US20180170992A1 - CAR T CELLS RECOGNIZING CANCER-SPECIFIC IL 13Ra2 - Google Patents

CAR T CELLS RECOGNIZING CANCER-SPECIFIC IL 13Ra2 Download PDF

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US20180170992A1
US20180170992A1 US15/545,950 US201615545950A US2018170992A1 US 20180170992 A1 US20180170992 A1 US 20180170992A1 US 201615545950 A US201615545950 A US 201615545950A US 2018170992 A1 US2018170992 A1 US 2018170992A1
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il13rα2
seq
cells
cell
antibody
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Irina V. Balyasnikova
Maciej S. Lesniak
Stephen M.G. Gottschalk
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University of Chicago
Baylor College of Medicine
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Baylor College of Medicine
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    • 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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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • 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
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    • C07K14/70521—CD28, CD152
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
    • C07K14/7155—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for interleukins [IL]
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    • C07—ORGANIC CHEMISTRY
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    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2866—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against receptors for cytokines, lymphokines, interferons
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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    • C07K2317/00—Immunoglobulins specific features
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    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
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    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
    • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
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    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment

Definitions

  • the disclosure relates generally to the fields of cancer biology and to molecular antibody-receptor technology.
  • Cancer is a major threat to human and non-human animal health, leading to reduced quality of life and, in too many cases, death.
  • the burden placed on national, regional and local healthcare organizations to treat and prevent the various forms of cancer is significant in terms of the resources and manpower required.
  • One of the main weapons vertebrates, including humans, have to combat disease is a functioning immune system.
  • a brief consideration of immunotherapies to treat or prevent cancer might lead one to conclude that the effort held out little hope of success because immune systems guard against foreign, or non-self, materials and cancer cells arise from within, i.e., they are self materials.
  • Mutant antigens are powerful targets for tumor destruction, e.g., in mice, and tumor-infiltrating lymphocytes targeting these mutations cause durable tumor regression in patients. Nevertheless, non-mutant antigens have been presumed by many scientists to be cancer-specific or “relatively cancer-specific” and safe antigens for vaccine approaches. However, adoptively transferred T cells can be orders of magnitude more effective and destructive than vaccinations. As a result, targeting MAGE-A3, HER-2 or CEA with T cells has caused death or serious toxicity in clinical trials now halted (8-11). As was shown in 2002, cancer cells with extremely high or very low expression levels of a target antigen differ only in the induction of immune responses, but not at the effector phase (15).
  • the high affinity interleukin-13 receptor ⁇ 2 (IL13R ⁇ 2) is selectively expressed at a high frequency by glioblastoma multiforme (GBM) as well as several other tumor types.
  • GBM glioblastoma multiforme
  • One approach for targeting this tumor-specific receptor utilizes the cognate ligand, IL-13, conjugated to cytotoxic molecules. This approach, however, lacks specificity because the lower affinity receptor for IL-13, IL13R ⁇ 1, is widely expressed by normal tissues.
  • T cells expressing a chimeric antigen receptor (i.e., CAR) that specifically recognizes and binds to the ⁇ 2 Interleukin 13 Receptor (i.e., IL13R ⁇ 2).
  • CAR Interleukin 13 Receptor
  • the IL13R ⁇ 2-specific CARs generally referred to herein as 47-CARs, when expressed in T cells effectively target and kill IL13R ⁇ 2-positive target cells.
  • 47-CARs with a short spacer region, or SSR (i.e., 47-CAR.SSR)
  • 47-CAR.SSR T cells have potent anti-tumor activity in vivo.
  • the disclosure provides (i) the sequences of heavy (SEQ ID NO:7) and light (SEQ ID NO:8) chain variable regions of a monoclonal antibody (i.e., the clone 47 antibody) specifically targeting human tumor-associated antigen, IL13R ⁇ 2, and (ii) data demonstrating the functionality of the protein encoded by the heavy and light chain cDNAs in the format of an scFv antibody or fusion to other functional moieties.
  • the sequences of the heavy and light chain constant regions were also determined and were found to be identical to the corresponding sequences in Genbank Acc. No. DQ381544.1.
  • the CH1 sequence of the clone 47 antibody is set forth in SEQ ID NO:104, CH2 in SEQ ID NO:105 and CH3 in SEQ ID NO:106; the light chain constant region sequence of the clone 47 antibody is set forth in SEQ ID NO:107; and the hinge region of the clone 47 antibody in SEQ ID NO:108.
  • the heavy and light chain can be arranged in different formats, such as single-chain antibody, diabodies, bi- and tri-specific antibodies, fusions with therapeutic proteins and other moieties, human or humanized whole antibodies as well as human or humanized Fab fragments and other functional derivatives.
  • the single-chain antibody or other arrangements of the protein encoded by the heavy and light chains may be expressed and conjugated to therapeutic carriers (e.g., viruses, cells, nanomaterials) for specific delivery of therapeutic to IL13R ⁇ 2-overexpressing tumors or for imaging tumor burden.
  • therapeutic carriers e.g., viruses, cells, nanomaterials
  • interleukin-13 receptor ⁇ 2 (IL13R ⁇ 2), the high affinity receptor for interleukin-13 (IL-13), is a promising candidate.
  • IL13R ⁇ 2 is expressed at a high frequency in the aggressive and incurable form of primary brain tumor known as glioblastoma multiforme (GBM) (1-3), as well as by other solid tumors (4).
  • GBM glioblastoma multiforme
  • normal tissues express little to no IL13R ⁇ 2, with the exception of the testes (6).
  • IL13R ⁇ 1 a different receptor with low affinity for IL-13, is expressed ubiquitously by many tissues (7-9), making it a poor candidate for selective targeting of tumor-specific immunotherapeutic applications.
  • IL-13PE Pseudomonas exotoxin A
  • the disclosure captures the tumor specificity of IL13R ⁇ 2 by providing protein binding partners specific for IL13R ⁇ 2, rather than mimicking IL13 itself, which would result in a molecule exhibiting a capacity to bind to both IL13R ⁇ 1 and IL13R ⁇ 2.
  • the disclosure provides a polynucleotide encoding one of these cancer-specific IL13R ⁇ 2 binding partners, including polynucleotides comprising codon-optimized coding regions for binding partners specific for an epitope of one of these IL13R ⁇ 2 binding partners.
  • fusion proteins or chimeras that comprise an IL13R ⁇ 2 binding partner as defined above in operable linkage to a peptide providing a second function, such as a signaling function of the signaling domain of a T cell signaling protein, a peptide modulator of T cell activation or an enzymatic component of a labeling system.
  • exemplary T cell signaling proteins include 4-1BB (CD137), CD3 ⁇ , and fusion proteins, e.g., CD28-CD3 ⁇ and 4-1BB-CD3 ⁇ .
  • 4-1BB (CD137) and CD28 are co-stimulatory molecules of T cells; CD3 ⁇ is a signal-transduction component of the T-cell antigen receptor.
  • the IL13R ⁇ 2-specific CAR may be expressed in two fragments that are inactive without the addition of an exogenous substance.
  • the CAR would consist of two molecules: 1) the first molecule would contain the IL13R ⁇ 2-specific scFc, a hinge, a transmembrane domain, a costimulatory domain, and a heterodimerizer domain (Exto-TM-HD), and 2) the first molecule would contain a transmembrane domain, a costimulatory domain, a heterodimerizer domain, a CD3 ⁇ activating domain (Cyto-HD) (Wu et al; Science. 2015 Oct. 16; 350(6258):aab407).
  • Exto-TM-HD and Cyto-HD in cells would result in an inactive IL13R ⁇ 2-CAR unless a small molecule, for example but not limited to, a rapalog A/C Heterodimerizer is added that links Exto-TM-HD and Cyto-HD, allowing for pharmacological control of IL13R ⁇ 2-CAR activity.
  • the peptide or protein providing a second function may provide a modulator of T cell activation, such as IL15, IL15R ⁇ , of an IL15/IL15R ⁇ fusion, or it may encode a label or an enzymatic component of a labeling system useful in monitoring the extent and/or location of binding, in vivo or in vitro.
  • T cells such as autologous T cells
  • Agent encoding these prophylactically and therapeutically active biomolecules placed in the context of T cells provide a powerful platform for recruiting adoptively transferred T cells to prevent or treat a variety of cancers in some embodiments of the disclosure. Codon optimization of the coding regions for binding partners specific for epitopes found on cancer cells provides an efficient approach to delivery of the diagnostic, prophylactic, and/or therapeutic proteins disclosed herein.
  • the disclosure provides an Interleukin 13 Receptor ⁇ 2 (IL13R ⁇ 2) binding partner comprising the antibody heavy chain variable fragment (V H ) complementarity determining region 1 (CDR1) of SEQ ID NO:1, the V H CDR2 of SEQ ID NO: 2, the V H CDR3 of SEQ ID NO: 3, the light chain (V L ) complementarity determining region 1 (CDR1) of SEQ ID NO: 4, the V L CDR2 of SEQ ID NO: 5, and the V L CDR3 of SEQ ID NO: 6, wherein the IL13R ⁇ 2 binding partner specifically binds to an epitope of IL13R ⁇ 2.
  • the V H sequence is set forth as SEQ ID NO: 7 and in some of the same and some different embodiments, the V L sequence is set forth as SEQ ID NO: 8.
  • a related aspect of the disclosure provides a bispecific binding molecule comprising a fragment of the IL13R ⁇ 2 binding partner described herein that binds to the IL13R ⁇ 2 epitope covalently linked to a peptide providing a second function to form a bispecific binding molecule.
  • the second function of the peptide is selected from the group consisting of a signaling function of the signaling domain of a T cell signaling protein, a peptide modulator of T cell activation, and an enzymatic component of a labeling system.
  • the fragment is a single-chain variable fragment (scFv), which may be contained within a bi-specific T-cell engager (BiTE) or a chimeric antigen receptor (CAR).
  • scFv single-chain variable fragment
  • BiTE bi-specific T-cell engager
  • CAR chimeric antigen receptor
  • Another aspect of the disclosure is drawn to a pharmaceutical composition
  • a pharmaceutical composition comprising the IL13R ⁇ 2 binding partner as described herein and a pharmaceutically acceptable carrier, adjuvant or diluent.
  • a related aspect provides a kit comprising the pharmaceutical composition described herein and a protocol for administration of the composition. Also related is an aspect providing a polynucleotide encoding the IL13R ⁇ 2 binding partner as described herein and a vector comprising the polynucleotide as described herein. Yet another aspect is directed to a host cell comprising the polynucleotide described herein or the vector described herein.
  • Yet another aspect of the disclosure provides a method of preventing, treating or ameliorating a symptom of a cancer disease comprising administering a therapeutically effective amount of the pharmaceutical composition as described herein.
