WO2024206274A2 - T cell receptors targeting y220c or r175h mutation in p53 - Google Patents
T cell receptors targeting y220c or r175h mutation in p53 Download PDFInfo
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- WO2024206274A2 WO2024206274A2 PCT/US2024/021425 US2024021425W WO2024206274A2 WO 2024206274 A2 WO2024206274 A2 WO 2024206274A2 US 2024021425 W US2024021425 W US 2024021425W WO 2024206274 A2 WO2024206274 A2 WO 2024206274A2
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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
- C07K14/435—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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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K40/00—Cellular immunotherapy
- A61K40/10—Cellular immunotherapy characterised by the cell type used
- A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K40/00—Cellular immunotherapy
- A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
- A61K40/32—T-cell receptors [TCR]
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K40/00—Cellular immunotherapy
- A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
- A61K40/41—Vertebrate antigens
- A61K40/42—Cancer antigens
- A61K40/4238—Regulators of development
- A61K40/424—Apoptosis related proteins, e.g. survivin or livin
- A61K40/4241—Apoptosis related proteins, e.g. survivin or livin p53
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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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
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
- C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
- C07K14/4746—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used p53
Definitions
- TCR T cell receptor
- Leydig 770310 HHS E-054-2023-0-PC-01 2 Further aspects of the invention polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, populations of cells, and pharmaceutical compositions relating to the TCRs of the invention. Still further aspects of the invention provide methods of detecting the presence of cancer in a mammal, methods of inducing an immune response against a cancer in a mammal, and methods of treating or preventing cancer in a mammal. Additional aspects of the invention provide methods of producing a host cell expressing the TCR and methods of producing the TCR, polypeptide, or protein.
- Figure 1A is a graph showing the frequency (%) of tetramer positive cells measured following each of culture conditions 1, 2, and 3 of Table 1. Tetramers were generated from HLA-A*02:01 monomer and were loaded with p53 R175H 9-mer peptide analogue to capture p53 R175H mutation-reactive T cells with HLA-A*02:01 restriction.
- Figures 1B-1E are graphs showing the percentage of mTCR+CD8+ cells expressing 4-1BB following co-culture of effector cells with target cells.
- Effector cells were healthy donor PBL transduced with 4196-C TCR (B), 4196-D TCR (C), 4196-E TCR (D) or TCR 4196_AV6_with_BV11-2 (E) (disclosed in US 2020/0277352; used as the “Comparison TCR”).
- Target cells were T2 cells that naturally expressed HLA-A2 and had been incubated with the WT peptide analogue or mutant p53 R175H 9-mer peptide analogue at the indicated concentrations.
- Figure 1F is a graph including the same data shown in Figures 1B-1E replotted together for comparison.
- Figure 1G is a graph showing the normalized tumor cell counts measured at 4 hour intervals following co-culture of effector cells with target cells.
- Effector cells were healthy donor PBL transduced with a retroviral vector encoding 4196-C TCR, 4196-D TCR, 4196-E TCR, or an irrelevant TCR.
- the target cells were TYK-nu human ovarian cancer cells that naturally expressed p53 R175H and HLA-A*02:01. P ⁇ 0.001.
- Figure 2A shows flow cytometry data obtained after staining TILs from Patient 4424 for CD8 and tetramer, which was used in Figure 1A.
- Figure 2B is a graph showing the percentage of mTCR+CD8+ cells expressing 4- 1BB as a marker for T cell activation following co-culture of effector cells with target cells.
- Effector cells were healthy donor PBL transduced with the 4424-R175H TCR.
- Target cells Leydig 770310 HHS E-054-2023-0-PC-01 3 were monkey kidney COS7 cells engineered express HLA-A2 and incubated with the WT peptide analogue or mutant p53 R175H 9-mer peptide analogue at the indicated concentrations.
- Figure 3 is a graph showing the normalized tumor cell counts measured at 3 hour intervals following co-culture of effector cells with target cells at an effector to target ratio of 2:1.
- Effector cells were healthy donor PBL transduced with a retroviral vector encoding the 4196-C TCR, 4196-D TCR, 4196-E TCR, 4424-R175H TCR, or 4141-TCR1a2 disclosed in US 2022/0332785 (another “Comparison TCR”).
- the target cells were TYK-nu human ovarian cancer cells.
- Figures 4A-4D are graphs showing the percentage of mTCR+CD3+ cells expressing 4-1BB following co-culture of effector cells with target cells.
- Effector cells were healthy donor PBL transduced with the 4402-Y220C-B TCR, 4402-Y220C-C TCR, or 4402- Y220C-L TCR or the 4343-D TCR (“Comparison TCR”).
- Target cells were autologous B cells pulsed with WT or mutant peptide at the indicated concentrations.
- Figure 4E is a graph showing the percentage of mTCR+CD3+ cells expressing 4- 1BB following co-culture of effector cells with target cells. Effector cells were healthy donor PBL transduced with the 4402-Y220C-C TCR or 4402-Y220C-L TCR.
- Target cells were autologous breast tumor organoid cells from Patient 4402 of passage 11 showing loss of DRB1*13:03 or passage 27 showing reduced but detectable levels of DRB1*13:03 expression (see Figure 4F).
- TCR-C and L show recognition of only the organoid passage 27 but not the passage 11, suggesting the two TCRs are restricted by DRB1*13:03.
- Target cells pulsed with DMSO served as a control.
- Figure 4F is a graph showing the Transcripts Per Kilobase Million (TPM) value measured for HLA-DRB1*15:01 and DRB1*13:03 in the autologous organoid cells from Patient 4402 of passages 11 and 27.
- TPM Transcripts Per Kilobase Million
- Figures 5A-5C show an alignment of the amino acid sequences of the nine p53 splice variants.
- P53_HUMAN SEQ ID NO: 1
- P53_HUMAN SEQ ID NO: 104
- P53_HUMAN SEQ ID NO: 105
- P53_HUMAN SEQ ID NO: 106
- P53_HUMAN SEQ ID NO: 107
- P53_HUMAN SEQ ID NO: 111).
- FIGS 6-7 are graphs showing mean tumor size (mm 2 ) measured at the indicated number of days after adoptive cell transfer (ACT) of transduced healthy donor T cells administered to tumor-bearing mice at a dose of 2 million cells/mouse ( Figure 6) or 10 million cells/mouse ( Figure 7).
- ACT adoptive cell transfer
- the healthy donor T cells were independently transduced with: (i) the retroviral vector encoding the 4196-C TCR of Example 4 (“4196 IVS-C”); (ii) an irrelevant TCR control (i.e., 4259) (“4259 (irrelevant)”); (iii) the TCR 4196_AV12- 1_with_BV6-1 disclosed in US 2020/0277352 (“12-6”); (iv) the TCR 4196_AV38- 1_with_BV10-3 disclosed in US 2020/0277352 (“38-10”); (v) the TCR 4196_AV6_with_BV11-2 disclosed in US 2020/0277352 (“6-11”); (vi) the TCR 4141- TCR1a2 disclosed in US 2022/0332785 (“41411a2”); or (vii) the 4141 IVS TCR disclosed in US Patent Application No.18/289,596 (“4141 IVS”).
- Tumor Protein P53 acts as a tumor suppressor by, for example, regulating cell division.
- the p53 protein is located in the nucleus of the cell, where it binds directly to DNA.
- the p53 protein is involved in determining whether the DNA will be repaired or the damaged cell will undergo apoptosis. If the DNA can be repaired, p53 activates other genes to fix the damage. If the DNA cannot be repaired, the p53 protein prevents the cell from dividing and signals it to undergo apoptosis. By stopping cells with mutated or damaged DNA from dividing, p53 helps prevent the development of tumors.
