WO2021211455A1 - Hla class i-restricted t cell receptors against lmp2 - Google Patents
Hla class i-restricted t cell receptors against lmp2 Download PDFInfo
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Classifications
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- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
- C07K14/70503—Immunoglobulin superfamily
- C07K14/7051—T-cell receptor (TcR)-CD3 complex
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- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/46—Cellular immunotherapy
- A61K39/461—Cellular immunotherapy characterised by the cell type used
- A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
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- A61K39/463—Cellular immunotherapy characterised by recombinant expression
- A61K39/4632—T-cell receptors [TCR]; antibody T-cell receptor constructs
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- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K39/00—Medicinal preparations containing antigens or antibodies
- A61K39/46—Cellular immunotherapy
- A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
- A61K39/464838—Viral antigens
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
- C12N5/06—Animal cells or tissues; Human cells or tissues
- C12N5/0602—Vertebrate cells
- C12N5/0634—Cells from the blood or the immune system
- C12N5/0636—T lymphocytes
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- A—HUMAN NECESSITIES
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- A61K2039/58—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation
- A61K2039/585—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation wherein the target is cancer
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2501/00—Active agents used in cell culture processes, e.g. differentation
- C12N2501/50—Cell markers; Cell surface determinants
- C12N2501/515—CD3, T-cell receptor complex
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
- C12N2710/00011—Details
- C12N2710/16011—Herpesviridae
- C12N2710/16211—Lymphocryptovirus, e.g. human herpesvirus 4, Epstein-Barr Virus
- C12N2710/16234—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N2710/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA dsDNA viruses
- C12N2710/00011—Details
- C12N2710/16011—Herpesviridae
- C12N2710/16211—Lymphocryptovirus, e.g. human herpesvirus 4, Epstein-Barr Virus
- C12N2710/16271—Demonstrated in vivo effect
Definitions
- Some cancers may have very limited treatment options, particularly when the cancer becomes metastatic and unresectable.
- treatments such as, for example, surgery, chemotherapy, and radiation therapy
- the prognosis for many cancers such as, for example, lymphomas and epithelial cancers, including Hodgkin lymphoma, T/NK cell lymphoma, post-transplant lymphoproliferative disorders, nasopharyngeal cancer, and gastric cancer
- lymphomas and epithelial cancers including Hodgkin lymphoma, T/NK cell lymphoma, post-transplant lymphoproliferative disorders, nasopharyngeal cancer, and gastric cancer.
- An embodiment of the invention provides an isolated or purified T-cell receptor (TCR) comprising the amino acid sequences of (a) SEQ ID NOs: 1-3, (b) SEQ ID NOs: 4-6, (c) SEQ ID NOs: 7-9, (d) SEQ ID NOs: 10-12, (e) SEQ ID NOs: 13-15, (f) SEQ ID NOs: 16- 18, (g) SEQ ID NOs: 1-6, (h) SEQ ID NOs: 7-12, or (i) SEQ ID NOs: 13-18, wherein the TCR has antigenic specificity for a LMP2 amino acid sequence presented by a human leukocyte antigen (HLA) Class I molecule.
- HLA human leukocyte antigen
- Another embodiment of the invention provides an isolated or purified polypeptide comprising a functional portion of the inventive TCR, wherein the functional portion comprises the amino acid sequences of: (a) SEQ ID NOs: 1-3, (b) SEQ ID NOs: 4-6, (c) SEQ ID NOs: 7-9, (d) SEQ ID NOs: 10-12, (e) SEQ ID NOs: 13-15, (f) SEQ ID NOs: 16-18,
- Still another embodiment of the invention provides an isolated or purified protein comprising at least one of the inventive polypeptides.
- nucleic acids recombinant expression vectors, host cells, populations of cells, and pharmaceutical compositions relating to the inventive TCRs, polypeptides, and proteins.
- An embodiment of the invention provides an isolated or purified nucleic acid comprising, from 5’ to 3’, a first nucleic acid sequence and a second nucleotide sequence, wherein the first and second nucleotide sequence, respectively, encode the amino sequences of SEQ ID NOs: 20, and 21 or 98; 21 or 98, and 20; 22, and 23 or 99; 23 or 99, and 22; 24, and 25 or 100; 25 or 100, and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 30 and 31; 31 and 30; 34, and 35 or 101; 35 or 101, and 34; 36, and 37 or 102; 37 or 102, and 36; 38, and 39 or 103; 39 or 103, and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 44 and 45; 45 and 44; 46, and 47 or 104; 47 or 104, and 46; 48, and 49 or 105; 49 or 105, and 48; 50, and 51 or 106; 51 or 106,
- Methods of detecting the presence of cancer in a mammal methods of treating or preventing cancer in a mammal, methods of inducing an immune response against a cancer in a mammal, methods of producing a host cell expressing a TCR that has antigenic specificity for the peptide of SEQ ID NO: 19, and methods of producing the inventive TCRs, polypeptides, and proteins, are further provided by embodiments of the invention.
- Figures 1A-1F present flow cytometry plots. Anti-LMP2 reactive T cells were enriched using LMP2426-434-HLA-A*02:01 tetramers. The tetramers were PE labeled. The antibody against CD8 was FITC labeled.
- Figure 1 A presents the TCR D2 before enrichment.
- Figure IB presents the TCR D2 after enrichment.
- Figure 1C presents the TCR D6 before enrichment.
- Figure ID presents the TCR D6 after enrichment.
- Figure IE presents the TCR D29 before enrichment.
- Figure IF presents the TCR D29 after enrichment.
- Figures 2A-2D present flow cytometry plots.
- HPV16 E7 TCR T cells and E7ii-i9- HLA-A*02:01 tetramers were used as control.
- the tetramers were PE-labeled.
- the antibody against mouse TCR constant region (mTRBC) was APC-labeled.
- Figure 2A shows detection of anti-LMP2 TCR D6 binding to LMP2.
- Figure 2B shows anti-LMP2 TCR D6 does not bind to E7.
- Figure 2C shows detection of anti-HPV16 E7 TCR binding E7.
- Figure 2D shows anti-HPV16 E7 TCR does not bind LMP2.
- FIG. 3 is a graph showing IFN ⁇ levels of an anti-LMP2 TCR based on alanine scanning of the LMP2426-434 epitope.
- An alanine residue was substituted for the native residue at each position of the peptide (CLGGLLTMV (SEQ ID NO: 19)).
- the residue substitutions are shown on the x axis.
- the assays shown were performed by co-culture of an anti-LMP2 TCR T cell (effector cells) with 293-A2 cells pulsed with 1 ⁇ g/ml peptide (target cells) indicated on the x axis. Co-culture supernatants were harvested after 18-24 hours, and the IFN ⁇ concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells pulsed with no peptide or treated with PMA and ionomycin instead of peptide served as control target cells.
- Figure 4 is a graph showing results of T cells transduced with the anti-LMP2 TCR D6 or untransduced T cells co-cultured with K562A2 loaded with 1 mM of peptide as indicated in the x-axis. The levels of IFN ⁇ in the overnight co-culture supernatant was measured with ELISA.
- Figure 5 is a graph showing results of T cells transduced with the anti-LMP2 TCR D6 or untransduced T cells co-cultured with K562A2 loaded with titrated concentrations of peptides as indicated in the x-axis. The levels of IFNy in the overnight co-culture supernatant was measured with ELISA.
- Figure 6 is a graph showing a functional avidity assay with the quantity of IFN- ⁇ produced in an overnight co-culture.
- the target cells are K562 cells pulsed with LMP2426-434 or E7II-I9 peptide at the concentrations indicated on the x axis.
- the TCR/target antigen combinations are shown in the key.
- Figure 7A presents Western Blots confirming the expression of LMP2 (or actin, as a control) on EBV-LCLs.
- FIG. 7B is a graph showing IFN ⁇ levels of an anti-LMP2 TCR tested for recognition of EBV-LCLs.
- the assay was performed by co-culture of TCR T cells (effector cells) with EBV-LCLs (target cells) indicated on the x axis. The effector-to-target ratio is 1:1. Co-culture supernatants were harvested after 18-24 hours, and the IFN ⁇ concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells treated with PMA and ionomycin served as control target cells.
- Figure 8A is a graph showing anti-LMP2 TCR T cells recognize HLA-A*02:01+ and LMP2+ cancer cell lines.
- the assay was performed by co-culture of TCR T cells (effector cells) with each cancer cell line (target cells) indicated on the x axis. The effector- to-target ratio is 1:1. Co-culture supernatants were harvested after 18-24 hours, and the IFN- ⁇ g concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells cultured alone or treated with PMA and ionomycin served as control target cells.
- Figures 8B and 8C are graphs showing results of T cells transduced to express anti-LMP2 TCR D6 co-cultured with target cell lines. Some donors’ PBMCs transduced to express the anti-LMP2 TCR demonstrate the data shown in Figure 8B (representative of 5 experiments) where the anti-LMP2 TCR-transduced T cells do not recognize the A2+ EBV LCLs.
- K562A2 and K562LMP2 is K562 retrovirally transduced to express HLA-A*02:01 and LMP2 (B95-8 strain), respectively.
- K562A2LMP2 is K562 retrovirally transduced to express both LMP2 (B95-8 strain) and HLA-A*02:01.
- K562A2 LMP2pep, K562A2 E7pep, and K562A2 CD22pep indicate K562A2 cell line loaded with 1 mM of peptides LMP2 P426 -434, HPV-16 E7 p11-19 , or CD22 P228- 236 , respectively.
- Figures 9A-9F are graphs showing LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer. The target cell line name and the expression of LMP2 and HLA-A*02:01 are indicated. The effector-to-target ratio is 1:1. The values plotted are the means of 3 technical replicates, and error bars represent the SEM.
- Figure 9A presents the cell line HONE1-EBV A2+/LMP2+.
- Figure 9B presents the cell line 4050-LMP2 A2+/LMP2+.
- Figure 9C presents the cell line 4050 A2+/LMP2-.
- Figure 9D presents the cell line HK1-EBV A2+/LMP2+.
- Figure 9E presents the cell line 293A2-LMP2 A2+/LMP2+.
- Figure 9F presents the cell line Hela A2- /LMP2-.
- Figure 10A is a graph showing a functional avidity assay with the quantity of IFN ⁇ produced in an overnight co-culture.
- the target cells are 293-A2 cells pulsed with LMP2426-434 peptide at the concentrations indicated on the x axis.
- the effector cells are cells transduced with the D2 or D6 TCR.
- Figure 10B is a graph showing anti-LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer.
- the target cell line is HK1-EBV.
- the effector-to-target ratio is 1:1.
- the values plotted are the means of 3 technical replicates, and error bars represent the SEM. UT, untransduced T cells; D2, LMP2 TCR D2 transduced T cells; D6, LMP2 TCR D6 transduced T cells; None, target cells alone.
- Figure IOC is a graph showing anti-LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer.
- the target cell line is HK1-EBV.
- the effector-to-target ratio is 1:5.
- the values plotted are the means of 3 technical replicates, and error bars represent the SEM. UT, untransduced T cells; D2, LMP2 TCR D2 transduced T cells; D6, LMP2 TCR D6 transduced T cells; None, target cells alone.
- Figure 10D is a graph showing LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer.
- the target cell line is HK1-EBV.
- the effector-to-target ratio is 1:1.
- UT untransduced T cells; D29, LMP2 TCR clone D29 transduced T cells; D6, LMP2 TCR clone D6 transduced T cells.
- An embodiment of the invention provides an isolated or purified TCR having antigenic specificity for an EBV antigen LMP2 amino acid sequence CLGGLLTMV (SEQ ID NO: 19) presented by a human leukocyte antigen (HLA) Class I molecule.
- HLA human leukocyte antigen
- the inventive TCR may have antigenic specificity for any LMP2 protein, polypeptide or peptide amino acid sequence, for example LMP2A (EBV strain B95- 8) (SEQ ID NO: 86), LMP2A (EBV strain AG876) (SEQ ID NO: 87), LMP2A (EBV strain GDI) (SEQ ID NO: 88), LMP2B (EBV strain B95-8) (SEQ ID NO: 89), LMP2B (EBV strain AG876) (SEQ ID NO: 90), or LMP2B (EBV strain GDI) (SEQ ID NO: 91).
- the LMP2 amino acid sequence comprises an LMP2 amino acid sequence with a substitution (with any other amino acid, in particular alanine or serine) at amino acid position 1, 3, 6, or 8, or any combination thereof that is within SEQ ID NO: 19 when within the full context of any of SEQ ID NOS: 86-91 or of any fragment of SEQ ID NOS: 86-91 that contains SEQ ID NO: 19. Positions 1, 3, 6, and 8 are underlined: CLGGLLTMV (SEQ ID NO: 19).
- “Peptide LMP2426-434” described herein consists of SEQ ID NO: 19 and is position 426 to 434 of LMP2A (EBV strain B95-8) (SEQ ID NO: 86) and LMP2A (EBV strain AG876) (SEQ ID NO: 87).
- SEQ ID NO: 19 starts at other positions in LMP2A (EBV strain GDI) (SEQ ID NO: 88), LMP2B (EBV strain B95-8) (SEQ ID NO: 89), LMP2B (EBV strain AG876) (SEQ ID NO: 90), and LMP2B (EBV strain GDI) (SEQ ID NO: 91).
- the TCR has antigenic specificity for an LMP2 peptide with a mutation at positions 1 and 3 as described above, wherein the mutated LMP2 peptide has any length.
- the mutated LMP2 peptide has any length suitable for binding to any of the HLA Class I molecules described herein.
- the TCR may have antigenic specificity for a LMP2 peptide with the mutation, the LMP2 peptide having a length of about 9 amino acid residues.
- the LMP2 peptide may comprise any contiguous amino acid residues of LMP2 protein which include the mutation.
- the TCR may have antigenic specificity for an LMP2 peptide with the mutation, the LMP2 peptide having a length of about 9 amino acid residues.
- the inventive TCRs are able to recognize LMP2 presented by an HLA Class I molecule.
- the TCR may elicit an immune response upon binding to LMP2 within the context of an HLA Class I molecule.
- the inventive TCRs may bind to the HLA Class I molecule in addition to LMP2.
- the HLA Class I molecule is an HLA-A molecule.
- the HLA-A molecule is a heterodimer of an a chain and ⁇ 2 microglobulin.
- the HLA-A a chain may be encoded by an HLA-A gene.
- ⁇ 2 microglobulin binds non-covalently to the alpha chain to build the HLA-A complex.
- the HLA-A molecule may be any HLA-A molecule.
- the HLA Class I molecule is an HLA-A02 molecule.
- the HLA-A02 molecule may be any HLA-A02 molecule.
- HLA-A02 molecules may include, but are not limited to, those expressed by the HLA-A*02:01, HLA- A*02:02, HLA-A*02:03, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, and HLA-A*02:11 alleles.
- the HLA-A02 molecule is expressed by the HLA-A*02:01 allele.
- the TCRs of the invention may provide any one or more of a variety of advantages, including when expressed by cells used for adoptive cell transfer.
- LMP2 is expressed by cancer cells and is not expressed by normal, noncancerous cells.
- inventive TCRs advantageously target the destruction of cancer cells while minimizing or eliminating the destruction of normal, non-cancerous cells, thereby reducing, for example, by minimizing or eliminating, toxicity.
- inventive TCRs may, advantageously, successfully treat or prevent LMP2-positive cancers that do not respond to other types of treatment such as, for example, chemotherapy, surgery, or radiation.
- the inventive TCRs may provide highly avid recognition of LMP2, which may provide the ability to recognize unmanipulated tumor cells (e.g., tumor cells that have not been treated with interferon (IFN)- ⁇ , transfected with a vector encoding one or both of LMP2 and HLA-A*02:01, pulsed with an LMP2 peptide, or a combination thereof). Accordingly, the inventive TCRs may increase the number of immunotherapy-eligible cancer patients to include those patients that express the HLA-A*02:01 allele who may not be eligible for immunotherapy using TCRs that recognize LMP2 presented by other MHC molecules. Moreover, the inventive TCRs, polypeptides and proteins comprise human amino acid sequences, which may reduce the risk of rejection by the human immune system as compared to, e.g., TCRs, polypeptides and proteins comprising mouse amino acid sequences.
- IFN interferon
- a TCR means that the TCR can specifically bind to and immunologically recognize LMP2 with high avidity.
- a TCR may be considered to have “antigenic specificity” for LMP2 if about 1 x 10 4 to about 1 x 10 5 T cells expressing the TCR secrete at least about 200 pg/mL or more (e.g., 200 pg/mL or more, 300 pg/mL or more, 400 pg/mL or more, 500 pg/mL or more, 600 pg/mL or more, 700 pg/mL or more, 1000 pg/mL or more, 5,000 pg/mL or more, 7,000 pg/mL or more, 10,000 pg/mL or more, 20,000 pg/mL or more, or a range defined by any two of the foregoing values) of IFN- ⁇ pon co-culture with (a) antigen-negative, HLA Class I
- HLA Class I molecule may be any of the HLA Class I molecules described herein (e.g., an HLA-A*02:01 molecule).
- a TCR may be considered to have “antigenic specificity” for LMP2 if T cells expressing the TCR secrete at least twice as much IFN ⁇ upon co-culture with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with a low concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2 as compared to the amount of IFN ⁇ expressed by a negative control.
- the negative control may be, for example, (i) T cells expressing the TCR, co-cultured with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with the same concentration of an irrelevant peptide (e.g., some other peptide with a different sequence from the LMP2 peptide) or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding an irrelevant peptide has been introduced such that the target cell expresses the irrelevant peptide, or (ii) untransduced T cells (e.g., derived from PBMC, which do not express the TCR) co-cultured with (a) antigen negative, HLA Class I molecule positive target cells pulsed with the same concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2.
- an irrelevant peptide
- the HLA Class I molecule expressed by the target cells of the negative control would be the same HLA Class I molecule expressed by the target cells that are co-cultured with the T cells being tested.
- the HLA Class I molecule may be any of the HLA Class I molecules described herein (e.g., an HLA-A*02:01 molecule).
- IFN ⁇ secretion may be measured by methods known in the art such as, for example, enzyme-linked immunosorbent assay (ELISA).
- a TCR may be considered to have “antigenic specificity” for LMP2 if at least twice as many of the numbers of T cells expressing the TCR secrete IFN- ⁇ upon co-culture with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with a low concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2 as compared to the numbers of negative control T cells that secrete IFN- ⁇ .
- the HLA Class I molecule, concentration of peptide, and the negative control may be as described herein with respect to other aspects of the invention.
- the numbers of cells secreting IFN- ⁇ may be measured by methods known in the art such as, for example, ELISPOT.
- a TCR may be considered to have “antigenic specificity” for LMP2 if T cells expressing the TCR upregulate expression of one or more T- cell activation markers as measured by, for example, flow cytometry after stimulation with target cells expressing LMP2.
- T-cell activation markers include 4-1BB, 0X40, CD107a, CD69, and cytokines that are upregulated upon antigen stimulation (e.g., tumor necrosis factor (TNF), interleukin (IL)-2, etc.).
- An embodiment of the invention provides a TCR comprising two polypeptides (i.e., polypeptide chains), such as an alpha (a) chain of a TCR, a beta ( ⁇ ) chain of a TCR, a gamma (g) chain of a TCR, a delta ( ⁇ ) chain of a TCR, or a combination thereof.
- the polypeptides of the inventive TCR can comprise any amino acid sequence, provided that the TCR has antigenic specificity for LMP2. In some embodiments, the TCR is non-naturally occurring.
- the TCR comprises two polypeptide chains, each of which comprises a variable region comprising a complementarity determining region (CDR)1, a CDR2, and a CDR3 of a TCR.
- the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 1 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 2 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 4 (CDR1 of ⁇ chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 5 (CDR2 of ⁇ chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 6 (CDR3 of ⁇ chain).
- the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 7 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 8 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 9 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 10 (CDR1 of ⁇ chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 11 (CDR2 of ⁇ chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 12 (CDR3 of ⁇ chain).
- the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 13 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 14 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 16 (CDR1 of ⁇ chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 17 (CDR2 of ⁇ chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 18 (CDR3 of ⁇ chain).
- the inventive TCR can comprise any one or more of the amino acid sequences selected from SEQ ID NOs: 1-6, 7-12, and 13-18.
- the TCR comprises the amino acid sequences of: (a) all of SEQ ID NOs: 1-3, (b) all of SEQ ID NOs: 4-6, (c) all of SEQ ID NOs: 7-9, (d) all of SEQ ID NOs: 10-12, (e) all of SEQ ID NOs: 13-15, (f) all of SEQ ID NOs: 16-18, (g) all of SEQ ID NOs: 1-6, (h) all of SEQ ID NOs: 7-12, or (i) all of SEQ ID NOs: 13-18.
- the TCR comprises the amino acid sequences of: (i) all of SEQ ID NOs: 1-6, (ii) all of SEQ ID NOs: 7-12, or (iii) all of SEQ ID NOs: 13-18.
- the CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or ⁇ chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
- the TCR comprises an amino acid sequence of a variable region of a TCR comprising the CDRs set forth above.
- the TCR may comprise a human variable region, e.g., a human a chain variable region and a human ⁇ chain variable region.
- the TCR can comprise the amino acid sequence of: SEQ ID NO: 20 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 21 or 98 (variable region of ⁇ chain with N-terminal signal peptide); SEQ ID NO: 22 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 23 or 99 (variable region of ⁇ chain with N- terminal signal peptide); SEQ ID NO: 24 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 25 or 100 (variable region of ⁇ chain with N-terminal signal peptide); SEQ ID NO: 26 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 27 (variable region of ⁇ chain without N-terminal signal peptide); SEQ ID NO: 28 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 29 (variable region of ⁇ chain without N-terminal peptid
- the inventive TCRs may further comprise an a chain constant region and a ⁇ chain constant region.
- the constant region may be derived from any suitable species such as, e.g., human or mouse.
- the TCRs further comprise murine a and ⁇ chain constant regions or human a and ⁇ chain constant regions.
- CDR complementarity determining region
- An embodiment of the invention provides a chimeric TCR comprising a human variable region and a murine constant region, wherein the TCR has antigenic specificity for an LMP2 amino acid sequence presented by an HLA Class I molecule.
- the murine constant region may provide any one or more advantages. For example, the murine constant region may diminish mispairing of the inventive TCR with the endogenous TCRs of the host cell into which the inventive TCR is introduced. Alternatively or additionally, the murine constant region may increase expression of the inventive TCR as compared to the same TCR with a human constant region.
- the chimeric TCR may comprise the amino acid sequence of SEQ ID NO: 32 (wild-type (WT) murine a chain constant region), SEQ ID NO: 33 (WT murine ⁇ chain constant region), or both SEQ ID NOs: 32 and 33.
- the inventive TCR comprises the amino acid sequences of both of SEQ ID NOs: 32 and 33.
- the chimeric TCR may comprise any of the murine constant regions described herein in combination with any of the CDR regions as described herein with respect to other aspects of the invention.
- the TCR may comprise the amino acid sequences of: (a) all of SEQ ID NOs: 1-3 and 32; (b) all of SEQ ID NOs: 4-6 and 33; (c) all of SEQ ID NOs: 7-9 and 32; (d) all of SEQ ID NOs: 10-12 and 33; (e) all of SEQ ID NOs: 13-15 and 32; (f) all of SEQ ID NOs: 16-18 and 33; (g) all of SEQ ID NOs: 1-6 and 32-33; (h) all of SEQ ID NOs: 7-12 and 32-33, or (i) all of SEQ ID NOs: 13-18 and 32-33.
- the chimeric TCR may comprise any of the murine constant regions described herein in combination with any of the variable regions described herein with respect to other aspects of the invention.
- the TCR may comprise the amino acid sequences of: (i) both of SEQ ID NOs: 20 and 32; (ii) both of SEQ ID NOs: 21 or 98, and 33; (iii) both of SEQ ID NOs: 22 and 32; (iv) both of SEQ ID NOs: 23 or 99, and 33; (v) both of SEQ ID NOs: 24 and 32; (vi) both of SEQ ID NOs: 25 or 100, and 33; (vii) both of SEQ ID NOs: 26 and 32; (vii) both of SEQ ID NOs: 27 and 33; (viii) both of SEQ ID NOs: 28 and 32; (ix) both of SEQ ID NOs: 29 and 33; (x) both of SEQ ID NOs: 30 and 32; (xi) both of SEQ ID NOs: 31 and
- the TCR comprises the amino acid sequence(s) of: SEQ ID NO: 34 (a chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 35 or 101 ( ⁇ chain with WT murine constant region and N- terminal signal peptide), SEQ ID NO: 36 (a chain with WT murine constant region and N- terminal signal peptide), SEQ ID NO: 37 or 102 ( ⁇ chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 38 (a chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 39 or 103 ( ⁇ chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 40 (a chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 41 ( ⁇ chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 42 (a chain with WT murine constant
- the TCR comprises an a chain comprising a variable region and a constant region and a ⁇ chain comprising a variable region and a constant region.