  • the cancer is a solid tumor, such as a glioblastoma multiforme (GBM).
  • GBM glioblastoma multiforme
  • the cancer is treated by inhibiting the growth rate of the solid tumor.
  • the symptom ameliorated is pain.
  • an IL13R ⁇ 2-specific chimeric antigen receptor comprising: (A) each of the amino acid sequences of: NYLMN (SEQ ID NO: 1); RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); GYGTAYGVDY (SEQ ID NO: 3); RASESVDNYGISFMN (SEQ ID NO: 4); AASRQGSG (SEQ ID NO: 5); and QQSKEVPWT (SEQ ID NO: 6), (B) a hinge region, (C) a transmembrane domain, and (D) an endodomain comprising a signaling domain a CD3 zeta chain and a signaling domain of CD28.
  • CAR chimeric antigen receptor
  • the endodomain further comprises a signaling domain of one or more of: CD137, CD134, CD27, CD40, ICOS, and Myd88, optionally, wherein the endodomain comprises one or more of the amino acid sequences of SEQ ID NOs: 68, 70, 72, 74, 76, and 78.
  • the hinge region comprises the amino acid sequence of SEQ ID NO: 35 or SEQ ID NO: 37.
  • the IL13R ⁇ 2-specific CAR comprises a transmembrane domain of CD28.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 39.
  • the CD3 zeta chain signaling domain comprises the amino acid sequence of SEQ ID NO: 41.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 47.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO 49 or 51.
  • the IL13R ⁇ 2-specific CAR comprises one or both of the amino acid sequences of SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the IL13R ⁇ 2-specific CAR of claim 9 wherein the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 13.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 53 or SEQ ID NO: 55.
  • the disclosure provides a nucleic acid encoding any of the IL13R ⁇ 2-specific CARs disclosed or described herein.
  • the nucleic acid comprises the sequence of SEQ ID NO: 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, or 65.
  • the disclosure provides a vector comprising a nucleic acid disclosed or described herein.
  • the vector is a retroviral vector.
  • the disclosure provides a host cell comprising a vector disclosed or described herein.
  • the host cell is a human host cell.
  • the host cell is a T-lymphocyte.
  • the host cell is a natural killer cell.
  • the disclosure provides a cell population comprising a host cell disclosed or described herein.
  • the cell population comprises at least 10 7 host cells.
  • Another aspect is drawn to a pharmaceutical composition
  • a pharmaceutical composition comprising an IL13R ⁇ 2-specific CAR as disclosed or described herein, a nucleic acid as disclosed or described herein, a vector as disclosed or described herein, a host cell as disclosed or described herein, or a cell population as disclosed or described herein, and a pharmaceutically acceptable carrier.
  • Another aspect of the disclosure provides a method of treating a cancer in a subject, comprising administering to the subject a cell population as disclosed or described herein, in an amount effective to treat the cancer in the subject.
  • the cancer is colon cancer.
  • the host cells of the cell population are cells obtained from the subject.
  • the cells obtained from the subject are T-lymphocytes.
  • the cells obtained from the subject are natural killer cells.
  • CAR IL13R ⁇ 2-specific chimeric antigen receptor
  • A an ectodomain comprising each of the amino acid sequences of: (i) NYLMN (SEQ ID NO: 1); (ii) RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); (III) GYGTAYGVDY (SEQ ID NO: 3); (iv) RASESVDNYGISFMN (SEQ ID NO: 4); (v) AASRQGSG (SEQ ID NO: 5); and (vi) QQSKEVPWT (SEQ ID NO: 6); (B) a spacer region; (C) a transmembrane domain; and (D) an endodomain selected from the group consisting of CD3. ⁇ , CD28. ⁇ , CD28.OX40. ⁇ , CD28.41BB. ⁇ and 41BB. ⁇ .
  • the spacer region comprises no more than 100 amino acids, or no more than 50 amino acids, or no more than 25 amino acids, or the spacer region comprises SEQ ID NO:103 (PKSCDKTHTCPPCPAPEL) from the IgG1 hinge region.
  • the transmembrane domain comprises the transmembrane domain of CD28, such as a transmembrane domain comprising the amino acid sequence of SEQ ID NO:39, or CD8a.
  • the endodomain further comprises a signaling domain of one or more of: CD137, CD134, CD27, CD40, ICOS, and Myd88.
  • the endodomain comprises one or more of the amino acid sequences of SEQ ID NOs: 68, 70, 72, 74, 76, and 78.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 41.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 47.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO 49 or 51.
  • the IL13R ⁇ 2-specific CAR comprises one or both of the amino acid sequences of SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the disclosure also contemplates embodiments wherein the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 13.
  • the IL13R ⁇ 2-specific CAR comprises the amino acid sequence of SEQ ID NO: 53 or SEQ ID NO: 55.
  • nucleic acid encoding the IL13R ⁇ 2-specific CAR disclosed herein.
  • the nucleic acid comprises the sequence of SEQ ID NO: 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, and 65.
  • Still another aspect of the disclosure is drawn to a vector comprising the nucleic acid disclosed herein.
  • the vector is a retroviral vector.
  • the host cell comprising the vector disclosed herein.
  • the host cell is a human host cell.
  • the host cell is a T-lymphocyte or a natural killer cell.
  • the cells obtained from the subject are T cells, and/or other lymphocytes including, but not limited to, NKT cells, ⁇ T cells, mucosa associated invariant T cells or MAIT cells, and innate lymphoid cells.
  • stem and/or progenitor cells may be obtained from the subject that are subsequently differentiated into the aforementioned immune cells.
  • Another aspect of the disclosure is a cell population comprising the host cell disclosed herein.
  • the cell population comprises at least 10 7 host cells.
  • the disclosure provides a pharmaceutical composition
  • a pharmaceutical composition comprising an IL13R ⁇ 2-specific CAR as disclosed herein, a nucleic acid as disclosed herein, a vector as disclosed herein, a host cell as disclosed herein, or a cell population as disclosed herein, and a pharmaceutically acceptable carrier.
  • Yet another aspect of the disclosure is a method of treating a cancer in a subject, comprising administering to the subject a cell population as disclosed herein, in an amount effective to treat the cancer in the subject.
  • the cancer is colon cancer.
  • the host cells of the cell population are cells obtained from the subject.
  • the cells obtained from the subject are T cells, and/or other lymphocytes including, but not limited to, NKT cells, ⁇ T cells, mucosa associated invariant T cells or MAIT cells, and innate lymphoid cells.
  • stem and/or progenitor cells may be obtained from the subject that are subsequently differentiated into the aforementioned immune cells.
  • the immune or stem and/or progenitor cells that are genetically modified to be IL13R ⁇ 2-specific by expressing a CAR or BITE molecule may be further genetically modified to enhance their anti-tumor activity.
  • additional genetic modification include, but are not limited to: i) CARs or BITEs that are specific for other antigens expressed on tumor cells or within the tumor environment, ii) cytokines (e.g., various interleukins such as IL7, IL12, IL15, IL21), iii) chimeric cytokine receptors (e.g., IL7R, IL15R), iv) chemokine receptors (e.g., CCR2b, CXCR2), iv) chimeric activating receptors (e.g., IL4/IL7R, IL4/IL2R, TGF ⁇ /TLR4R), v) silencing negative regulators (e.g., PD
  • FIG. 1 Characterization of antigen recognition and screening of hybridoma clones.
  • A binding of B-D13 mAb to ELISA plates coated with rhIL13R ⁇ 2hFc at 0.1 and 1 ⁇ g/ml.
  • B binding of IL13R ⁇ 2 mAb to native and denatured (at 95° C. in the presence of (3-mercaptoethanol) rhIL13R ⁇ 2hFc in a plate-bound ELISA.
  • C screening of selected hybridoma populations against rhIL13R ⁇ 2hFc in a plate-bound ELISA.
  • D screening of selected hybridoma populations against rhIL13R ⁇ 2hFC using a Western blot.
  • FIG. 2 The IL13R ⁇ 2 (clone 47) mAb specifically binds to rhIL13R ⁇ 2 and IL13R ⁇ 2 expressed on the cell surface of CHO cells.
  • A binding of IL13R ⁇ 2 (clone 47, 83807, and B-D13) mAbs to rhIL13R ⁇ 2 in a plate-bound ELISA.
  • B binding of the IL13R ⁇ 2 (clone 47) mAb to human IL13R ⁇ 2 expressed on the surface of CHO cells.
  • C cross-reactivity of the IL13R ⁇ 2 (clone 47) mAb with hrIL13R ⁇ 1.
  • D cross-reactivity of IL13R ⁇ 2 (clones 47, 83807, and B-D13) mAbs with mouse rIL13R ⁇ 2. Error bars represent S.D.
  • FIG. 3 Binding of IL13R ⁇ 2 mAb to glioma cells.
  • A flow charts of IL13R ⁇ 2 (clones 47, 83807, and B-D13) mAbs binding to the surface of glioma cells, normal human primary astrocytes, and HEK cells transfected with IL13R ⁇ 2.
  • B data of the median fluorescence intensity of binding between the IL13R ⁇ 2 (clones 47, 83807, and B-D13) mAbs to various cell lines analyzed by flow cytometry. Numbers above the bars represent the difference in the binding of clone 47 when compared with clone B-D13 for each cell line. The color key is the same for A and B.
  • C mRNA expression for IL13R ⁇ 2 in glioma cells as well as normal human primary astrocytes.
  • D panels a-c, flow cytometry demonstrating the specific binding of the IL13R ⁇ 2 (clone 47) mAb to GFP-tagged U251 glioma cells from an intracranial xenograft (xeno).
  • the curve with a clear area under the curve in sub-panel b depicts the binding of mAb IL13R ⁇ 2 (clone 47) to GFP negative cells;
  • the curve with a clear area under the curve in sub-panel c depicts the binding of mAb IL13R ⁇ 2 (clone 47) to GFP positive cells.
  • Curves in sub-panels b and c with gray areas under the curves show the results when exposing control IgG to GFP-negative (sub-panel b) or GFP-positive (sub-panel c) cells. neg, negative.
  • A area; SSC-A, side scatter area; APC-A, allophycocyanin area.
  • FIG. 4 The affinity between the IL13R ⁇ 2 (clone 47) mAb and rhIL13R ⁇ 2.
  • the kinetics of interaction of IL13R ⁇ 2 (clone 47) mAb (A) and the commercially available mAb clones 83807 (B) and B-D13 (C) with rhIL13R ⁇ 2 as visualized by SPR in a Biacore 3000 are shown.