- WT (normal) full-length p53 comprises the amino acid sequence of SEQ ID NO: 1. Mutations in the p53 protein may reduce or eliminate the p53 protein’s tumor suppressor function. Alternatively or additionally, a p53 mutation may be a gain-of-function mutation by interfering with WT p53 in a dominant negative fashion. Mutated p53 protein may be expressed in any of a variety of human cancers such as, for example, cholangiocarcinoma, melanoma, colon cancer, rectal cancer, ovarian cancer, endometrial cancer, non-small cell lung cancer (NSCLC), glioblastoma, uterine cervical cancer, head and neck cancer, breast cancer, pancreatic cancer, or bladder cancer.
- human cancers such as, for example, cholangiocarcinoma, melanoma, colon cancer, rectal cancer, ovarian cancer, endometrial cancer, non-small cell lung cancer (NSCLC), glioblastoma, uterine cervical cancer,
- An aspect of the invention provides an isolated or purified T cell receptor (TCR) having antigenic specificity for a human p53 Y220C or human p53 R175H amino acid sequence Leydig 770310 HHS E-054-2023-0-PC-01 5 (hereinafter, “mutated p53”).
- TCR T cell receptor
- a p53 amino acid sequence may comprise fewer than all of the amino acid residues of the full-length, WT p53 protein. Accordingly, the position numbers are defined herein by reference to the WT full-length p53 protein (namely, SEQ ID NO: 1) with the understanding that the actual position of the corresponding residue in a particular example of a p53 amino acid sequence may be different. Because the positions are as defined by SEQ ID NO: 1, the term “Y220C” indicates that the tyrosine present at position 220 of SEQ ID NO: 1 is replaced by cysteine, and “R175H” indicates that the arginine present at position 175 of SEQ ID NO: 1 has been replaced with histidine.
- Y220C refers to a substitution of the underlined tyrosine in SEQ ID NO: 114 with cysteine, even though the actual position of the underlined tyrosine in SEQ ID NO: 114 is 13.
- Human p53 amino acid sequences with the Y220C mutation are hereinafter referred to as “Y220C” or “p53 Y220C .”
- Human p53 amino acid sequences with the R175H mutation are hereinafter referred to as “R175H” or “p53 R175H .”
- “mutated p53” refers to human p53 Y220C or human p53 R175H .
- P53 has nine known splice variants. The p53 mutations described herein are conserved over all nine p53 splice variants. An alignment of the nine p53 splice variants is shown in Figures 5A-5C.
- the inventive TCRs may have antigenic specificity for any mutated p53 amino acid sequence described herein encoded by any of the nine p53 splice variants. Because the positions are as defined by SEQ ID NO: 1, then the actual positions of the amino acid sequence of a particular splice variant of p53 are defined relative to the corresponding positions of SEQ ID NO: 1, and the positions as defined by SEQ ID NO: 1 may be different than the actual positions in a particular splice variant.
- mutations refer to a replacement of an amino acid residue in the amino acid sequence of a particular splice variant of p53 corresponding to the indicated position of the 393-amino acid Leydig 770310 HHS E-054-2023-0-PC-01 6 sequence of SEQ ID NO: 1 with the that the actual positions in the splice variant may be different.
- the TCR has antigenic specificity for human p53 with a mutation at position 220, as defined by SEQ ID NO: 1.
- the p53 mutation at position 220 may be a missense mutation.
- the mutation at position 220 may be a substitution of the native (WT) tyrosine residue present at position 220 with any amino acid residue other than tyrosine.
- the TCR has antigenic specificity for a human p53 Y220C amino acid sequence.
- the TCR may have antigenic specificity for the human p53 Y220C amino acid sequence of DRNTFRHSVVVPCEPPEVGSDCTTI (SEQ ID NO: 114).
- the TCR does not have antigenic specificity for the wild-type human p53 amino acid sequence of DRNTFRHSVVVPYEPPEVGSDCTTI (SEQ ID NO: 115).
- the TCR has antigenic specificity for human p53 with a mutation at position 175, as defined by SEQ ID NO: 1.
- the p53 mutation at position 175 may be a missense mutation. Accordingly, the mutation at position 175 may be a substitution of the native (WT) arginine residue present at position 175 with any amino acid residue other than arginine.
- the TCR has antigenic specificity for a human p53 R175H amino acid sequence.
- the TCR may have antigenic specificity for the human p53 R175H amino acid sequence of HMTEVVRHC (SEQ ID NO: 112).
- the TCR does not have antigenic specificity for the wild- type human p53 amino acid sequence of HMTEVVRRC (SEQ ID NO: 113).
- the inventive TCRs may be able to recognize mutated p53 in an HLA (human leukocyte antigen)-molecule-dependent manner.
- HLA- molecule-dependent manner means that the TCR elicits an immune response upon binding to mutated p53 within the context of an HLA molecule, which HLA molecule is expressed by the patient from which the TCR was isolated.
- the inventive TCRs may be able to recognize mutated p53 that is presented by the applicable HLA molecule and may bind to the HLA molecule in addition to mutated p53.
- the inventive TCRs are able to recognize Y220C presented by an HLA Class II molecule.
- the TCR may elicit an immune response upon binding to Y220C within the context of an HLA Class II molecule.
- the inventive TCRs are able to recognize Y220C that is presented by an HLA Class II molecule and may bind to the HLA Class II molecule in addition to Y220C.
- the Class II molecule is an HLA-DR heterodimer.
- the HLA-DR heterodimer is a cell surface receptor including an ⁇ chain and a ⁇ chain.
- the HLA-DR ⁇ chain is encoded by the HLA-DRA gene.
- the HLA-DR ⁇ chain is encoded by the HLA-DRB1 gene, the HLA-DRB3 gene, HLA-DRB4 gene, or the HLA- DRB5 gene.
- Examples of molecules encoded by the HLA-DRB1 gene may include, but are not limited to, HLA-DR1, HLA-DR2, HLA-DR3, HLA-DR4, HLA-DR5, HLA-DR6, HLA- DR7, HLA-DR8, HLA-DR9, HLA-DR10, HLA-DR11, HLA-DR12, HLA-DR13, HLA- DR14, HLA-DR15, HLA-DR16, and HLA-DR17.
- the HLA-DRB3 gene encodes HLA- DR52.
- the HLA-DRB4 gene encodes HLA-DR53.
- the HLA-DRB5 gene encodes HLA- DR51.
- the alpha chain of the HLA Class II molecule is expressed by the HLA-DRA1*01:01 allele.
- the beta chain of the HLA Class II molecule is expressed by the HLA-DRB3*02:02 allele.
- the HLA Class II molecule is an HLA-DRB3:HLA-DRA heterodimer.
- the HLA Class II molecule is a heterodimer of an HLA-DRA1*01:01 chain and an HLA-DRB3*02:02 chain.
- the mutated p53 is Y220C and the HLA Class II molecule is a heterodimer of an HLA-DRA1*01:01 chain and an HLA-DRB3*02:02 chain.
- the alpha chain of the HLA Class II molecule is expressed by the HLA-DRA1*01:01 allele.
- the beta chain of the HLA Class II molecule is expressed by the HLA-DRB1*13:03 allele.
- the HLA Class II molecule is an HLA-DRB1:HLA-DRA heterodimer.
- the HLA Class II molecule is a heterodimer of an HLA-DRA1*01:01 chain and an HLA-DRB1*13:03 chain.
- the mutated p53 is Y220C and the HLA Class II molecule is a heterodimer of an HLA-DRA1*01:01 chain and an HLA-DRB1*13:03 chain.
- the inventive TCRs are able to recognize R175H presented by an HLA Class I molecule. In this regard, the TCR may elicit an immune response upon binding to R175H within the context of an HLA Class I molecule.
- the inventive TCRs are able to recognize R175H that is presented by an HLA Class I molecule and may bind to the HLA Class I molecule in addition to R175H.
- the HLA Class I molecule is an HLA-A molecule.
- the HLA-A molecule is a heterodimer of an ⁇ chain and ⁇ 2 microglobulin.
- the HLA-A ⁇ chain may be encoded by an HLA-A gene.
- ⁇ 2 microglobulin binds non-covalently to the alpha1, alpha2 and alpha3 domains of the alpha chain to build the HLA-A complex.