- the TCR may comprise (a) an a chain comprising the amino acid sequence of SEQ ID NO: 46 (a chain with N-terminal signal peptide), wherein: (i) X at position 179 of SEQ ID NO: 46 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a ⁇ chain comprising the amino acid sequence
- X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (d) a ⁇ chain comprising the amino acid sequence of SEQ ID NO: 49 or 105 ( ⁇ chain with N-terminal signal peptide), wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys; (e) an a comprising the amino acid sequence of SEQ ID NO: 50 (a chain with N- terminal signal peptide), wherein: (i) X at position 179 of SEQ ID NO: 50 is Thr or Cys; (ii)
- X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (f) a ⁇ chain comprising the amino acid sequence of SEQ ID NO: 51 or 106 ( ⁇ chain with N-terminal signal peptide), wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys; (g) both (a) and (b); (h) both (c) and (d); or (i) both (e) and (f); (j) an a chain comprising the amino acid sequence of SEQ ID NO: 52 (a chain without N-terminal signal peptide), wherein:
- the TCR comprising SEQ ID NO: 47 or 104 does not comprise SEQ ID NO: 35 or
- the TCR comprising SEQ ID NO: 48 does not comprise SEQ ID NO: 36 (unsubstituted a chain).
- the TCR comprising SEQ ID NO: 49 or 105 does not comprise SEQ ID NO: 37 or
- the TCR comprising SEQ ID NO: 50 does not comprise SEQ ID NO: 38 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 51 or 106 does not comprise SEQ ID NO: 39 or
- the TCR comprising SEQ ID NO: 52 does not comprise SEQ ID NO: 40 (unsubstituted a chain).
- the TCR comprising SEQ ID NO: 53 does not comprise SEQ ID NO: 41 (unsubstituted ⁇ chain).
- the TCR comprising SEQ ID NO: 54 does not comprise SEQ ID NO: 42 (unsubstituted a chain).
- the TCR comprising SEQ ID NO: 55 does not comprise SEQ ID NO: 43 (unsubstituted ⁇ chain).
- the TCR comprising SEQ ID NO: 56 does not comprise SEQ ID NO: 44 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 57 does not comprise SEQ ID NO: 45 (unsubstituted ⁇ chain).
- the TCR comprises a substituted constant region. In this regard, the TCR may comprise the amino acid sequence of any of the TCRs described herein with one, two, three, or four amino acid substitution(s) in the constant region of one or both of the a and ⁇ chain.
- the TCR comprises a murine constant region with one, two, three, or four amino acid substitution(s) in the murine constant region of one or both of the a and ⁇ chains.
- the TCR comprises a murine constant region with one, two, three, or four amino acid substitution(s) in the murine constant region of the a chain and one amino acid substitution in the murine constant region of the ⁇ chain.
- the TCRs comprising the substituted constant region advantageously provide one or more of increased recognition of LMP2 + targets, increased expression by a host cell, diminished mispairing with endogenous TCRs, and increased anti tumor activity as compared to the parent TCR comprising an unsubstituted (wild-type) constant region.
- substituted amino acid sequences of the murine constant regions of the TCR a and ⁇ chains correspond with all or portions of the unsubstituted murine constant region amino acid sequences SEQ ID NOs: 32 and 33, respectively, with SEQ ID NO: 58 having one, two, three, or four amino acid substitution(s) when compared to SEQ ID NO: 32 and SEQ ID NO: 59 having one amino acid substitution when compared to SEQ ID NO: 33.
- an embodiment of the invention provides a TCR comprising the amino acid sequences of (a) SEQ ID NO: 58 (constant region of a chain), wherein (i) X at position 48 is Thr or Cys; (ii) X at position 112 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) SEQ ID NO: 59 (constant region of ⁇ chain), wherein X at position 57 is Ser or Cys; or (c) both of SEQ ID NOs: 58 and 59.
- the TCR comprising SEQ ID NO: 58 does not comprise SEQ ID NO: 32 (unsubstituted murine constant region of a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 59 does not comprise SEQ ID NO: 33 (unsubstituted murine constant region of ⁇ chain).
- the first amino acid of any of the mouse alpha constant regions described herein may be different from N as provided in SEQ ID NOS: 32 and 58.
- this first amino acid can be encoded by a split codon (having nucleotides from both a variable region and a constant region) such that any of the murine alpha constant regions may have a different amino acid at that position.
- the first amino acid of any of the mouse beta constant regions described herein may be different from E as provided in SEQ ID NOS: 33 and 59, e.g., this first amino acid can be encoded by a split codon.
- the substituted constant region includes cysteine substitutions in the constant region of one or both of the a and ⁇ chains to provide a cysteine- substituted TCR.
- Opposing cysteines in the a and the ⁇ chains provide a disulfide bond that links the constant regions of the a and the ⁇ chains of the substituted TCR to one another and which is not present in a TCR comprising the unsubstituted murine constant regions.
- the TCR may be a cysteine-substituted TCR in which one or both of the native Thr at position 48 (Thr48) of SEQ ID NO: 32 and the native Ser at position 57 (Ser57) of SEQ ID NO: 33 may be substituted with Cys.
- Thr48 native Thr at position 48
- Ser57 native Ser at position 57
- both of the native Thr48 of SEQ ID NO: 32 and the native Ser57 of SEQ ID NO: 33 are substituted with Cys.
- Examples of cysteine- substituted TCR constant regions sequences are set forth in Table 1.
- the cysteine-substituted TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined in Table 1.
- the cysteine-substituted TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
- the cysteine-substituted, chimeric TCR comprises a full length alpha chain and a full-length beta chain.
- Examples of cysteine- substituted, chimeric TCR alpha chain and beta chain sequences are set forth in Table 1.
- the TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv) SEQ ID NO: 56, (xv) SEQ ID NO: 57, (xvi) both of SEQ ID NOs: 52 and 53, (xv) both of SEQ ID NOs: 54 and 55, or (xvi) both of SEQ ID NOs: 56
- the substituted amino acid sequence includes substitutions of one, two, or three amino acids in the transmembrane (TM) domain of the constant region of one or both of the a and ⁇ chains with a hydrophobic amino acid to provide a hydrophobic amino acid-substituted TCR (also referred to herein as an “LVL- modified TCR”).
- the hydrophobic amino acid substitution(s) in the TM domain of the TCR may increase the hydrophobicity of the TM domain of the TCR as compared to a TCR that lacks the hydrophobic amino acid substitution(s) in the TM domain.
- the TCR is an LVL-modified TCR in which one, two, or three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; preferably with Leu, lie, or Val.
- all three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; preferably with Leu, Ile, or Val.
- the LVL-modified TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined in Table 2.
- the LVL-modified TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
- the LVL-modified TCR comprises a full length alpha chain and a full-length beta chain.
- Examples of LVL-modified TCR alpha chain and beta chain sequences are set forth in Table 2.
- the LVL- modified TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv
- the substituted amino acid sequence includes the cysteine substitutions in the constant region of one or both of the a and ⁇ chains in combination with the substitution(s) of one, two, or three amino acids in the transmembrane (TM) domain of the constant region of one or both of the a and ⁇ chains with a hydrophobic amino acid (also referred to herein as “cysteine-substituted, LVL-modified TCR”).
- the TCR is a cysteine-substituted, LVL-modified, chimeric TCR in which the native Thr48 of SEQ ID NO: 32 is substituted with Cys; one, two, or three of the native Seri 12,
- Metl 14, and Gly 115 of SEQ ID NO: 32 are, independently, substituted with Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; preferably with Leu, lie, or Val; and the native Ser57 of SEQ ID NO: 33 is substituted with Cys.
- all three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; preferably with Leu, Ile, or Val.
- the cysteine-substituted, LVL-modified TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined in Table 3.
- the cysteine-substituted, LVL-modified TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
- the cysteine-substituted, LVL-modified TCR comprises a full- length alpha chain and a full-length beta chain.
- the LVL- modified TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv) SEQ ID NO: 56, (xv) SEQ ID NO:
- polypeptide comprising a functional portion of any of the TCRs described herein.
- polypeptide includes oligopeptides and refers to a single chain of amino acids connected by one or more peptide bonds.
- the functional portion can be any portion comprising contiguous amino acids of the TCR of which it is a part, provided that the functional portion specifically binds to LMP2.
- Functional portions encompass, for example, those parts of a TCR that retain the ability to specifically bind to LMP2 (e.g., within the context of an HLA-A*02:01 molecule), or detect, treat, or prevent cancer, to a similar extent, the same extent, or to a higher extent, as the parent TCR.
- the functional portion can comprise, for instance, about 10%, about 25%, about 30%, about 50%, about 70%, about 80%, about 90%, about 95%, or more, of the parent TCR.
- the functional portion can comprise additional amino acids at the amino or carboxy terminus of the portion, or at both termini, which additional amino acids are not found in the amino acid sequence of the parent TCR.
- the additional amino acids do not interfere with the biological function of the functional portion, e.g., specifically binding to LMP2; and/or having the ability to detect cancer, treat or prevent cancer, etc.
- the additional amino acids enhance the biological activity, as compared to the biological activity of the parent TCR.
- the polypeptide can comprise a functional portion of either or both of the a and ⁇ chains of the TCRs of the invention, such as a functional portion comprising one or more of the CDR1, CDR2, and CDR3 of the variable region(s) of the a chain and/or ⁇ chain of a TCR of the invention.
- the polypeptide can comprise the amino acid sequence of SEQ ID NO: 1 (CDR1 of a chain), SEQ ID NO: 2 (CDR2 of a chain), SEQ ID NO: 3 (CDR3 of a chain), SEQ ID NO: 4 (CDR1 of ⁇ chain), SEQ ID NO: 5 (CDR2 of ⁇ chain), SEQ ID NO: 6 (CDR3 of ⁇ chain), or a combination thereof.
- the polypeptide can comprise the amino acid sequence of SEQ ID NO: 7 (CDR1 of a chain), SEQ ID NO: 8 (CDR2 of a chain), SEQ ID NO: 9 (CDR3 of a chain), SEQ ID NO: 10 (CDR1 of ⁇ chain), SEQ ID NO: 11 (CDR2 of ⁇ chain), SEQ ID NO: 12 (CDR3 of ⁇ chain), or a combination thereof.
- the polypeptide can comprise the amino acid sequence of SEQ ID NO: 13 (CDR1 of a chain), SEQ ID NO: 14 (CDR2 of a chain), SEQ ID NO: 15 (CDR3 of a chain), SEQ ID NO: 16 (CDR1 of ⁇ chain), SEQ ID NO: 17 (CDR2 of ⁇ chain), SEQ ID NO: 18 (CDR3 of ⁇ chain), or a combination thereof.
- the CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or ⁇ chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
- the inventive polypeptide can comprise any one or more of the amino acid sequences selected from SEQ ID NOs: 1-6, 7-12, and 13-18.
- the TCR comprises the amino acid sequences of: (a) all of SEQ ID NOs: 1- 3, (b) all of SEQ ID NOs: 4-6, (c) all of SEQ ID NOs: 7-9, (d) all of SEQ ID NOs: 10-12, (e) all of SEQ ID NOs: 13-15, (f) all of SEQ ID NOs: 16-18, (g) all of SEQ ID NOs: 1-6, (h) all of SEQ ID NOs: 7-12, or (i) all of SEQ ID NOs: 13-18.
- the polypeptide comprises the amino acid sequences of: (i) all of SEQ ID NOs: 1-6, (ii) all of SEQ ID NOs: 7-12, or (iii) all of SEQ ID NOs: 13-18.
- the inventive polypeptide can comprise, for instance, the variable region of the inventive TCR comprising a combination of the CDR regions set forth above.
- the polypeptide can comprise the amino acid sequence of SEQ ID NO: 20 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 21 or 98 (variable region of ⁇ chain with N-terminal signal peptide); SEQ ID NO: 22 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 23 or 99 (variable region of ⁇ chain with N-terminal signal peptide); SEQ ID NO: 24 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 25 or 100 (variable region of ⁇ chain with N- terminal signal peptide); SEQ ID NO: 26 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 27 (variable region of ⁇ chain without N-terminal signal peptid
- the inventive polypeptide can further comprise the constant region of the inventive TCR set forth above.
- polypeptide can further comprise the amino acid sequence of SEQ ID NO: 32 (WT murine constant region of a chain), SEQ ID NO: 33 (WT murine constant region of ⁇ chain), SEQ ID NO: 58, (substituted murine constant region of a chain), SEQ ID NO: 59 (substituted murine constant region of ⁇ chain), both SEQ ID NOs: 32 and 33, or both SEQ ID NOs: 58 and 59.
- the polypeptide further comprises the amino acid sequences of both of SEQ ID NOs: 32 and 33 or both of SEQ ID NO: 58 and 59 in combination with any of the CDR regions or variable regions described herein with respect to other aspects of the invention.
- the polypeptide comprises: (a) the amino acid sequence of SEQ ID NO: 58, wherein: (i) X at position 48 of SEQ ID NO: 58 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or (c) both (a) and (b). In embodiments of the invention, one or both of SEQ ID NOs:
- the inventive polypeptide can comprise the entire length of an a or ⁇ chain of the TCR described herein.
- the inventive polypeptide can comprise the amino acid sequence of (i) SEQ ID NO: 20, (ii) SEQ ID NO: 21 or 98, (iii) SEQ ID NO: 26, (iv) SEQ ID NO: 27, (v) both of SEQ ID NOs: 20, and 21 or 98, (vi) both of SEQ ID NOs: 26 and 27, (vii) SEQ ID NO: 22, (viii) SEQ ID NO: 23 or 99, (ix) SEQ ID NO: 28, (x) SEQ ID NO: 29, (xi) both of SEQ ID NOs: 22, and 23 or 99, (xii) both of SEQ ID NOs: 28 and 29, (xiii) SEQ ID NO: 24, (xiv) SEQ ID NO: 25 or 100, (xv) SEQ ID NO: 30, (xvi) SEQ ID NO: 31, (xvii) both of
- the polypeptide comprises: (a) the amino acid sequence of SEQ ID NO: 46, wherein: (i) X at position 179 of SEQ ID NO: 46 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
- An embodiment of the invention further provides a protein comprising at least one of the polypeptides described herein.
- protein is meant a molecule comprising one or more polypeptide chains.
- the protein of the invention can comprise (a) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 1-3 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 4-6; (b) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 7-9 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 10-12; or (c) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 13-15 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 16-18.
- the CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or ⁇ chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
- the protein may comprise (i) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 20 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 21 or 98; (ii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 26 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 27; (iii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 22 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 23 or 99; (iv) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 28 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 29; (v) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 24 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 25 or 100; or (vi)
- the inventive protein may further comprise any of the constant regions described herein with respect to other aspects of the invention.
- the first polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 32 and the second polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 33.
- the first polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 58 and the second polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 59.
- the protein comprises: (a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 58, wherein: (i) X at position 48 of SEQ ID NO: 58 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or (c) both (a) and (b).
- a first polypeptide chain comprising the
- the protein of an embodiment of the invention can comprise (a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:
- 51 or 106, and 52-57 are as defined in any one of Tables 1-3.
- the protein of the invention can be a TCR.
- the inventive protein can be a fusion protein.
- an embodiment of the invention also provides a fusion protein comprising at least one of the inventive polypeptides described 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 polypeptide, which is expressed in frame (in tandem) with one of the inventive polypeptides described herein.
- the other polypeptide can encode any peptidic or proteinaceous molecule, or a portion thereof, including, but not limited to an immunoglobulin, CD3, CD4, CD8, an MHC molecule, a CD1 molecule, e.g., CDla, CDlb, CDlc, CD Id, etc.
- the fusion protein can comprise one or more copies of the inventive polypeptide and/or one or more copies of the other polypeptide.
- the fusion protein can comprise 1, 2, 3, 4, 5, or more, copies of the inventive polypeptide and/or of the other polypeptide.
- Suitable methods of making fusion proteins are known in the art, and include, for example, recombinant methods.
- the TCRs, polypeptides, and proteins of the invention may be expressed as a single protein comprising a linker peptide linking the a chain and the ⁇ chain.
- the TCRs, polypeptides, and proteins of the invention may further comprise a linker peptide.
- the linker peptide may advantageously facilitate the expression of a recombinant TCR, polypeptide, and/or protein in a host cell.
- the linker peptide may comprise any suitable amino acid sequence.
- the linker peptide may be a furin-SGSG-P2A linker comprising the amino acid sequence of RAKRS GS GATNF SLLKQ AGD VEENPGP (SEQ ID NO: 60).
- the linker peptide may be cleaved, resulting in separated a and ⁇ chains.
- the TCR, polypeptide, or protein may comprise an amino acid sequence comprising a full-length a chain, a full-length ⁇ chain, and a linker peptide positioned between the a and ⁇ chains, for example a chain-linker- ⁇ chain or ⁇ chain-linker-a chain.
- the protein of the invention can be a recombinant antibody, or an antigen binding portion thereof, comprising at least one of the inventive polypeptides described herein.
- "recombinant antibody” refers to a recombinant (e.g., genetically engineered) protein comprising at least one of the polypeptides of the invention and a polypeptide chain of an antibody, or an antigen binding portion thereof.
- the polypeptide of an antibody, or antigen binding portion thereof can be a heavy chain, a light chain, a variable or constant region of a heavy or light chain, a single chain variable fragment (scFv), or an Fc, Fab, or F(ab)2' fragment of an antibody, etc.
- polypeptide chain of an antibody, or an antigen binding portion thereof can exist as a separate polypeptide of the recombinant antibody.
- the polypeptide chain of an antibody, or an antigen binding portion thereof can exist as a polypeptide, which is expressed in frame (in tandem) with the polypeptide of the invention.
- the polypeptide of an antibody, or an antigen binding portion thereof can be a polypeptide of any antibody or any antibody fragment, including any of the antibodies and antibody fragments described herein.
- Functional variants encompass, for example, those variants of the TCR, polypeptide, or protein described herein (the parent TCR, polypeptide, or protein) that retain the ability to specifically bind to LMP2 for which the parent TCR has antigenic specificity or to which the parent polypeptide or protein specifically binds, to a similar extent, the same extent, or to a higher extent, as the parent TCR, polypeptide, or protein.
- the functional variant can, for instance, be at least about 30%, about 50%, about 75%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or more identical in amino acid sequence to the parent TCR, polypeptide, or protein, respectively.
- the functional variant can, for example, comprise the amino acid sequence of the parent TCR, polypeptide, or protein with at least one conservative amino acid substitution.
- Conservative amino acid substitutions are known in the art, and include amino acid substitutions in which one amino acid having certain physical and/or chemical properties is exchanged for another amino acid that has the same chemical or physical properties.
- the conservative amino acid substitution can be an acidic amino acid substituted for another acidic amino acid (e.g., Asp or Glu), an amino acid with a nonpolar side chain substituted for another amino acid with a nonpolar side chain (e.g., Ala, Gly, Val, lie, Leu, Met, Phe, Pro, Trp, Val, etc.), a basic amino acid substituted for another basic amino acid (Lys, Arg, etc.), an amino acid with a polar side chain substituted for another amino acid with a polar side chain (Asn, Cys, Gin, Ser, Thr, Tyr, etc.), etc.
- an amino acid with a nonpolar side chain substituted for another amino acid with a nonpolar side chain e.g., Ala, Gly, Val, lie, Leu, Met, Phe, Pro, Trp, Val, etc.
- a basic amino acid substituted for another basic amino acid Lys, Arg, etc.
- the functional variants can comprise the amino acid sequence of the parent TCR, polypeptide, or protein with at least one non-conservative amino acid substitution.
- the non-conservative amino acid substitution it is preferable for the non-conservative amino acid substitution to not interfere with or inhibit the biological activity of the functional variant.
- the non-conservative amino acid substitution enhances the biological activity of the functional variant, such that the biological activity of the functional variant is increased as compared to the parent TCR, polypeptide, or protein.
- Each signal peptide of the TCRs, polypeptides, proteins, functional variants, and functional portions described herein, when present, can be any suitable TCR signal peptide, so long as the TCR, polypeptide, protein, or functional variant is expressed and has antigenic specificity for an LMP2 amino acid sequence presented by an HLA Class I molecule.
- the TCR, polypeptide, or protein can consist essentially of the specified amino acid sequence or sequences described herein, such that other components of the TCR, polypeptide, or protein, e.g., other amino acids, do not materially change the biological activity of the TCR, polypeptide, or protein.
- the inventive TCR, polypeptide, or protein can, for example, consist essentially of the amino acid sequence of SEQ ID NO:
- SEQ ID NO: 21 or 98 SEQ ID NO: 22, SEQ ID NO: 23 or 99, SEQ ID NO: 24, SEQ ID NO: 25 or 100, both of SEQ ID NOs: 20, and 21 or 98, both of SEQ ID NO: 22, and 23 or 99, both of SEQ ID NO: 24, and 25 or 100
- SEQ ID NO: 26 SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, both of SEQ ID NOs: 26-27, both of SEQ ID NO: 28-29, or both of SEQ ID NO: 30-31.
- inventive TCRs, polypeptides, or proteins can consist essentially of the amino acid sequences of (a) any one or more of SEQ ID NOs: 1-6, 7-12, 13-18; (b) all of SEQ ID NO: 1-3; (c) all of SEQ ID NO: 4- 6; (d) all of SEQ ID NO: 7-9; (e) all of SEQ ID NOs: 10-12; (f) all of SEQ ID NOs: 13-15;
- the TCRs, polypeptides, and proteins of the invention can be of any length, i.e., can comprise any number of amino acids, provided that the TCRs, polypeptides, or proteins retain their biological activity, e.g., the ability to specifically bind to LMP2; detect cancer in a mammal; or treat or prevent cancer in a mammal, etc.
- the polypeptide can be in the range of from about 50 to about 5000 amino acids long, such as about 50, about 70, about 75, about 100, about 125, about 150, about 175, about 200, about 300, about 400, about 500, about 600, about 700, about 800, about 900, about 1000 or more amino acids in length.
- the polypeptides of the invention also include oligopeptides.
- the TCRs, polypeptides, and proteins of the invention can comprise synthetic amino acids in place of one or more naturally-occurring amino acids.
- synthetic amino acids include, for example, aminocyclohexane carboxylic acid, norleucine, oc-amino n-decanoic acid, homoserine, S-acetylaminomethyl-cysteine, trans-3- and trans-4-hydroxyproline, 4-aminophenylalanine, 4-nitrophenylalanine, 4- chlorophenylalanine, 4-carboxyphenylalanine, ⁇ -phenylserine ⁇ -hydroxyphenylalanine, phenylglycine, oc-naphthylalanine, cyclohexylalanine, cyclohexylglycine, indoline-2- carboxylic acid, l,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, aminomalonic
- TCRs, polypeptides, and proteins of the invention can be glycosylated, amidated, carboxylated, phosphorylated, esterified, N-acylated, cyclized via, e.g., a disulfide bridge, or converted into an acid addition salt and/or optionally dimerized or polymerized, or conjugated.
- the TCR, polypeptide, and/or protein of the invention can be obtained by methods known in the art such as, for example, de novo synthesis.
- polypeptides and proteins can be recombinantly produced using the nucleic acids described herein using standard recombinant methods. See, for instance, Green and Sambrook, Molecular Cloning: A Laboratory Manual. 4 th ed., Cold Spring Harbor Press, Cold Spring Harbor, NY (2012).
- the TCRs, polypeptides, and/or proteins described herein can be commercially synthesized by commercial entities.
- the inventive TCRs, polypeptides, and proteins can be synthetic, recombinant, isolated, and/or purified.
- An embodiment of the invention provides an isolated or purified TCR, polypeptide, or protein encoded by any of the nucleic acids or vectors described herein with respect to other aspects of the invention.
- Another embodiment of the invention provides an isolated or purified TCR, polypeptide, or protein that results from expression of any of the nucleic acids or vectors described herein with respect to other aspects of the invention in a cell.
- Still another embodiment of the invention provides a method of producing any of the TCRs, polypeptides, or proteins described herein, the method comprising culturing any of the host cells or populations of host cells described herein so that the TCR, polypeptide, or protein is produced.
- conjugates e.g., bioconjugates, comprising any of the inventive TCRs, polypeptides, or proteins (including any of the functional portions or variants thereof), nucleic acids, recombinant expression vectors, host cells, populations of host cells, or antibodies, or antigen binding portions thereof.
- An embodiment of the invention provides a nucleic acid comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein.