  • the rhIL13R ⁇ 2 was injected at concentrations ranging from 1 to 100 nM (1 nM, 2.5 nM, 5 nM, 7.5 nM, 10 nM, 15 nM, 20 nM, 25 nM concentrations shown, lower to upper curves) at a constant flow rate of 20 ⁇ l/minute over immobilized antibodies and over a control dextran surface (these values were subtracted from the signal).
  • the association and dissociation phases were monitored for 300 s by following the change in SPR signal (colored curves) given in RU. Black curves represent the fit of the data to a one-site binding model. For derived kinetic parameters, see Table 1. Lower panels show residuals from a one-site binding model, indicating an excellent fit.
  • FIG. 5 The IL13R ⁇ 2 (clone 47) mAb competes with rhIL-13 for the binding site of IL13R ⁇ 2.
  • A using a competitive binding plate assay, the IL13R ⁇ 2 (clone 47) mAb but not control mIgG or antibody clones 83807, B-D13, and YY-23Z significantly abolished the binding of rhIL-13 to the rhIL13R ⁇ 2Fc chimera absorbed to plastic.
  • One-way analysis of variance followed by Dunnett's post hoc test was performed. Data from a single representative experiment are shown.
  • IL13R ⁇ 2 recombinant human IL-13 competes with the IL13R ⁇ 2 (clone 47) mAb for the binding site of WT IL13R ⁇ 2 but not with the 4-amino acid (4aa) mutant IL13R ⁇ 2 expressed on the surface of HEK cells.
  • C the IL13R ⁇ 2 (clone 47) mAb competes with rhIL-13 for the binding site of the WT and 4-amino acid mutant form of IL13R ⁇ 2.
  • a paired t test was performed. Data represent the summary of three independent experiments shown in B and C. *, p ⁇ 0.05; **, p ⁇ 0.01; ***, p ⁇ 0.001. Error bars represent S.D.
  • FIG. 6 The contribution of Tyr207, Asp271, Tyr315, and Asp318 residues of IL13R ⁇ 2 to the binding of the IL13R ⁇ 2 (clone 47) mAb.
  • A variants of cDNA encoding individual mutations to Ala or a combinatorial 4-amino acid mutant (4aa mut) of IL13R ⁇ 2 was generated.
  • HEK cells were transfected with a control vector or a vector encoding the IL13R ⁇ 2 variants. After 48 hours, binding of the IL13R ⁇ 2 (clone 47) mAb to the surface of transfected cells was analyzed by flow cytometry.
  • Anti-IL13R ⁇ 2 antibody clones 83807 and B-D13 were used as reference antibodies in this assay. Binding of antibodies was determined as the percentage of positive cells. The ratio of bound clones was determined for each IL13R ⁇ 2 mutant and compared with that of the wild-type receptor. One-way analysis of variance followed by Dunnett's post hoc test was performed. Data represent a summary of four independent experiments. Error bars represent S.D. B, representative graphs of flow cytometry data demonstrating the binding of clone 47 or rhIL-13 to the WT and 4-amino acid-mutated variant of the IL13R ⁇ 2 receptor expressed on the surface of HEK cells.
  • Filled curves negative control, staining with isotype control IgG+secondary antibody; Open curves: staining with the anti-IL13R ⁇ 2 (clone 47) monoclonal antibody+secondary antibody.
  • A area; APC-A, allophycocyanin area; FITC-A, fluorescein isothiocyanate area.
  • FIG. 7 Effect of N-linked glycosylation on the binding of IL13R ⁇ 2 to recombinant IL13R ⁇ 2.
  • A binding of IL13R ⁇ 2 to control and Pngase F-treated rhIL13R ⁇ 2. Plates were coated with hrIL13R ⁇ 2 at 1 ⁇ g/ml and treated with native buffer or with 1 milliunit/well Pngase F in native buffer for 3 hours at 37° C.
  • An ELISA for binding of the IL13R ⁇ 2 (clone 47) mAb in comparison with antibody clones B-D13, 83807, and YY-23Z and rhIL-13 was performed, and the data of one representative experiment from three independent experiments are shown.
  • B a Western blot shows the lower molecular weight of Pngase F-treated rhIL13R ⁇ 2 due to removal of N-linked glycosylation adducts from the molecule.
  • C flow cytometry shows the binding of IL13R ⁇ 2 mAbs to IL13R ⁇ 2-expressing U251 and HEK293 cells treated with 1 milliunit of Pngase F for 1 hour at 37° C. The data are representative of three independent experiments.
  • a paired t test was used to evaluate the difference between control and Pngase F-treated groups. *, p ⁇ 0.5.
  • MFI mean fluorescence intensity. Error bars represent S.D.
  • FIG. 9 The IL13R ⁇ 2 (clone 47) mAb improves the survival of mice in an orthotopic human glioma xenograft model.
  • A the survival of animals injected with U251 glioma cells (2.5 ⁇ 10 4 ) alone or in combination with either control IgG or the IL13R ⁇ 2 (clone 47) mAb.
  • FIG. 10 A competitive binding assay for the IL13R ⁇ 2 (clone 47) mAb to the surface of N10 glioma cells.
  • N10 glioma cells were pre-incubated either with 10 ⁇ excess rhIL13 (left panel) or with 10 ⁇ excess of IL13R ⁇ 2 (clone 47) mAb for 30 minutes on ice (right panel). N10 cells were subsequently incubated with isotype control mIgG, IL13R ⁇ 2 (clone 47) mAb or rhIL13. Bound antibodies or rhIL13 were detected with secondary antibodies and analyzed by flow cytometry. Data are presented as % of positive cells.
  • FIG. 12 Binding of IL13R ⁇ 2 clone 47 phages with IL13R ⁇ 2hFc in plate ELISA.
  • FIG. 13 Specificity of binding scFv IL13R ⁇ 2 clone 47 with IL13R ⁇ 2hFc—competitive assay.
  • FIG. 14 Binding of soluble scFv IL13R ⁇ 2 (clone 47) with IL13R ⁇ 2hFc chimera. These data show that soluble scFvIL13R ⁇ 2 (clone47) generated in a prokaryotic expression system ( E. coli ) binds specifically to IL13R ⁇ 2Fc recombinant protein. Parental antibody, mAb IL13R ⁇ 2 (clone 47), and control mouse IgG served as positive and negative controls, respectively
  • FIG. 15 The effect of mesenchymal stem cells secreting scFvIL13R ⁇ 2-sTRAIL fusion protein on the U87-IL13R ⁇ 2 glioma cell line.
  • the amount of cancer cell killing is equivalent to the use of TRAIL alone without the scFV, but it is expected that the scFV-TRAIL would be less harmful to non-cancer tissues, given the specificity conferred by the scFv targeting IL13R ⁇ 2.
  • FIG. 16 Schematic maps of retroviral vector encoding IL13R ⁇ 2-specific scFv CARs.
  • the CAR consists of the immunoglobulin heavy-chain leader peptide, the IL13R ⁇ 2-specific scFv clone 47 (M47), a short hinge (SH) or long hinge (LH), a transmembrane domain (TM) derived from CD28, and a CD28. ⁇ endodomain.
  • LTR long terminal repeat (retroviral backbone). Domains are identified as block structures. Maps are not to scale.
  • FIG. 17 IL13R ⁇ 2-scFv CAR T cell agent: Expression of ⁇ CD3. ⁇ relative to ⁇ GAPDH of CAR agent in T cells.
  • SH short hinge.
  • LH long hinge.
  • FIG. 18 IL13R ⁇ 2-scFv CARs are expressed on the surface of T cells.
  • IL13R ⁇ 2-CAR T cells were generated by retroviral transduction and CAR expression was determined by FACS analysis. Short hinge CARs were detected with an antibody specific for murine scFV. Long hinge CARs were detected with an antibody specific for the long hinge. Isotype antibody control: open curve; Specific Antibody: filled curve.
  • FIG. 19 Functional characterization of IL13R ⁇ 2-CAR T cells—Cytotoxicity.
  • Standard 51 Chromium cytotoxicity assays were performed with Raji (IL13R ⁇ 1-/IL13R ⁇ 2-), 293T (IL13R ⁇ 1+/IL13R ⁇ 2 ⁇ ), 293T genetically modified to express IL13R ⁇ 2 cells (293T-IL13R ⁇ 2; IL13R ⁇ 1+/IL13R ⁇ 2+), or U373 (IL13R ⁇ 1+/IL13R ⁇ 2+) cells as targets.
  • T cells expressing nonfunctional CARs had not cytolytic activity, demonstrating that the killing activity depends on the expression of a functional IL13R ⁇ 2-CAR.
  • NT T cells killed none of the targets, further confirming specificity.
  • FIG. 20 Functional characterization of IL13R ⁇ 2-CAR T cells—IFN ⁇ and IL2 Cytokine secretions.
  • IL13R ⁇ 2-CAR.SH.CD28. ⁇ T cells and IL13R ⁇ 2-CAR.LH.CD28. ⁇ T cells secreted IFN ⁇ demonstrating target cell recognition in contrast to IL13R ⁇ 2-CAR.SH. ⁇ T cells, IL13R ⁇ 2-CAR.LH. ⁇ T cells or NT T cells.
  • IL13R ⁇ 2-CAR.SH.CD28. ⁇ T cells secreted IL2, demonstrating that IL13R ⁇ 2-CAR.SH.CD28. ⁇ induces superior T cell activation in comparison to IL13R ⁇ 2-CAR.LH.CD28. ⁇ .
  • IL13R ⁇ 2-CAR.SH. ⁇ T cells, IL13R ⁇ 2-CAR.LH. ⁇ T cells or NT T cells also did not induce IL2 production.
  • FIG. 21 IL13R ⁇ 2-SH CARs have anti-glioma activity in vivo.
  • Severe combined immunodeficient (SCID) mice were injected with 1 ⁇ 10 5 firefly luciferase expressing U373 cells intracranially.
  • mice were treated either with 1 ⁇ 10 6 IL13R ⁇ 2-CAR.SH.CD28. ⁇ T cells, IL13R ⁇ 2-CAR.LH.CD28. ⁇ T cells, IL13R ⁇ 2-CAR.SH. ⁇ T cells, or IL13R ⁇ 2-CAR.LH. ⁇ T cells (5 mice per group). Tumor growth was monitored by bioluminescence imaging. Only IL13R ⁇ 2-CAR.SH.CD28. ⁇ T cells had significant anti-glioma effects with 4/5 mice having a complete response.
  • FIG. 22 Properties of m47 CAR T cell agent.
  • the m47-CAR T cells recognize IL13R ⁇ 2 + , but not IL13R ⁇ 1 + targets.
  • the data show that the short hinge CD28z-CAR (SH2) T cells perform better in terms of effector function than CD28z-CAR (SH3), CD28z-CAR (LH2), CD28z-CAR (LH3), CD28z-CAR (SH2 ⁇ ), or CD28z-CAR (SH3 ⁇ ).