- the HLA-A molecule may be any HLA-A
- the HLA Class I molecule is an HLA-A2 molecule.
- the HLA-A2 molecule may be any HLA- A2 molecule.
- Examples of HLA-A2 molecules may include, but are not limited to, those encoded by the HLA-A*02:01, HLA-A*02:02, HLA-A*02:03 allele, HLA-A*02:05, HLA- A*02:06, HLA-A*02:07 allele, or HLA-A*02:11 allele.
- the HLA Class I molecule is encoded by the HLA-A*02:01 allele.
- the TCRs of the invention may provide any one or more of many advantages, including when expressed by cells used for adoptive cell transfer. Mutated p53 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 mutated p53-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 mutated p53, 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 mutated p53 and the applicable HLA molecule, pulsed with a p53 peptide with the p53 mutation, or a combination thereof).
- unmanipulated tumor cells e.g., tumor cells that have not been treated with interferon (IFN)- ⁇ , transfected with a vector encoding one or both of mutated p53 and the applicable HLA molecule, pulsed with a p53 peptide with the p53 mutation, or a combination thereof.
- Mutations in p53 are common across different tumor types. Roughly half of all tumors harbor a mutation in p53, about half of which will be a missense mutation. The R175H mutation is common, affecting about 5% of all patients with solid cancers.
- the Y220C mutation is also highly recurrent and affects about 0.4% of all cancer patients. Accordingly, the inventive TCRs may increase the number of patients who may be eligible for treatment with immunotherapy.
- the phrase “antigenic specificity,” as used herein, means that the TCR can specifically bind to and immunologically recognize mutated p53 with high avidity.
- a TCR may be considered to have “antigenic specificity” for mutated p53 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- ⁇ upon co-culture with (a) antigen-negative, applicable HLA molecule positive target cells pulsed with mutated p53 peptide (e.g., about 0.1 ng/mL to Leydig 770310 H
- TCRs expressing the inventive TCRs may also secrete IFN- ⁇ upon co-culture with antigen-negative, applicable HLA molecule positive target cells pulsed with higher concentrations of mutated p53 peptide.
- a TCR may be considered to have “antigenic specificity” for mutated p53 if T cells expressing the TCR secrete at least twice as much IFN- ⁇ upon co-culture with (a) antigen-negative, applicable HLA molecule positive target cells pulsed with mutated p53 peptide or (b) antigen-negative, applicable HLA molecule positive target cells into which a nucleotide sequence encoding mutated p53 has been introduced such that the target cell expresses mutated p53 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, applicable HLA molecule positive target cells pulsed with the same concentration of an irrelevant peptide (e.g., some other peptide with a different sequence from the mutated p53 peptide) or (b) antigen-negative, applicable HLA 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, applicable HLA molecule positive target cells pulsed with the same concentration of mutated p53 peptide or (b) antigen-negative, applicable HLA molecule positive target cells into which a nucleotide sequence encoding mutated p53 has been introduced such that the target cell expresses mutated p
- IFN- ⁇ secretion may be measured by methods known in the art such as, for example, enzyme-linked immunosorbent assay (ELISA).
- concentration of pulsed peptide may be as described herein with respect to other aspects of the invention.
- a TCR may be considered to have “antigenic specificity” for mutated p53 if at least twice as many of the numbers of T cells expressing the TCR secrete IFN- ⁇ upon co-culture with (a) antigen-negative, applicable HLA molecule positive target cells pulsed with mutated p53 peptide or (b) antigen-negative, applicable HLA molecule positive target cells into which a nucleotide sequence encoding mutated p53 has been introduced such that the target cell expresses mutated p53 as compared to the numbers Leydig 770310 HHS E-054-2023-0-PC-01 10 of negative control T cells that secrete ⁇ .
- the 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, enzyme-linked immunospot (ELISPOT) assay.
- ELISPOT enzyme-linked immunospot
- a TCR may be considered to have “antigenic specificity” for mutated p53 if at least twice as many spots are detected by ELISPOT for the T cells expressing the TCR upon co-culture with (a) antigen-negative, applicable HLA molecule positive target cells pulsed with mutated p53 peptide or (b) antigen-negative, applicable HLA molecule positive target cells into which a nucleotide sequence encoding mutated p53 has been introduced such that the target cell expresses mutated p53 as compared to the number of spots detected by ELISPOT for negative control T cells co-cultured with the same target cells.
- concentration of peptide and the negative control may be as described herein with respect to other aspects of the invention.
- a TCR may be considered to have “antigenic specificity” for mutated p53 if T cells expressing the TCR upregulate expression of one or both of 4-1BB and OX40 as measured by, for example, flow cytometry after stimulation with target cells expressing mutated p53.
- An aspect of the invention provides a TCR comprising two polypeptides (i.e., polypeptide chains), such as an alpha ( ⁇ ) chain of a TCR, a beta ( ⁇ ) chain of a TCR, a gamma ( ⁇ ) 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 mutated p53.
- 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.
- CDR complementarity determining region
- the TCR comprises a first polypeptide chain comprising an ⁇ chain CDR1 (CDR1 ⁇ ), an ⁇ chain CDR2 (CDR2 ⁇ ), and an ⁇ chain CDR3 (CDR3 ⁇ ), and a second polypeptide chain comprising a ⁇ chain CDR1 (CDR1 ⁇ ), a ⁇ chain CDR2 (CDR2 ⁇ ), and a ⁇ chain CDR3 (CDR3 ⁇ ).
- the TCR comprises the amino acid sequences of: (1) all of SEQ ID NOs: 2-7 (4196-C TCR); (2) all of SEQ ID NOs: 16-21 (4196-D TCR); (3) all of SEQ ID NOs: 30-35 (4196-E TCR); (4) all of SEQ ID NOs: 44-49 (4424-R175H TCR); (5) all of SEQ ID NOs: 58-63 (4402-Y220C-B TCR); (6) all of SEQ ID NOs: 72-77 (4402-Y220C-C TCR); or (7) all of SEQ ID NOs: 86-91 (4402-Y220C-L TCR).
- the six amino acid sequences in each collection correspond to the CDR1 ⁇ , CDR2 ⁇ , CDR3 ⁇ , CDR1 ⁇ , CDR2 ⁇ , and CDR3 ⁇ of a TCR, respectively.
- the TCR may comprise the amino acid sequences of any one or more of: SEQ ID NOs: 2-7, 16-21, 30-35, 44-49, 58-63, 72-77, and 86-91.
- the TCR comprises an isolated or purified T cell receptor (TCR) having antigenic specificity for a human p53 Y220C or human p53 R175H amino acid sequence, wherein the TCR comprises the amino acid sequences of: (1) all of SEQ ID NOs: 2-7; (2) all of SEQ ID NOs: 16-21; (3) all of SEQ ID NOs: 30-35; (4) all of SEQ ID NOs: 44-49; (5) all of SEQ ID NOs: 58-63; (6) all of SEQ ID NOs: 72-77; or (7) all of SEQ ID NOs: 86-91.
- TCR T cell receptor
- the TCR comprises an ⁇ chain variable region amino acid sequence and a ⁇ chain variable region amino acid sequence, which together comprise one of the collections of CDRs set forth above.
- the TCR can comprise the amino acid sequences of: (1) both of SEQ ID NOs: 8 and 9 (4196-C TCR); (2) both of SEQ ID NOs: 10 and 11 (4196-C TCR); (3) both of SEQ ID NOs: 22 and 23 (4196-D TCR); (4) both of SEQ ID NOs: 24 and 25 (4196-D TCR); (5) both of SEQ ID NOs: 36 and 37 (4196-E TCR); (6) both of SEQ ID NOs: 38 and 39 (4196-E TCR); (7) both of SEQ ID NOs: 50 and 51 (4424-R175H TCR); (8) both of SEQ ID NOs: 52 and 53 (4424-R175H TCR); (9) both of SEQ ID NOs: 64 and 65 (4402-Y220C-B TCR); (10)
- Each one of the foregoing collections of amino acid sequences in this paragraph sets forth the two variable regions of each of seven different TCRs having antigenic specificity for mutated human p53.