- Nucleic acid includes “polynucleotide,” “oligonucleotide,” and “nucleic acid molecule,” and generally means a polymer of DNA or RNA, which can be single-stranded or double-stranded, which can contain natural, non-natural or altered nucleotides, and which can contain a natural, non-natural or altered intemucleotide linkage, such as a phosphoroamidate linkage or a phosphorothioate linkage, instead of the phosphodiester found between the nucleotides of an unmodified oligonucleotide.
- the nucleic acid comprises complementary DNA (cDNA).
- the nucleic acid does not comprise any insertions, deletions, inversions, and/or substitutions. However, it may be suitable in some instances, as discussed herein, for the nucleic acid to comprise one or more insertions, deletions, inversions, and/or substitutions.
- the nucleic acids of the invention are recombinant.
- the term “recombinant” refers to (i) molecules that are constructed outside living cells by joining natural or synthetic nucleic acid segments to nucleic acid molecules that can replicate in a living cell, or (ii) molecules that result from the replication of those described in (i) above.
- the replication can be in vitro replication or in vivo replication.
- the nucleic acids can be constructed based on chemical synthesis and/or enzymatic ligation reactions using procedures known in the art. See, for example, Green and Sambrook et al., supra.
- a nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed upon hybridization (e.g., phosphorothioate derivatives and acridine substituted nucleotides).
- modified nucleotides that can be used to generate the nucleic acids include, but are not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxymethyl) uracil, 5-carboxymethylaminomethyl- 2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N 6 -isopentenyladenine, 1 -methylguanine, 1-methybnosine, 2,2-dimethylguanine, 2- methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N 6 -substituted adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-
- the nucleic acid can comprise any nucleotide sequence which encodes any of the TCRs, polypeptides, or proteins described herein.
- the nucleic acid may comprise the nucleotide sequences of any one of SEQ ID NOs: 92-97 and 107-109 (Table 4).
- the nucleic acid comprises the nucleotide sequences of both of SEQ ID NOs: 92, and 93 or 107, or both of SEQ ID NOs: 94, and 95 or 108, or both of SEQ ID NOs: 96, and 97 or 109.
- the nucleic acid comprises a codon-optimized nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein.
- codon optimization of the nucleotide sequence increases the translation efficiency of the mRNA transcripts. Codon optimization of the nucleotide sequence may involve substituting a native codon for another codon that encodes the same amino acid, but can be translated by tRNA that is more readily available within a cell, thus increasing translation efficiency. Optimization of the nucleotide sequence may also reduce secondary mRNA structures that would interfere with translation, thus increasing translation efficiency.
- the invention also provides a nucleic acid comprising a nucleotide sequence which is complementary to the nucleotide sequence of any of the nucleic acids described herein or a nucleotide sequence which hybridizes under stringent conditions to the nucleotide sequence of any of the nucleic acids described herein.
- the nucleotide sequence which hybridizes under stringent conditions preferably hybridizes under high stringency conditions.
- high stringency conditions is meant that the nucleotide sequence specifically hybridizes to a target sequence (the nucleotide sequence of any of the nucleic acids described herein) in an amount that is detectably stronger than non-specific hybridization.
- High stringency conditions include conditions which would distinguish a polynucleotide with an exact complementary sequence, or one containing only a few scattered mismatches from a random sequence that happened to have a few small regions (e.g., 3-10 bases) that matched the nucleotide sequence.
- Relatively high stringency conditions would include, for example, low salt and/or high temperature conditions, such as provided by about 0.02-0.1 M NaCl or the equivalent, at temperatures of about 50-70 °C.
- Such high stringency conditions tolerate little, if any, mismatch between the nucleotide sequence and the template or target strand, and are particularly suitable for detecting expression of any of the inventive TCRs. It is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide.
- the invention also provides a nucleic acid comprising a nucleotide sequence that is at least about 70% or more, e.g., about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to any of the nucleic acids described herein.
- the nucleic acid may consist essentially of any of the nucleotide sequences described herein.
- An embodiment of the invention provides an isolated or purified nucleic acid comprising, from 5’ to 3’, a first nucleic acid sequence and a second nucleotide sequence, wherein the first and second nucleotide sequence, respectively, encode the amino sequences of SEQ ID NOs: 20, and 21 or 98; 21 or 98, and 20; 22, and 23 or 99; 23 or 99, and 22; 24, and 25 or 100; 25 or 100, and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 30 and 31; 31 and 30; 34, and 35 or 101; 35 or 101, and 34; 36, and 37 or 102; 37 or 102, and 36; 38, and 39 or 103; 39 or 103, and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 44 and 45; 45 and 44; 46, and 47 or 104; 47 or 104, and 46; 48, and 49 or 105; 49 or 105, and 48; 50, and 51 or 106; 51 or 106,
- the isolated or purified nucleic acid further comprises a third nucleotide sequence interposed between the first and second nucleotide sequence, wherein the third nucleotide sequence encodes a cleavable linker peptide.
- the cleavable linker peptide comprises the amino acid sequence of SEQ ID NO: 60.
- the nucleic acids of the invention can be incorporated into a recombinant expression vector.
- the invention provides a recombinant expression vector comprising any of the nucleic acids of the invention.
- the recombinant expression vector comprises a nucleotide sequence encoding the a chain, the ⁇ chain, and linker peptide.
- the term "recombinant expression vector” means a genetically -modified oligonucleotide or polynucleotide construct that permits the expression of an mRNA, protein, polypeptide, or peptide by a host cell, when the construct comprises a nucleotide sequence encoding the mRNA, protein, polypeptide, or peptide, and the vector is contacted with the cell under conditions sufficient to have the mRNA, protein, polypeptide, or peptide expressed within the cell.
- the vectors of the invention are not naturally-occurring as a whole. However, parts of the vectors can be naturally-occurring.
- the inventive recombinant expression vectors can comprise any type of nucleotide, including, but not limited to DNA and RNA, which can be single-stranded or double-stranded, synthesized or obtained in part from natural sources, and which can contain natural, non-natural or altered nucleotides.
- the recombinant expression vectors can comprise naturally-occurring, non- naturally-occurring intemucleotide linkages, or both types of linkages.
- the non- naturally occurring or altered nucleotides or intemucleotide linkages do not hinder the transcription or replication of the vector.
- the recombinant expression vector of the invention can be any suitable recombinant expression vector, and can be used to transform or transfect any suitable host cell.
- Suitable vectors include those designed for propagation and expansion or for expression or both, such as plasmids and viruses.
- the vector can be selected from the pUC series (Fermentas Life Sciences), the pBluescript series (Stratagene, LaJolla, CA), the pET series (Novagen, Madison, WI), the pGEX series (Pharmacia Biotech, Uppsala, Sweden), and the pEX series (Clontech, Palo Alto, CA).
- Bacteriophage vectors such as /.GTK).
- the recombinant expression vector is a viral vector, e.g., a retroviral vector.
- the recombinant expression vector is an MSGV1 vector.
- the recombinant expression vector is a transposon or a lentiviral vector.
- the recombinant expression vectors of the invention can be prepared using standard recombinant DNA techniques described in, for example, Green and Sambrook et al., supra. Constructs of expression vectors, which are circular or linear, can be prepared to contain a replication system functional in a prokaryotic or eukaryotic host cell. Replication systems can be derived, e.g., from ColEl, 2 m plasmid, l, SV40, bovine papillomavirus, and the like.
- the recombinant expression vector comprises regulatory sequences, such as transcription and translation initiation and termination codons, which are specific to the type of host cell (e.g., bacterium, fungus, plant, or animal) into which the vector is to be introduced, as appropriate and taking into consideration whether the vector is DNA- or RNA- based.
- regulatory sequences such as transcription and translation initiation and termination codons, which are specific to the type of host cell (e.g., bacterium, fungus, plant, or animal) into which the vector is to be introduced, as appropriate and taking into consideration whether the vector is DNA- or RNA- based.
- the recombinant expression vector can include one or more marker genes, which allow for selection of transformed or transfected host cells.
- Marker genes include biocide resistance, e.g., resistance to antibiotics, heavy metals, etc., complementation in an auxotrophic host cell to provide prototrophy, and the like.
- Suitable marker genes for the inventive expression vectors include, for instance, neomycin/G418 resistance genes, hygromycin resistance genes, histidinol resistance genes, tetracycline resistance genes, and ampicillin resistance genes.
- the recombinant expression vector can comprise a native or normative promoter operably linked to the nucleotide sequence encoding the TCR, polypeptide, or protein, or to the nucleotide sequence which is complementary to or which hybridizes to the nucleotide sequence encoding the TCR, polypeptide, or protein.
- a native or normative promoter operably linked to the nucleotide sequence encoding the TCR, polypeptide, or protein, or to the nucleotide sequence which is complementary to or which hybridizes to the nucleotide sequence encoding the TCR, polypeptide, or protein.
- the promoter can be a non-viral promoter or a viral promoter, e.g., a cytomegalovirus (CMV) promoter, an SV40 promoter, an RSV promoter, and a promoter found in the long-terminal repeat of the murine stem cell virus.
- CMV cytomegalovirus
- inventive recombinant expression vectors can be designed for either transient expression, for stable expression, or for both. Also, the recombinant expression vectors can be made for constitutive expression or for inducible expression.
- the recombinant expression vectors can be made to include a suicide gene.
- suicide gene refers to a gene that causes the cell expressing the suicide gene to die.
- the suicide gene can be a gene that confers sensitivity to an agent, e.g., a drug, upon the cell in which the gene is expressed, and causes the cell to die when the cell is contacted with or exposed to the agent.
- Suicide genes are known in the art and include, for example, the Herpes Simplex Virus (HSV) thymidine kinase (TK) gene, cytosine deaminase, purine nucleoside phosphorylase, nitroreductase, and the inducible caspase 9 gene system.
- HSV Herpes Simplex Virus
- TK thymidine kinase
- Another embodiment of the invention further provides a host cell comprising any of the recombinant expression vectors described herein.
- the term "host cell” refers to any type of cell that can contain the inventive recombinant expression vector.
- the host cell can be a eukaryotic cell, e.g., plant, animal, fungi, or algae, or can be a prokaryotic cell, e.g., bacteria or protozoa.
- the host cell can be a cultured cell or a primary cell, i.e., isolated directly from an organism, e.g., a human.
- the host cell can be an adherent cell or a suspended cell, i.e., a cell that grows in suspension.
- Suitable host cells are known in the art and include, for instance, DH5a A. coli cells, Chinese hamster ovarian cells, monkey VERO cells, COS cells, HEK293 cells, and the like.
- the host cell is preferably a prokaryotic cell, e.g., a DH5oc cell.
- the host cell is preferably a mammalian cell. Most preferably, the host cell is a human cell.
- the host cell can be of any cell type, can originate from any type of tissue, and can be of any developmental stage, the host cell preferably is a peripheral blood lymphocyte (PBL) or a peripheral blood mononuclear cell (PBMC). More preferably, the host cell is a T cell. In an embodiment of the invention, the host cell is a human lymphocyte. In another embodiment of the invention, the host cell is selected from any of a T cell, a natural killer T (NKT) cell, an invariant natural killer T (iNKT) cell, and a natural killer (NK) cell.
- PBL peripheral blood lymphocyte
- PBMC peripheral blood mononuclear cell
- the host cell is a T cell.
- the host cell is a human lymphocyte.
- the host cell is selected from any of a T cell, a natural killer T (NKT) cell, an invariant natural killer T (iNKT) cell, and a natural killer (NK) cell.
- Still another embodiment of the invention provides a method of producing a host cell expressing a TCR that has antigenic specificity for the peptide of SEQ ID NO: 19, the method comprising contacting a cell with any of the vectors described herein under conditions that allow introduction of the vector into the cell.
- the T cell can be any T cell, such as a cultured T cell, e.g., a primary T cell, or a T cell from a cultured T cell line, e.g., Jurkat, SupTl, etc., or a T cell obtained from a mammal. If obtained from a mammal, the T cell can be obtained from numerous sources, including but not limited to blood, bone marrow, lymph node, the thymus, or other tissues or fluids. T cells can also be enriched for or purified. Preferably, the T cell is a human T cell.
- the T cell can be any type of T cell and can be of any developmental stage, including but not limited to, CD4 + /CD8 + double positive T cells, CD4 + helper T cells, e.g., Thi and Th2 cells, CD4 + T cells, CD8 + T cells (e.g., cytotoxic T cells), tumor infiltrating lymphocytes (TILs), memory T cells (e.g., central memory T cells and effector memory T cells), naive T cells, and the like.
- CD4 + /CD8 + double positive T cells CD4 + helper T cells, e.g., Thi and Th2 cells
- CD4 + T cells e.g., CD4 + T cells
- CD8 + T cells e.g., cytotoxic T cells
- TILs tumor infiltrating lymphocytes
- memory T cells e.g., central memory T cells and effector memory T cells
- naive T cells e.g., naive T cells, and the like.
- the population of cells can be a heterogeneous population comprising the host cell comprising any of the recombinant expression vectors described, in addition to at least one other cell, e.g., a host cell (e.g., a T cell), which does not comprise any of the recombinant expression vectors, or a cell other than a T cell, e.g., a B cell, a macrophage, a neutrophil, an erythrocyte, a hepatocyte, an endothelial cell, an epithelial cell, a muscle cell, a brain cell, etc.
- a host cell e.g., a T cell
- a cell other than a T cell e.g., a B cell, a macrophage, a neutrophil, an erythrocyte, a hepatocyte, an endothelial cell, an epithelial cell, a muscle cell, a brain cell, etc.
- the population of cells can be a substantially homogeneous population, in which the population comprises mainly of host cells (e.g., consisting essentially of) comprising the recombinant expression vector.
- the population also can be a clonal population of cells, in which all cells of the population are clones of a single host cell comprising a recombinant expression vector, such that all cells of the population comprise the recombinant expression vector.
- the population of cells is a clonal population comprising host cells comprising a recombinant expression vector as described herein.
- the numbers of cells in the population may be rapidly expanded. Expansion of the numbers of T cells can be accomplished by any of a number of methods as are known in the art as described in, for example, U.S. Patent 8,034,334; U.S. Patent 8,383,099; U.S. Patent Application Publication No. 2012/0244133; Dudley et ak, J. Immunother., 26:332-42 (2003); and Riddell et ak, J. Immunol. Methods, 128:189-201 (1990). In embodiments, expansion of the numbers of T cells is carried out by culturing the T cells with 0KT3 antibody, IL-2, and feeder PBMC (e.g., irradiated allogeneic PBMC).
- PBMC e.g., irradiated allogeneic PBMC
- inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, and host cells can be isolated and/or purified.
- isolated means having been removed from its natural environment.
- purified means having been increased in purity, wherein “purity” is a relative term, and not to be necessarily construed as absolute purity.
- the purity can be at least about 50%, can be greater than about 60%, about 70%, about 80%, about 90%, about 95%, or can be about 100%.
- inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, and host cells (including populations thereof), all of which are collectively referred to as "inventive TCR materials" hereinafter, can be formulated into a composition, such as a pharmaceutical composition.
- the invention provides a pharmaceutical composition comprising any of the TCRs, polypeptides, proteins, nucleic acids, expression vectors, and host cells (including populations thereof), described herein, and a pharmaceutically acceptable carrier.
- inventive pharmaceutical compositions containing any of the inventive TCR materials can comprise more than one inventive TCR material, e.g., a polypeptide and a nucleic acid, or two or more different TCRs.
- the pharmaceutical composition can comprise an inventive TCR material in combination with another pharmaceutically active agent(s) or drug(s), such as a chemotherapeutic agent, e.g., asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, vincristine, etc.
- a chemotherapeutic agent e.g., asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, vincristine, etc.
- the carrier is a pharmaceutically acceptable carrier.
- the carrier can be any of those conventionally used for the particular inventive TCR material under consideration
- compositions are known or apparent to those skilled in the art and are described in more detail in, for example, Remington : The Science and Practice of Pharmacy, 22 nd Ed., Pharmaceutical Press (2012). ft is preferred that the pharmaceutically acceptable carrier be one which has no detrimental side effects or toxicity under the conditions of use.
- Suitable formulations may include any of those for parenteral, subcutaneous, intravenous, intramuscular, intraarterial, intrathecal, intratumoral, or interperitoneal administration. More than one route can be used to administer the inventive TCR materials, and in certain instances, a particular route can provide a more immediate and more effective response than another route.
- the inventive TCR material is administered by injection, e.g., intravenously.
- the pharmaceutically acceptable carrier for the cells for injection may include any isotonic carrier such as, for example, normal saline (about 0.90% w/v of NaCl in water, about 300 mOsm/L NaC1 in water, or about 9.0 g NaCl per liter of water), NORMOSOL R electrolyte solution (Abbott, Chicago, IL), PLASMA-LYTE A (Baxter, Deerfield, IL), about 5% dextrose in water, or Ringer's lactate.
- the pharmaceutically acceptable carrier is supplemented with human serum albumin.
- the amount or dose (e.g., numbers of cells when the inventive TCR material is one or more cells) of the inventive TCR material administered should be sufficient to effect, e.g., a therapeutic or prophylactic response, in the subject or animal over a reasonable time frame.
- the dose of the inventive TCR material should be sufficient to bind to a cancer antigen (e.g., LMP2), or detect, treat or prevent cancer in a period of from about 2 hours or longer, e.g., 12 to 24 or more hours, from the time of administration. In certain embodiments, the time period could be even longer.
- a cancer antigen e.g., LMP2
- the dose will be determined by the efficacy of the particular inventive TCR material and the condition of the animal (e.g., human), as well as the body weight of the animal (e.g., human) to be treated.
- Many assays for determining an administered dose are known in the art.
- an assay which comprises comparing the extent to which target cells are lysed or IFN- ⁇ is secreted by T cells expressing the inventive TCR, polypeptide, or protein upon administration of a given dose of such T cells to a mammal among a set of mammals of which each is given a different dose of the T cells, could be used to determine a starting dose to be administered to a mammal.
- the extent to which target cells are lysed or IFN- ⁇ is secreted upon administration of a certain dose can be assayed by methods known in the art.
- the dose of the inventive TCR material also will be determined by the existence, nature and extent of any adverse side effects that might accompany the administration of a particular inventive TCR material. Typically, the attending physician will decide the dosage of the inventive TCR material with which to treat each individual patient, taking into consideration a variety of factors, such as age, body weight, general health, diet, sex, inventive TCR material to be administered, route of administration, and the severity of the cancer being treated.
- the inventive TCR material is a population of cells
- the number of cells administered per infusion may vary, e.g., from about 1 x 10 6 to about 1 x 10 12 cells or more. In certain embodiments, fewer than 1 x 10 6 cells may be administered.
- inventive TCR materials of the invention can be modified in any number of ways, such that the therapeutic or prophylactic efficacy of the inventive TCR materials is increased through the modification.
- inventive TCR materials can be conjugated either directly or indirectly through a bridge to a chemotherapeutic agent.
- the practice of conjugating compounds to a chemotherapeutic agent is known in the art.
- sites on the inventive TCR materials which are not necessary for the function of the inventive TCR materials, are suitable sites for attaching a bridge and/or a chemotherapeutic agent, provided that the bridge and/or chemotherapeutic agent, once attached to the inventive TCR materials, do(es) not interfere with the function of the inventive TCR materials, i.e., the ability to bind to LMP2 or to detect, treat, or prevent cancer.
- inventive pharmaceutical compositions TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, and populations of cells can be used in methods of treating or preventing cancer.
- inventive TCRs are believed to bind specifically to LMP2, such that the TCR (or related inventive polypeptide or protein), when expressed by a cell, is able to mediate an immune response against a target cell expressing LMP2.
- the invention provides a method of treating or preventing cancer in a mammal, comprising administering to the mammal any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, in an amount effective to treat or prevent cancer in the mammal.
- An embodiment of the invention provides a method of inducing an immune response against a cancer in a mammal, comprising administering to the mammal any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, in an amount effective to induce an immune response against the cancer in the mammal.
- An embodiment of the invention provides any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, for use in the treatment or prevention of cancer in a mammal.
- An embodiment of the invention provides any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, for use in inducing an immune response against a cancer in a mammal.
- inventive methods can provide any amount of any level of treatment or prevention of cancer in a mammal.
- the treatment or prevention provided by the inventive method can include treatment or prevention of one or more conditions or symptoms of the cancer being treated or prevented.
- treatment or prevention can include promoting the regression of a tumor.
- prevention can encompass delaying the onset of the cancer, or a symptom or condition thereof. Alternatively or additionally, “prevention” may encompass preventing or delaying the recurrence of cancer, or a symptom or condition thereof.
- a method of detecting the presence of cancer in a mammal comprises (i) contacting a sample comprising one or more cells from the mammal with any of the inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, populations of cells, or pharmaceutical compositions described herein, thereby forming a complex, and (ii) detecting the complex, wherein detection of the complex is indicative of the presence of cancer in the mammal.
- the sample of cells can be a sample comprising whole cells, lysates thereof, or a fraction of the whole cell lysates, e.g., a nuclear or cytoplasmic fraction, a whole protein fraction, or a nucleic acid fraction.
- the contacting can take place in vitro or in vivo with respect to the mammal.
- the contacting is in vitro.
- detection of the complex can occur through any number of ways known in the art.
- the inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, or populations of cells, described herein can be labeled with a detectable label such as, for instance, a radioisotope, a fluorophore (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), an enzyme (e.g., alkaline phosphatase, horseradish peroxidase), and element particles (e.g., gold particles).
- a detectable label such as, for instance, a radioisotope, a fluorophore (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), an enzyme (e.g., alkaline phosphatase, horseradish peroxidase), and element particles (e.g., gold particles).
- the cells can be cells that are allogeneic or autologous to the mammal.
- the cells are autologous to the mammal.
- the cancer can be any cancer, including, e.g., any of acute lymphocytic cancer, acute myeloid leukemia, alveolar rhabdomyosarcoma, bone cancer, brain cancer, breast cancer, cancer of the anus, anal canal, or anorectum, cancer of the eye, cancer of the intrahepatic bile duct, cancer of the joints, cancer of the neck, gallbladder, or pleura, cancer of the nose, nasal cavity, or middle ear, cancer of the oral cavity, cancer of the vagina, cancer of the vulva, chronic lymphocytic leukemia, chronic myeloid cancer, colon cancer, colorectal cancer, endometrial cancer, esophageal cancer, uterine cervical cancer, gastrointestinal carcinoid tumor, glioma, Hodgkin lymphoma, hypopharynx cancer, kidney cancer, larynx cancer, liver cancer, lung cancer, malignant mesothelioma,
- any cancer including, e.g.
- a preferred cancer is an epithelial cancer (such as nasopharyngeal cancer or gastric cancer) or a lymphoma (such as Hodgkin lymphoma, T/NK cell lymphoma, or post-transplant lymphoproliferative disorders).
- the cancer expresses an LMP2 amino acid sequence, wherein the LMP2 amino acid sequence is SEQ ID NO: 19.
- the LMP2 expressed by the cancer may be as described herein with respect to other aspects of the invention.
- the mammal referred to in the inventive methods can be any mammal.
- the term "mammal” refers to any mammal, including, but not limited to, mammals of the order Rodentia, such as mice and hamsters, and mammals of the order Logomorpha, such as rabbits. It is preferred that the mammals are from the order Carnivora, including Felines (cats) and Canines (dogs). It is more preferred that the mammals are from the order Artiodactyla, including Bovines (cows) and Swines (pigs) or of the order Perssodactyla, including Equines (horses). It is most preferred that the mammals are of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). An especially preferred mammal is the human.
- Flow cytometry was performed in the various Examples below using the following materials and software.
- PE- conjugated antibody against tetramer, or APC-conjugated antibody against mouse constant region Biolegend, San Diego, CA, USA or BD Biosciences, San Jose, CA, USA
- FlowJo software FlowJo, LLC, Ashland, OR, USA.
- CD8+ T cells and dendritic cells were isolated from healthy donors. Matured DCs were pulsed with LMP2 peptide LMP2426-434 for four hours. CD8+ T cells were stimulated with peptide pulsed autologous DCs. After two rounds of stimulation, T cells were tested for reactivity against 293-A2 cells expressing the full length LMP2 protein and were found to possess LMP2-reactive T cells. LMP2 reactive T cells were enriched using LMP2426-434-HLA-A*02:01 tetramers. The enriched T cells were confirmed to be tetramer positive and CD8 positive ( Figures 1A-1F). Subsequently, these LMP2 reactive CD8+ T cells were sequenced using single cell sequencing to identify paired T-cell receptor (TCR) TCRoc and TCR ⁇ chain sequences (TCRoc (TCRAV) and TCR ⁇ (TCRBV)).