  • FIG. 23 Functional comparison of m47 CAR T cell agents. Open curve: secondary antibody; Filled curve: IL13R ⁇ 2Fc+secondary antibody.
  • FIG. 24 The m47 CAR T cell agent is highly expressed after transduction. Open curve: secondary antibody; Filled curve: IL13R ⁇ 2Fc+secondary antibody.
  • FIG. 25 The m47 CAR T cell produce interferon ⁇ and interleukin 2, but only after IL13R ⁇ 2 stimulation.
  • FIG. 26 IL13R ⁇ 2- and IL13R ⁇ 1-positive cell lines are made by genetic modification of HEK 293T cells. Filled curve: isotype antibody control; Open curve: specific antibody.
  • FIG. 27 The m47 CAR T cells kill only IL13R ⁇ 2 + cell lines.
  • the in vitro experiments provide data establishing that m47 CAR T cells present a recombinant CAR protein on the cell surface that does not recognize IL4R, IL13R ⁇ 1 or any receptor other than its specific recognition of IL13R ⁇ 2.
  • the specificity of the recognition extends to a specificity for only those cell lines expressing IL13R ⁇ 2.
  • FIG. 28 In vivo data comparing effect of m47 CAR T cell agent, untreated and NT-treated glioblastoma multiforme xenografts in nude mice.
  • FIG. 29 The m47 CAR T cell agent prolonged the survival of nude mice with glioblastoma multiforme.
  • FIG. 30 Characterization of IL13R ⁇ 2-CAR T cells.
  • A, B Co-culture assay with recombinant protein demonstrated interferon ⁇ and interleukin 2 production in an IL14R ⁇ 2-dependent fashion;
  • C Cytolytic activity in standard chromium release assay.
  • FIG. 31 Generation of 47 CAR T cells.
  • A Scheme of M47 CARs. All CARs contained an N-terminal leader sequence, a codon-optimized synthetic gene encoding M47 in scFv format, a spacer region, a CD28 transmembrane domain, and signaling domains derived from CD28 and CD3- ⁇ .
  • the spacer region was either the IgG1 hinge (16 amino acids; short spacer region; M47-CAR.SSR.CD28. ⁇ ) or the IgG1-CH2CH3 domain.
  • LSR. ⁇ and SSR. ⁇ M47-CARs without signaling domains were constructed and served as controls.
  • C,B CAR expression was confirmed using FACS analysis.
  • FIG. 32 Phenotypic analysis of 47-CAR T cell lines.
  • CAR T cells were analyzed for CD4 and CD8 surface expression using CD4-PacBlue and CD8-PerCP antibodies (BD Biosciences).
  • the four CAR T cell lines analyzed for surface expression of CD4 and CD8 were SSR. ⁇ , SSR.CD28. ⁇ , LSR. ⁇ , and LSR.CD28. ⁇ .
  • the histogram provides the results of the analysis, with light gray bars indicating CD4 expression and black bars indicating CD8 expression.
  • FIG. 33 47-CAR T cells release cytokines after stimulation with recombinant IL13R ⁇ 2 protein or IL13R ⁇ 2-positive cells.
  • 47-CAR or non-transduced (NT) T cells were stimulated with recombinant IL13R ⁇ 1, IL13R ⁇ 2, or IL4R ⁇ proteins.
  • C U373 and 293T-GFP-IL13R ⁇ 2 (IL2); SSR. ⁇ vs SSR.CD28. ⁇ : p ⁇ 0.01; LSR. ⁇ vs LSR.CD28. ⁇ : NS.
  • FIG. 34 LSR.CD28. ⁇ T cells show a self-activation phenotype during ex vivo expansion. T cells were analyzed for phosphor-CD3- ⁇ expression using CD247 (pY142)-AF647 antibody (BD Biosciences).
  • FIG. 35 Cell surface expression of IL13R ⁇ 1 and IL13R ⁇ 2.
  • Cell lines were analyzed for IL13R ⁇ 1 and IL13R ⁇ expression using primary goat anti-IL13R ⁇ 1 and anti-IL13R ⁇ 2 antibodies (AF152 and AF146, respectively; R&D) followed by secondary rabbit anti-goat IgG Alexa647 antibody (Life Technologies). Filled curve: isotype antibody control; Open curve: specific antibody.
  • FIG. 36 Generation of SSR 47-CARs with CD28.OX40. ⁇ , CD28.41BB. ⁇ or 41BB. ⁇ endodomains.
  • A Scheme of SSR 47-CARs.
  • B, C CAR expression was confirmed using FACS analysis. Representative plots (B) and summary data (C) are shown.
  • Open curve secondary antibody; Filled curve: IL13R ⁇ 2Fc+secondary antibody.
  • D Expression of 47-CAR.SSR.41BB. ⁇ , M47-CAR.SSR.OX40.CD28. ⁇ and M47-CAR.SSR.41BB.CD28. ⁇ by Western blot analysis.
  • FIG. 37 Comparison of 47-CAR.SSR.CD28. ⁇ , 47-CAR.SSR.41BB. ⁇ , and 47-CAR.SSR.CD28.OX40. ⁇ T cells.
  • FIG. 38 Treatment of glioma xenograft with T cells expressing 47-CARs results in tumor regression and improved overall survival.
  • A Representative images for each group and
  • FIG. 39 Analysis of U373 cells isolated from recurrent tumors.
  • U373 cells were isolated from recurrent tumors of mice that were treated with 47-CAR T cells. After short-term culture (2 to 7 days), FACS analysis and cytotoxicity assays were performed.
  • A FACS analysis for IL13R ⁇ 2.
  • B 47-CAR T cells killed U373 tumor cells isolated from recurrent tumors in contrast to Raji cells in a standard four-hour cytotoxicity assay for Cr release from labeled cells. Open curve: isotype antibody control; Filled curve: specific antibody.
  • FIG. 40 Limited persistence of 47-CAR T cell in vivo.
  • 47.SSR.CD28. ⁇ -CAR T cells were transduced to express eGFP.ffLuc.
  • A FACS analysis confirmed the expression of the CAR and eGFP.ffLuc transgenes.
  • B C
  • 1 ⁇ 10 5 unmodified U373 cells were injected intracranially into mice.
  • mice received 2 ⁇ 10 6 47.SSR.CD28. ⁇ eGFP.ffLuc CAR T cells intracranially using the same tumor coordinates. Bioluminescence imaging was used to monitor T cell persistence.
  • FIG. 41 Generation and characterization of LSR-CD28.41BB. ⁇ CAR T cells.
  • A Scheme of LSR.CD28.41BB. ⁇ CAR construct.
  • B CAR expression was confirmed using FACS analysis. Representative plot. Open curve: secondary antibody; Filled curve: IL13R ⁇ 2Fc+secondary antibody.
  • FIG. 42 Generation of SSR. ⁇ .CD28.41BB. ⁇ CAR T cells.
  • A Scheme of SSR. ⁇ .CD28.41BB. ⁇ CAR construct.
  • B CAR expression was tested using FACS analysis (representative plot shown).
  • FIG. 43 FACS analysis of PD-L1 expression on U373 cell surface with and without IFN ⁇ stimulation.
  • U373 cells were cultured with or without IFN ⁇ (100 units/ml). After 24 hours, U373 cells were analyzed for PD-L1 expression using a CD271 PE antibody (BD Biosciences).
  • FIG. 44 Transgenic expression of IL15 in SSR.CD28. ⁇ T cells results in enhanced antigen-dependent IL15 secretion.
  • T cells were stimulated with (A) recombinant proteins or (B) cell lines.
  • FIG. 45 Transgenic expression of IL15 results in (A) enhanced in vivo persistence of SSR.CD28. ⁇ T cells resulting in improved (B) progression-free survival (PFS).
  • the disclosure provides binding agents, or partners, that specifically recognize interleukin 13 receptor ⁇ 2 (IL13R ⁇ 2) for use in diagnosing, preventing, treating or ameliorating a symptom of any of a wide range of cancers characterized by cells presenting IL13R ⁇ 2. More particularly, the disclosure provides (i) the sequences of the six complementarity determining regions of a monoclonal antibody (m47) that specifically targets human tumor-associated antigen, i.e., interleukin 13 receptor ⁇ 2 (IL13R ⁇ 2), and (ii) data demonstrating the functionality of the protein encoded by the heavy and light chain cDNAs in the format of an scFv antibody or conjugate (e.g., fusion) to other functional moieties.
  • m47 monoclonal antibody
  • IL13R ⁇ 2 interleukin 13 receptor ⁇ 2
  • the six complementarity determining regions of the m47 monoclonal antibody confer binding specificity for IL13R ⁇ 2, consistent with the understanding in the immunological arts.
  • the scFv comprises the complete heavy and light chain variable regions of antibody m47, or the complete heavy and light chains of antibody m47.
  • the heavy and light chain fragments comprise, e.g., the m47 CDRs, or the m47 variable regions, and these domains can be arranged in different formats, such as a single-chain variable fragment of an antibody, i.e., a scFv, a diabody, a bi-specific antibody fragment, a tri-specific antibody fragment, a fusion protein with any of a wide variety of therapeutic proteins and/or other moieties, a humanized antibody fragment, a Fab fragment, a Fab′ fragment, a F(ab)2′ fragment and any other functional format for a bi-functional peptide providing a targeting function and an effector function.
  • a single-chain variable fragment of an antibody i.e., a scFv, a diabody, a bi-specific antibody fragment, a tri-specific antibody fragment, a fusion protein with any of a wide variety of therapeutic proteins and/or other moieties
  • a humanized antibody fragment a Fab fragment,
  • the single-chain antibody or other arrangements of the protein encoded by the heavy and light chains could be expressed and conjugated to therapeutic carriers (e.g., viruses, cells, nanomaterials) for specific delivery of a therapeutic to an IL13R ⁇ 2-expressing tumor.
  • therapeutic carriers e.g., viruses, cells, nanomaterials
  • the materials according to the disclosure are also useful in imaging tumor burden.
  • the technology addresses the most serious obstacle to progress in immunotherapy, i.e., the virtual absence of defined, tumor-specific antigens that can be predictably found on at least a larger subgroup of human cancers and that can serve as effective targets for cancer eradication. Finding such antigens would move the field beyond the methods for treating CD19/CD20-expressing B cell malignancies.
  • the disclosure describes the development and characterization of a monoclonal antibody (mAb) fragment specific to IL13R ⁇ 2 for the therapeutic purpose of targeting IL13R ⁇ 2-expressing tumors.