- the two amino acid sequences in each collection correspond to the variable region of the ⁇ chain and the variable region of the ⁇ chain of a TCR, respectively.
- the TCR may, e.g., comprise the amino acid sequence of any one or more of SEQ ID NOs: 8, 9, 10, 11, 22, 23, 24, 25, 36, 37, 38, 39, 50, 51, 52, 53, 64, 65, 66, 67, 78, 79, 80, 81, 92, 93, 94, and 95.
- the TCR comprises the amino acid sequence(s) of: (1) SEQ ID NO: 8; (2) SEQ ID NO: 9; (3) both of SEQ ID NOs: 8 and 9; (4) SEQ ID NO: 10; (5) SEQ ID NO: 11; (6) both of SEQ ID NOs: 10 and 11; (7) SEQ ID NO: 22; (8) SEQ ID NO: 23; (9) both of SEQ ID NOs: 22 and 23; (10) SEQ ID NO: 24; (11) SEQ Leydig 770310 HHS E-054-2023-0-PC-01 12 ID NO: 25; (12) both of SEQ ID NOs: 24 (13) SEQ ID NO: 36; (14) SEQ ID NOs: 37; (15) both of SEQ ID NOs: 36 and 37; (16) SEQ ID NO: 38; (17) SEQ ID NO: 39; (18) both of SEQ ID NOs: 38 and 39; (19) SEQ ID NO: 50; (20) SEQ ID NO: 51; (21) both of SEQ ID NOs: 50; (20) SEQ ID
- the inventive TCRs may further comprise a constant region.
- the constant region may be derived from any suitable species such as, e.g., human or mouse.
- the TCRs further comprise a murine constant region.
- 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, alpha chain, and/or beta 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.
- CDR complementarity determining region
- the TCR may comprise a murine ⁇ chain constant region and a murine ⁇ chain constant region.
- the murine ⁇ chain constant region may be modified or unmodified.
- a modified murine ⁇ chain constant region may be, e.g., cysteine-substituted, LVL-modified, or both cysteine-substituted and LVL-modified, as described, for example, in U.S. Patent No. 10,174,098.
- the murine ⁇ chain constant region may be modified or unmodified.
- a modified murine ⁇ chain constant region may be, e.g., cysteine-substituted, as described, for example, in U.S. Patent No.10,174,098.
- the TCR comprises a cysteine-substituted, LVL-modified murine ⁇ chain constant region comprising the amino acid sequence of SEQ ID NO: 100 or 101.
- the TCR comprises a cysteine-substituted murine ⁇ chain constant region comprising the amino acid sequence of SEQ ID NO: 102.
- the inventive TCR can comprise an ⁇ chain of a TCR and a ⁇ chain of a TCR.
- the ⁇ chain of the TCR may comprise a variable region of an ⁇ chain and a constant region of an ⁇ chain.
- An ⁇ chain of this type can be paired with any ⁇ Leydig 770310 HHS E-054-2023-0-PC-01 13 chain of a TCR.
- the ⁇ chain may a region of a ⁇ chain and a constant region of a ⁇ chain.
- the TCR can comprise the amino acid sequences of: (1) both of SEQ ID NOs: 12 and 13 (4196-C TCR); (2) both of SEQ ID NOs: 14 and 15 (4196-C TCR); (3) both of SEQ ID NOs: 26 and 27 (4196-D TCR); (4) both of SEQ ID NOs: 28 and 29 (4196-D TCR); (5) both of SEQ ID NOs: 40 and 41 (4196-E TCR); (6) both of SEQ ID NOs: 42 and 43 (4196-E TCR); (7) both of SEQ ID NOs: 54 and 55 (4424-R175H TCR); (8) both of SEQ ID NOs: 56 and 57 (4424-R175H); (9) both of SEQ ID NOs: 68 and 69 (4402-Y220C-B TCR); (10) both of SEQ ID NOs: 70 and 71 (4402-Y220C-B TCR); (11) SEQ ID NO: 82 and 83 (4402-Y220C
- the TCR may comprise the amino acid sequence of any one or more of SEQ ID NOs: 12, 13, 14, 15, 26, 27, 28, 29, 40, 41, 42, 43, 54, 55, 56, 57, 68, 69, 70, 71, 82, 83, 84, 85, 96, 97, 98, and 99.
- the TCR comprises the amino acid sequences of: (1) SEQ ID NO: 12; (2) SEQ ID NO: 13; (3) both of SEQ ID NOs: 12 and 13; (4) SEQ ID NO: 14; (5) SEQ ID NO: 15; (6) both of SEQ ID NOs: 14 and 15; (7) SEQ ID NO: 26; (8) SEQ ID NO: 27; (9) both of SEQ ID NOs: 26 and 27; (10) SEQ ID NO: 28; (11) SEQ ID NO: 29; (12) both of SEQ ID NOs: 28 and 29; (13) SEQ ID NO: 40; (14) SEQ ID NO: 41; (15) both of SEQ ID NOs: 40 and 41; (16) SEQ ID NO: 42; (17) SEQ ID NO: 43; (18) both of SEQ ID NOs: 42 and 43; (19) SEQ ID NO: 54; (20) SEQ ID NO: 55; (21) both of SEQ ID NOs: 54 and 55; (22) SEQ ID NO: 56; (23) SEQ ID NO:
- the term “functional variant,” as used herein, refers to a TCR, Leydig 770310 HHS E-054-2023-0-PC-01 14 polypeptide, or protein having substantial or 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 mutated p53 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%, at least about 50%, at least about 75%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least 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, Ile, 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, Gln, Ser, Thr, Tyr, etc.), etc.
- an amino acid with a polar side chain substituted for another amino acid with a polar side chain 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, Ile, Leu, Met, Phe, Pro, Trp, Val, 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.
- 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, Leydig 770310 HHS E-054-2023-0-PC-01 15 polypeptide, or protein, e.g., other amino do not materially change the biological activity of the TCR, polypeptide, or protein.
- a polypeptide comprising a functional portion of any of the TCRs described herein.
- 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 mutated p53.
- Functional portions encompass, for example, those parts of a TCR that retain the ability to specifically bind to mutated p53 (e.g., in an applicable HLA molecule-dependent manner), 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 mutated p53; 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.
- the polypeptide can comprise a functional portion of either or both of the ⁇ and ⁇ chains of the TCRs of the invention, such as a functional portion comprising one of more of CDR1, CDR2, and CDR3 of the variable region(s) of the ⁇ chain and/or ⁇ chain of a TCR of the invention.
- the polypeptide comprises the amino acid sequences of: (1) all of SEQ ID NOs: 2-7; (2) all of SEQ ID NOs: 16-21; (3) all of SEQ ID NOs: 30-35; (4) all of SEQ ID NOs: 44-49; (5) all of SEQ ID NOs: 58-63; (6) all of SEQ ID NOs: 72-77; or (7) all of SEQ ID NOs: 86-91.
- the polypeptide may comprise the amino acid sequences of any one or more of: SEQ ID NOs: 2-7, 16-21, 30-35, 44-49, 58-63, 72-77, and 86-91.
- 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, e.g., the amino acid sequences of: (1) both of SEQ ID NOs: 8 and 9; (2) both of SEQ ID NOs: 10 and 11; (3) both of SEQ ID NOs: 22 and 23; (4) both of SEQ ID NOs: 24 and 25; (5) both of SEQ ID NOs: 36 and 37; (6) both of SEQ ID NOs: 38 and 39; (7) both of SEQ ID NOs: 50 and 51; (8) both of SEQ ID NOs: 52 and 53; (9) both of SEQ ID NOs: 64 and 65; (10) both of SEQ ID NOs: 66 and 67; (11) both of SEQ ID NOs: 78 and 79; (12) both of SEQ ID NOs: 80 and 81; (13) both of
- the polypeptide may, e.g., comprise the amino acid sequence of any one or more of SEQ ID NOs: 8, 9, 10, 11, 22, 23, 24, 25, 36, 37, 38, 39, 50, 51, 52, 53, 64, 65, 66, 67, 78, 79, 80, 81, 92, 93, 94 and 95.