- This Example demonstrates construction of a retroviral vector encoding anti- LMP2 TCRs.
- MSGV1 based-retroviral vectors were constructed which encoded TCR alpha and beta chain variable regions which were identical to each of the TCRs of Example 1 with the exception that the amino acid residue at position 2 of the N-terminal signal peptide of the beta chain was changed to an alanine in order to facilitate cloning into the vector. Additional modifications to the wild-type TCR were made, as described in more detail below. [0137] Construction of LMP2-specific TCRs was done as previously described (Jin et al.,
- the murine TCRoc and TCR ⁇ constant chains were cysteine-modified, and transmembrane hydrophobic mutations were introduced into the murine TCRoc constant chain. Without being bound to a particular theory or mechanism, it is believed that these modifications result in preferential pairing of the introduced TCR chains and enhanced TCR surface expression and functionality (Cohen et al., Cancer Res., 67(8):3898-903 (2007); Haga-Friedman et al., J. Immu., 188: 5538-5546 (2012)).
- TCR ⁇ and TCRoc chains were separated by a Furin SGSG P2A linker (RAKRS GS GATNF S LLKQ AGD VEENPGP) (SEQ ID NO: 60) to ensure a comparable expression efficiency of the two chains (Szymczak et al., Nat. Biotechnol., 22(5):589-94 (2004)).
- RAKRS GS GATNF S LLKQ AGD VEENPGP SEQ ID NO: 60
- the second amino acid in the TCR ⁇ chain (the second amino acid within the N-terminal signal peptide) was changed to an alanine (A).
- the expression cassette had the following configuration: 5 NcoI-VDJ ⁇ -mC ⁇ -Furin/SGSG/P2A-VJ ⁇ -mC ⁇ .-EcoRI3 .
- the nucleotide sequences of each TCR were codon optimized for human tissue expression.
- Retrovirus encoding the TCR D6 anti-LMP2 TCR was produced and used to transduce peripheral blood T cells with the TCR D6-encoding MSGV1 vector of Example 2.
- Human peripheral blood mononuclear cells (PBMCs) were isolated from the huffy coats. Before transduction, PBMCs were cultured in T cell media plus 50 ng/mL anti-CD3 (OKT3, Miltenyi Biotec, Bergisch Gladbach, Germany) for two days. Retroviral supernatants were generated by co-transfection of 293GP cells with MSGV1 vector expressing TCR and RD114 packaging plasmids. Two days after transfection, retroviral supernatants were harvested.
- Transduction was performed by adding 5 ml retroviral supernatant to one well of a six-well plate coated with RetroNectin and centrifuged at 2000g for 2 hours at 32°C. The retroviral supernatant was discarded and 1 million T cells were added. On the following day, T cells were harvested and cultured in normal condition.
- TCR The expression of the introduced TCR was assessed by flow cytometry using an antibody specific for the mouse TCR ⁇ chain. The results indicated that the TCR specifically binds to LMP2426-434-HLA-A*02:01 tetramers, but it does not bind to E7-HLA-A*02:01 tetramers ( Figures 2A-2D).
- the anti-LMP2 TCR transduced T cells were co- cultured with 293-A2 cells pulsed with serial diluted LMP2426-434 peptide.
- Anti-LMP2 TCR transduced T cells displayed high functional avidity in the range of 10 -9 -10 -10 M LMP2426-434 peptide ( Figure 6).
- This Example demonstrates EBV -transformed lymphoblastoid cell line (EBV- LCL) recognition by the anti-LMP2 TCR D6.
- EBV-LCLs naturally express all latent proteins including: EBNA1, EBNA2, EBNA3, LMP1, and LMP2.
- EBV-LCLs are HLA-intact.
- Several EBV-LCLs were made. LMP2 protein expression was confirmed by Western Blot (Figure 7A). When anti-LMP2 TCR T cells were co-cultured with EBV-LCLs, the T cells showed production of IFN- ⁇ in response to each of the HLA-A*02:01+ EBV-LCLs ( Figure 7B). EBV-LCLs lacking HLA-A*02:01 were not recognized.
- This Example demonstrates tumor cell line recognition by the anti-LMP2 TCR D6.
- Anti-LMP2426-434 TCR transduced CD8+ T cells produced the inflammatory effector cytokine IFN- ⁇ when co-cultured with four nasopharyngeal cancer cell lines expressing LMP2 and HLA-A*02:01, but not when co-cultured with several tumor cell lines lacking LMP2 or HLA-A*02:01 ( Figure 8A).
- introduction of the target antigen LMP2 into two tumor cell lines naturally expressing HLA-A*02:01 but not the target antigen conferred their recognition by the anti-LMP2426-434 TCR transduced CD8+ T cells Figure 8A).
- Figures 8B and 8C are graphs showing additional results of T cells transduced to express the anti-LMP2 TCR D6 co-cultured with target cell lines as indicated on the x-axis, at an E:T ratio of 1:1, 5e4 cells each in 96-well round-bottom plate for a final total volume of 200 pL/well. The levels of IFN ⁇ in the overnight co-culture supernatant was measured with ELISA. [0154] The results indicate that LMP2 TCR can recognize processed and presented epitope of LMP2 antigen on tumor cell lines in an antigen- and HLA-A*02:01- dependent fashion.
- This Example demonstrates tumor cell cytoloysis induced by the anti-LMP2 TCR D6.
- the anti-LMP2 TCR D2 was constructed, and T cells transduced, similarly as was detailed above for TCR D6.
- TCR D6 T cells recognized LMP2426-434 peptide at lower concentrations than TCR D2 T cells (Figure 10A). TCR D6 T cells showed IFN- ⁇ release at concentration as low as 10 picomoles, whereas TCR D2 T cells showed IFN- ⁇ release at concentration as low as 100 picomoles. These findings indicated that TCR D2 T cells had lower avidity for LMP2426-434 peptide than TCR D6 T cells.
- TCR D2 and TCR D6 T cells were compared ( Figures 10B and C).
- effector-to-target ratio (E:T) was 1:1
- the TCRs showed similar ability in killing tumor cells ( Figure 10B).
- effector-to-target ratio (E:T) was 1:5, TCR D6 was able to continuously kill tumor cells in 48 h, while TCR D2 showed limited killing ability (Figure IOC), possibly due to its lower avidity than TCR D6 in lower concentrations.
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Abstract
Disclosed are isolated or purified T cell receptors (TCRs), wherein the TCRs have antigenic specificity for a LMP2 amino acid sequence presented by a human leukocyte antigen (HLA) Class I molecule. Related polypeptides and proteins, as well as related nucleic acids, recombinant expression vectors, host cells, populations of cells, and pharmaceutical compositions are also provided. Also disclosed are methods of detecting the presence of cancer in a mammal and methods of treating or preventing cancer in a mammal.
Description
HLA CLASS I-RESTRICTED T CELL RECEPTORS AGAINST LMP2
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This patent application claims the benefit of U.S. Provisional Patent Application No. 63/008,949, filed April 13, 2020, and U.S. Provisional Patent Application No. 63/032,954, filed June 1, 2020, each of which is incorporated by reference in its entirety herein.
STATEMENT REGARDING
FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
[0002] This invention was made with Government support under project number ZIA BC 011871 by the National Institutes of Health, National Cancer Institute. The Government has certain rights in the invention.
INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED
ELECTRONICALLY
[0003] Incorporated by reference in its entirety herein is a computer-readable nucleotide/amino acid sequence listing submitted concurrently herewith and identified as follows: One 147,121 Byte ASCII (Text) file named “753310_ST25.txt” dated April 12, 2021
BACKGROUND OF THE INVENTION
[0004] Some cancers may have very limited treatment options, particularly when the cancer becomes metastatic and unresectable. Despite advances in treatments such as, for example, surgery, chemotherapy, and radiation therapy, the prognosis for many cancers, such as, for example, lymphomas and epithelial cancers, including Hodgkin lymphoma, T/NK cell lymphoma, post-transplant lymphoproliferative disorders, nasopharyngeal cancer, and gastric cancer, may be poor. Accordingly, there exists an unmet need for additional treatments for cancer.
BRIEF SUMMARY OF THE INVENTION
[0005] An embodiment of the invention provides an isolated or purified T-cell receptor (TCR) comprising the amino acid sequences of (a) SEQ ID NOs: 1-3, (b) SEQ ID NOs: 4-6, (c) SEQ ID NOs: 7-9, (d) SEQ ID NOs: 10-12, (e) SEQ ID NOs: 13-15, (f) SEQ ID NOs: 16- 18, (g) SEQ ID NOs: 1-6, (h) SEQ ID NOs: 7-12, or (i) SEQ ID NOs: 13-18, wherein the TCR has antigenic specificity for a LMP2 amino acid sequence presented by a human leukocyte antigen (HLA) Class I molecule.
[0006] Another embodiment of the invention provides an isolated or purified polypeptide comprising a functional portion of the inventive TCR, wherein the functional portion comprises the amino acid sequences of: (a) SEQ ID NOs: 1-3, (b) SEQ ID NOs: 4-6, (c) SEQ ID NOs: 7-9, (d) SEQ ID NOs: 10-12, (e) SEQ ID NOs: 13-15, (f) SEQ ID NOs: 16-18,
(g) SEQ ID NOs: 1-6, (h) SEQ ID NOs: 7-12, or (i) SEQ ID NOs: 13-18.
[0007] Still another embodiment of the invention provides an isolated or purified protein comprising at least one of the inventive polypeptides.
[0008] Further embodiments of the invention provide nucleic acids, recombinant expression vectors, host cells, populations of cells, and pharmaceutical compositions relating to the inventive TCRs, polypeptides, and proteins.
[0009] An embodiment of the invention provides an isolated or purified nucleic acid comprising, from 5’ to 3’, a first nucleic acid sequence and a second nucleotide sequence, wherein the first and second nucleotide sequence, respectively, encode the amino sequences of SEQ ID NOs: 20, and 21 or 98; 21 or 98, and 20; 22, and 23 or 99; 23 or 99, and 22; 24, and 25 or 100; 25 or 100, and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 30 and 31; 31 and 30; 34, and 35 or 101; 35 or 101, and 34; 36, and 37 or 102; 37 or 102, and 36; 38, and 39 or 103; 39 or 103, and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 44 and 45; 45 and 44; 46, and 47 or 104; 47 or 104, and 46; 48, and 49 or 105; 49 or 105, and 48; 50, and 51 or 106; 51 or 106, and 50; 52 and 53; 53 and 52; 54 and 55; 55 and 54; 56 and 57; 57 and 56. [0010] Methods of detecting the presence of cancer in a mammal, methods of treating or preventing cancer in a mammal, methods of inducing an immune response against a cancer in a mammal, methods of producing a host cell expressing a TCR that has antigenic specificity for the peptide of SEQ ID NO: 19, and methods of producing the inventive TCRs, polypeptides, and proteins, are further provided by embodiments of the invention.
[0011] Additional embodiments are as described herein.
BRIEF DESCRIPTION OF THE DRAWINGS
[0012] Figures 1A-1F present flow cytometry plots. Anti-LMP2 reactive T cells were enriched using LMP2426-434-HLA-A*02:01 tetramers. The tetramers were PE labeled. The antibody against CD8 was FITC labeled. Figure 1 A presents the TCR D2 before enrichment. Figure IB presents the TCR D2 after enrichment. Figure 1C presents the TCR D6 before enrichment. Figure ID presents the TCR D6 after enrichment. Figure IE presents the TCR D29 before enrichment. Figure IF presents the TCR D29 after enrichment.
[0013] Figures 2A-2D present flow cytometry plots. HPV16 E7 TCR T cells and E7ii-i9- HLA-A*02:01 tetramers were used as control. The tetramers were PE-labeled. The antibody against mouse TCR constant region (mTRBC) was APC-labeled. Figure 2A shows detection of anti-LMP2 TCR D6 binding to LMP2. Figure 2B shows anti-LMP2 TCR D6 does not bind to E7. Figure 2C shows detection of anti-HPV16 E7 TCR binding E7. Figure 2D shows anti-HPV16 E7 TCR does not bind LMP2.
[0014] Figure 3 is a graph showing IFNγ levels of an anti-LMP2 TCR based on alanine scanning of the LMP2426-434 epitope. An alanine residue was substituted for the native residue at each position of the peptide (CLGGLLTMV (SEQ ID NO: 19)). The residue substitutions are shown on the x axis. The assays shown were performed by co-culture of an anti-LMP2 TCR T cell (effector cells) with 293-A2 cells pulsed with 1 μg/ml peptide (target cells) indicated on the x axis. Co-culture supernatants were harvested after 18-24 hours, and the IFNγ concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells pulsed with no peptide or treated with PMA and ionomycin instead of peptide served as control target cells.
[0015] Figure 4 is a graph showing results of T cells transduced with the anti-LMP2 TCR D6 or untransduced T cells co-cultured with K562A2 loaded with 1 mM of peptide as indicated in the x-axis. The levels of IFNγ in the overnight co-culture supernatant was measured with ELISA.
[0016] Figure 5 is a graph showing results of T cells transduced with the anti-LMP2 TCR D6 or untransduced T cells co-cultured with K562A2 loaded with titrated concentrations of peptides as indicated in the x-axis. The levels of IFNy in the overnight co-culture supernatant was measured with ELISA.
[0017] Figure 6 is a graph showing a functional avidity assay with the quantity of IFN-γ produced in an overnight co-culture. The target cells are K562 cells pulsed with LMP2426-434 or E7II-I9 peptide at the concentrations indicated on the x axis. The TCR/target antigen combinations are shown in the key.
[0018] Figure 7A presents Western Blots confirming the expression of LMP2 (or actin, as a control) on EBV-LCLs.
[0019] Figure 7B is a graph showing IFNγ levels of an anti-LMP2 TCR tested for recognition of EBV-LCLs. The assay was performed by co-culture of TCR T cells (effector cells) with EBV-LCLs (target cells) indicated on the x axis. The effector-to-target ratio is 1:1. Co-culture supernatants were harvested after 18-24 hours, and the IFNγ concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells treated with PMA and ionomycin served as control target cells. Positive expression of LMP2 and HLA- A*02:01 by target cells is indicated by the symbol “+”; lack of expression expression of HLA-A*02:01 by target cells is indicated by the symbol The target cells in the x axis cell lines are derived from multiple patients.
[0020] Figure 8A is a graph showing anti-LMP2 TCR T cells recognize HLA-A*02:01+ and LMP2+ cancer cell lines. The assay was performed by co-culture of TCR T cells (effector cells) with each cancer cell line (target cells) indicated on the x axis. The effector- to-target ratio is 1:1. Co-culture supernatants were harvested after 18-24 hours, and the IFN-γ g concentration was measured by ELISA. Error bars represent the SEM of 3 technical replicates. Untransduced (UT) T cells served as a control effector cell. Target cells cultured alone or treated with PMA and ionomycin served as control target cells. Positive expression of LMP2 and HLA-A*02:01 by target cells is indicated by the symbol “+”; lack of expression of LMP2 and HLA-A*02:01 by target cells is indicated by the symbol [0021] Figures 8B and 8C are graphs showing results of T cells transduced to express anti-LMP2 TCR D6 co-cultured with target cell lines. Some donors’ PBMCs transduced to express the anti-LMP2 TCR demonstrate the data shown in Figure 8B (representative of 5 experiments) where the anti-LMP2 TCR-transduced T cells do not recognize the A2+ EBV LCLs. In some donors’ PBMCs, the anti-LMP2 TCR-transduced T cells recognized some A2+ EBV-LCLs as shown in Figure 8C. K562A2 and K562LMP2 is K562 retrovirally transduced to express HLA-A*02:01 and LMP2 (B95-8 strain), respectively. K562A2LMP2 is K562 retrovirally transduced to express both LMP2 (B95-8 strain) and HLA-A*02:01.
K562A2 LMP2pep, K562A2 E7pep, and K562A2 CD22pep indicate K562A2 cell line loaded with 1 mM of peptides LMP2P426-434, HPV-16 E7p11-19, or CD22P228- 236, respectively. [0022] Figures 9A-9F are graphs showing LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer. The target cell line name and the expression of LMP2 and HLA-A*02:01 are indicated. The effector-to-target ratio is 1:1. The values plotted are the means of 3 technical replicates, and error bars represent the SEM. UT, untransduced T cells; LMP2 TCR, LMP2 TCR-transduced T cells; None, target cells alone. Figure 9A presents the cell line HONE1-EBV A2+/LMP2+. Figure 9B presents the cell line 4050-LMP2 A2+/LMP2+. Figure 9C presents the cell line 4050 A2+/LMP2-. Figure 9D presents the cell line HK1-EBV A2+/LMP2+. Figure 9E presents the cell line 293A2-LMP2 A2+/LMP2+. Figure 9F presents the cell line Hela A2- /LMP2-.
[0023] Figure 10A is a graph showing a functional avidity assay with the quantity of IFNγ produced in an overnight co-culture. The target cells are 293-A2 cells pulsed with LMP2426-434 peptide at the concentrations indicated on the x axis. The effector cells are cells transduced with the D2 or D6 TCR.
[0024] Figure 10B is a graph showing anti-LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer. The target cell line is HK1-EBV. The effector-to-target ratio is 1:1. The values plotted are the means of 3 technical replicates, and error bars represent the SEM. UT, untransduced T cells; D2, LMP2 TCR D2 transduced T cells; D6, LMP2 TCR D6 transduced T cells; None, target cells alone.
[0025] Figure IOC is a graph showing anti-LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer. The target cell line is HK1-EBV. The effector-to-target ratio is 1:5. The values plotted are the means of 3 technical replicates, and error bars represent the SEM. UT, untransduced T cells; D2, LMP2 TCR D2 transduced T cells; D6, LMP2 TCR D6 transduced T cells; None, target cells alone.
[0026] Figure 10D is a graph showing LMP2 TCR T cell-mediated cytolysis of tumor cell lines, as determined by an ACEA xCELLigence Real Time Cell Analyzer. The target cell line is HK1-EBV. The effector-to-target ratio is 1:1. UT, untransduced T cells; D29, LMP2 TCR clone D29 transduced T cells; D6, LMP2 TCR clone D6 transduced T cells.
DETAILED DESCRIPTION OF THE INVENTION
[0027] An embodiment of the invention provides an isolated or purified TCR having antigenic specificity for an EBV antigen LMP2 amino acid sequence CLGGLLTMV (SEQ ID NO: 19) presented by a human leukocyte antigen (HLA) Class I molecule. Hereinafter, references to a “TCR” also refer to functional portions and functional variants of the TCR, unless specified otherwise. The inventive TCR may have antigenic specificity for any LMP2 protein, polypeptide or peptide amino acid sequence, for example LMP2A (EBV strain B95- 8) (SEQ ID NO: 86), LMP2A (EBV strain AG876) (SEQ ID NO: 87), LMP2A (EBV strain GDI) (SEQ ID NO: 88), LMP2B (EBV strain B95-8) (SEQ ID NO: 89), LMP2B (EBV strain AG876) (SEQ ID NO: 90), or LMP2B (EBV strain GDI) (SEQ ID NO: 91).
[0028] In embodiments of the invention, the LMP2 amino acid sequence comprises an LMP2 amino acid sequence with a substitution (with any other amino acid, in particular alanine or serine) at amino acid position 1, 3, 6, or 8, or any combination thereof that is within SEQ ID NO: 19 when within the full context of any of SEQ ID NOS: 86-91 or of any fragment of SEQ ID NOS: 86-91 that contains SEQ ID NO: 19. Positions 1, 3, 6, and 8 are underlined: CLGGLLTMV (SEQ ID NO: 19). “Peptide LMP2426-434” described herein consists of SEQ ID NO: 19 and is position 426 to 434 of LMP2A (EBV strain B95-8) (SEQ ID NO: 86) and LMP2A (EBV strain AG876) (SEQ ID NO: 87). SEQ ID NO: 19 starts at other positions in LMP2A (EBV strain GDI) (SEQ ID NO: 88), LMP2B (EBV strain B95-8) (SEQ ID NO: 89), LMP2B (EBV strain AG876) (SEQ ID NO: 90), and LMP2B (EBV strain GDI) (SEQ ID NO: 91).
[0029] In embodiments of the invention, the TCR has antigenic specificity for an LMP2 peptide with a mutation at positions 1 and 3 as described above, wherein the mutated LMP2 peptide has any length. In embodiments of the invention, the mutated LMP2 peptide has any length suitable for binding to any of the HLA Class I molecules described herein. For example, the TCR may have antigenic specificity for a LMP2 peptide with the mutation, the LMP2 peptide having a length of about 9 amino acid residues. The LMP2 peptide may comprise any contiguous amino acid residues of LMP2 protein which include the mutation.
In embodiments of the invention, the TCR may have antigenic specificity for an LMP2 peptide with the mutation, the LMP2 peptide having a length of about 9 amino acid residues. [0030] In embodiments of the invention, the inventive TCRs are able to recognize LMP2 presented by an HLA Class I molecule. In this regard, the TCR may elicit an immune
response upon binding to LMP2 within the context of an HLA Class I molecule. The inventive TCRs may bind to the HLA Class I molecule in addition to LMP2.
[0031] In an embodiment of the invention, the HLA Class I molecule is an HLA-A molecule. The HLA-A molecule is a heterodimer of an a chain and β2 microglobulin. The HLA-A a chain may be encoded by an HLA-A gene. β2 microglobulin binds non-covalently to the alpha chain to build the HLA-A complex. The HLA-A molecule may be any HLA-A molecule. In embodiments of the invention, the HLA Class I molecule is an HLA-A02 molecule. The HLA-A02 molecule may be any HLA-A02 molecule. Examples of HLA-A02 molecules may include, but are not limited to, those expressed by the HLA-A*02:01, HLA- A*02:02, HLA-A*02:03, HLA-A*02:05, HLA-A*02:06, HLA-A*02:07, and HLA-A*02:11 alleles. Preferably, the HLA-A02 molecule is expressed by the HLA-A*02:01 allele.
[0032] The TCRs of the invention may provide any one or more of a variety of advantages, including when expressed by cells used for adoptive cell transfer. LMP2 is expressed by cancer cells and is not expressed by normal, noncancerous cells. Without being bound to a particular theory or mechanism, it is believed that the inventive TCRs advantageously target the destruction of cancer cells while minimizing or eliminating the destruction of normal, non-cancerous cells, thereby reducing, for example, by minimizing or eliminating, toxicity. Moreover, the inventive TCRs may, advantageously, successfully treat or prevent LMP2-positive cancers that do not respond to other types of treatment such as, for example, chemotherapy, surgery, or radiation. Additionally, the inventive TCRs may provide highly avid recognition of LMP2, which may provide the ability to recognize unmanipulated tumor cells (e.g., tumor cells that have not been treated with interferon (IFN)-γ, transfected with a vector encoding one or both of LMP2 and HLA-A*02:01, pulsed with an LMP2 peptide, or a combination thereof). Accordingly, the inventive TCRs may increase the number of immunotherapy-eligible cancer patients to include those patients that express the HLA-A*02:01 allele who may not be eligible for immunotherapy using TCRs that recognize LMP2 presented by other MHC molecules. Moreover, the inventive TCRs, polypeptides and proteins comprise human amino acid sequences, which may reduce the risk of rejection by the human immune system as compared to, e.g., TCRs, polypeptides and proteins comprising mouse amino acid sequences.
[0033] The phrase “antigenic specificity,” as used herein, means that the TCR can specifically bind to and immunologically recognize LMP2 with high avidity. For example, a TCR may be considered to have “antigenic specificity” for LMP2 if about 1 x 104 to about 1
x 105 T cells expressing the TCR secrete at least about 200 pg/mL or more (e.g., 200 pg/mL or more, 300 pg/mL or more, 400 pg/mL or more, 500 pg/mL or more, 600 pg/mL or more, 700 pg/mL or more, 1000 pg/mL or more, 5,000 pg/mL or more, 7,000 pg/mL or more, 10,000 pg/mL or more, 20,000 pg/mL or more, or a range defined by any two of the foregoing values) of IFN-γ pon co-culture with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with a low concentration of LMP2 peptide (e.g., about 0.05 ng/mL to about 10 ng/mL, 1 ng/mL, 2 ng/mL, 5 ng/mL, 8 ng/mL, 10 ng/mL, or a range defined by any two of the foregoing values) or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2. Cells expressing the inventive TCRs may also secrete IFNγ upon co-culture with antigen-negative, HLA Class I molecule positive target cells pulsed with higher concentrations of LMP2 peptide. The HLA Class I molecule may be any of the HLA Class I molecules described herein (e.g., an HLA-A*02:01 molecule).