  • mAb monoclonal antibody
  • the high affinity IL13R ⁇ 2 is selectively expressed at a high frequency by glioblastoma multiforme (GBM) as well as several other tumor types.
  • GBM glioblastoma multiforme
  • One approach for targeting this tumor-specific receptor utilizes the cognate ligand, IL-13, conjugated to cytotoxic molecules. This approach, however, lacks specificity because the lower affinity receptor for IL-13, IL13R ⁇ 1, is widely expressed by normal tissues.
  • a monoclonal antibody (mAb) specific to IL13R ⁇ 2 was expected to overcome the lack of specificity afflicting methodologies that recognized both IL13 receptors, i.e., IL13R ⁇ 1 as well as IL13R ⁇ 2. Such a mAb would be therapeutically useful in targeting and treating IL13R ⁇ 2-expressing cancers, including tumors.
  • hybridoma cell lines were generated and compared for binding affinities to recombinant human IL13R ⁇ 2 (rhIL13R ⁇ 2).
  • Clone 47 demonstrated binding to the native conformation of IL13R ⁇ 2 and was therefore chosen for further studies.
  • clone 47 specifically recognized wild-type IL13R ⁇ 2 expressed on the surface of CHO and HEK cells as well as several glioma cell lines.
  • clone 47 also significantly inhibited the interaction between human soluble IL-13 and IL13R ⁇ 2 receptor. Moreover, N-linked glycosylation of IL13R ⁇ 2 contributes in part to the interaction of the antibody to IL13R ⁇ 2. In vivo, the IL13R ⁇ 2 mAb improved the survival of nude mice intracranially implanted with a human U251 glioma xenograft.
  • the IL13R ⁇ 2-specific, scFv-based CAR, 47-CAR, constructed as disclosed herein, provided the material used in exploring the influence of long and short spacer regions, as well as endodomains, on its function.
  • 47-CAR.SSR.CD28. ⁇ i.e., the 47-CAR binding region provided as an scFv joined to a short spacer region as defined herein, in turn joined to an unmodified or chimeric endodomain or T cell cytoplasmic domain
  • 47-CAR.LSR.CD28. ⁇ similar construct substituting a long spacer region (LSR)) recognized target cells as judged by IFN ⁇ production, only 47-CAR.SSR.CD28. ⁇ induced IL2 production, indicating better T-cell activation.
  • mice treated with 47-CAR.SSR.CD28. ⁇ T cells had the longest median survival in comparison to 47-CAR.SSR.41BB. ⁇ or 47-CAR.SSR.CD28.OX40. ⁇ T-cell treated mice, this difference did not reach significance.
  • the experimental results also showed that addition of a second costimulatory endodomain did not improve antitumor activity in vivo. Limited T-cell persistence in vivo was identified as the principal limitation on therapy.
  • gliomas such as U373 express PD-L1, which is upregulated in the presence of IFN ⁇ ( FIG. 43 ), and could be targeted in future studies.
  • the disclosure is based, at least in part, on the discovery that IL13R ⁇ 2 is found preferentially on cancer cells such as tumor cells.
  • This receptor functions as a cancer-, or tumor-, specific antigen that has been used to elicit the high-affinity monoclonal antibody m47, along with antigen binding fragments of that antibody.
  • the VL and VH variable regions of the m47 antibody have been engineered into a single chain (sc) variable fragment (scFv) to generate conjugates, such as chimeric antigen receptors (i.e., CARs), for introduction into T cells for adoptive transfer.
  • CAR-transduced T cells are expected to target a tumor-specific IL13R ⁇ 2 epitope, leading to eradication of cancer cells presenting the receptor. It is believed that CAR-transduced T cells recognizing IL13R ⁇ 2 will destroy large solid tumors. CAR-transduced T cells, however, target cancer cells only directly and antigen-negative cancer cells may escape. It is expected that CAR-transduced T cells also will be effective in eliminating antigen-negative cancer cells via the bystander effect.
  • 47-CARs IL13R ⁇ 2-specific CARs with a scFv47-based antigen-binding domain
  • the data show that 47-CARs perform better with a short spacer region, which provides for optimal functionality, and that 47-CAR T cells are able to recognize and kill only IL13R ⁇ 2-positive and not IL13R ⁇ 1-positive target cells in vitro.
  • 47-CAR T cells induce tumor regression in an orthotopic xenograft mouse model of GBM, which was associated with a significant survival advantage.
  • the protein conjugates according to the disclosure are specific for IL13R ⁇ 2, which is associated with cancers, e.g., tumors.
  • the disclosure provides a polynucleotide encoding one of these cancer-specific binding partners, including polynucleotides comprising codon-optimized coding regions for binding partners specific for an epitope of IL13R ⁇ 2.
  • the polynucleotides of the disclosure encode conjugates, or bi-functional polypeptides, useful in diagnosing, preventing, treating, or ameliorating a symptom of cancer, such as any of a variety of human cancers, including those forming solid tumors.
  • vectors comprising a polynucleotide as disclosed herein, a host cell comprising such a polynucleotide and/or a vector as described above, and methods of treating, preventing or ameliorating a symptom of, a cancer disease, e.g., a solid tumor, a primary cancer site or a metastasized cancer.
  • a cancer disease e.g., a solid tumor, a primary cancer site or a metastasized cancer.
  • conjugates provide appropriately cancer—as well as protein-specific antibody receptors that can be incorporated into a variety of backbones providing effector function, such as bispecific T cell Engagers (BiTEs) or chimeric antigen receptors (CARs), as noted below.
  • BiTEs bispecific T cell Engagers
  • CARs chimeric antigen receptors
  • Exemplary conjugates of the disclosure include CARs, fusion proteins, including fusions comprising single-chain variable (antibody) fragment (scFv) multimers or scFv fusions to coding regions encoding products useful in treating cancer, e.g., IL15, IL15R ⁇ , or IL15/IL15R ⁇ agent, diabodies, tribodies, tetrabodies, and bispecific bivalent scFvs, including bispecific tandem bivalent scFvs, also known as bispecific T cell engagers, or BiTEs.
  • CARs CARs
  • fusion proteins including fusions comprising single-chain variable (antibody) fragment (scFv) multimers or scFv fusions to coding regions encoding products useful in treating cancer, e.g., IL15, IL15R ⁇ , or IL15/IL15R ⁇ agent, diabodies, tribodies, tetrabodies, and bispecific bivalent scFv
  • any of these conjugate forms may exhibit any of various relative structures, as it is known in the art that different domain orders (e.g., H 2 N-VH-linker-VL-CO 2 H and H 2 N-VL-linker-VH-CO 2 H) are compatible with specific binding.
  • Higher order forms of the conjugates described herein are also contemplated, such as peptibodies comprising at least one form of the conjugates disclosed herein.
  • the conjugates of the disclosure specifically bind to a cancer-specific epitope (e.g., an IL13R ⁇ 2) and the polynucleotides encoding them may be codon-optimized, e.g., for maximal translation, for expression in the targeted cells (e.g., human or mouse cells). Codon optimization in the context of expressing the conjugates of the disclosure, such as CARs, is important to ensuring that production of the protein is both efficient and robust enough to be useful as a source of therapeutic.
  • a cancer-specific epitope e.g., an IL13R ⁇ 2
  • the polynucleotides encoding them may be codon-optimized, e.g., for maximal translation, for expression in the targeted cells (e.g., human or mouse cells). Codon optimization in the context of expressing the conjugates of the disclosure, such as CARs, is important to ensuring that production of the protein is both efficient and robust enough to be useful as a source of therapeutic.
  • the disclosure also contemplates conjugates in which a targeting moiety (an anti-IL13R ⁇ 2 antibody or fragment thereof) is linked to a peptide providing a second function, e.g., an effector function, such as a T cell signaling domain involved in T cell activation, a peptide that affects or modulates an immunological response to cancer cells, or an enzymatic component of a labeling system that results in a CAR encoded by a polynucleotide according to the disclosure, if the coding region for the conjugate is codon-optimized for expression in a target cell.
  • a targeting moiety an anti-IL13R ⁇ 2 antibody or fragment thereof
  • a peptide providing a second function e.g., an effector function, such as a T cell signaling domain involved in T cell activation, a peptide that affects or modulates an immunological response to cancer cells, or an enzymatic component of a labeling system that results in a CAR encoded by a poly
  • Exemplary conjugates include an anti-IL13R ⁇ 2 scFv linked to a hinge, a transmembrane domain, and an effector compound or domain, e.g., CD28, CD3 ⁇ , CD134 (OX40), CD137 (41BB), ICOS, CD40, CD27, or Myd88, thereby yielding a CAR.
  • an effector compound or domain e.g., CD28, CD3 ⁇ , CD134 (OX40), CD137 (41BB), ICOS, CD40, CD27, or Myd88, thereby yielding a CAR.
  • the polynucleotide aspect of the disclosure comprises embodiments in which an unexpected variation on codon optimization in slower-growing higher eukaryotes such as vertebrates, e.g., humans, is provided that is focused on translation optimization (maximizing high-fidelity translation rates) rather than the typical codon optimization used in such organisms, which is designed to accommodate mutational bias and thereby minimize mutation. Also disclosed are the methods of diagnosing, preventing, treating or ameliorating a symptom of a cancer.
  • the polynucleotides comprise a codon-optimized coding region for an antigen receptor specifically recognizing an IL13R ⁇ 2 epitope linked to any one of the following: a coding region for a T cell signaling domain involved in T cell activation, a gene product that affects or modulates an immunological response to cancer cells such as an IL15/IL15R ⁇ fusion, or a labeling component such as an enzymatic component of a labeling system.
  • the linked coding regions result in polynucleotides encoding conjugates according to the disclosure, such as BiTEs or chimeric antigen receptors (CARs).
  • compositions of the disclosure are typically administered in the form of a conjugate-transduced cell, such as a T cell, an NK cell, or a lymphocyte including, but not limited to, NKT cells, ⁇ T cells, mucosa associated invariant T cells or MAIT cells, or innate lymphoid cells, although administration of a vector comprising a polynucleotide of the disclosure or administration of a polynucleotide of the disclosure are also contemplated, depending on the functionalities of the conjugate.
  • a conjugate-transduced cell such as a T cell, an NK cell, or a lymphocyte including, but not limited to, NKT cells, ⁇ T cells, mucosa associated invariant T cells or MAIT cells, or innate lymphoid cells
  • a pharmaceutical composition according to the disclosure, and these pharmaceutical compositions are suitable for administration to diagnose, prevent, treat, or ameliorate a symptom of, a cancer.
  • hybridoma cell lines were generated and compared for binding affinities to recombinant human IL13R ⁇ 2 (rhIL13R ⁇ 2).
  • Clone 47 demonstrated binding to the native conformation of IL13R ⁇ 2 and was therefore characterized further.