- the polypeptide comprises the amino acid sequence(s) of: (1) SEQ ID NO: 8; (2) SEQ ID NO: 9; (3) both of SEQ ID NOs: 8 and 9; (4) SEQ ID NO: 10; (5) SEQ ID NO: 11; (6) both of SEQ ID NOs: 10 and 11; (7) SEQ ID NO: 22; (8) SEQ ID NO: 23; (9) both of SEQ ID NOs: 22 and 23; (10) SEQ ID NO: 24; (11) SEQ ID NO: 25; (12) both of SEQ ID NOs: 24 and 25; (13) SEQ ID NO: 36; (14) SEQ ID NOs: 37; (15) both of SEQ ID NOs: 36 and 37; (16) SEQ ID NO: 38; (17) SEQ ID NO: 39; (18) both of SEQ ID NOs: 38 and 39; (19) SEQ ID NO: 50; (20) SEQ ID NO: 51; (21) both of SEQ ID NOs: 50 and 51; (22) SEQ ID NO: 52; (23) SEQ ID NO: 10;
- the inventive polypeptide can further comprise the constant region of the inventive TCR set forth above.
- the polypeptide can comprise, e.g., the amino acid sequence of (i) one of SEQ ID NOs 100-102 or (ii) SEQ ID NO: 102 and one of SEQ ID NOs: 100 and 101.
- the inventive polypeptide may comprise an ⁇ chain and a ⁇ chain of the inventive TCR.
- the polypeptide can comprise, e.g., the amino acid sequences of: (1) both of SEQ ID NOs: 12 and 13; (2) both of SEQ ID NOs: 14 and 15; (3) both of SEQ ID NOs: 26 and 27; (4) both of SEQ ID NOs: 28 and 29; (5) both of Leydig 770310 HHS E-054-2023-0-PC-01 17 SEQ ID NOs: 40 and 41; (6) both of SEQ 42 and 43; (7) both of SEQ ID NOs: 54 and 55; (8) both of SEQ ID NOs: 56 and 57; (9) both of SEQ ID NOs: 68 and 69; (10) both of SEQ ID NOs: 70 and 71; (11) SEQ ID NO: 82 and 83; (12) SEQ ID NO: 84 and 85; (13) SEQ ID NO: 96 and 97; or (14) SEQ ID NO: 98 and 99.
- the polypeptide may comprise the amino acid sequence of any one or more of SEQ ID NOs: 12, 13, 14, 15, 26, 27, 28, 29, 40, 41, 42, 43, 54, 55, 56, 57, 68, 69, 70, 71, 82, 83, 84, 85, 96, 97, 98, and 99.
- the polypeptide comprises the amino acid sequences of: (1) SEQ ID NO: 12; (2) SEQ ID NO: 13; (3) both of SEQ ID NOs: 12 and 13; (4) SEQ ID NO: 14; (5) SEQ ID NO: 15; (6) both of SEQ ID NOs: 14 and 15; (7) SEQ ID NO: 26; (8) SEQ ID NO: 27; (9) both of SEQ ID NOs: 26 and 27; (10) SEQ ID NO: 28; (11) SEQ ID NO: 29; (12) both of SEQ ID NOs: 28 and 29; (13) SEQ ID NO: 40; (14) SEQ ID NO: 41; (15) both of SEQ ID NOs: 40 and 41; (16) SEQ ID NO: 42; (17) SEQ ID NO: 43; (18) both of SEQ ID NOs: 42 and 43; (19) SEQ ID NO: 54; (20) SEQ ID NO: 55; (21) both of SEQ ID NOs: 54 and 55; (22) SEQ ID NO: 56; (23) SEQ ID NO:
- an aspect of the invention further provides a protein comprising a functional portion of any of the inventive TCRs described herein.
- protein is meant a molecule comprising one or more polypeptide chains.
- the protein of the invention can comprise: first and second polypeptide chains, wherein: (1) the first polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 2-4; (2) the second polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 5-7; (3) the first polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 2-4 and the second polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 5-7; (4) the first polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 16-18; (5) the second polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 19-21; (6) the first polypeptide chain comprises the amino acid sequences of all of SEQ ID NOs: 16-18 and the second polypeptide chain comprises
- the protein comprises first and second polypeptide chains, wherein: (1) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 8; (2) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 9; (3) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 8 and the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 9; (4) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 10; (5) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 11; (6) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 10 and the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 11; (7) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 22; (8) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 23; (9) the first Leydig 770310 HHS E-054-2023-0-PC-01 19 polypeptide chain comprises the amino acid
- the protein comprises first and second polypeptide chains, wherein: (1) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 12; (2) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 13; (3) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 12 and the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 13; (4) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 14; (5) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 15; (6) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 14 and the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 15; (7) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 26; (8) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 27; (9) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 26 and the second polypeptide chain comprises the amino acid
- the protein of the invention may be a TCR.
- 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.
- an aspect 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., CD1a, CD1b, CD1c, CD1d, 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 ⁇ 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 comprise the amino acid sequence of RAKRSGSGATNFSLLKQAGDVEENPGP (SEQ ID NO: 103).
- the linker peptide may be cleaved, resulting in separated ⁇ and ⁇ chains.
- the TCR, polypeptide, or protein may comprise an amino acid sequence comprising a full-length ⁇ chain, a full-length ⁇ chain, and a linker peptide positioned between the ⁇ and ⁇ chains.
- Leydig 770310 HHS E-054-2023-0-PC-01 23 the TCR, or protein disclosed herein comprises an ⁇ chain and/or a ⁇ chain, as disclosed herein, comprising a signal peptide.
- the sequence of the signal peptide of any of the ⁇ chains and/or ⁇ chains disclosed herein comprises an leucine, lysine, alanine or histidine residue substituted for the wild-type residue at position 2.
- the TCR, polypeptide or protein disclosed herein comprises a mature version of an ⁇ chain and/or a ⁇ chain, as disclosed herein, that lacks a signal peptide.
- 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.
- the 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.
- 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 mutated p53; 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 50, 70, 75, 100, 125, 150, 175, 200, 300, 400, 500, 600, 700, 800, 900, 1000 or more amino acids in length.
- the polypeptides of the invention also include oligopeptides.
- the TCRs, polypeptides, and proteins of the invention of the invention can comprise synthetic amino acids in place of one or more naturally-occurring amino acids.
- Such synthetic amino acids include, for example, aminocyclohexane carboxylic acid, norleucine, ⁇ -amino n-decanoic acid, homoserine, S-acetylaminomethyl- cysteine, trans-3- and trans-4-hydroxyproline, 4-aminophenylalanine, 4-nitrophenylalanine, Leydig 770310 HHS E-054-2023-0-PC-01 24 4-chlorophenylalanine, 4- ⁇ -phenylserine ⁇ -hydroxyphenylalanine, phenylglycine, ⁇ -naphthylalanine, cyclohexylalanine, cyclohexylglycine, indoline-2- carboxylic acid, 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, aminomalonic acid, aminomalonic acid monoamide, N’-benzyl-N’-methyl-lysine, N’,N’-d
- the TCRs, polypeptides, and proteins of the invention can be, e.g., 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.
- inventive TCRs, polypeptides, and proteins described herein are also contemplated to be useful as the soluble TCR component of bispecific engager TCR fusion proteins (e.g., IMMTAC (immune- mobilizing monoclonal TCRs against cancer) molecules).
- Bispecific engager TCR fusion proteins have two components.
- the other component comprises an anti-CD3 effector.
- the anti-CD3 effector may be any molecule that engages with a CD3 molecule on T cells and activates a T cell immune response.