[0034] Alternatively or additionally, a TCR may be considered to have “antigenic specificity” for LMP2 if T cells expressing the TCR secrete at least twice as much IFNγ upon co-culture with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with a low concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2 as compared to the amount of IFNγ expressed by a negative control. The negative control may be, for example, (i) T cells expressing the TCR, co-cultured with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with the same concentration of an irrelevant peptide (e.g., some other peptide with a different sequence from the LMP2 peptide) or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding an irrelevant peptide has been introduced such that the target cell expresses the irrelevant peptide, or (ii) untransduced T cells (e.g., derived from PBMC, which do not express the TCR) co-cultured with (a) antigen negative, HLA Class I molecule positive target cells pulsed with the same concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2. The HLA Class I molecule expressed by the target cells of the negative control would be the same HLA Class I molecule expressed by the target cells that are co-cultured with the T cells being tested. The HLA Class I molecule may be any of the HLA Class I molecules described herein (e.g., an HLA-A*02:01 molecule). IFNγ secretion may be
measured by methods known in the art such as, for example, enzyme-linked immunosorbent assay (ELISA).
[0035] Alternatively or additionally, a TCR may be considered to have “antigenic specificity” for LMP2 if at least twice as many of the numbers of T cells expressing the TCR secrete IFN-γ upon co-culture with (a) antigen-negative, HLA Class I molecule positive target cells pulsed with a low concentration of LMP2 peptide or (b) antigen-negative, HLA Class I molecule positive target cells into which a nucleotide sequence encoding LMP2 has been introduced such that the target cell expresses LMP2 as compared to the numbers of negative control T cells that secrete IFN-γ . The HLA Class I molecule, concentration of peptide, and the negative control may be as described herein with respect to other aspects of the invention. The numbers of cells secreting IFN-γ may be measured by methods known in the art such as, for example, ELISPOT.
[0036] Alternatively or additionally, a TCR may be considered to have “antigenic specificity” for LMP2 if T cells expressing the TCR upregulate expression of one or more T- cell activation markers as measured by, for example, flow cytometry after stimulation with target cells expressing LMP2. Examples of T-cell activation markers include 4-1BB, 0X40, CD107a, CD69, and cytokines that are upregulated upon antigen stimulation (e.g., tumor necrosis factor (TNF), interleukin (IL)-2, etc.).
[0037] An embodiment of the invention provides a TCR comprising two polypeptides (i.e., polypeptide chains), such as an alpha (a) chain of a TCR, a beta (β) chain of a TCR, a gamma (g) chain of a TCR, a delta (δ) chain of a TCR, or a combination thereof. The polypeptides of the inventive TCR can comprise any amino acid sequence, provided that the TCR has antigenic specificity for LMP2. In some embodiments, the TCR is non-naturally occurring.
[0038] In an embodiment of the invention, the TCR comprises two polypeptide chains, each of which comprises a variable region comprising a complementarity determining region (CDR)1, a CDR2, and a CDR3 of a TCR. In an embodiment of the invention, the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 1 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 2 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 4 (CDR1 of β chain), a CDR2 comprising the amino
acid sequence of SEQ ID NO: 5 (CDR2 of β chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 6 (CDR3 of β chain).
[0039] In another embodiment of the invention, the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 7 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 8 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 9 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 10 (CDR1 of β chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 11 (CDR2 of β chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 12 (CDR3 of β chain).
[0040] In another embodiment of the invention, the TCR comprises a first polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 13 (CDR1 of a chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 14 (CDR2 of a chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15 (CDR3 of a chain), and a second polypeptide chain comprising a CDR1 comprising the amino acid sequence of SEQ ID NO: 16 (CDR1 of β chain), a CDR2 comprising the amino acid sequence of SEQ ID NO: 17 (CDR2 of β chain), and a CDR3 comprising the amino acid sequence of SEQ ID NO: 18 (CDR3 of β chain).
[0041] In this regard, the inventive TCR can comprise any one or more of the amino acid sequences selected from SEQ ID NOs: 1-6, 7-12, and 13-18. In an embodiment of the invention, the TCR comprises the amino acid sequences of: (a) all of SEQ ID NOs: 1-3, (b) all of SEQ ID NOs: 4-6, (c) all of SEQ ID NOs: 7-9, (d) all of SEQ ID NOs: 10-12, (e) all of SEQ ID NOs: 13-15, (f) all of SEQ ID NOs: 16-18, (g) all of SEQ ID NOs: 1-6, (h) all of SEQ ID NOs: 7-12, or (i) all of SEQ ID NOs: 13-18. In an especially preferred embodiment, the TCR comprises the amino acid sequences of: (i) all of SEQ ID NOs: 1-6, (ii) all of SEQ ID NOs: 7-12, or (iii) all of SEQ ID NOs: 13-18.
[0042] The CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or β chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
[0043] In embodiments of the invention, the TCR comprises an amino acid sequence of a variable region of a TCR comprising the CDRs set forth above. The TCR may comprise a human variable region, e.g., a human a chain variable region and a human β chain variable region. In this regard, the TCR can comprise the amino acid sequence of: SEQ ID NO: 20
(variable region of a chain with N-terminal signal peptide); SEQ ID NO: 21 or 98 (variable region of β chain with N-terminal signal peptide); SEQ ID NO: 22 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 23 or 99 (variable region of β chain with N- terminal signal peptide); SEQ ID NO: 24 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 25 or 100 (variable region of β chain with N-terminal signal peptide); SEQ ID NO: 26 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 27 (variable region of β chain without N-terminal signal peptide); SEQ ID NO: 28 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 29 (variable region of β chain without N-terminal signal peptide); SEQ ID NO: 30 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 31 (variable region of β chain without N-terminal signal peptide); both of SEQ ID NOs: 20, and 21 or 98; both of SEQ ID NOs: 22, and 23 or 99; both of SEQ ID NOs: 24, and 25 or 100; both of SEQ ID NOs: 26 and 27; both of SEQ ID NOs: 28 and 29; or both of SEQ ID NOs: 30 and 31.
[0044] The inventive TCRs may further comprise an a chain constant region and a β chain constant region. The constant region may be derived from any suitable species such as, e.g., human or mouse. In embodiments of the invention, the TCRs further comprise murine a and β chain constant regions or human a and β chain constant regions. As used herein, the term “murine” or “human,” when referring to a TCR or any component of a TCR described herein (e.g., complementarity determining region (CDR), variable region, constant region, a chain, and/or β chain), means a TCR (or component thereof) which is derived from a mouse or a human, respectively, i.e., a TCR (or component thereof) that originated from or was, at one time, expressed by a mouse T cell or a human T cell, respectively.
[0045] An embodiment of the invention provides a chimeric TCR comprising a human variable region and a murine constant region, wherein the TCR has antigenic specificity for an LMP2 amino acid sequence presented by an HLA Class I molecule. The murine constant region may provide any one or more advantages. For example, the murine constant region may diminish mispairing of the inventive TCR with the endogenous TCRs of the host cell into which the inventive TCR is introduced. Alternatively or additionally, the murine constant region may increase expression of the inventive TCR as compared to the same TCR with a human constant region. The chimeric TCR may comprise the amino acid sequence of SEQ ID NO: 32 (wild-type (WT) murine a chain constant region), SEQ ID NO: 33 (WT murine β chain constant region), or both SEQ ID NOs: 32 and 33. Preferably, the inventive TCR comprises the amino acid sequences of both of SEQ ID NOs: 32 and 33. The chimeric
TCR may comprise any of the murine constant regions described herein in combination with any of the CDR regions as described herein with respect to other aspects of the invention. In this regard, the TCR may comprise the amino acid sequences of: (a) all of SEQ ID NOs: 1-3 and 32; (b) all of SEQ ID NOs: 4-6 and 33; (c) all of SEQ ID NOs: 7-9 and 32; (d) all of SEQ ID NOs: 10-12 and 33; (e) all of SEQ ID NOs: 13-15 and 32; (f) all of SEQ ID NOs: 16-18 and 33; (g) all of SEQ ID NOs: 1-6 and 32-33; (h) all of SEQ ID NOs: 7-12 and 32-33, or (i) all of SEQ ID NOs: 13-18 and 32-33. In another embodiment of the invention, the chimeric TCR may comprise any of the murine constant regions described herein in combination with any of the variable regions described herein with respect to other aspects of the invention. In this regard, the TCR may comprise the amino acid sequences of: (i) both of SEQ ID NOs: 20 and 32; (ii) both of SEQ ID NOs: 21 or 98, and 33; (iii) both of SEQ ID NOs: 22 and 32; (iv) both of SEQ ID NOs: 23 or 99, and 33; (v) both of SEQ ID NOs: 24 and 32; (vi) both of SEQ ID NOs: 25 or 100, and 33; (vii) both of SEQ ID NOs: 26 and 32; (vii) both of SEQ ID NOs: 27 and 33; (viii) both of SEQ ID NOs: 28 and 32; (ix) both of SEQ ID NOs: 29 and 33; (x) both of SEQ ID NOs: 30 and 32; (xi) both of SEQ ID NOs: 31 and 33; (xii) all of SEQ ID NOs: 20, 21 or 98, and 32-33; (xiii) all of SEQ ID NOs: 22, 23 or 99, and 32-33; (xiv) all of SEQ ID NOs: 24, 25 or 100, and 32-33; (xv) all of SEQ ID NOs: 26-27 and 32-33; (xvi) all of SEQ ID NOs: 28-29 and 32-33; or (xvii) all of SEQ ID NOs: 30-31 and 32-33.
[0046] In another embodiment of the invention, the TCR comprises the amino acid sequence(s) of: SEQ ID NO: 34 (a chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 35 or 101 (β chain with WT murine constant region and N- terminal signal peptide), SEQ ID NO: 36 (a chain with WT murine constant region and N- terminal signal peptide), SEQ ID NO: 37 or 102 (β chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 38 (a chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 39 or 103 (β chain with WT murine constant region and N-terminal signal peptide), SEQ ID NO: 40 (a chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 41 (β chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 42 (a chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 43 (β chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 44 (a chain with WT murine constant region and without N-terminal signal peptide), SEQ ID NO: 45 (β chain with WT murine constant region and without N-terminal signal peptide), both of SEQ ID NO: 34, and 35 or 101, both of SEQ ID NO: 36, and 37 or 102, both of SEQ ID NO: 38,
and 39 or 103, both of SEQ ID NO: 40-41, both of SEQ ID NO: 42-43, or both of SEQ ID NO: 44-45.
[0047] In embodiments of the invention, the TCR comprises an a chain comprising a variable region and a constant region and a β chain comprising a variable region and a constant region. In this regard, the TCR may comprise (a) an a chain comprising the amino acid sequence of SEQ ID NO: 46 (a chain with N-terminal signal peptide), wherein: (i) X at position 179 of SEQ ID NO: 46 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a β chain comprising the amino acid sequence of SEQ ID NO: 47 or 104 (β chain with N-terminal signal peptide), wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys; (c) an a comprising the amino acid sequence of SEQ ID NO: 48 (a chain with N-terminal signal peptide), wherein: (i) X at position 177 of SEQ ID NO: 48 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro,
Phe, or Trp; and (iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (d) a β chain comprising the amino acid sequence of SEQ ID NO: 49 or 105 (β chain with N-terminal signal peptide), wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys; (e) an a comprising the amino acid sequence of SEQ ID NO: 50 (a chain with N- terminal signal peptide), wherein: (i) X at position 179 of SEQ ID NO: 50 is Thr or Cys; (ii)
X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (f) a β chain comprising the amino acid sequence of SEQ ID NO: 51 or 106 (β chain with N-terminal signal peptide), wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys; (g) both (a) and (b); (h) both (c) and (d); or (i) both (e) and (f); (j) an a chain comprising the amino acid sequence of SEQ ID NO: 52 (a chain without N-terminal signal peptide), wherein: (i) X at position 160 of SEQ ID NO: 52 is Thr or Cys; (ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (k) a β chain comprising the amino acid sequence of SEQ ID NO: 53 (β chain without N-terminal signal peptide), wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys; (1) an a comprising the amino acid sequence of SEQ ID NO:
54 (a chain without N-terminal signal peptide), wherein: (i) X at position 159 of SEQ ID NO: 54 is Thr or Cys; (ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (m) a β chain comprising the amino acid sequence of SEQ ID NO: 55 (β chain without N-terminal signal peptide), wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys; (n) an a comprising the amino acid sequence of SEQ ID NO: 56 (a chain without N-terminal signal peptide), wherein: (i) X at position 161 of SEQ ID NO: 56 is Thr or Cys; (ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (o) a β chain comprising the amino acid sequence of SEQ ID NO: 57 (β chain without N-terminal signal peptide), wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys; (p) both (j) and (k); (q) both (1) and (m); or (r) both (n) and (o). In embodiments of the invention, the TCR comprising SEQ ID NO:
46 does not comprise SEQ ID NO: 34 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 47 or 104 does not comprise SEQ ID NO: 35 or
101 (unsubstituted β chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 48 does not comprise SEQ ID NO: 36 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 49 or 105 does not comprise SEQ ID NO: 37 or
102 (unsubstituted β chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 50 does not comprise SEQ ID NO: 38 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 51 or 106 does not comprise SEQ ID NO: 39 or
103 (unsubstituted β chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 52 does not comprise SEQ ID NO: 40 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 53 does not comprise SEQ ID NO: 41 (unsubstituted β chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 54 does not comprise SEQ ID NO: 42 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 55 does not comprise SEQ ID NO: 43 (unsubstituted β chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 56 does not comprise SEQ ID NO: 44 (unsubstituted a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 57 does not comprise SEQ ID NO: 45 (unsubstituted β chain).
[0048] In embodiments of the invention, the TCR comprises a substituted constant region. In this regard, the TCR may comprise the amino acid sequence of any of the TCRs described herein with one, two, three, or four amino acid substitution(s) in the constant region of one or both of the a and β chain. Preferably, the TCR comprises a murine constant region with one, two, three, or four amino acid substitution(s) in the murine constant region of one or both of the a and β chains. In an especially preferred embodiment, the TCR comprises a murine constant region with one, two, three, or four amino acid substitution(s) in the murine constant region of the a chain and one amino acid substitution in the murine constant region of the β chain. In some embodiments, the TCRs comprising the substituted constant region advantageously provide one or more of increased recognition of LMP2+ targets, increased expression by a host cell, diminished mispairing with endogenous TCRs, and increased anti tumor activity as compared to the parent TCR comprising an unsubstituted (wild-type) constant region. In general, the substituted amino acid sequences of the murine constant regions of the TCR a and β chains, SEQ ID NOs: 58 and 59, respectively, correspond with all or portions of the unsubstituted murine constant region amino acid sequences SEQ ID NOs: 32 and 33, respectively, with SEQ ID NO: 58 having one, two, three, or four amino acid substitution(s) when compared to SEQ ID NO: 32 and SEQ ID NO: 59 having one amino acid substitution when compared to SEQ ID NO: 33. In this regard, an embodiment of the invention provides a TCR comprising the amino acid sequences of (a) SEQ ID NO: 58 (constant region of a chain), wherein (i) X at position 48 is Thr or Cys; (ii) X at position 112 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) SEQ ID NO: 59 (constant region of β chain), wherein X at position 57 is Ser or Cys; or (c) both of SEQ ID NOs: 58 and 59. In embodiments of the invention, the TCR comprising SEQ ID NO: 58 does not comprise SEQ ID NO: 32 (unsubstituted murine constant region of a chain). In embodiments of the invention, the TCR comprising SEQ ID NO: 59 does not comprise SEQ ID NO: 33 (unsubstituted murine constant region of β chain). [0049] The first amino acid of any of the mouse alpha constant regions described herein may be different from N as provided in SEQ ID NOS: 32 and 58. For example, in any TCR construct, polypeptide, protein, etc., as described herein, this first amino acid can be encoded by a split codon (having nucleotides from both a variable region and a constant region) such that any of the murine alpha constant regions may have a different amino acid at that position. Similarly, the first amino acid of any of the mouse beta constant regions described
herein may be different from E as provided in SEQ ID NOS: 33 and 59, e.g., this first amino acid can be encoded by a split codon.
[0050] In embodiments of the invention, the substituted constant region includes cysteine substitutions in the constant region of one or both of the a and β chains to provide a cysteine- substituted TCR. Opposing cysteines in the a and the β chains provide a disulfide bond that links the constant regions of the a and the β chains of the substituted TCR to one another and which is not present in a TCR comprising the unsubstituted murine constant regions. In this regard, the TCR may be a cysteine-substituted TCR in which one or both of the native Thr at position 48 (Thr48) of SEQ ID NO: 32 and the native Ser at position 57 (Ser57) of SEQ ID NO: 33 may be substituted with Cys. Preferably, both of the native Thr48 of SEQ ID NO: 32 and the native Ser57 of SEQ ID NO: 33 are substituted with Cys. Examples of cysteine- substituted TCR constant regions sequences are set forth in Table 1. In embodiments of the invention, the cysteine-substituted TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined in Table 1. The cysteine-substituted TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
[0051] In embodiments of the invention, the cysteine-substituted, chimeric TCR comprises a full length alpha chain and a full-length beta chain. Examples of cysteine- substituted, chimeric TCR alpha chain and beta chain sequences are set forth in Table 1. In embodiments of the invention, the TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv) SEQ ID NO: 56, (xv) SEQ ID NO: 57, (xvi) both of SEQ ID NOs: 52 and 53, (xv) both of SEQ ID NOs: 54 and 55, or (xvi) both of SEQ ID NOs: 56 and 57, wherein all of the seqeunces are as defined in Table 1.
TABLE 1
[0052] In embodiments of the invention, the substituted amino acid sequence includes substitutions of one, two, or three amino acids in the transmembrane (TM) domain of the constant region of one or both of the a and β chains with a hydrophobic amino acid to provide a hydrophobic amino acid-substituted TCR (also referred to herein as an “LVL- modified TCR”). The hydrophobic amino acid substitution(s) in the TM domain of the TCR may increase the hydrophobicity of the TM domain of the TCR as compared to a TCR that lacks the hydrophobic amino acid substitution(s) in the TM domain. In this regard, the TCR is an LVL-modified TCR in which one, two, or three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; preferably with Leu, lie, or Val. Preferably, all three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; preferably with Leu, Ile, or Val. In embodiments of the invention, the LVL-modified TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined
in Table 2. The LVL-modified TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
[0053] In embodiments of the invention, the LVL-modified TCR comprises a full length alpha chain and a full-length beta chain. Examples of LVL-modified TCR alpha chain and beta chain sequences are set forth in Table 2. In embodiments of the invention, the LVL- modified TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv) SEQ ID NO: 56, (xv) SEQ ID NO: 57, (xvi) both of SEQ ID NOs: 52 and 53, (xv) both of SEQ ID NOs: 54 and 55, or (xvi) both of SEQ ID NOs: 56 and 57, wherein all of the sequences are as defined in Table 2.
[0054] In embodiments of the invention, the substituted amino acid sequence includes the cysteine substitutions in the constant region of one or both of the a and β chains in combination with the substitution(s) of one, two, or three amino acids in the transmembrane (TM) domain of the constant region of one or both of the a and β chains with a hydrophobic
amino acid (also referred to herein as “cysteine-substituted, LVL-modified TCR”). In this regard, the TCR is a cysteine-substituted, LVL-modified, chimeric TCR in which the native Thr48 of SEQ ID NO: 32 is substituted with Cys; one, two, or three of the native Seri 12,
Metl 14, and Gly 115 of SEQ ID NO: 32 are, independently, substituted with Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; preferably with Leu, lie, or Val; and the native Ser57 of SEQ ID NO: 33 is substituted with Cys. Preferably, all three of the native Seri 12, Metl 14, and Gly 115 of SEQ ID NO: 32 may, independently, be substituted with Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; preferably with Leu, Ile, or Val. In embodiments of the invention, the cysteine-substituted, LVL-modified TCR comprises (i) SEQ ID NO: 58, (ii) SEQ ID NO: 59, or (iii) both of SEQ ID NOs: 58 and 59, wherein both of SEQ ID NOs: 58 and 59 are as defined in Table 3. The cysteine-substituted, LVL-modified TCRs of the invention may include the substituted constant region in addition to any of the CDRs or variable regions described herein.
[0055] In embodiments, the cysteine-substituted, LVL-modified TCR comprises a full- length alpha chain and a full-length beta chain. In embodiments of the invention, the LVL- modified TCR comprises (i) SEQ ID NO: 46, (ii) SEQ ID NO: 47 or 104, (iii) SEQ ID NO: 48, (iv) SEQ ID NO: 49 or 105, (v) SEQ ID NO: 50, (vi) SEQ ID NO: 51 or 106, (vii) both of SEQ ID NO: 46, and 47 or 104, (viii) both of SEQ ID NO: 48, and 49 or 105, (ix) both of SEQ ID NO: 50, and 51 or 106, (x) SEQ ID NO: 52, (xi) SEQ ID NO: 53, (xii) SEQ ID NO: 54, (xiii) SEQ ID NO: 55, (xiv) SEQ ID NO: 56, (xv) SEQ ID NO: 57, (xvi) both of SEQ ID NOs: 52 and 53, (xv) both of SEQ ID NOs: 54 and 55, or (xvi) both of SEQ ID NOs: 56 and 57, wherein all of the sequences are as defined in Table 3.
[0056] Also provided by an embodiment of the invention is a polypeptide comprising a functional portion of any of the TCRs described herein. The term "polypeptide," as used herein, includes oligopeptides and refers to a single chain of amino acids connected by one or more peptide bonds.
[0057] With respect to the inventive polypeptides, the functional portion can be any portion comprising contiguous amino acids of the TCR of which it is a part, provided that the functional portion specifically binds to LMP2. The term “functional portion,” when used in reference to a TCR, refers to any part or fragment of the TCR of the invention, which part or fragment retains the biological activity of the TCR of which it is a part (the parent TCR). Functional portions encompass, for example, those parts of a TCR that retain the ability to specifically bind to LMP2 (e.g., within the context of an HLA-A*02:01 molecule), or detect, treat, or prevent cancer, to a similar extent, the same extent, or to a higher extent, as the parent TCR. In reference to the parent TCR, the functional portion can comprise, for instance, about 10%, about 25%, about 30%, about 50%, about 70%, about 80%, about 90%, about 95%, or more, of the parent TCR.
[0058] The functional portion can comprise additional amino acids at the amino or carboxy terminus of the portion, or at both termini, which additional amino acids are not found in the amino acid sequence of the parent TCR. Desirably, the additional amino acids
do not interfere with the biological function of the functional portion, e.g., specifically binding to LMP2; and/or having the ability to detect cancer, treat or prevent cancer, etc.
More desirably, the additional amino acids enhance the biological activity, as compared to the biological activity of the parent TCR.
[0059] The polypeptide can comprise a functional portion of either or both of the a and β chains of the TCRs of the invention, such as a functional portion comprising one or more of the CDR1, CDR2, and CDR3 of the variable region(s) of the a chain and/or β chain of a TCR of the invention. In an embodiment of the invention, the polypeptide can comprise the amino acid sequence of SEQ ID NO: 1 (CDR1 of a chain), SEQ ID NO: 2 (CDR2 of a chain), SEQ ID NO: 3 (CDR3 of a chain), SEQ ID NO: 4 (CDR1 of β chain), SEQ ID NO: 5 (CDR2 of β chain), SEQ ID NO: 6 (CDR3 of β chain), or a combination thereof. In another embodiment of the invention, the polypeptide can comprise the amino acid sequence of SEQ ID NO: 7 (CDR1 of a chain), SEQ ID NO: 8 (CDR2 of a chain), SEQ ID NO: 9 (CDR3 of a chain), SEQ ID NO: 10 (CDR1 of β chain), SEQ ID NO: 11 (CDR2 of β chain), SEQ ID NO: 12 (CDR3 of β chain), or a combination thereof. In another embodiment of the invention, the polypeptide can comprise the amino acid sequence of SEQ ID NO: 13 (CDR1 of a chain), SEQ ID NO: 14 (CDR2 of a chain), SEQ ID NO: 15 (CDR3 of a chain), SEQ ID NO: 16 (CDR1 of β chain), SEQ ID NO: 17 (CDR2 of β chain), SEQ ID NO: 18 (CDR3 of β chain), or a combination thereof. The CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or β chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
[0060] In this regard, the inventive polypeptide can comprise any one or more of the amino acid sequences selected from SEQ ID NOs: 1-6, 7-12, and 13-18. In an embodiment of the invention, the TCR comprises the amino acid sequences of: (a) all of SEQ ID NOs: 1- 3, (b) all of SEQ ID NOs: 4-6, (c) all of SEQ ID NOs: 7-9, (d) all of SEQ ID NOs: 10-12, (e) all of SEQ ID NOs: 13-15, (f) all of SEQ ID NOs: 16-18, (g) all of SEQ ID NOs: 1-6, (h) all of SEQ ID NOs: 7-12, or (i) all of SEQ ID NOs: 13-18. In a preferred embodiment, the polypeptide comprises the amino acid sequences of: (i) all of SEQ ID NOs: 1-6, (ii) all of SEQ ID NOs: 7-12, or (iii) all of SEQ ID NOs: 13-18.