  • Clone 47 bound specifically and with high affinity (KD 1.39 ⁇ 10 ⁇ 9 M) to rhIL13R ⁇ 2 but not to rhIL13R ⁇ 1 or murine IL13R ⁇ 2.
  • clone 47 specifically recognized wild-type IL13R ⁇ 2 expressed on the surface of CHO and HEK cells as well as several glioma cell lines.
  • GBM glioblastoma multiforme
  • a phage display library approach has been used to select small antibody fragments specific to human IL13R ⁇ 2, followed by their evaluation in vitro and in vivo (23).
  • IL13R ⁇ 2 conjugation with toxins has failed to increase cytotoxicity in IL13R ⁇ 2-expressing glioma and renal cell carcinoma cell lines when compared with the effects of IL-13PE38.
  • the low affinity of generated antibody fragments is the most reasonable explanation for the lack of success.
  • Antibody fragments derived from phage display libraries are known to be lower in affinity and avidity than antibodies generated by conventional hybridoma technology (24). Modifications of those small antibody fragments are often required to enhance their affinity and avidity to targeted proteins.
  • Monoclonal antibodies appear to be valuable research and diagnostic tools as well as therapeutic agents. Monoclonal antibodies specific for tumor-associated antigens have significant advantages over systemic chemotherapies due to the ability to specifically target cancer cells while avoiding interaction with untransformed tissue. Therefore, the search for novel “magic bullets” continues to grow, confirmed by a global market for therapeutic antibodies worth $48 billion as of 2010. Therapeutic antibodies are products of traditional hybridoma technology or screening of libraries for antibody fragments and their subsequent engineering into humanized fragments or full size molecules. Prior to this study, the hybridoma cell line secreting a high affinity antibody to the tumor-specific antigen IL13R ⁇ 2 was unavailable to the scientific community. Here, we describe the generation and characterization of a high affinity antibody to the tumor-specific antigen IL13R ⁇ 2 and discuss its potential use in different applications.
  • the specificity of interaction of newly discovered antibodies to human IL13R ⁇ 2 was analyzed by ELISA using the rhIL13R ⁇ 2hFc fusion protein, recombinant human IL13R ⁇ 2 expressed on the surface of CHO and HEK cells, and several glioma cell lines expressing IL13R ⁇ 2 at various levels by flow cytometry.
  • IL13R ⁇ 2 (clone 47) mAb competed with recombinant human IL-13 for its epitope and was able to block about 80% of the binding between IL-13 and IL13R ⁇ 2. Conversely, human recombinant IL-13 was able to block about 50% of antibody binding to IL13R ⁇ 2.
  • IL-13 is a small 10-kDa molecule (31), whereas an antibody is about 15 times greater in molecular mass.
  • the ability of rhIL-13 to compete with an antibody for a binding site suggests that the inhibitory property of the antibody is likely due to the specific interaction with amino acid residues contributing to the binding of IL-13 to the cognate receptor rather than to steric hindrance, which can also prevent the interaction of IL-13 with its receptor.
  • Tyr207, Asp271, Tyr315, and Asp318 were identified as critical residues of IL13R ⁇ 2 necessary for interaction with IL-13 (28).
  • the affinity of the IL13R ⁇ 2 mAb was measured and compared with the binding properties of two commercially available antibodies using the surface plasmon resonance method.
  • the affinity of the IL13R ⁇ 2 mAb was determined to be equal to 1.39 ⁇ 10 ⁇ 9 M, greatly exceeding the affinity of comparable commercially available antibodies by up to 75-fold.
  • the IL13R ⁇ 2 mAb (clone 47) demonstrated superiority to two commercial antibodies in binding to the IL13R ⁇ 2 expressed on the surface of various glioma cells and in ELISA.
  • the N-linked glycosylation of IL13R ⁇ 2 has been identified as a necessary requirement for efficient binding to IL-13 (30). Taking into consideration that the IL13R ⁇ 2 mAb disclosed herein inhibits about 80% of IL-13 binding to the cognate receptor, IL13R ⁇ 2, it is reasonable to expect that the binding of this antibody, or an agent containing its binding domain, with the deglycosylated form of IL13R ⁇ 2 could also be affected.
  • the IL13R ⁇ 2 molecule has four potential sites of N-linked glycosylation.
  • the binding of the antibody to rhIL13R ⁇ 2 or to IL13R ⁇ 2 expressed on the surface of HEK or U251 cells treated with Pngase F was decreased by 35 and 30%, respectively, when compared with non-treated control.
  • a partial change in binding activity for the clone 47 when compared with clones 83807 and B-D13 suggests that removal of carbohydrate adducts from IL13R ⁇ 2 with Pngase F causes conformational changes of the receptor, indirectly affecting the binding of both IL-13 (30) and the IL13R ⁇ 2 mAb to IL13R ⁇ 2.
  • IL13R ⁇ 2 mAb To investigate the therapeutic properties of the IL13R ⁇ 2 mAb and its agent, an in vivo study was performed whereby glioma cells and the IL13R ⁇ 2 (clone 47) mAb were intracranially co-injected into brain, or antibody was injected into established tumor-bearing mice. Interestingly, the IL13R ⁇ 2 mAb was able to delay tumor progression and improve survival of animals with intracranial U251 glioma xenografts most significantly in the co-injected model, demonstrating a trend in the improvement of median survival in animals with established glioma.
  • Cancers amenable to the described treatments include cancers in which IL13R ⁇ 2 has been found to be expressed, including glioblastoma; medulloblastoma; Kaposi sarcoma; and head and neck, ovarian, pancreatic, kidney, and colorectal cancers (2, 43-47).
  • IL13R ⁇ 2 contributes to the invasive phenotype of ovarian, pancreatic, and colorectal cancers (5, 13).
  • Minn et al. (42) have suggested a relationship between IL13R ⁇ 2 expression and breast cancer metastasis to the lung.
  • Fichtner-Feigl et al. (11) demonstrated that the interaction of IL-13 with IL13R ⁇ 2 upregulates TGF- ⁇ 1, mediating fibrosis in a bleomycin-induced model of lung fibrosis.
  • the anti-IL13R ⁇ 2 antibody (clone 47) and binding agents thereof will be able to attenuate TGF- ⁇ 1-induced pulmonary fibrosis.
  • the described experiments led to the generation of an anti-IL13R ⁇ 2 antibody and binding agents thereof, all of which are specific to human IL13R ⁇ 2.
  • the antibody and its agent possess a high affinity for IL13R ⁇ 2 and compete with IL-13 for the binding site on IL13R ⁇ 2.
  • the antibody recognizes antigen expressed on the cell surface of glioma cells as well as other IL13R ⁇ 2-expressing cells, establishing the suitability for targeting IL13R ⁇ 2-expressing tumor cells in vivo.
  • the anti-IL13R ⁇ 2 antibody and binding agents thereof are also expected to be efficacious and cost effective in diagnostic imaging, delivery of antibody radionuclide conjugates, bioassays for the detection of IL13R ⁇ 2, and as a carrier for therapeutic agents in various types of IL13R ⁇ 2-overexpressing tumors.
  • compositions of the disclosure are typically administered in the form of conjugate-transduced T cells, although administration of a vector comprising a polynucleotide of the disclosure or administration of a polynucleotide of the disclosure are also contemplated, depending on the functionalities of the conjugate.
  • a polynucleotide, vector or host cell of the disclosure with a physiologically suitable buffer, adjuvant or diluent yields a pharmaceutical composition according to the disclosure, and these pharmaceutical compositions are suitable for administration to diagnose, prevent, treat, or ameliorate a symptom of, a cancer.
  • a conjugate according to the disclosure such as a fusion protein composed of an scFv-receptor for an IL13R ⁇ 2 epitope fused to IL15/IL15R ⁇ , is also contemplated. It is expected that the fusion protein will eliminate clinical size tumors or only incipient and microdisseminated cancer cells.
  • the disclosure further contemplates the simultaneous targeting of two independent IL13R ⁇ 2 epitopes on a human cancer, which may be essential for preventing escape from treatment, such as CAR treatment.
  • the disclosure provides materials and methods that are adaptable and can serve as the basis for a platform technology with considerable growth potential.
  • the cancer-specific nature of IL13R ⁇ 2 is expected to provide targets for cancer diagnostics, prophylactics and therapeutics that offer major advantages over previously and presently used targets.
  • IL13R ⁇ 2 binding agents comprising each of the amino acid sequences of NYLMN (SEQ ID NO: 1); RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); GYGTAYGVDY (SEQ ID NO: 3); RASESVDNYGISFMN (SEQ ID NO: 4); AASRQGSG (SEQ ID NO: 5); and QQSKEVPWT (SEQ ID NO: 6).
  • the binding agent comprises each of the foregoing six amino acid sequences in addition to further sequences which provide a framework to support a three-dimensional conformation that binds to IL13R ⁇ 2.
  • the IL13R ⁇ 2 binding agent comprises one or both of the amino acid sequences of SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the IL13R ⁇ 2 binding agent comprises the amino acid sequence of SEQ ID NO: 7.
  • the IL13R ⁇ 2 binding agent comprises the amino acid sequence of SEQ ID NO: 8.
  • the IL13R ⁇ 2 binding agent comprises both the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8.
  • the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • linker comprises a short amino acid sequence of about 5 to about 25 amino acids, e.g., about 10 to about 20 amino acids.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the linker comprises the amino acid sequence of AKTTPPKLEEGEFSEARV (SEQ ID NO: 80).
  • IL13R ⁇ 2 binding agent comprises the amino acid sequence of SEQ ID NO: 13.
  • the binding agent provided herein further comprises additional amino acid sequences.
  • the binding agent further comprises a constant region of a heavy chain and/or a constant region of a light chain. Sequences for heavy and light chain constant regions are publically available. For example, the National Center of Biotechnology Information (NCBI) nucleotide database provides a sequence of the constant region of the IgG1 kappa light chain. See GenBank Accession No. DQ381549.1, incorporated herein by reference.
  • the binding agent comprises an amino acid sequence of SEQ ID NO: 28.
  • the binding agent comprises a modified amino acid sequence of SEQ ID NO: 28.
  • the binding agent comprises an amino acid sequence which is at least 90%, at least 93%, at least 95%, or at least 98% identical to SEQ ID NO: 28.
  • the NCBI nucleotide database provides a sequence of the constant region of the Mus musculus IgG1. See GenBank Accession No. DQ381544.1.
  • the binding agent comprises an amino acid sequence of SEQ ID NO: 29.
  • the binding agent comprises a modified amino acid sequence of SEQ ID NO: 29.
  • the binding agent comprises an amino acid sequence which is at least 90%, at least 93%, at least 95%, or at least 98% identical to SEQ ID NO: 29.