- the anti-CD3 effector may be an anti-CD3 antibody or anti-CD3 antibody fragment.
- the soluble TCR component of the bispecific engager TCR fusion protein binds to the target antigen presented on the surface of cancer cells presented by an HLA molecule.
- the anti- CD3 effector component engages a CD3 molecule on T cells. The engagement of these components of the bispecific engager TCR fusion protein triggers the activation and recruitment of T cells and redirects T-cell killing to tumor cells.
- An aspect of the invention provides a bispecific engager TCR fusion protein comprising (i) any of the inventive TCRs, polypeptides, or proteins (including any of the functional portions or variants thereof) described herein and (ii) an anti-CD3 effector.
- references to “protein(s)” also encompass the bispecific engager TCR fusion proteins described herein, unless specified otherwise.
- 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 Leydig 770310 HHS E-054-2023-0-PC-01 25 recombinant methods.
- TCRs, polypeptides, and/or proteins described herein can be synthesized by any of a variety of commercial entities.
- inventive TCRs, polypeptides, and proteins can be synthetic, recombinant, isolated, and/or purified.
- An aspect 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 internucleotide 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.
- An aspect 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: 8 and 9; 9 and 8; 10 and 11; 11 and 10; 12 and 13; 13 and 12; 14 and 15; 15 and 14; 22 and 23; 23 and 22; 24 and 25; 25 and 24; 26 and 27; 27 and 26; 28 and 29; 29 and 28; 36 and 37; 37 and 36; 38 and 39; 39 and 38; 40 and 41; 41 and 40; 42 and 43; 43 and 42; 50 and 51; 51 and 50; 52 and 53; 53 and 52; 54 and 55; 55 and 54; 56 and 57; 57 and 56; 64 and 65; 65 and 64; 66 and 67; 67 and 66; 68 and 69; 69 and 68; 70 and 71; 71 and 70; 78 and 79; 79 and 78
- the nucleic acid further comprises a third nucleotide acid sequence interposed between the first and second nucleotide sequence, wherein the third nucleotide sequence encodes a cleavable linker peptide.
- the cleavable linker peptide may comprise the amino acid sequence of RAKRSGSGATNFSLLKQAGDVEENPGP (SEQ ID NO: 103).
- the nucleic acids of 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-methylinosine, 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-mannosyl
- nucleic acid comprising a nucleotide sequence which is complementary to the nucleotide sequence of any of the nucleic acids described herein.
- the nucleic acids of the invention can be incorporated into a recombinant expression vector.
- an aspect of 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 ⁇ 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 internucleotide linkages, or both types of linkages.
- the non- naturally occurring or altered nucleotides or internucleotide 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 group consisting of the transposon/transposase series, 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 ⁇ GT10, ⁇ GT11, ⁇ ZapII (Stratagene), ⁇ EMBL4, and ⁇ NM1149, also can be used.
- animal expression vectors include pEUK-Cl, pMAM and pMAMneo (Clontech).
- the recombinant expression vector is a transposon or a viral vector, e.g., a lentiviral vector or a retroviral vector.
- Leydig 770310 HHS E-054-2023-0-PC-01 28 The recombinant expression 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 ⁇ plasmid, ⁇ , 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.
- 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 nonnative promoter operably linked to the nucleotide sequence encoding the TCR, polypeptide, or protein, or to the nucleotide sequence which is complementary to the nucleotide sequence encoding the TCR, polypeptide, or protein.
- the selection of promoters is within the ordinary skill of the artisan.
- 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, e.g., a human elongation factor-1 ⁇ 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
- the inventive recombinant expression vectors can be designed for either transient expression, for stable expression, or for both.
- the recombinant expression vectors can be made for constitutive expression or for inducible expression. Further, the recombinant expression vectors can be made to include a suicide gene.
- suicide gene refers to a gene that causes the cell expressing Leydig 770310 HHS E-054-2023-0-PC-01 29 the suicide gene to die.
- the suicide gene can 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.
- 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, DH5 ⁇ E. 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 DH5 ⁇ cell.
- the host cell is preferably a mammalian cell. Most preferably, the host cell is a human cell.
- the host cell may be a human lymphocyte.
- the host cell is selected from the group consisting of a T cell, a natural killer T (NKT) cell, an invariant natural killer T (iNKT) cell, a natural killer (NK) cell, a macrophage, a pluripotent cell, and a multipotent 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.
- PBL peripheral blood lymphocyte
- PBMC peripheral blood mononuclear 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, SupT1, etc., or a T cell obtained from a mammal. If obtained from a mammal, the T cell can be obtained from Leydig 770310 HHS E-054-2023-0-PC-01 30 numerous sources, including but not limited 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.
- Pluripotent cells may comprise, for example, stem cells, e.g., embryonic stem cells, nuclear transfer derived embryonic stem cells, induced pluripotent stem cells (iPSC), etc.
- Multipotent cells may comprise, for example, hematopoietic stem cells.
- Modifying, e.g., reprogramming, cells to a pluripotent state refers to the reversion of a cell to a pluripotent cell and is described for example, in Crompton et al., Trends Immunol., 35(4): 178-185 (2014).
- Exemplary techniques may include somatic cell nuclear transfer (SCNT), cell–cell fusion, and direct reprogramming.
- Examples of methods for carrying out cell-cell fusion are described, for example, in Ogle et al., Nat. Rev. Mol. Cell Biol.6: 567-75 (2005) and Zhou et al., Cell Stem Cell, 3: 382-388 (2008).
- Examples of methods for carrying out SCNT are described, for example, in Hanna et al., Cell, 143: 508- 525 (2010); Stadtfeld et al., Genes Dev., 24: 2239-2263 (2010); Wilmut et al., Nature, 385: 810-813 (1997); Vizcardo et al., Cell Stem Cell, 12: 31-36 (2013); and Crompton et al., Cell Stem Cell, 12: 6-8 (2013).
- the host cell is an iPSC that was prepared by reprogramming, any of the host cells described herein (e.g., T cells, NK cells, or invariant natural killer T cells) to a pluripotent state.
- 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.
- 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.
- 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 Nos. 8,034,334; 8,383,099; and 11,401,503; Dudley et al., J. Immunother., 26:332-42 (2003); and Riddell et al., J. Immunol. Methods, 128:189-201 (1990).
- expansion of the numbers of T cells is carried out by culturing the T cells with OKT3 antibody, IL-2, and feeder PBMC (e.g., irradiated allogeneic PBMC).
- Another aspect of the invention provides a method of producing an engineered human cell (or an engineered population of human cells), the method comprising introducing any of the inventive nucleic acids or recombinant expression vectors described herein to an isolated human cell (or an isolated population of human cells), wherein the nucleic acid or recombinant expression vector comprises a nucleotide sequence encoding any of the inventive TCRs, polypeptides, or proteins described herein.
- the isolated human cell, or isolated population of human cells, to which the nucleic acid or recombinant expression vector is introduced may be as described herein with respect to other aspects of the invention.
- the inventive TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, and host cells can be isolated and/or purified.
- isolated as used herein means having been removed from its natural Leydig 770310 HHS E-054-2023-0-PC-01 32 environment.
- purified as used 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%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least 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.
- 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 of the invention 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.
- Leydig 770310 HHS E-054-2023-0-PC-01 33 Preferably, the inventive TCR 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 NaCl 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., mutated p53), 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 aspects, 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.
- Many assays for determining an administered dose are known in the art. For example, 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.
- inventive TCR material 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.
- 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 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 aspects, fewer than 1 x 10 6 cells may be administered.
- Leydig 770310 HHS E-054-2023-0-PC-01 34 One of ordinary skill in the art 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.
- 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.
- inventive TCR materials which are not necessary for the function of the inventive TCR materials, are ideal 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 mutated p53 or to detect, treat, or prevent cancer.
- inventive pharmaceutical compositions, TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, or populations of cells can be used in methods of treating or preventing cancer.
- inventive TCRs are believed to bind specifically to mutated p53, 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 mutated p53.