[0061] In an embodiment of the invention, the inventive polypeptide can comprise, for instance, the variable region of the inventive TCR comprising a combination of the CDR regions set forth above. In this regard, the polypeptide can comprise the amino acid sequence
of SEQ ID NO: 20 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 21 or 98 (variable region of β chain with N-terminal signal peptide); SEQ ID NO: 22 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 23 or 99 (variable region of β chain with N-terminal signal peptide); SEQ ID NO: 24 (variable region of a chain with N-terminal signal peptide); SEQ ID NO: 25 or 100 (variable region of β chain with N- terminal signal peptide); SEQ ID NO: 26 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 27 (variable region of β chain without N-terminal signal peptide); SEQ ID NO: 28 (variable region of a chain without N-terminal signal peptide);
SEQ ID NO: 29 (variable region of β chain without N-terminal signal peptide); SEQ ID NO: 30 (variable region of a chain without N-terminal signal peptide); SEQ ID NO: 31 (variable region of β chain without N-terminal signal peptide); both of SEQ ID NOs: 20, and 21 or 98; both of SEQ ID NOs: 22, and 23 or 99; both of SEQ ID NOs: 24, and 25 or 100; both of SEQ ID NOs: 26 and 27; both of SEQ ID NOs: 28 and 29; or both of SEQ ID NOs: 30 and 31. [0062] In embodiments of the invention, the inventive polypeptide can further comprise the constant region of the inventive TCR set forth above. In this regard, the polypeptide can further comprise the amino acid sequence of SEQ ID NO: 32 (WT murine constant region of a chain), SEQ ID NO: 33 (WT murine constant region of β chain), SEQ ID NO: 58, (substituted murine constant region of a chain), SEQ ID NO: 59 (substituted murine constant region of β chain), both SEQ ID NOs: 32 and 33, or both SEQ ID NOs: 58 and 59.
Preferably, the polypeptide further comprises the amino acid sequences of both of SEQ ID NOs: 32 and 33 or both of SEQ ID NO: 58 and 59 in combination with any of the CDR regions or variable regions described herein with respect to other aspects of the invention. [0063] In embodiments of the invention, the polypeptide comprises: (a) the amino acid sequence of SEQ ID NO: 58, wherein: (i) X at position 48 of SEQ ID NO: 58 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or (c) both (a) and (b). In embodiments of the invention, one or both of SEQ ID NOs: 58 and 59 of the polypeptide are as defined in any one of Tables 1-3.
[0064] In embodiments of the invention, the inventive polypeptide can comprise the entire length of an a or β chain of the TCR described herein. In this regard, the inventive polypeptide can comprise the amino acid sequence of (i) SEQ ID NO: 20, (ii) SEQ ID NO:
21 or 98, (iii) SEQ ID NO: 26, (iv) SEQ ID NO: 27, (v) both of SEQ ID NOs: 20, and 21 or 98, (vi) both of SEQ ID NOs: 26 and 27, (vii) SEQ ID NO: 22, (viii) SEQ ID NO: 23 or 99, (ix) SEQ ID NO: 28, (x) SEQ ID NO: 29, (xi) both of SEQ ID NOs: 22, and 23 or 99, (xii) both of SEQ ID NOs: 28 and 29, (xiii) SEQ ID NO: 24, (xiv) SEQ ID NO: 25 or 100, (xv) SEQ ID NO: 30, (xvi) SEQ ID NO: 31, (xvii) both of SEQ ID NOs: 24, and 25 or 100, or (xviii) both of SEQ ID NOs: 30 and 31. The polypeptide of the invention can comprise both chains of the TCRs described herein.
[0065] In embodiments of the invention, the polypeptide comprises: (a) the amino acid sequence of SEQ ID NO: 46, wherein: (i) X at position 179 of SEQ ID NO: 46 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) the amino acid sequence of SEQ ID NO: 47 or 104, wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys; (c) the amino acid sequence of SEQ ID NO: 48, wherein: (i) X at position 177 of SEQ ID NO: 48 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (d) the amino acid sequence of SEQ ID NO: 49 or 105, wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys; (e) the amino acid sequence of SEQ ID NO: 50, wherein: (i) X at position 179 of SEQ ID NO: 50 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (1) the amino acid sequence of SEQ ID NO: 51 or 106, wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys; (g) both (a) and (b); (h) both (c) and (d); (i) both (e) and (1); (j) the amino acid sequence of SEQ ID NO: 52, wherein: (i) X at position 160 of SEQ ID NO: 52 is Thr or Cys; (ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (k) the amino acid sequence of SEQ ID NO: 53, wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys; (1) the amino acid sequence of SEQ ID NO: 54, wherein: (i) X at position 159 of SEQ ID NO: 54 is Thr or Cys; (ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val,
Leu, lie, Pro, Phe, or Trp; and (iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (m) the amino acid sequence of SEQ ID NO: 55, wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys; (n) the amino acid sequence of SEQ ID NO:
56, wherein: (i) X at position 161 of SEQ ID NO: 56 is Thr or Cys; (ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (o) the amino acid sequence of SEQ ID NO: 57, wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys; (p) both (j) and (k); (q) both (1) and (m); or (r) both (n) and (o). In an embodiment of the invention, any one or more of SEQ ID NOs: 46, 47 or 104, 48, 49 or 105, 50, 51 or 106, and 52-57 of the polypeptide are as defined in any one of Tables 1-3.
[0066] An embodiment of the invention further provides a protein comprising at least one of the polypeptides described herein. By "protein" is meant a molecule comprising one or more polypeptide chains.
[0067] In an embodiment, the protein of the invention can comprise (a) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 1-3 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 4-6; (b) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 7-9 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 10-12; or (c) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 13-15 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 16-18. The CDR3 of SEQ ID NOs: 3, 6, 9, 12, 15, or 18 i.e., of the a chain or β chain or both, may further comprise a cysteine immediately N-terminal to the first amino acid of the CDR or a phenylalanine immediately C-terminal to the final amino acid or both.
[0068] In another embodiment of the invention, the protein may comprise (i) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 20 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 21 or 98; (ii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 26 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 27; (iii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 22 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 23 or 99; (iv) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 28 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 29; (v) a first
polypeptide chain comprising the amino acid sequence of SEQ ID NO: 24 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 25 or 100; or (vi) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 30 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 31.
[0069] The inventive protein may further comprise any of the constant regions described herein with respect to other aspects of the invention. In this regard, in embodiments of the invention, the first polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 32 and the second polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 33. In embodiments of the invention, the first polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 58 and the second polypeptide chain may further comprise the amino acid sequence of SEQ ID NO: 59.
[0070] In embodiments of the invention, the protein comprises: (a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 58, wherein: (i) X at position 48 of SEQ ID NO: 58 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or (c) both (a) and (b). In embodiments of the invention, one or both of SEQ ID NOs: 58 and 59 of the protein are as defined in any one of Tables 1-3.
[0071] Alternatively or additionally, the protein of an embodiment of the invention can comprise (a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO:
46, wherein: (i) X at position 179 of SEQ ID NO: 46 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 47 or 104, wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys; (c) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 48, wherein: (i) X at position 177 of SEQ ID NO: 48 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(d) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 49 or 105, wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys; (e) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 50, wherein: (i) X at position 179 of SEQ ID NO: 50 is Thr or Cys; (ii) X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp; (iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and (iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (f) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 51 or 106, wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys; (g) both (a) and (b); (h) both (c) and (d); (i) both (e) and (f); (j) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 52, wherein: (i) X at position 160 of SEQ ID NO: 52 is Thr or Cys; (ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (k) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 53, wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys; (1) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 54, wherein: (i) X at position 159 of SEQ ID NO: 54 is Thr or Cys; (ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (m) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 55, wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys; (n) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 56, wherein: (i) X at position 161 of SEQ ID NO: 56 is Thr or Cys; (ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (o) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 57, wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys; (p) both (j) and (k); (q) both (1) and (m); or(r) both (n) and (o). In an embodiment of the invention, one or more of SEQ ID NOs: SEQ ID NOs: 46, 47 or 104, 48, 49 or 105, 50,
51 or 106, and 52-57 are as defined in any one of Tables 1-3.
[0072] The protein of the invention can be a TCR. Alternatively, if, for example, the protein comprises a single polypeptide chain or if the first and/or second polypeptide chain(s) of the protein further comprise(s) other amino acid sequences, e.g., an amino acid sequence
encoding an immunoglobulin or a portion thereof, then the inventive protein can be a fusion protein. In this regard, an embodiment of the invention also provides a fusion protein comprising at least one of the inventive polypeptides described 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 polypeptide, which is expressed in frame (in tandem) with one of the inventive polypeptides described herein. The other polypeptide can encode any peptidic or proteinaceous molecule, or a portion thereof, including, but not limited to an immunoglobulin, CD3, CD4, CD8, an MHC molecule, a CD1 molecule, e.g., CDla, CDlb, CDlc, CD Id, etc.
[0073] The fusion protein can comprise 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 polypeptide and/or of the other polypeptide. Suitable methods of making fusion proteins are known in the art, and include, for example, recombinant methods.
[0074] In some embodiments of the invention, the TCRs, polypeptides, and proteins of the invention may be expressed as a single protein comprising a linker peptide linking the a chain and the β chain. In this regard, the TCRs, polypeptides, and proteins of the invention may further comprise a linker peptide. The linker peptide may advantageously facilitate the expression of a recombinant TCR, polypeptide, and/or protein in a host cell. The linker peptide may comprise any suitable amino acid sequence. For example, the linker peptide may be a furin-SGSG-P2A linker comprising the amino acid sequence of RAKRS GS GATNF SLLKQ AGD VEENPGP (SEQ ID NO: 60). Upon expression of the construct including the linker peptide by a host cell, the linker peptide may be cleaved, resulting in separated a and β chains. In embodiments of the invention, the TCR, polypeptide, or protein may comprise an amino acid sequence comprising a full-length a chain, a full-length β chain, and a linker peptide positioned between the a and β chains, for example a chain-linker-β chain or β chain-linker-a chain.
[0075] The protein of the invention can be a recombinant antibody, or an antigen binding portion thereof, comprising at least one of the inventive polypeptides described herein. As used herein, "recombinant antibody" refers to a recombinant (e.g., genetically engineered) protein comprising at least one of the polypeptides of the invention and a polypeptide chain of an antibody, or an antigen binding portion thereof. The polypeptide of an antibody, or antigen binding portion thereof, can be a heavy chain, a light chain, a variable or constant
region of a heavy or light chain, a single chain variable fragment (scFv), or an Fc, Fab, or F(ab)2' fragment of an antibody, etc. The polypeptide chain of an antibody, or an antigen binding portion thereof, can exist as a separate polypeptide of the recombinant antibody. Alternatively, the polypeptide chain of an antibody, or an antigen binding portion thereof, can exist as a polypeptide, which is expressed in frame (in tandem) with the polypeptide of the invention. The polypeptide of an antibody, or an antigen binding portion thereof, can be a polypeptide of any antibody or any antibody fragment, including any of the antibodies and antibody fragments described herein.
[0076] Included in the scope of the invention are functional variants of the inventive TCRs, polypeptides, or proteins described herein. The term “functional variant,” as used herein, refers to a TCR, polypeptide, or protein having substantial or significant sequence identity or similarity to a parent TCR, polypeptide, or protein, which functional variant retains the biological activity of the TCR, polypeptide, or protein of which it is a variant. Functional variants encompass, for example, those variants of the TCR, polypeptide, or protein described herein (the parent TCR, polypeptide, or protein) that retain the ability to specifically bind to LMP2 for which the parent TCR has antigenic specificity or to which the parent polypeptide or protein specifically binds, to a similar extent, the same extent, or to a higher extent, as the parent TCR, polypeptide, or protein. In reference to the parent TCR, polypeptide, or protein, the functional variant can, for instance, be at least about 30%, about 50%, about 75%, about 80%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or more identical in amino acid sequence to the parent TCR, polypeptide, or protein, respectively.
[0077] The functional variant can, for example, comprise the amino acid sequence of the parent TCR, polypeptide, or protein with at least one conservative amino acid substitution. Conservative amino acid substitutions are known in the art, and include amino acid substitutions in which one amino acid having certain physical and/or chemical properties is exchanged for another amino acid that has the same chemical or physical properties. For instance, the conservative amino acid substitution can be an acidic amino acid substituted for another acidic amino acid (e.g., Asp or Glu), an amino acid with a nonpolar side chain substituted for another amino acid with a nonpolar side chain (e.g., Ala, Gly, Val, lie, Leu, Met, Phe, Pro, Trp, Val, etc.), a basic amino acid substituted for another basic amino acid (Lys, Arg, etc.), an amino acid with a polar side chain substituted for another amino acid with a polar side chain (Asn, Cys, Gin, Ser, Thr, Tyr, etc.), etc.
[0078] Alternatively or additionally, the functional variants can comprise the amino acid sequence of the parent TCR, polypeptide, or protein with at least one non-conservative amino acid substitution. In this case, it is preferable for the non-conservative amino acid substitution to not interfere with or inhibit the biological activity of the functional variant. Preferably, the non-conservative amino acid substitution enhances the biological activity of the functional variant, such that the biological activity of the functional variant is increased as compared to the parent TCR, polypeptide, or protein.
[0079] Each signal peptide of the TCRs, polypeptides, proteins, functional variants, and functional portions described herein, when present, can be any suitable TCR signal peptide, so long as the TCR, polypeptide, protein, or functional variant is expressed and has antigenic specificity for an LMP2 amino acid sequence presented by an HLA Class I molecule.
[0080] The TCR, polypeptide, or protein can consist essentially of the specified amino acid sequence or sequences described herein, such that other components of the TCR, polypeptide, or protein, e.g., other amino acids, do not materially change the biological activity of the TCR, polypeptide, or protein. In this regard, the inventive TCR, polypeptide, or protein can, for example, consist essentially of the amino acid sequence of SEQ ID NO:
20, SEQ ID NO: 21 or 98, SEQ ID NO: 22, SEQ ID NO: 23 or 99, SEQ ID NO: 24, SEQ ID NO: 25 or 100, both of SEQ ID NOs: 20, and 21 or 98, both of SEQ ID NO: 22, and 23 or 99, both of SEQ ID NO: 24, and 25 or 100, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, both of SEQ ID NOs: 26-27, both of SEQ ID NO: 28-29, or both of SEQ ID NO: 30-31. Furthermore, the inventive TCRs, polypeptides, or proteins can consist essentially of the amino acid sequences of (a) any one or more of SEQ ID NOs: 1-6, 7-12, 13-18; (b) all of SEQ ID NO: 1-3; (c) all of SEQ ID NO: 4- 6; (d) all of SEQ ID NO: 7-9; (e) all of SEQ ID NOs: 10-12; (f) all of SEQ ID NOs: 13-15;
(g) all of SEQ ID NOs: 16-18; (h) all of SEQ ID NOs: 1-6; (i) all of SEQ ID NOs: 7-12; (j) all of SEQ ID NOs: 13-18.
[0081] The TCRs, polypeptides, and proteins of the invention can be of any length, i.e., can comprise any number of amino acids, provided that the TCRs, polypeptides, or proteins retain their biological activity, e.g., the ability to specifically bind to LMP2; detect cancer in a mammal; or treat or prevent cancer in a mammal, etc. For example, the polypeptide can be in the range of from about 50 to about 5000 amino acids long, such as about 50, about 70, about 75, about 100, about 125, about 150, about 175, about 200, about 300, about 400, about 500,
about 600, about 700, about 800, about 900, about 1000 or more amino acids in length. In this regard, the polypeptides of the invention also include oligopeptides.
[0082] The TCRs, polypeptides, and proteins of the invention can comprise synthetic amino acids in place of one or more naturally-occurring amino acids. Such synthetic amino acids are known in the art, and include, for example, aminocyclohexane carboxylic acid, norleucine, oc-amino n-decanoic acid, homoserine, S-acetylaminomethyl-cysteine, trans-3- and trans-4-hydroxyproline, 4-aminophenylalanine, 4-nitrophenylalanine, 4- chlorophenylalanine, 4-carboxyphenylalanine, β-phenylserine β-hydroxyphenylalanine, phenylglycine, oc-naphthylalanine, cyclohexylalanine, cyclohexylglycine, indoline-2- carboxylic acid, l,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, aminomalonic acid, aminomalonic acid monoamide, N’-benzyl-N’-methyl-lysine, N’,N’-dibenzyl-lysine, 6- hydroxylysine, ornithine, oc-aminocyclopentane carboxylic acid, a-aminocyclohexane carboxylic acid, oc-aminocycloheptane carboxylic acid, a-(2-amino-2-norbomane)-carboxylic acid, a,g-diaminobutyric acid, a,β-diaminopropionic acid, homophenylalanine, and oc-tert- butylglycine.
[0083] The TCRs, polypeptides, and proteins of the invention can be glycosylated, amidated, carboxylated, phosphorylated, esterified, N-acylated, cyclized via, e.g., a disulfide bridge, or converted into an acid addition salt and/or optionally dimerized or polymerized, or conjugated.
[0084] The TCR, polypeptide, and/or protein of the invention can be obtained by methods known in the art such as, for example, de novo synthesis. Also, polypeptides and proteins can be recombinantly produced using the nucleic acids described herein using standard recombinant methods. See, for instance, Green and Sambrook, Molecular Cloning: A Laboratory Manual. 4th ed., Cold Spring Harbor Press, Cold Spring Harbor, NY (2012). Alternatively, the TCRs, polypeptides, and/or proteins described herein can be commercially synthesized by commercial entities. In this respect, the inventive TCRs, polypeptides, and proteins can be synthetic, recombinant, isolated, and/or purified. An embodiment of the invention provides an isolated or purified TCR, polypeptide, or protein encoded by any of the nucleic acids or vectors described herein with respect to other aspects of the invention. Another embodiment of the invention provides an isolated or purified TCR, polypeptide, or protein that results from expression of any of the nucleic acids or vectors described herein with respect to other aspects of the invention in a cell. Still another embodiment of the
invention provides a method of producing any of the TCRs, polypeptides, or proteins described herein, the method comprising culturing any of the host cells or populations of host cells described herein so that the TCR, polypeptide, or protein is produced.
[0085] Included in the scope of the invention are conjugates, e.g., bioconjugates, comprising any of the inventive TCRs, polypeptides, or proteins (including any of the functional portions or variants thereof), nucleic acids, recombinant expression vectors, host cells, populations of host cells, or antibodies, or antigen binding portions thereof.
Conjugates, as well as methods of synthesizing conjugates in general, are known in the art. [0086] An embodiment of the invention provides a nucleic acid comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein. "Nucleic acid," as used herein, includes "polynucleotide," "oligonucleotide," and "nucleic acid molecule," and generally means a polymer of DNA or RNA, which can be single-stranded or double-stranded, which can contain natural, non-natural or altered nucleotides, and which can contain a natural, non-natural or altered intemucleotide linkage, such as a phosphoroamidate linkage or a phosphorothioate linkage, instead of the phosphodiester found between the nucleotides of an unmodified oligonucleotide. In embodiments, the nucleic acid comprises complementary DNA (cDNA). It is generally preferred that the nucleic acid does not comprise any insertions, deletions, inversions, and/or substitutions. However, it may be suitable in some instances, as discussed herein, for the nucleic acid to comprise one or more insertions, deletions, inversions, and/or substitutions.
[0087] Preferably, the nucleic acids of the invention are recombinant. As used herein, the term "recombinant" refers to (i) molecules that are constructed outside living cells by joining natural or synthetic nucleic acid segments to nucleic acid molecules that can replicate in a living cell, or (ii) molecules that result from the replication of those described in (i) above.
For purposes herein, the replication can be in vitro replication or in vivo replication.
[0088] The nucleic acids can be constructed based on chemical synthesis and/or enzymatic ligation reactions using procedures known in the art. See, for example, Green and Sambrook et al., supra. For example, a nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed upon hybridization (e.g., phosphorothioate derivatives and acridine substituted nucleotides). Examples of modified nucleotides that can be used to generate the nucleic acids include, but are not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine,
xanthine, 4-acetylcytosine, 5-(carboxyhydroxymethyl) uracil, 5-carboxymethylaminomethyl- 2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1 -methylguanine, 1-methybnosine, 2,2-dimethylguanine, 2- methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-substituted adenine, 7-methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil, 5 -methoxy uracil, 2-methylthio- N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5- oxyacetic acid methylester, 3-(3-amino-3-N-2-carboxypropyl) uracil, and 2,6-diaminopurine. Alternatively, one or more of the nucleic acids of the invention can be purchased from commercial entities.
[0089] The nucleic acid can comprise any nucleotide sequence which encodes any of the TCRs, polypeptides, or proteins described herein. In embodiments of the invention, the nucleic acid may comprise the nucleotide sequences of any one of SEQ ID NOs: 92-97 and 107-109 (Table 4). In embodiments of the invention, the nucleic acid comprises the nucleotide sequences of both of SEQ ID NOs: 92, and 93 or 107, or both of SEQ ID NOs: 94, and 95 or 108, or both of SEQ ID NOs: 96, and 97 or 109.
[0090] In embodiments of the invention, the nucleic acid comprises a codon-optimized nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein. Without being bound to any particular theory or mechanism, it is believed that codon optimization of the nucleotide sequence increases the translation efficiency of the mRNA transcripts. Codon optimization of the nucleotide sequence may involve substituting a native codon for another codon that encodes the same amino acid, but can be translated by tRNA that is more readily available within a cell, thus increasing translation efficiency. Optimization of the nucleotide sequence may also reduce secondary mRNA structures that would interfere with translation, thus increasing translation efficiency.
[0091] The invention also provides a nucleic acid comprising a nucleotide sequence which is complementary to the nucleotide sequence of any of the nucleic acids described herein or a nucleotide sequence which hybridizes under stringent conditions to the nucleotide sequence of any of the nucleic acids described herein.
[0092] The nucleotide sequence which hybridizes under stringent conditions preferably hybridizes under high stringency conditions. By “high stringency conditions” is meant that the nucleotide sequence specifically hybridizes to a target sequence (the nucleotide sequence of any of the nucleic acids described herein) in an amount that is detectably stronger than non-specific hybridization. High stringency conditions include conditions which would distinguish a polynucleotide with an exact complementary sequence, or one containing only a few scattered mismatches from a random sequence that happened to have a few small regions (e.g., 3-10 bases) that matched the nucleotide sequence. Such small regions of complementarity are more easily melted than a full-length complement of 14-17 or more bases, and high stringency hybridization makes them easily distinguishable. Relatively high stringency conditions would include, for example, low salt and/or high temperature conditions, such as provided by about 0.02-0.1 M NaCl or the equivalent, at temperatures of about 50-70 °C. Such high stringency conditions tolerate little, if any, mismatch between the nucleotide sequence and the template or target strand, and are particularly suitable for detecting expression of any of the inventive TCRs. It is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide.
[0093] The invention also provides a nucleic acid comprising a nucleotide sequence that is at least about 70% or more, e.g., about 80%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% identical to any of the nucleic acids described herein. In this regard, the nucleic acid may consist essentially of any of the nucleotide sequences described herein.
[0094] An embodiment of the invention provides an isolated or purified nucleic acid comprising, from 5’ to 3’, a first nucleic acid sequence and a second nucleotide sequence, wherein the first and second nucleotide sequence, respectively, encode the amino sequences of SEQ ID NOs: 20, and 21 or 98; 21 or 98, and 20; 22, and 23 or 99; 23 or 99, and 22; 24, and 25 or 100; 25 or 100, and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 30 and 31; 31 and 30; 34, and 35 or 101; 35 or 101, and 34; 36, and 37 or 102; 37 or 102, and 36; 38, and 39 or 103; 39 or 103, and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 44 and 45; 45 and
44; 46, and 47 or 104; 47 or 104, and 46; 48, and 49 or 105; 49 or 105, and 48; 50, and 51 or 106; 51 or 106, and 50; 52 and 53; 53 and 52; 54 and 55; 55 and 54; 56 and 57; 57 and 56. [0095] In an embodiment of the invention, the isolated or purified nucleic acid further comprises a third nucleotide sequence interposed between the first and second nucleotide sequence, wherein the third nucleotide sequence encodes a cleavable linker peptide. In an embodiment of the invention, the cleavable linker peptide comprises the amino acid sequence of SEQ ID NO: 60.