  • the IL13R ⁇ 2 binding agent is an antibody, or an antigen-binding fragment thereof.
  • the antibody comprises each of the amino acid sequences of SEQ ID NOs: 1-6.
  • the antibody comprises the amino acid sequence of SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the antibody comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8.
  • the antibody comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8 and the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • the linker comprises a short amino acid sequence of about 5 to about 25 amino acids, e.g., about 10 to about 20 amino acids.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the linker comprises the amino acid sequence of AKTTPPKLEEGEFSEARV (SEQ ID NO: 80).
  • the antibody comprises the amino acid sequence of SEQ ID NO: 13.
  • the antibody can be any type of immunoglobulin that is known in the art.
  • the antibody can be of any isotype, e.g., IgA, IgD, IgE, IgG, or IgM.
  • the antibody can be monoclonal or polyclonal.
  • the antibody can be a naturally-occurring antibody, i.e., an antibody isolated and/or purified from a mammal, e.g., mouse, rabbit, goat, horse, chicken, hamster, human, and the like.
  • the antibody may be considered to be a mammalian antibody, e.g., a mouse antibody, rabbit antibody, goat antibody, horse antibody, chicken antibody, hamster antibody, human antibody, and the like.
  • isolated means having been removed from its natural environment.
  • purified as used herein relates to the isolation of a molecule or compound in a form that is substantially free of contaminants normally associated with the molecule or compound in a native or natural environment and means having been increased in purity as a result of being separated from other components of the original composition. It is recognized that “purity” is a relative term, and not to be necessarily construed as absolute purity or absolute enrichment or absolute selection.
  • the purity is at least or about 50%, is at least or about 60%, at least or about 70%, at least or about 80%, or at least or about 90% (e.g., at least or about 91%, at least or about 92%, at least or about 93%, at least or about 94%, at least or about 95%, at least or about 96%, at least or about 97%, at least or about 98%, at least or about 99% or is approximately 100%.
  • the antibody comprises a constant region of an IgG. In exemplary aspects, the antibody comprises a constant region of an IgG 1 . In exemplary aspects, the antibody comprises a constant region of an IgG kappa light chain. For instance, the antibody may comprise the amino acid sequence of SEQ ID NO: 28. In exemplary aspects, the antibody comprises an amino acid sequence that is highly similar to SEQ ID NO: 28.
  • the antibody may comprise an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 28, or an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 28, or an amino acid sequence having at least 93% sequence identity to SEQ ID NO: 28, or an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 28, or an amino acid sequence having at least 98% sequence identity to SEQ ID NO: 28.
  • the antibody comprises a constant region of a Mus musculus IgG 1 .
  • the antibody may comprise the amino acid sequence of SEQ ID NO: 30.
  • the antibody comprises an amino acid sequence which is highly similar to SEQ ID NO: 30.
  • the antibody may comprise an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 30, or an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 30, or an amino acid sequence having at least 93% sequence identity to SEQ ID NO: 30, or an amino acid sequence having at least 95% sequence identity to SEQ ID NO: 30, or an amino acid sequence having at least 98% sequence identity to SEQ ID NO: 30.
  • the anti-IL13R ⁇ 2 antibodies and fragments thereof of the disclosure can have any level of affinity or avidity for IL13R ⁇ 2.
  • the dissociation constant (IQ may be any of those exemplary dissociation constants described herein with regard to binding units. Binding constants, including dissociation constants, are determined by methods known in the art, including, for example, methods that utilize the principles of surface plasmon resonance, e.g., methods utilizing a BiacoreTM system. In accordance with the foregoing, in some embodiments, the antibody is in monomeric form, while in other embodiments, the antibody is in polymeric form.
  • the antibody comprises two or more distinct antigen binding regions or fragments
  • the antibody is considered bispecific, trispecific, or multi-specific, or bivalent, trivalent, or multivalent, depending on the number of distinct epitopes that are recognized and bound by the binding agent.
  • the antibody in exemplary aspects is considered to be a blocking antibody or neutralizing antibody.
  • the K D of the binding agent is about the same as the K D of the native ligand, IL13, for IL13R ⁇ 2.
  • the K D of the binding agent is lower (e.g., at least 0.5-fold lower, at least 1-fold lower, at least 2-fold lower, at least 5-fold lower, at least 10-fold lower, at least 25-fold lower, at least 50-fold lower, at least 75-fold lower, at least 100-fold lower) than the K D of IL13 for IL13R ⁇ 2.
  • the K D is between about 0.0001 nM and about 100 nM. In some embodiments, the K D is at least or about 0.0001 nM, at least or about 0.001 nM, at least or about 0.01 nM, at least or about 0.1 nM, at least or about 1 nM, or at least or about 10 nM. In some embodiments, the K D is no more than or about 100 nM, no more than or about 75 nM, no more than or about 50 nM, or no more than or about 25 nM. In exemplary aspects, the antibody has a K D for human IL13R ⁇ 2 that is no greater than about 1.39 ⁇ 10 ⁇ 9 M.
  • the binding agent e.g., antibody, or antigen binding fragment thereof, does not bind to human IL13R ⁇ 1.
  • the antibody is a genetically engineered antibody, e.g., a single chain antibody, a humanized antibody, a chimeric antibody, a CDR-grafted antibody, an antibody that includes portions of CDR sequences specific for IL13R ⁇ 2 (e.g., an antibody that includes CDR sequences of SEQ ID NOs: 1-6), a humaneered or humanized antibody, a bispecific antibody, a trispecific antibody, and the like, as defined in greater detail herein. Genetic engineering techniques also provide the ability to make fully human antibodies in a non-human.
  • the antibody is a chimeric antibody.
  • chimeric antibody is used herein to refer to an antibody containing constant domains from one species and the variable domains from a second, or more generally, containing stretches of amino acid sequence from at least two species.
  • the antibody is a humanized antibody.
  • humanized when used in relation to antibodies is used to refer to antibodies having at least CDR regions from a nonhuman source that are engineered to have a structure and immunological function more similar to true human antibodies than the original source antibodies.
  • humanizing can involve grafting CDR from a non-human antibody, such as a mouse antibody, into a human antibody.
  • Humanizing also can involve select amino acid substitutions to make a non-human sequence look more like a human sequence, as would be known in the art.
  • chimeric or humanized is not meant to be mutually exclusive; rather, is meant to encompass chimeric antibodies, humanized antibodies, and chimeric antibodies that have been further humanized. Except where context otherwise indicates, statements about (properties of, uses of, testing, and so on) chimeric antibodies apply to humanized antibodies, and statements about humanized antibodies pertain also to chimeric antibodies. Likewise, except where context dictates, such statements also should be understood to be applicable to antibodies and antigen binding fragments of such antibodies.
  • the binding agent is an antigen binding fragment of an antibody that specifically binds to an IL13R ⁇ 2 in accordance with the disclosure.
  • the antigen binding fragment (also referred to herein as “antigen binding portion”) may be an antigen binding fragment of any of the antibodies described herein.
  • the antigen binding fragment can be any part of an antibody that has at least one antigen binding site, including, but not limited to, Fab, F(ab′) 2 , dsFv, sFv, scFv, diabodies, triabodies, bis-scFvs, fragments expressed by a Fab expression library, domain antibodies, VhH domains, V-NAR domains, VH domains, VL domains, and the like.
  • Antibody fragments of the invention are not limited to these exemplary types of antibody fragments.
  • the IL13R ⁇ 2 binding agent is an antigen binding fragment.
  • the antigen binding fragment comprises each of the amino acid sequences of SEQ ID NOs: 1-6.
  • the antigen binding fragment comprises the amino acid sequence of SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the antigen binding fragment comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8.
  • the antigen binding fragment comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8 and the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • the linker comprises a short amino acid sequence of about 5 to about 25 amino acids, e.g., about 10 to about 20 amino acids.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the linker comprises the amino acid sequence of AKTTPPKLEEGEFSEARV (SEQ ID NO: 80).
  • the antigen binding fragment provided herein comprises the amino acid sequence of SEQ ID NO: 13.
  • the antigen binding fragment comprises a leader sequence.
  • the leader sequence in some aspects, is located N-terminal to the heavy chain variable region.
  • the antigen binding fragment comprises an Ig kappa leader sequence.
  • Suitable leader sequences are known in the art, and include, for example, an Ig kappa leader sequence of METDTLLLWVLLLWVPGSTGD (SEQ ID NO: 9).
  • an antigen binding fragment comprises one more tag sequences.
  • Tag sequences may assist in the production and characterization of the manufactured antigen binding fragment.
  • the antigen binding fragment comprises one or more tag sequences C-terminal to the light chain variable region. Suitable tag sequences are known in the art and include, but are not limited to, Myc tags, His tags, and the like.
  • an antigen binding fragment comprises a Myc tag of GGPEQKLISEEDLN (SEQ ID NO: 11).
  • an antigen binding fragment comprises a His tag sequence of HHHHHH (SEQ ID NO: 12).
  • the antigen binding fragment of the disclosures comprises, from the N- to the C-terminus, a leader sequence, a heavy chain variable region, a linker sequence, a light chain variable region, a Myc tag (e.g., SEQ ID NO: 11), and a His tag (e.g., SEQ ID NO: 12).
  • the antigen binding fragment of the disclosure comprises the amino acid sequence of SEQ ID NO: 14.
  • the antigen binding fragment is a domain antibody.
  • a domain antibody comprises a functional binding unit of an antibody, and can correspond to the variable regions of either the heavy (V H ) or light (V L ) chains of antibodies.
  • a domain antibody can have a molecular weight of approximately 13 kDa, or approximately one-tenth the weight of a full antibody. Domain antibodies may be derived from full antibodies, such as those described herein.
  • the antigen binding fragments in some embodiments are monomeric or polymeric, bispecific or trispecific, and bivalent or trivalent.
  • Antibody fragments that contain the antigen binding, or idiotope, of the antibody molecule share a common idiotype and are contemplated by the disclosure.
  • Such antibody fragments may be generated by techniques known in the art and include, but are not limited to, the F(ab′) 2 fragment which may be produced by pepsin digestion of the antibody molecule; the Fab′ fragments which may be generated by reducing the disulfide bridges of the F(ab′) 2 fragment, and the two Fab′ fragments which may be generated by treating the antibody molecule with papain and a reducing agent.
  • the binding agent provided herein is a single-chain variable region fragment (scFv) antibody fragment.
  • An scFv may consist of a truncated Fab fragment comprising the variable (V) domain of an antibody heavy chain linked to a V domain of an antibody light chain via a synthetic peptide, and it can be generated using routine recombinant DNA technology techniques (see, e.g., Janeway et al., Immunobiology, 2 nd Edition, Garland Publishing, New York, (1996)).