- an aspect of 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 aspect 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.
- the terms “treat,” and “prevent” as well as words stemming therefrom, as used herein, do not necessarily imply 100% or complete treatment or prevention.
- the 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.
- inventive pharmaceutical compositions TCRs, polypeptides, proteins, nucleic acids, recombinant expression vectors, host cells, or populations of cells can be used in methods of inducing an immune response against a cancer in a mammal.
- an aspect 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, 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 aspect 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 inducement of an immune response against a cancer in a mammal. Also provided by an aspect of the invention 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.
- 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).
- a detectable label such as, for instance, a radioiso
- 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, colocrectal cancer, endometrial cancer, esophageal cancer, uterine cervical cancer, gastrointestinal carcinoid tumor, glioma, Hodgkin lymphoma, hypopharynx cancer, kidney cancer, larynx cancer, liver cancer, lung cancer,
- the cancer is a cancer which expresses mutated p53.
- the cancer may express p53 with a mutation at one or both of positions 220 and 175, as defined by SEQ ID NO: 1.
- the cancer may express p53 with one or both of the following human p53 mutations: Y220C and R175H.
- the cancer is an epithelial cancer.
- the cancer is colon cancer, rectal cancer, ovarian cancer, endometrial cancer, non-small cell lung cancer (NSCLC), glioblastoma, uterine cervical cancer, head and neck cancer, breast cancer, pancreatic cancer, or bladder cancer.
- NSCLC non-small cell lung cancer
- the cancer may be known to comprise a Y220C or R175H mutation in human p53.
- 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 Lagomorpha, 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).
- EXAMPLE 1 This example demonstrates the isolation of TCRs from Patient 4196.
- the p53 R175H 9-amino acid epitope (HMTEVVRHC) (SEQ ID NO: 112) contains cysteine at its C-terminus.
- Cysteine residues can oxidize and form disulfide bonds with other cysteine residues under oxidizing conditions, thus potentially interfering with their ability to bind to MHC molecules (Sachs et al., J. Immunol., 205(2): 539–549 (2020)). This may lead to reduced T cell activity.
- HMTEVVRHC HMTEVVRHC
- AABA alpha-aminobutyric acid
- AABA is a cysteine analogue containing a methyl group in place of the sulfhydryl group present in cysteine.
- the native cysteine at position 9 of (HMTEVVRRC) (SEQ ID NO: 113) was replaced with AABA to produce the corresponding wild-type analogue peptide HMTEVVRRX (SEQ ID NO: 117), wherein X at position 9 of SEQ ID NO: 117 is AABA.
- Three different culture conditions were tested prior to isolating TCRs specific for p53 R175H from TILs from Patient 4196 (4196 TILs).
- the HLA-A2 tetramer was oligomerized HLA-A2 monomers loaded with the p53 R175H 9-amino acid epitope analogue HMTEVVRHX (SEQ ID NO: 116), wherein X at position 9 of SEQ ID NO: 116 is AABA.
- SEQ ID NO: 116 9-amino acid epitope analogue HMTEVVRHX
- TCR alpha and beta chain variable regions were identified by single-cell TCR sequencing.
- the amino acid sequences of the alpha and beta chain variable regions are shown in Table 2.
- the CDRs are underlined.
- the N-terminal signal peptides are in bold font.
- T cells were Leydig 770310 HHS E-054-2023-0-PC-01 40 stained for the HLA-A2 tetramer.
- the tetramer was oligomerized HLA-A2 loaded with the p53 R175H 9-amino acid epitope analogue HMTEVVRHX (SEQ ID NO: 116), wherein X at position 9 of SEQ ID NO: 116 is AABA.
- the flow cytometry staining for CD8 and tetramer is shown in Figure 2A.
- the 4424-R175H TCR was isolated from the tetramer.
- the 4424-R175H TCR was the first TCR that was identified by use of a tetramer.
- the sequences of the TCR alpha and beta chain variable regions were identified by single-cell TCR sequencing. The amino acid sequences of the alpha and beta chain variable regions are shown in Table 3. The CDRs are underlined. The N-terminal signal peptides are in bold font.
- a R S T This example demonstrates the isolation of TCRs from Patient 4402.
- TIL from Patient 4402 showed specific recognition of antigen presenting cells (APCs) pulsed with p53 Y220C peptide (DRNTFRHSVVVPCEPPEVGSDCTTI) (SEQ ID NO: 114), but not the corresponding WT peptide (DRNTFRHSVVVPYEPPEVGSDCTTI) (SEQ Leydig 770310 HHS E-054-2023-0-PC-01 41 ID NO: 115).
- APCs antigen presenting cells
- DRNTFRHSVVVPCEPPEVGSDCTTI p53 Y220C peptide
- DRNTFRHSVVVPYEPPEVGSDCTTI SEQ Leydig 770310 HHS E-054-2023-0-PC-01 41
- TCRs Twenty-one (21) TCRs (4402-Y220C-A to -U, respectively) were isolated from TIL from Patient 4402. ELISpot analysis was performed to detect IFN- ⁇ release following co-culture of healthy donor PBL expressing the respective 21 TCRs that were isolated from Patient 4402 TIL (effector cells).
- the 4402-Y220C-B TCR, 4402-Y220C-C TCR, and 4402-Y220C-L TCR showed increased IFN- ⁇ release against B cells pulsed with 1 ⁇ g/mL mutant p53 Y220C peptide (DRNTFRHSVVVPCEPPEVGSDCTTI) (SEQ ID NO: 114) (target cells) relative to the DMSO controls, while the other 18 TCRs did not. Effector cells treated with phorbol 12- myristate 13-acetate (PMA) and ionomycin were used as a positive control. Controls included: cultures with only effector cells, cultures with target cells pulsed with DMSO, and cultures with PBL transduced with an empty vector (mock).
- PMA phorbol 12- myristate 13-acetate
- the sequences of the TCR alpha and beta chain variable regions were identified by single-cell TCR sequencing.
- the amino acid sequences of the alpha and beta chain variable regions of three of the TCRs (4402-Y220C-B TCR (TRAV12-3/TRBV7-2), 4402- Y220C-C TCR (TRAV26-2/TRBV5-6), and 4402-Y220C-L TCR (TRAV23/TRBV5-1)) are shown in Table 4.
- the CDRs are underlined.
- the N-terminal signal peptides are in bold font.
- Nucleotide sequences encoding the variable regions of the ⁇ and ⁇ chains of the TCRs of Tables 2-4 were obtained and codon optimized.
- the TCR ⁇ VDJ regions were fused to the mouse TCR ⁇ constant chain.
- the TCR ⁇ VJ regions were fused to the mouse TCR ⁇ constant chain.
- Leydig 770310 HHS E-054-2023-0-PC-01 43 replacing the constant regions of the human and TCR ⁇ chains with the corresponding murine constant regions improves TCR expression and functionality (Cohen et al., Cancer Res., 66(17): 8878-86 (2006)).
- the murine TCR ⁇ and TCR ⁇ constant chains were cysteine-modified.
- TCR ⁇ and TCR ⁇ chains were separated by a Furin Ser/Gly P2A linker RAKRSGSGATNFSLLKQAGDVEENPGP (SEQ ID NO: 103). Without being bound to a particular theory or mechanism, it is believed that the linker provides comparable expression efficiency of the two chains (Szymczak et al., Nat. Biotechnol., 22(5):589-94 (2004)).
- EXAMPLE 5 This example demonstrates the specificity and avidity of the 4196-C TCR, 4196-D TCR, and 4196-E TCR.
- Healthy donor PBL were transduced with the retroviral vector encoding the 4196- C TCR, 4196-D TCR, or 4196-E TCR of Example 4 or the TCR 4196_AV6_with_BV11-2 disclosed in US 2020/0277352.