[0096] The nucleic acids of the invention can be incorporated into a recombinant expression vector. In this regard, the invention provides a recombinant expression vector comprising any of the nucleic acids of the invention. In embodiments of the invention, the recombinant expression vector comprises a nucleotide sequence encoding the a chain, the β chain, and linker peptide.
[0097] For purposes herein, the term "recombinant expression vector" means a genetically -modified oligonucleotide or polynucleotide construct that permits the expression of an mRNA, protein, polypeptide, or peptide by a host cell, when the construct comprises a nucleotide sequence encoding the mRNA, protein, polypeptide, or peptide, and the vector is contacted with the cell under conditions sufficient to have the mRNA, protein, polypeptide, or peptide expressed within the cell. The vectors of the invention are not naturally-occurring as a whole. However, parts of the vectors can be naturally-occurring. The inventive recombinant expression vectors can comprise any type of nucleotide, including, but not limited to DNA and RNA, which can be single-stranded or double-stranded, synthesized or obtained in part from natural sources, and which can contain natural, non-natural or altered nucleotides. The recombinant expression vectors can comprise naturally-occurring, non- naturally-occurring intemucleotide linkages, or both types of linkages. Preferably, the non- naturally occurring or altered nucleotides or intemucleotide linkages do not hinder the transcription or replication of the vector.
[0098] The recombinant expression vector of the invention can be any suitable recombinant expression vector, and can be used to transform or transfect any suitable host cell. Suitable vectors include those designed for propagation and expansion or for expression or both, such as plasmids and viruses. The vector can be selected from the pUC series (Fermentas Life Sciences), the pBluescript series (Stratagene, LaJolla, CA), the pET series (Novagen, Madison, WI), the pGEX series (Pharmacia Biotech, Uppsala, Sweden), and the pEX series (Clontech, Palo Alto, CA). Bacteriophage vectors, such as /.GTK). /.GTl 1,
/.Zap 11 (Stratagene), ZEMBL4, and lNMI 149, also can be used. Examples of plant expression vectors include pBIOl, pBI101.2, pBI101.3, pBI121 and pBIN19 (Clontech). Examples of animal expression vectors include pEUK-Cl, pMAM and pMAMneo (Clontech). Preferably, the recombinant expression vector is a viral vector, e.g., a retroviral vector. In an especially preferred embodiment, the recombinant expression vector is an MSGV1 vector. In an embodiment of the invention, the recombinant expression vector is a transposon or a lentiviral vector.
[0099] The recombinant expression vectors of the invention can be prepared using standard recombinant DNA techniques described in, for example, Green and Sambrook et al., supra. Constructs of expression vectors, which are circular or linear, can be prepared to contain a replication system functional in a prokaryotic or eukaryotic host cell. Replication systems can be derived, e.g., from ColEl, 2 m plasmid, l, SV40, bovine papillomavirus, and the like.
[0100] Desirably, the recombinant expression vector comprises regulatory sequences, such as transcription and translation initiation and termination codons, which are specific to the type of host cell (e.g., bacterium, fungus, plant, or animal) into which the vector is to be introduced, as appropriate and taking into consideration whether the vector is DNA- or RNA- based.
[0101] The recombinant expression vector can include one or more marker genes, which allow for selection of transformed or transfected host cells. Marker genes include biocide resistance, e.g., resistance to antibiotics, heavy metals, etc., complementation in an auxotrophic host cell to provide prototrophy, and the like. Suitable marker genes for the inventive expression vectors include, for instance, neomycin/G418 resistance genes, hygromycin resistance genes, histidinol resistance genes, tetracycline resistance genes, and ampicillin resistance genes.
[0102] The recombinant expression vector can comprise a native or normative promoter operably linked to the nucleotide sequence encoding the TCR, polypeptide, or protein, or to the nucleotide sequence which is complementary to or which hybridizes to the nucleotide sequence encoding the TCR, polypeptide, or protein. The selection of promoters, e.g., strong, weak, inducible, tissue-specific and developmental-specific, is within the ordinary skill of the artisan. Similarly, the combining of a nucleotide sequence with a promoter is also within the skill of the artisan. The promoter can be a non-viral promoter or a viral promoter, e.g., a
cytomegalovirus (CMV) promoter, an SV40 promoter, an RSV promoter, and a promoter found in the long-terminal repeat of the murine stem cell virus.
[0103] The inventive recombinant expression vectors can be designed for either transient expression, for stable expression, or for both. Also, the recombinant expression vectors can be made for constitutive expression or for inducible expression.
[0104] Further, the recombinant expression vectors can be made to include a suicide gene. As used herein, the term "suicide gene" refers to a gene that causes the cell expressing the suicide gene to die. The suicide gene can be a gene that confers sensitivity to an agent, e.g., a drug, upon the cell in which the gene is expressed, and causes the cell to die when the cell is contacted with or exposed to the agent. Suicide genes are known in the art and include, for example, the Herpes Simplex Virus (HSV) thymidine kinase (TK) gene, cytosine deaminase, purine nucleoside phosphorylase, nitroreductase, and the inducible caspase 9 gene system.
[0105] Another embodiment of the invention further provides a host cell comprising any of the recombinant expression vectors described herein. As used herein, the term "host cell" refers to any type of cell that can contain the inventive recombinant expression vector. The host cell can be a eukaryotic cell, e.g., plant, animal, fungi, or algae, or can be a prokaryotic cell, e.g., bacteria or protozoa. The host cell can be a cultured cell or a primary cell, i.e., isolated directly from an organism, e.g., a human. The host cell can be an adherent cell or a suspended cell, i.e., a cell that grows in suspension. Suitable host cells are known in the art and include, for instance, DH5a A. coli cells, Chinese hamster ovarian cells, monkey VERO cells, COS cells, HEK293 cells, and the like. For purposes of amplifying or replicating the recombinant expression vector, the host cell is preferably a prokaryotic cell, e.g., a DH5oc cell. For purposes of producing a recombinant TCR, polypeptide, or protein, the host cell is preferably a mammalian cell. Most preferably, the host cell is a human cell. While the host cell can be of any cell type, can originate from any type of tissue, and can be of any developmental stage, the host cell preferably is a peripheral blood lymphocyte (PBL) or a peripheral blood mononuclear cell (PBMC). More preferably, the host cell is a T cell. In an embodiment of the invention, the host cell is a human lymphocyte. In another embodiment of the invention, the host cell is selected from any of a T cell, a natural killer T (NKT) cell, an invariant natural killer T (iNKT) cell, and a natural killer (NK) cell. Still another embodiment of the invention provides a method of producing a host cell expressing a TCR that has antigenic specificity for the peptide of SEQ ID NO: 19, the method comprising
contacting a cell with any of the vectors described herein under conditions that allow introduction of the vector into the cell.
[0106] For purposes herein, the T cell can be any T cell, such as a cultured T cell, e.g., a primary T cell, or a T cell from a cultured T cell line, e.g., Jurkat, SupTl, etc., or a T cell obtained from a mammal. If obtained from a mammal, the T cell can be obtained from numerous sources, including but not limited to blood, bone marrow, lymph node, the thymus, or other tissues or fluids. T cells can also be enriched for or purified. Preferably, the T cell is a human T cell. The T cell can be any type of T cell and can be of any developmental stage, including but not limited to, CD4+/CD8+ double positive T cells, CD4+ helper T cells, e.g., Thi and Th2 cells, CD4+ T cells, CD8+ T cells (e.g., cytotoxic T cells), tumor infiltrating lymphocytes (TILs), memory T cells (e.g., central memory T cells and effector memory T cells), naive T cells, and the like.
[0107] Also provided by the invention is a population of cells comprising at least one host cell described herein. The population of cells can be a heterogeneous population comprising the host cell comprising any of the recombinant expression vectors described, in addition to at least one other cell, e.g., a host cell (e.g., a T cell), which does not comprise any of the recombinant expression vectors, or a cell other than a T cell, e.g., a B cell, a macrophage, a neutrophil, an erythrocyte, a hepatocyte, an endothelial cell, an epithelial cell, a muscle cell, a brain cell, etc. Alternatively, the population of cells can be a substantially homogeneous population, in which the population comprises mainly of host cells (e.g., consisting essentially of) comprising the recombinant expression vector. The population also can be a clonal population of cells, in which all cells of the population are clones of a single host cell comprising a recombinant expression vector, such that all cells of the population comprise the recombinant expression vector. In one embodiment of the invention, the population of cells is a clonal population comprising host cells comprising a recombinant expression vector as described herein.
[0108] In embodiments of the invention, the numbers of cells in the population may be rapidly expanded. Expansion of the numbers of T cells can be accomplished by any of a number of methods as are known in the art as described in, for example, U.S. Patent 8,034,334; U.S. Patent 8,383,099; U.S. Patent Application Publication No. 2012/0244133; Dudley et ak, J. Immunother., 26:332-42 (2003); and Riddell et ak, J. Immunol. Methods, 128:189-201 (1990). In embodiments, expansion of the numbers of T cells is carried out by
culturing the T cells with 0KT3 antibody, IL-2, and feeder PBMC (e.g., irradiated allogeneic PBMC).
[0109] The inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, and host cells (including populations thereof), can be isolated and/or purified. The term "isolated," as used herein, means having been removed from its natural environment. The term "purified," as used herein, means having been increased in purity, wherein "purity" is a relative term, and not to be necessarily construed as absolute purity. For example, the purity can be at least about 50%, can be greater than about 60%, about 70%, about 80%, about 90%, about 95%, or can be about 100%.
[0110] The inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, and host cells (including populations thereof), all of which are collectively referred to as "inventive TCR materials" hereinafter, can be formulated into a composition, such as a pharmaceutical composition. In this regard, the invention provides a pharmaceutical composition comprising any of the TCRs, polypeptides, proteins, nucleic acids, expression vectors, and host cells (including populations thereof), described herein, and a pharmaceutically acceptable carrier. The inventive pharmaceutical compositions containing any of the inventive TCR materials can comprise more than one inventive TCR material, e.g., a polypeptide and a nucleic acid, or two or more different TCRs. Alternatively, the pharmaceutical composition can comprise an inventive TCR material in combination with another pharmaceutically active agent(s) or drug(s), such as a chemotherapeutic agent, e.g., asparaginase, busulfan, carboplatin, cisplatin, daunorubicin, doxorubicin, fluorouracil, gemcitabine, hydroxyurea, methotrexate, paclitaxel, rituximab, vinblastine, vincristine, etc. [0111] Preferably, the carrier is a pharmaceutically acceptable carrier. With respect to pharmaceutical compositions, the carrier can be any of those conventionally used for the particular inventive TCR material under consideration. Methods for preparing administrable compositions are known or apparent to those skilled in the art and are described in more detail in, for example, Remington : The Science and Practice of Pharmacy, 22nd Ed., Pharmaceutical Press (2012). ft is preferred that the pharmaceutically acceptable carrier be one which has no detrimental side effects or toxicity under the conditions of use.
[0112] The choice of carrier will be determined in part by the particular inventive TCR material, as well as by the particular method used to administer the inventive TCR material. Accordingly, there are a variety of suitable formulations of the pharmaceutical composition of the invention. Suitable formulations may include any of those for parenteral,
subcutaneous, intravenous, intramuscular, intraarterial, intrathecal, intratumoral, or interperitoneal administration. More than one route can be used to administer the inventive TCR materials, and in certain instances, a particular route can provide a more immediate and more effective response than another route.
[0113] Preferably, the inventive TCR material is administered by injection, e.g., intravenously. When the inventive TCR material is a host cell (or population thereof) expressing the inventive TCR, the pharmaceutically acceptable carrier for the cells for injection may include any isotonic carrier such as, for example, normal saline (about 0.90% w/v of NaCl in water, about 300 mOsm/L NaC1 in water, or about 9.0 g NaCl per liter of water), NORMOSOL R electrolyte solution (Abbott, Chicago, IL), PLASMA-LYTE A (Baxter, Deerfield, IL), about 5% dextrose in water, or Ringer's lactate. In embodiments, the pharmaceutically acceptable carrier is supplemented with human serum albumin.
[0114] For purposes of the invention, the amount or dose (e.g., numbers of cells when the inventive TCR material is one or more cells) of the inventive TCR material administered should be sufficient to effect, e.g., a therapeutic or prophylactic response, in the subject or animal over a reasonable time frame. For example, the dose of the inventive TCR material should be sufficient to bind to a cancer antigen (e.g., LMP2), or detect, treat or prevent cancer in a period of from about 2 hours or longer, e.g., 12 to 24 or more hours, from the time of administration. In certain embodiments, the time period could be even longer. The dose will be determined by the efficacy of the particular inventive TCR material and the condition of the animal (e.g., human), as well as the body weight of the animal (e.g., human) to be treated. [0115] Many assays for determining an administered dose are known in the art. For purposes of the invention, an assay, which comprises comparing the extent to which target cells are lysed or IFN-γ is secreted by T cells expressing the inventive TCR, polypeptide, or protein upon administration of a given dose of such T cells to a mammal among a set of mammals of which each is given a different dose of the T cells, could be used to determine a starting dose to be administered to a mammal. The extent to which target cells are lysed or IFN-γ is secreted upon administration of a certain dose can be assayed by methods known in the art.
[0116] The dose of the inventive TCR material also will be determined by the existence, nature and extent of any adverse side effects that might accompany the administration of a particular inventive TCR material. Typically, the attending physician will decide the dosage of the inventive TCR material with which to treat each individual patient, taking into
consideration a variety of factors, such as age, body weight, general health, diet, sex, inventive TCR material to be administered, route of administration, and the severity of the cancer being treated. In embodiments in which the inventive TCR material is a population of cells, the number of cells administered per infusion may vary, e.g., from about 1 x 106 to about 1 x 1012 cells or more. In certain embodiments, fewer than 1 x 106 cells may be administered.
[0117] One of ordinary skill in the art will readily appreciate that the inventive TCR materials of the invention can be modified in any number of ways, such that the therapeutic or prophylactic efficacy of the inventive TCR materials is increased through the modification. For instance, the inventive TCR materials can be conjugated either directly or indirectly through a bridge to a chemotherapeutic agent. The practice of conjugating compounds to a chemotherapeutic agent is known in the art. One of ordinary skill in the art recognizes that sites on the inventive TCR materials, which are not necessary for the function of the inventive TCR materials, are suitable sites for attaching a bridge and/or a chemotherapeutic agent, provided that the bridge and/or chemotherapeutic agent, once attached to the inventive TCR materials, do(es) not interfere with the function of the inventive TCR materials, i.e., the ability to bind to LMP2 or to detect, treat, or prevent cancer.
[0118] It is contemplated that the inventive pharmaceutical compositions, TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, and populations of cells can be used in methods of treating or preventing cancer. Without being bound to a particular theory, the inventive TCRs are believed to bind specifically to LMP2, such that the TCR (or related inventive polypeptide or protein), when expressed by a cell, is able to mediate an immune response against a target cell expressing LMP2. In this regard, the invention provides a method of treating or preventing cancer in a mammal, comprising administering to the mammal any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, in an amount effective to treat or prevent cancer in the mammal.
[0119] An embodiment of the invention provides a method of inducing an immune response against a cancer in a mammal, comprising administering to the mammal any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic
acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, in an amount effective to induce an immune response against the cancer in the mammal.
[0120] An embodiment of the invention provides any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, for use in the treatment or prevention of cancer in a mammal.
[0121] An embodiment of the invention provides any of the pharmaceutical compositions, TCRs, polypeptides, or proteins described herein, any nucleic acid or recombinant expression vector comprising a nucleotide sequence encoding any of the TCRs, polypeptides, or proteins described herein, or any host cell or population of cells comprising a recombinant vector which encodes any of the TCRs, polypeptides, or proteins described herein, for use in inducing an immune response against a cancer in a mammal.
[0122] The terms "treat," and "prevent" as well as words stemming therefrom, as used herein, do not necessarily imply 100% or complete treatment or prevention. Rather, there are varying degrees of treatment or prevention of which one of ordinary skill in the art recognizes as having a potential benefit or therapeutic effect. In this respect, the inventive methods can provide any amount of any level of treatment or prevention of cancer in a mammal. Furthermore, the treatment or prevention provided by the inventive method can include treatment or prevention of one or more conditions or symptoms of the cancer being treated or prevented. For example, treatment or prevention can include promoting the regression of a tumor. Also, for purposes herein, "prevention" can encompass delaying the onset of the cancer, or a symptom or condition thereof. Alternatively or additionally, “prevention” may encompass preventing or delaying the recurrence of cancer, or a symptom or condition thereof.
[0123] Also provided is a method of detecting the presence of cancer in a mammal. The method comprises (i) contacting a sample comprising one or more cells from the mammal with any of the inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, populations of cells, or pharmaceutical compositions described
herein, thereby forming a complex, and (ii) detecting the complex, wherein detection of the complex is indicative of the presence of cancer in the mammal.
[0124] With respect to the inventive method of detecting cancer in a mammal, the sample of cells can be a sample comprising whole cells, lysates thereof, or a fraction of the whole cell lysates, e.g., a nuclear or cytoplasmic fraction, a whole protein fraction, or a nucleic acid fraction.
[0125] For purposes of the inventive method of detecting cancer, the contacting can take place in vitro or in vivo with respect to the mammal. Preferably, the contacting is in vitro. [0126] Also, detection of the complex can occur through any number of ways known in the art. For instance, the inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, or populations of cells, described herein, can be labeled with a detectable label such as, for instance, a radioisotope, a fluorophore (e.g., fluorescein isothiocyanate (FITC), phycoerythrin (PE)), an enzyme (e.g., alkaline phosphatase, horseradish peroxidase), and element particles (e.g., gold particles).
[0127] For purposes of the inventive methods, wherein host cells or populations of cells are administered, the cells can be cells that are allogeneic or autologous to the mammal. Preferably, the cells are autologous to the mammal.
[0128] With respect to the inventive methods, the cancer can be any cancer, including, e.g., any of acute lymphocytic cancer, acute myeloid leukemia, alveolar rhabdomyosarcoma, bone cancer, brain cancer, breast cancer, cancer of the anus, anal canal, or anorectum, cancer of the eye, cancer of the intrahepatic bile duct, cancer of the joints, cancer of the neck, gallbladder, or pleura, cancer of the nose, nasal cavity, or middle ear, cancer of the oral cavity, cancer of the vagina, cancer of the vulva, chronic lymphocytic leukemia, chronic myeloid cancer, colon cancer, colorectal cancer, endometrial cancer, esophageal cancer, uterine cervical cancer, gastrointestinal carcinoid tumor, glioma, Hodgkin lymphoma, hypopharynx cancer, kidney cancer, larynx cancer, liver cancer, lung cancer, malignant mesothelioma, melanoma, multiple myeloma, nasopharynx cancer, non-Hodgkin lymphoma, cancer of the oropharynx, ovarian cancer, cancer of the penis, pancreatic cancer, peritoneum, omentum, and mesentery cancer, pharynx cancer, prostate cancer, rectal cancer, renal cancer, skin cancer, small intestine cancer, soft tissue cancer, stomach cancer, testicular cancer, thyroid cancer, cancer of the uterus, ureter cancer, and urinary bladder cancer. A preferred cancer is an epithelial cancer (such as nasopharyngeal cancer or gastric cancer) or a lymphoma (such as Hodgkin lymphoma, T/NK cell lymphoma, or post-transplant
lymphoproliferative disorders). In embodiments of the invention, the cancer expresses an LMP2 amino acid sequence, wherein the LMP2 amino acid sequence is SEQ ID NO: 19. The LMP2 expressed by the cancer may be as described herein with respect to other aspects of the invention.
[0129] The mammal referred to in the inventive methods can be any mammal. As used herein, the term "mammal" refers to any mammal, including, but not limited to, mammals of the order Rodentia, such as mice and hamsters, and mammals of the order Logomorpha, such as rabbits. It is preferred that the mammals are from the order Carnivora, including Felines (cats) and Canines (dogs). It is more preferred that the mammals are from the order Artiodactyla, including Bovines (cows) and Swines (pigs) or of the order Perssodactyla, including Equines (horses). It is most preferred that the mammals are of the order Primates, Ceboids, or Simoids (monkeys) or of the order Anthropoids (humans and apes). An especially preferred mammal is the human.
[0130] It shall be noted that the preceding are merely examples of embodiments. Other exemplary embodiments are apparent from the entirety of the description herein. It will also be understood by one of ordinary skill in the art that each of these embodiments may be used in various combinations with the other embodiments provided herein.
[0131] The following examples further illustrate the invention but, of course, should not be construed as in any way limiting its scope.
EXAMPLES
[0132] Flow cytometry was performed in the various Examples below using the following materials and software. To detect TCR expression in transduced cells, PE- conjugated antibody against tetramer, or APC-conjugated antibody against mouse constant region (Biolegend, San Diego, CA, USA or BD Biosciences, San Jose, CA, USA) were used to label cells. Data were acquired with a BD Fortessa or LSRII flow cytometer (BD Biosciences) and analyzed with FlowJo software (FlowJo, LLC, Ashland, OR, USA).
EXAMPLE 1
[0133] This Example demonstrates isolation of anti-LMP2 TCRs.
[0134] CD8+ T cells and dendritic cells (DCs) were isolated from healthy donors. Matured DCs were pulsed with LMP2 peptide LMP2426-434 for four hours. CD8+ T cells were stimulated with peptide pulsed autologous DCs. After two rounds of stimulation, T cells
were tested for reactivity against 293-A2 cells expressing the full length LMP2 protein and were found to possess LMP2-reactive T cells. LMP2 reactive T cells were enriched using LMP2426-434-HLA-A*02:01 tetramers. The enriched T cells were confirmed to be tetramer positive and CD8 positive (Figures 1A-1F). Subsequently, these LMP2 reactive CD8+ T cells were sequenced using single cell sequencing to identify paired T-cell receptor (TCR) TCRoc and TCRβ chain sequences (TCRoc (TCRAV) and TCRβ (TCRBV)).
EXAMPLE 2
[0135] This Example demonstrates construction of a retroviral vector encoding anti- LMP2 TCRs.
[0136] Separate MSGV1 based-retroviral vectors were constructed which encoded TCR alpha and beta chain variable regions which were identical to each of the TCRs of Example 1 with the exception that the amino acid residue at position 2 of the N-terminal signal peptide of the beta chain was changed to an alanine in order to facilitate cloning into the vector. Additional modifications to the wild-type TCR were made, as described in more detail below. [0137] Construction of LMP2-specific TCRs was done as previously described (Jin et al.,
JCI Insight, 3(8): e99488 (2018), incorporated herein by reference in its entirety). Briefly, the TCRβ VDJ regions were fused to the mouse TCRβ constant chain, and the TCRoc VJ regions were fused to the mouse TCRoc constant chain. Without being bound to a particular theory or mechanism, it is believed that replacement of the constant regions of the human TCRoc and TCRβ chains by those encoding the corresponding murine constant regions improves TCR expression and functionality (Cohen et al., Cancer Res., 66(17): 8878-8886 (2006)).
[0138] In addition, the murine TCRoc and TCRβ constant chains were cysteine-modified, and transmembrane hydrophobic mutations were introduced into the murine TCRoc constant chain. Without being bound to a particular theory or mechanism, it is believed that these modifications result in preferential pairing of the introduced TCR chains and enhanced TCR surface expression and functionality (Cohen et al., Cancer Res., 67(8):3898-903 (2007); Haga-Friedman et al., J. Immu., 188: 5538-5546 (2012)).
[0139] The TCRβ and TCRoc chains were separated by a Furin SGSG P2A linker (RAKRS GS GATNF S LLKQ AGD VEENPGP) (SEQ ID NO: 60) to ensure a comparable
expression efficiency of the two chains (Szymczak et al., Nat. Biotechnol., 22(5):589-94 (2004)).
[0140] To allow cloning of the LMP2-specific TCR expression cassette into the MSGV1 vector 5’NcoI site, the second amino acid in the TCRβ chain (the second amino acid within the N-terminal signal peptide) was changed to an alanine (A). The expression cassette had the following configuration: 5 NcoI-VDJβ -mC β-Furin/SGSG/P2A-VJα-mCα.-EcoRI3 . The nucleotide sequences of each TCR were codon optimized for human tissue expression.
[0141] After the modifications described in this Example were made, the sequences were as in the following table.
EXAMPLE 3
[0142] This Example demonstrates characterization of an anti-LMP2 TCR D6.