- TCR-expressing T cells were co-cultured for 18 hours (h) with T2 cells that expressed HLA-A2 and had been incubated with the WT epitope analogue HMTEVVRRX (SEQ ID NO: 117), wherein X at position 9 of SEQ ID NO: 117 is AABA, or p53 R175H 9-amino acid epitope analogue at the concentration of peptides denoted Leydig 770310 HHS E-054-2023-0-PC-01 48 in Figures 1B-1E.
- T cell activation marker was measured by flow cytometry following the co-culture.
- the 4196-C TCR, 4196-D TCR, and 4196-E TCR all showed specificity for the mutant p53 epitope analogue.
- the TCR 4196_AV6_with_BV11-2 showed significant wild-type epitope analogue recognition at the 1000 ng/mL and 100 ng/mL concentration.
- Effector cells were prepared by transducing healthy donor PBL with the retroviral vector encoding the 4196-C TCR, 4196-D TCR, or 4196-E TCR of Example 4.
- the anti- tumor activity of the 4196-C TCR, 4196-D TCR, and 4196-E TCR was determined using an INCUCYTE immune cell killing assay.
- TYK-nu human ovarian cancer cells target cells that naturally expressed p53 R175H and HLA-A2 were labeled with red fluorescent protein (RFP).
- Fifty thousand effector cells were co-cultured with ten thousand TYK-nu cells over 3 days. The number of viable RFP+ TYK-nu cells were counted at 4h intervals. The results are shown in Figure 1G.
- EXAMPLE 7 This example demonstrates the specificity and avidity of the 4424-R175H TCR. Effector cells were healthy donor PBL transduced with the retroviral vector encoding the 4424-R175H TCR of Example 4.
- Target cells were monkey kidney COS7 cells that were engineered to express HLA-A2 and incubated with the WT peptide analogue HMTEVVRRX (SEQ ID NO: 117), wherein X at position 9 of SEQ ID NO: 117 is AABA or Leydig 770310 HHS E-054-2023-0-PC-01 49 the mutant p53 R175H peptide analogue (SEQ ID NO: 116), wherein X at position 9 of SEQ ID NO: 116 is AABA at the concentrations denoted in Fig.2B. Following 18 h co-culture, T cell activation marker 4-1BB expression was measured by flow cytometry. The results are shown in Fig.2B.
- T cells expressing the 4196-C TCR, 4196-D TCR, 4196-E TCR, or 4424-R175H TCR encoded by the respective retroviral vectors of Example 4 or 4141- TCR1a2 were co-cultured with ten thousand human ovarian cancer TYK-nu cells (target cells) for 72 h at an effector to target ratio of 2:1. Viable RFP+ TYK-nu cells were counted every 3 h. The results are shown in Figure 3. All of the T cell-treated conditions showed a significant delay in tumor growth relative to the tumor-only condition.
- EXAMPLE 9 This example demonstrates tumor cell recognition by the 4402-Y220C-B TCR, 4402-Y220C-C TCR, and 4402-Y220C-L TCR. Healthy donor PBL were independently transduced with the respective retroviral vectors of Example 4 encoding the 4402-Y220C-B TCR, 4402-Y220C-C TCR, or 4402- Y220C-L TCR (effector cells). Effector cells were co-cultured with target cells under conditions shown in Table 6.
- the 4402-Y220C-C TCR and 4402-Y220C-L TCR released IFN- ⁇ when the autologous organoid tumor cells were pulsed with p53 Y220C 25-mer (DRNTFRHSVVVPCEPPEVGSDCTTI) (SEQ ID NO: 114).
- DRNTFRHSVVVPCEPPEVGSDCTTI DRNTFRHSVVVPCEPPEVGSDCTTI
- the autologous organoid tumor cells exhibited HLA loss of heterozygosity, and they may have lost the HLA-DRB3*02:02 molecule restricting the 4402-Y220C-B TCR.
- Leydig 770310 HHS E-054-2023-0-PC-01 51 10 This example demonstrates the avidity and specificity of the 4402-Y220C-B TCR, 4402-Y220C-C TCR, and 4402-Y220C-L TCR.
- Healthy donor PBL were independently transduced with the retroviral vector of Example 4 encoding the 4402-Y220C-B TCR, 4402-Y220C-C TCR, or 4402-Y220C-L TCR or the 4343-D TCR disclosed in US 2023/0321240 (effector cells).
- Target cells were autologous B cells pulsed with WT (DRNTFRHSVVVPYEPPEVGSDCTTI) (SEQ ID NO: 115) or mutant (DRNTFRHSVVVPCEPPEVGSDCTTI) (SEQ ID NO: 114) peptides at the concentrations denoted in Figures 4A-4D. After the effector cells were co-cultured with the target cells, 4-1BB expression was measured by flow cytometry.
- Healthy donor PBL were transduced with the retroviral vector of Example 4 encoding the 4402-Y220C-B TCR (effector cells).
- Target cells were COS7 cells independently transfected with the individual Class II HLA molecules expressed by Patient 4402 (Table 7). TABLE 7 HLA molecule(s) Transfected into Target Cells Leydig 770310 HHS E-054-2023-0-PC-01 52 secretion was measured by ELISpot.
- 4402-Y220C-B TCR-expressing cells showed significant IFN- ⁇ secretion when co-cultured with COS7 cells expressing HLA-DRB3*02:02.
- EXAMPLE 12 This example demonstrates differential autologous tumor organoid recognition by 4402-Y220C-C TCR and 4402-Y220C-L TCR. Healthy donor PBL were independently transduced with the retroviral vector of Example 4 encoding the 4402-Y220C-C TCR or 4402-Y220C-L TCR (effector cells).
- Target cells were autologous breast tumor organoid cells from Patient 4402 of passage 11 or passage 27.
- Target cells pulsed with DMSO served as a control. Effector cells were co-cultured with target cells. T cell activation was measured by 4-1BB upregulation. The results are shown in Figure 4E.
- EXAMPLE 13 This example demonstrates the differential expression of the HLA-DRB1*15:01 and DRB1*13:03 molecules by the autologous organoid cells of passage 11 and 27 of Example 12.
- the expression of HLA-DRB1*15:01 and DRB1*13:03 by the autologous organoid cells of passage 11 and 27 of Example 12 was measured by transcriptome analysis (RNA sequencing). The results are shown in Figure 4F.
- HLA-DRB1*13:03 is the restriction element for the 4402-Y220C-C TCR and 4402-Y220C-L TCR.
- Leydig 770310 HHS E-054-2023-0-PC-01 53 14 This example demonstrates that adoptive transfer of cells transduced with the retroviral vector encoding the 4196-C TCR of Example 4 reduce tumor size in tumor-bearing mice.
- NSG mice (immunocompromised) were subcutaneously injected with TYK-nu human ovarian cancer cells, which naturally expressed the p53 R175H mutation and HLA- A*02:01. Two weeks later, the tumor-bearing mice were randomized and treated with adoptive cell transfer of healthy donor T cells independently transduced with: 1. the retroviral vector encoding the 4196-C TCR of Example 4; 2. an irrelevant TCR control (i.e., 4259); 3. the TCR 4196_AV12-1_with_BV6-1 disclosed in US 2020/0277352; 4. the TCR 4196_AV38-1_with_BV10-3 disclosed in US 2020/0277352; 5.
- TCR 4196_AV6_with_BV11-2 disclosed in US 2020/0277352; 6. the TCR 4141-TCR1a2 disclosed in US 2022/0332785; or 7. the 4141 IVS TCR disclosed in US Patent Application No.18/289,596.
- Two T-cell dose levels were tested: 2 million or 10 million T cells/mouse. The mean tumor size was measured at various time points up to 40 days after adoptive transfer of the transduced cells. The results obtained with the 2 million T cells/mouse dose are shown in Figure 6. As shown in Figure 6, only the 4196-C TCR showed statistical significance relative to 4259 TCR, the irrelevant TCR control. The results obtained with the 10 million T cells/mouse dose are shown in Figure 7.
- Leydig 770310 HHS E-054-2023-0-PC-01 54 followed by a list of one or more items (for “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.
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