[0143] Retrovirus encoding the TCR D6 anti-LMP2 TCR was produced and used to transduce peripheral blood T cells with the TCR D6-encoding MSGV1 vector of Example 2. Human peripheral blood mononuclear cells (PBMCs) were isolated from the huffy coats. Before transduction, PBMCs were cultured in T cell media plus 50 ng/mL anti-CD3 (OKT3, Miltenyi Biotec, Bergisch Gladbach, Germany) for two days. Retroviral supernatants were generated by co-transfection of 293GP cells with MSGV1 vector expressing TCR and RD114 packaging plasmids. Two days after transfection, retroviral supernatants were harvested. Transduction was performed by adding 5 ml retroviral supernatant to one well of a six-well plate coated with RetroNectin and centrifuged at 2000g for 2 hours at 32°C. The retroviral supernatant was discarded and 1 million T cells were added. On the following day, T cells were harvested and cultured in normal condition.
[0144] The expression of the introduced TCR was assessed by flow cytometry using an antibody specific for the mouse TCRβ chain. The results indicated that the TCR specifically binds to LMP2426-434-HLA-A*02:01 tetramers, but it does not bind to E7-HLA-A*02:01 tetramers (Figures 2A-2D).
[0145] To evaluate key residues that mediate recognition by the anti-LMP2 TCR, individual residues of LMP2 peptide were mutated to alanine (Figure 3). 293-A2 cells were pulsed with LMP2426-434, or alanine mutated peptides, then co-cultured with LMP2 TCR T cells. The inflammatory effector cytokine IFN-γ concentration in the supernatant was measured by ELISA. Alanine substitutions at positions 2 and 9 reduced IFN-γ production; these positions have been demonstrated to be anchoring positions for binding with HLA-A2 molecule. Alanine substitutions at positions 4, 5, 6, 7, and 8 reduced IFN-γ , suggesting that these residues contribute to the anti-LMP2 TCR recognition of LMP2426-434 peptide.
[0146] In silico search was performed for human peptides with amino acid sequences that are similar to the TCR recognition motif and/or human peptides with high levels of sequence homology (ScanProsite tool, NCBI protein BLAST). After filtering for predicted HLA- A*02:01 IC50 of 1000 or below, a total of 48 candidate peptides (Table 6) were curated as candidates for cross-reactivity screening.
Results of screeing for possible cross-reactivity are in Figures 4 and 5.
[0147] To define the functional avidity, the anti-LMP2 TCR transduced T cells were co- cultured with 293-A2 cells pulsed with serial diluted LMP2426-434 peptide. Anti-LMP2 TCR transduced T cells displayed high functional avidity in the range of 10-9-10-10 M LMP2426-434 peptide (Figure 6).
EXAMPLE 4
[0148] This Example demonstrates EBV -transformed lymphoblastoid cell line (EBV- LCL) recognition by the anti-LMP2 TCR D6.
[0149] EBV-LCLs naturally express all latent proteins including: EBNA1, EBNA2, EBNA3, LMP1, and LMP2. In addition, EBV-LCLs are HLA-intact. Several EBV-LCLs were made. LMP2 protein expression was confirmed by Western Blot (Figure 7A). When anti-LMP2 TCR T cells were co-cultured with EBV-LCLs, the T cells showed production of IFN-γ in response to each of the HLA-A*02:01+ EBV-LCLs (Figure 7B). EBV-LCLs lacking HLA-A*02:01 were not recognized. These results indicate that LMP2 TCR can recognize naturally processed and presented epitope of LMP2 antigen on EBV-LCLs in an antigen- and HLA-A*02:01- dependent fashion.
EXAMPLE 5
[0150] This Example demonstrates tumor cell line recognition by the anti-LMP2 TCR D6.
[0151] To evaluate whether anti-LMP2426-434 TCR transduced CD8+ T cells could recognize tumor cell lines expressing the LMP2 antigen in the context of HLA-A*02:01, a number of tumor cell lines derived from different cancer histologies were tested for recognition. Nasopharyngeal cancer cell lines, including C666-1, HK1-EBV, HONE1-EBV, and NPC43, were transduced with LMP2 since these cell lines lose LMP2 expression in vitro. [0152] Anti-LMP2426-434 TCR transduced CD8+ T cells produced the inflammatory effector cytokine IFN-γ when co-cultured with four nasopharyngeal cancer cell lines expressing LMP2 and HLA-A*02:01, but not when co-cultured with several tumor cell lines lacking LMP2 or HLA-A*02:01 (Figure 8A). In addition, introduction of the target antigen LMP2 into two tumor cell lines naturally expressing HLA-A*02:01 but not the target antigen conferred their recognition by the anti-LMP2426-434 TCR transduced CD8+ T cells (Figure 8A).
[0153] Figures 8B and 8C are graphs showing additional results of T cells transduced to express the anti-LMP2 TCR D6 co-cultured with target cell lines as indicated on the x-axis, at an E:T ratio of 1:1, 5e4 cells each in 96-well round-bottom plate for a final total volume of 200 pL/well. The levels of IFNγ in the overnight co-culture supernatant was measured with ELISA.
[0154] The results indicate that LMP2 TCR can recognize processed and presented epitope of LMP2 antigen on tumor cell lines in an antigen- and HLA-A*02:01- dependent fashion.
EXAMPLE 6
[0155] This Example demonstrates tumor cell cytoloysis induced by the anti-LMP2 TCR D6.
[0156] The ability of anti-LMP2 TCR T cells to kill tumor cells was assessed with a real- time impedance-based cytolysis assay (Figures 9A-9F). Each of the target cell lines that expressed HLA-A*02:01 and LMP2 were killed at a effector-to-target ratio 1:1, including two nasopharyngeal cancer cell lines (HK1-EBV and HONE1-EBV) and two HLA-A*02:01+ cell lines engineered to express LMP2 (4050-LMP2 and 293A2-LMP2) (Figures 9A-9F). Tumor cell lines that did not express the HLA-A*02:01 molecule or the EBV LMP2 molecule were not killed (4050 and Hela). These results demonstrate that LMP2 TCR T cells could specifically engage and mediate T cell effector functions against LMP2+ tumor lines.
EXAMPLE 7
[0157] This Example demonstrates comparison of anti-LMP2 TCRs.
[0158] The anti-LMP2 TCR D2 was constructed, and T cells transduced, similarly as was detailed above for TCR D6.
[0159] In a functional avidity assay, TCR D6 T cells recognized LMP2426-434 peptide at lower concentrations than TCR D2 T cells (Figure 10A). TCR D6 T cells showed IFN-γ release at concentration as low as 10 picomoles, whereas TCR D2 T cells showed IFN-γ release at concentration as low as 100 picomoles. These findings indicated that TCR D2 T cells had lower avidity for LMP2426-434 peptide than TCR D6 T cells.
[0160] In addition, the ability of TCR D2 and TCR D6 T cells to kill tumor cells was compared (Figures 10B and C). When effector-to-target ratio (E:T) was 1:1, the TCRs showed similar ability in killing tumor cells (Figure 10B). When effector-to-target ratio (E:T) was 1:5, TCR D6 was able to continuously kill tumor cells in 48 h, while TCR D2 showed limited killing ability (Figure IOC), possibly due to its lower avidity than TCR D6 in lower concentrations.
[0161] Results for TCR D29 are presented in Figure 10D.
[0162] All references, including publications, patent applications, and patents, cited herein are hereby incorporated by reference to the same extent as if each reference were individually and specifically indicated to be incorporated by reference and were set forth in its entirety herein.
[0163] The use of the terms “a” and “an” and “the” and “at least one” and similar referents in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The use of the term “at least one” followed by a list of one or more items (for example, “at least one of A and B”) is to be construed to mean one item selected from the listed items (A or B) or any combination of two or more of the listed items (A and B), unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention unless otherwise claimed. No language in the specification should be construed as indicating any non-claimed element as essential to the practice of the invention.
[0164] Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations of those preferred embodiments may become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventors expect skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than as specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.
Claims
1. An isolated or purified T-cell receptor (TCR) comprising the amino acid sequences of
(a) all of SEQ ID NOs: 1-3,
(b) all of SEQ ID NOs: 4-6,
(c) all of SEQ ID NOs: 7-9,
(d) all of SEQ ID NOs: 10-12,
(e) all of SEQ ID NOs: 13-15,
(f) all of SEQ ID NOs: 16-18,
(g) all of SEQ ID NOs: 1-6,
(h) all of SEQ ID NOs: 7-12, or
(i) all of SEQ ID NOs: 13-18, wherein the TCR has antigenic specificity for an LMP2 amino acid sequence presented by a human leukocyte antigen (HLA) Class I molecule.
2. The isolated or purified TCR according to claim 1, wherein the LMP2 amino acid sequence is SEQ ID NO: 19.
3. The isolated or purified TCR according to claim 2, wherein the LMP2 amino acid sequence is SEQ ID NO: 19 from any one of SEQ ID NOs: 86-91.
4. The isolated or purified TCR according to any one of claims 1-3, wherein the HLA Class I molecule is an HLA-A molecule.
5. The isolated or purified TCR according to any one of claims 1-4, wherein the HLA Class I molecule is an HLA-A*02 molecule.
6. The isolated or purified TCR according to any one of claims 1-5, wherein the HLA Class I molecule is encoded by the HLA-A*02:01 allele.
7. The isolated or purified TCR according to any one of claims 1-6, comprising the amino acid sequences of:
(i) SEQ ID NO: 20,
(ii) SEQ ID NO: 21 or 98,
(iii) SEQ ID NO: 26,
(iv) SEQ ID NO: 27,
(v) both of SEQ ID NOs: 20, and 21 or 98,
(vi) both of SEQ ID NOs: 26 and 27,
(vii) SEQ ID NO: 22,
(viii) SEQ ID NO: 23 or 99,
(ix) SEQ ID NO: 28,
(x) SEQ ID NO: 29,
(xi) both of SEQ ID NOs: 22, and 23 or 99,
(xii) both of SEQ ID NOs: 28 and 29.
(xiii) SEQ ID NO: 24,
(xiv) SEQ ID NO: 25 or 100,
(xv) SEQ ID NO: 30,
(xvi) SEQ ID NO: 31,
(xvii) both of SEQ ID NOs: 24, and 25 or 100, or (xviii) both of SEQ ID NOs: 30 and 31.
8. The isolated or purified TCR of any one of claims 1-7, further comprising:
(a) an a chain constant region comprising the amino acid sequence of SEQ ID NO: 58, wherein:
(i) X at position 48 of SEQ ID NO: 58 is Thr or Cys;
(ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) a β chain constant region comprising the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or
(c) both (a) and (b).
9. The isolated or purified TCR of any one of claims 1-8, comprising:
(a) an a chain comprising the amino acid sequence of SEQ ID NO: 46, wherein:
(i) X at position 179 of SEQ ID NO: 46 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) a β chain comprising the amino acid sequence of SEQ ID NO: 47 or 104, wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys;
(c) an a chain comprising the amino acid sequence of SEQ ID NO: 48, wherein:
(i) X at position 177 of SEQ ID NO: 48 is Thr or Cys;
(ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(d) a β chain comprising the amino acid sequence of SEQ ID NO: 49 or 105, wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys;
(e) an a chain comprising the amino acid sequence of SEQ ID NO: 50, wherein:
(i) X at position 179 of SEQ ID NO: 50 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(f) a β chain comprising the amino acid sequence of SEQ ID NO: 51 or 106, wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys;
(g) both (a) and (b);
(h) both (c) and (d);
(i) both (e) and (f);
(j) an a chain comprising the amino acid sequence of SEQ ID NO: 52, wherein:
(i) X at position 160 of SEQ ID NO: 52 is Thr or Cys;
(ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(k) a β chain comprising the amino acid sequence of SEQ ID NO: 53, wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys;
(l) an a chain comprising the amino acid sequence of SEQ ID NO: 54, wherein:
(i) X at position 159 of SEQ ID NO: 54 is Thr or Cys;
(ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(m) a β chain comprising the amino acid sequence of SEQ ID NO: 55, wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys;
(n) an a chain comprising the amino acid sequence of SEQ ID NO: 56, wherein:
(i) X at position 161 of SEQ ID NO: 56 is Thr or Cys;
(ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(o) a β chain comprising the amino acid sequence of SEQ ID NO: 57, wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys;
(p) both (j) and (k);
(q) both (1) and (m); or
(r) both (n) and (o).
10. An isolated or purified polypeptide comprising a functional portion of the TCR of any one of claims 1-9, wherein the functional portion comprises the amino acid sequences of:
(a) all of SEQ ID NOs: 1-3,
(b) all of SEQ ID NOs: 4-6,
(c) all of SEQ ID NOs: 7-9,
(d) all of SEQ ID NOs: 10-12,
(e) all of SEQ ID NOs: 13-15,
(f) all of SEQ ID NOs: 16-18,
(g) all of SEQ ID NOs: 1-6,
(h) all of SEQ ID NOs: 7-12, or
(i) all of SEQ ID NOs: 13-18.
11. The isolated or purified polypeptide according to claim 10, wherein the functional portion comprises the amino acid sequence(s) of:
(i) SEQ ID NO: 20,
(ii) SEQ ID NO: 21 or 98,
(iii) SEQ ID NO: 26,
(iv) SEQ ID NO: 27,
(v) both of SEQ ID NOs: 20, and 21 or 98,
(vi) both of SEQ ID NOs: 26 and 27,
(vii) SEQ ID NO: 22,
(viii) SEQ ID NO: 23 or 99,
(ix) SEQ ID NO: 28,
(x) SEQ ID NO: 29,
(xi) both of SEQ ID NOs: 22, and 23 or 99,
(xii) both of SEQ ID NOs: 28 and 29,
(xiii) SEQ ID NO: 24,
(xiv) SEQ ID NO: 25 or 100,
(xv) SEQ ID NO: 30,
(xvi) SEQ ID NO: 31,
(xvii) both of SEQ ID NOs: 24, and 25 or 100, or (xviii) both of SEQ ID NOs: 30 and 31.
12. The isolated or purified polypeptide of claim 10 or 11, further comprising:
(a) the amino acid sequence of SEQ ID NO: 58, wherein:
(i) X at position 48 of SEQ ID NO: 58 is Thr or Cys;
(ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or
(c) both (a) and (b).
13. The isolated or purified polypeptide of any one of claims 10-12, comprising:
(a) the amino acid sequence of SEQ ID NO: 46, wherein:
(i) X at position 179 of SEQ ID NO: 46 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) the amino acid sequence of SEQ ID NO: 47 or 104, wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys;
(c) the amino acid sequence of SEQ ID NO: 48, wherein:
(i) X at position 177 of SEQ ID NO: 48 is Thr or Cys;
(ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(d) the amino acid sequence of SEQ ID NO: 49 or 105, wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys;
(e) the amino acid sequence of SEQ ID NO: 50, wherein:
(i) X at position 179 of SEQ ID NO: 50 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(f) the amino acid sequence of SEQ ID NO: 51 or 106, wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys;
(g) both (a) and (b);
(h) both (c) and (d);
(i) both (e) and (f);
(j) the amino acid sequence of SEQ ID NO: 52, wherein:
(i) X at position 160 of SEQ ID NO: 52 is Thr or Cys;
(ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(k) the amino acid sequence of SEQ ID NO: 53, wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys;
(l) the amino acid sequence of SEQ ID NO: 54, wherein:
(i) X at position 159 of SEQ ID NO: 54 is Thr or Cys;
(ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(m) the amino acid sequence of SEQ ID NO: 55, wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys;
(n) the amino acid sequence of SEQ ID NO: 56, wherein:
(i) X at position 1601of SEQ ID NO: 56 is Thr or Cys;
(ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(o) the amino acid sequence of SEQ ID NO: 57, wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys;
(p) both (j) and (k);
(q) both (1) and (m); or
(r) both (n) and (o).
14. An isolated or purified protein comprising at least one of the polypeptides of any one of claims 10-13.
15. The isolated or purified protein according to claim 14, comprising:
(a) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 1- 3 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 4-6;
(b) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 7- 9 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 10- 12; or
(c) a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 13-15 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 16-18.
16. The isolated or purified protein according to claim 14 or 15, comprising:
(i) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 20 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 21 or 98;
(ii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 26 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 27;
(iii) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 22 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 23 or
99;
(iv) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 28 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 29;
(v) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 24 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 25 or 100; or
(vi) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 30 and a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 31.
17. The isolated or purified protein of any one of claims 14-16, further comprising:
(a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 58, wherein:
(i) X at position 48 of SEQ ID NO: 58 is Thr or Cys;
(ii) X at position 112 of SEQ ID NO: 58 is Ser, Ala, Val, Leu, lie, Pro, Phe,
Met, or Trp;
(iii) X at position 114 of SEQ ID NO: 58 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 115 of SEQ ID NO: 58 is Gly, Ala, Val, Leu, Ile, Pro, Phe,
Met, or Trp;
(b) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 59, wherein X at position 57 of SEQ ID NO: 59 is Ser or Cys; or
(c) both (a) and (b).
18. The isolated or purified protein of any one of claims 14-17, comprising:
(a) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 46, wherein:
(i) X at position 179 of SEQ ID NO: 46 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 46 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 46 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 46 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(b) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 47 or 104, wherein X at position 189 of SEQ ID NO: 47 or 104 is Ser or Cys;
(c) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 48, wherein:
(i) X at position 177 of SEQ ID NO: 48 is Thr or Cys;
(ii) X at position 241 of SEQ ID NO: 48 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 243 of SEQ ID NO: 48 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 244 of SEQ ID NO: 48 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(d) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 49 or 105, wherein X at position 191 of SEQ ID NO: 49 or 105 is Ser or Cys;
(e) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 50, wherein:
(i) X at position 179 of SEQ ID NO: 50 is Thr or Cys;
(ii) X at position 243 of SEQ ID NO: 50 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 245 of SEQ ID NO: 50 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 246 of SEQ ID NO: 50 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(f) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 51 or 106, wherein X at position 189 of SEQ ID NO: 51 or 106 is Ser or Cys;
(g) both (a) and (b);
(h) both (c) and (d);
(i) both (e) and (f);
(j) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 52, wherein:
(i) X at position 160 of SEQ ID NO: 52 is Thr or Cys;
(ii) X at position 224 of SEQ ID NO: 52 is Ser, Ala, Val, Leu, lie, Pro, Phe, Met, or Trp;
(iii) X at position 226 of SEQ ID NO: 52 is Met, Ala, Val, Leu, lie, Pro, Phe, or Trp; and
(iv) X at position 227 of SEQ ID NO: 52 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(k) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 53, wherein X at position 170 of SEQ ID NO: 53 is Ser or Cys;
(l) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 54, wherein:
(i) X at position 159 of SEQ ID NO: 54 is Thr or Cys;
(ii) X at position 223 of SEQ ID NO: 54 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 225 of SEQ ID NO: 54 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 226 of SEQ ID NO: 54 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(m) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 55, wherein X at position 172 of SEQ ID NO: 55 is Ser or Cys;
(n) a first polypeptide chain comprising the amino acid sequence of SEQ ID NO: 56, wherein:
(i) X at position 161 of SEQ ID NO: 56 is Thr or Cys;
(ii) X at position 225 of SEQ ID NO: 56 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp;
(iii) X at position 227 of SEQ ID NO: 56 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and
(iv) X at position 228 of SEQ ID NO: 56 is Gly, Ala, Val, Leu, lie, Pro, Phe,
Met, or Trp;
(o) a second polypeptide chain comprising the amino acid sequence of SEQ ID NO: 57, wherein X at position 175 of SEQ ID NO: 57 is Ser or Cys;
(p) both (j) and (k);
(q) both (1) and (m); or
(r) both (n) and (o).
19. An isolated or purified nucleic acid comprising a nucleotide sequence encoding the TCR according to any one of claims 1-9, the polypeptide according to any one of claims 10-13, or the protein according to any one of claims 14-18.
20. An isolated or purified nucleic acid comprising, from 5’ to 3’, a first nucleic acid sequence and a second nucleotide sequence, wherein the first and second nucleotide sequence, respectively, encode the amino sequences of SEQ ID NOs: 20, and 21 or 98; 21 or 98, and 20; 22, and 23 or 99; 23 or 99, and 22; 24, and 25 or 100; 25 or 100, and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 30 and 31; 31 and 30; 34, and 35 or 101; 35 or 101, and 34; 36, and 37 or 102; 37 or 102, and 36; 38, and 39 or 103; 39 or 103, and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 44 and 45; 45 and 44; 46, and 47 or 104; 47 or 104, and 46; 48, and 49 or 105; 49 or 105, and 48; 50, and 51 or 106; 51 or 106, and 50; 52 and 53; 53 and 52; 54 and 55; 55 and 54; 56 and 57; 57 and 56.
21. The isolated or purified nucleic acid according to claim 20, further comprising a third nucleotide sequence interposed between the first and second nucleotide sequence, wherein the third nucleotide sequence encodes a cleavable linker peptide.
22. The isolated or purified nucleic acid according to claim 21, wherein the cleavable linker peptide comprises the amino acid sequence of SEQ ID NO: 60.
23. A recombinant expression vector comprising the nucleic acid according to any one of claims 19-22.
24. The recombinant expression vector according to claim 23, which is a transposon or a lentiviral vector.
25. An isolated or purified TCR, polypeptide, or protein encoded by the nucleic acid according to any one of claims 19-22 or the vector according to claim 23 or 24.
26. An isolated or purified TCR, polypeptide, or protein that results from expression of the nucleic acid according to any one of claims 19-22 or the vector according to claim 23 or 24 in a cell.
27. A method of producing a host cell expressing a TCR that has antigenic specificity for the peptide of SEQ ID NO: 30, the method comprising contacting a cell with the vector according to claim 23 or 24 under conditions that allow introduction of the vector into the cell.
28. An isolated or purified host cell comprising the nucleic acid according to any one of claims 19-22 or the recombinant expression vector according to claim 23 or 24.
29. The host cell according to claim 28 wherein the cell is a human lymphocyte.
30. The host cell according to claim 28 or 29, wherein the cell is selected from a T cell, a natural killer T (NKT) cell, an invariant natural killer T (iNKT) cell, and a natural killer (NK) cell.
31. An isolated or purified population of cells comprising the host cell according to any one of claims 28-30.
32. A method of producing the TCR according to any one of claims 1-9, 25, or 26, the polypeptide according to any one of claims 10-13, 25, or 26, or the protein according to any one of claims 14-18, 25, or 26, the method comprising culturing the host cell according to any one of claims 28-30, or the population of host cells according to claim 31, so that the TCR, polypeptide, or protein is produced.
33. A pharmaceutical composition comprising (a) the TCR according to any one of claims 1-9, 25, or 26, the polypeptide according to any one of claims 10-13, 25, or 26, or the protein according to any one of claims 14-18, 25, or 26, the nucleic acid according to any one of claims 19-22, the recombinant expression vector according to claim 23 or 24, the host cell according to any one of claims 28-30, or the population of cells according to claim 31 and (b) a pharmaceutically acceptable carrier.
34. A method of detecting the presence of cancer in mammal, the method comprising:
(a) contacting a sample comprising cells of the cancer with the TCR according to any one of claims 1-9, 25, or 26, the polypeptide according to any one of claims 10-13, 25, or 26, or the protein according to any one of claims 14-18, 25, or 26, the nucleic acid according to any one of claims 19-22, the recombinant expression vector according to claim 23 or 24, the host cell according to any one of claims 28-30, the population of cells according to claim 31, or the pharmaceutical composition of claim 33, thereby forming a complex; and
(b) detecting the complex, wherein detection of the complex is indicative of the presence of cancer in the mammal.
35. The TCR according to any one of claims 1-9, 25, or 26, the polypeptide according to any one of claims 10-13, 25 or 26, or the protein according to any one of claims 14-18, 25, or 26, the nucleic acid according to any one of claims 19-22, the recombinant expression vector according to claim 23 or 24, the host cell according to any one of claims 28-30, the population of cells according to claim 31, or the pharmaceutical composition according to claim 33, for use in inducing an immune response against a cancer in a mammal.
36. The TCR according to any one of claims 1-9, 25, or 26, the polypeptide according to any one of claims 10-13, 25, or 26, or the protein according to any one of claims 14-18, 25, or 26, the nucleic acid according to any one of claims 19-22, the recombinant expression vector according to claim 23 or 24, the host cell according to any one of claims 28-30, the population of cells according to claim 31, or the pharmaceutical composition of claim 33, for use in treating or preventing cancer in a mammal.
37. The method of claim 34 or the TCR, polypeptide, protein, nucleic acid, recombinant expression vector, host cell, population of cells, or pharmaceutical composition for the use of claim 35 or 36, wherein the cancer expresses an LMP2 amino acid sequence.
38. The method according to claim 34 or 37 or the TCR, polypeptide, protein, nucleic acid, recombinant expression vector, host cell, population of cells, or pharmaceutical composition for the use according to claim 35 or 36, wherein the cancer is Hodgkin lymphoma, T/NK cell lymphoma, post-transplant lymphoproliferative disorders, nasopharyngeal cancer, or gastric cancer.
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