  • disulfide-stabilized variable region fragments (dsFv) can be prepared by recombinant DNA technology (see, e.g., Reiter et al., Protein Engineering, 7, 697-704 (1994)).
  • the IL13R ⁇ 2 binding agent provided herein is an scFv.
  • the scFv comprises each of the amino acid sequences of SEQ ID NOs: 1-6.
  • the scFv comprises the amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 8.
  • the scFv comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8.
  • the scFv comprises the amino acid sequences of SEQ ID NO: 7 and SEQ ID NO: 8 and the amino acid sequence of SEQ ID NO: 7 is fused to the amino acid sequence of SEQ ID NO: 8 through a linker.
  • the linker comprises a short amino acid sequence of about 5 to about 25 amino acids, e.g., about 10 to about 20 amino acids.
  • the linker comprises the amino acid sequence of EEGEFSEAR (SEQ ID NO 10).
  • the linker comprises the amino acid sequence of AKTTPPKLEEGEFSEARV (SEQ ID NO: 80).
  • the scFv provided herein comprises the amino acid sequence of SEQ ID NO: 13.
  • Recombinant antibody fragments e.g., scFvs of the disclosure
  • Such diabodies (dimers), triabodies (trimers) or tetrabodies (tetramers) are well known in the art. See e.g., Kortt et al., Biomol Eng. 2001 18:95-108, (2001) and Todorovska et al., J Immunol Methods. 248:47-66, (2001).
  • the binding agent is a bispecific antibody (bscAb).
  • Bispecific antibodies are molecules comprising two single-chain Fv fragments joined via a glycine-serine linker using recombinant methods.
  • the V light-chain (V L ) and V heavy-chain (V H ) domains of two antibodies of interest in exemplary embodiments are isolated using standard PCR methods.
  • the V L and V H cDNAs obtained from each hybridoma are then joined to form a single-chain fragment in a two-step fusion PCR.
  • Bispecific fusion proteins are prepared in a similar manner.
  • Bispecific single-chain antibodies and bispecific fusion proteins are antibody substances included within the scope of the present invention.
  • Exemplary bispecific antibodies are taught in U.S. Patent Application Publication No. 2005-0282233A1 and International Patent Application Publication No. WO 2005/087812, both applications of which are incorporated herein by reference in their entireties.
  • the binding agent is a bispecific T-cell engaging antibody (BiTE) containing two scFvs produced as a single polypeptide chain.
  • the binding agent is a BiTE comprising two scFvs, wherein at least one comprises each of the amino acid sequences of SEQ ID NOs: 1-6 or comprises SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the binding agent is a dual affinity re-targeting antibody (DART).
  • DARTs are produced as separate polypeptides joined by a stabilizing interchain disulphide bond.
  • the binding agent is a DART comprising an scFv comprising each of the amino acid sequences of SEQ ID NOs: 1-6 or comprises SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the binding agent is a tetravalent tandem diabody (TandAbs) in which an antibody fragment is produced as a non-covalent homodimer folder in a head-to-tail arrangement.
  • the binding agent is a TandAbs comprising an scFv comprising each of the amino acid sequences of SEQ ID NOs: 1-6 or comprises SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • TandAbs are known in the art.
  • the BiTE, DART, or TandAbs comprises the CDRs of SEQ ID NOs: 1-6. In exemplary aspects, the BiTE, DART, or TandAbs comprises the amino acid sequence of SEQ ID NOs: 7 and 8. In exemplary aspects, the BiTE, DART, or TandAbs comprises SEQ ID NOs: 13.
  • Suitable methods of making antibodies are known in the art. For instance, standard hybridoma methods are described in, e.g., Harlow and Lane (eds.), Antibodies: A Laboratory Manual, CSH Press (1988), and CA. Janeway et al. (eds.), Immunobiology, 5 th Ed., Garland Publishing, New York, N.Y. (2001)).
  • Monoclonal antibodies for use in the invention may be prepared using any technique that provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique originally described by Koehler and Milstein (Nature 256: 495-497, 1975), the human B-cell hybridoma technique (Kosbor et al., Immunol Today 4:72, 1983; Cote et al., Proc Natl Acad Sci 80: 2026-2030, 1983) and the EBV-hybridoma technique (Cole et al., Monoclonal Antibodies and Cancer Therapy, Alan R Liss Inc, New York N.Y., pp 77-96, (1985).
  • a polyclonal antibody is prepared by immunizing an animal with an immunogen comprising a polypeptide of the present invention and collecting antisera from that immunized animal.
  • an animal used for production of anti-antisera is a non-human animal including rabbits, mice, rats, hamsters, goat, sheep, pigs or horses. Because of the relatively large blood volume of rabbits, a rabbit, in some exemplary aspects, is a preferred choice for production of polyclonal antibodies.
  • IL13R ⁇ 2 antigen is emulsified in Freund's Complete Adjuvant for immunization of rabbits.
  • 50 ⁇ g of epitope are emulsified in Freund's Incomplete Adjuvant for boosts.
  • Polyclonal antisera may be obtained, after allowing time for antibody generation, simply by bleeding the animal and preparing serum samples from the whole blood.
  • a mouse is injected periodically with recombinant IL13R ⁇ 2 against which the antibody is to be raised (e.g., 10-20 ⁇ g IL13R ⁇ 2 emulsified in Freund's Complete Adjuvant).
  • IL13R ⁇ 2 emulsified in Freund's Complete Adjuvant.
  • the mouse is given a final pre-fusion boost of a IL13R ⁇ 2 polypeptide containing the epitope that allows specific recognition of lymphatic endothelial cells in PBS, and four days later the mouse is sacrificed and its spleen removed.
  • the spleen is placed in 10 ml serum-free RPMI 1640, and a single cell suspension is formed by grinding the spleen between the frosted ends of two glass microscope slides submerged in serum-free RPMI 1640, supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin, and 100 ⁇ g/ml streptomycin (RPMI) (Gibco, Canada).
  • RPMI streptomycin
  • the cell suspension is filtered through sterile 70-mesh Nitex cell strainer (Becton Dickinson, Parsippany, N.J.), and is washed twice by centrifuging at 200 g for 5 minutes and resuspending the pellet in 20 ml serum-free RPMI.
  • Splenocytes taken from three naive Balb/c mice are prepared in a similar manner and used as a control.
  • NS-1 myeloma cells kept in log phase in RPMI with 11% fetal bovine serum (FBS) (Hyclone Laboratories, Inc., Logan, Utah) for three days prior to fusion, are centrifuged at 200 g for 5 minutes, and the pellet is washed twice.
  • FBS fetal bovine serum
  • Spleen cells (1 ⁇ 10 8 ) are combined with 2.0 ⁇ 10 7 NS-1 cells and centrifuged, and the supernatant is aspirated.
  • the cell pellet is dislodged by tapping the tube, and 1 ml of 37° C.
  • PEG 1500 (50% in 75 mM Hepes, pH 8.0) (Boehringer Mannheim) is added with stirring over the course of 1 minute, followed by the addition of 7 ml of serum-free RPMI over 7 minutes. An additional 8 ml RPMI is added and the cells are centrifuged at 200 g for 10 minutes.
  • the pellet After discarding the supernatant, the pellet is resuspended in 200 ml RPMI containing 15% FBS, 100 ⁇ M sodium hypoxanthine, 0.4 ⁇ M aminopterin, 16 ⁇ M thymidine (HAT) (Gibco), 25 units/ml IL-6 (Boehringer Mannheim) and 1.5 ⁇ 10 6 splenocytes/ml and plated into 10 Corning flat-bottom 96-well tissue culture plates (Corning, Corning N.Y.).
  • Plates are washed three times with PBS containing 0.05% Tween 20 (PBST) and 50 ⁇ l culture supernatant is added. After incubation at 37° C. for 30 minutes, and washing as above, 50 ⁇ l of horseradish peroxidase-conjugated goat anti-mouse IgG(Fc) (Jackson ImmunoResearch, West Grove, Pa.) diluted 1:3500 in PBST is added. Plates are incubated as above, washed four times with PBST, and 100 ⁇ l substrate, consisting of 1 mg/ml o-phenylene diamine (Sigma) and 0.1 ⁇ l/ml 30% H 2 O 2 in 100 mM citrate, pH 4.5, are added. The color reaction is stopped after 5 minutes with the addition of 50 ⁇ l of 15% H 2 SO 4 . The A 490 absorbance is determined using a plate reader (Dynatech).
  • Selected fusion wells are cloned twice by dilution into 96-well plates and visual scoring of the number of colonies/well after 5 days.
  • the monoclonal antibodies produced by hybridomas are isotyped using the Isostrip system (Boehringer Mannheim, Indianapolis, Ind.).
  • myeloma cell lines may be used.
  • Such cell lines suited for use in hybridoma-producing fusion procedures preferably are non-antibody-producing, have high fusion efficiency, and enzyme deficiencies that render them incapable of growing in certain selective media that support the growth of only the desired fused cells (hybridomas).
  • the immunized animal is a mouse
  • rats one may use R210.RCY3, Y3-Ag 1.2.3, IR983F and 4B210
  • U-266, GM1500-GRG2, LICR-LON-HMy2 and UC729-6 are all useful in connection with cell fusions.
  • the hybridomas and cell lines produced by such techniques for producing the monoclonal antibodies are contemplated to be compositions of the disclosure.
  • adjuvants may be used to increase an immunological response.
  • adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol.
  • BCG Bacilli Calmette-Guerin
  • Corynebacterium parvum are potentially useful human adjuvants.
  • Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening recombinant immunoglobulin libraries or panels of highly specific binding reagents as disclosed in Orlandi et al. (Proc. Natl. Acad. Sci. 86: 3833-3837; 1989), and Winter and Milstein (Nature 349: 293-299, 1991).
  • phage display can be used to generate an antibody of the disclosure.
  • phage libraries encoding antigen-binding variable (V) domains of antibodies can be generated using standard molecular biology and recombinant DNA techniques (see, e.g., Sambrook et al. (eds.), Molecular Cloning, A Laboratory Manual, 3 rd Edition, Cold Spring Harbor Laboratory Press, New York (2001)). Phage encoding a variable region with the desired specificity are selected for specific binding to the desired antigen, and a complete or partial antibody is reconstituted comprising the selected variable domain.
  • Nucleic acid sequences encoding the reconstituted antibody are introduced into a suitable cell line, such as a myeloma cell used for hybridoma production, such that antibodies having the characteristics of monoclonal antibodies are secreted by the cell (see, e.g., Janeway et al., supra, Huse et al., supra, and U.S. Pat. No. 6,265,150).
  • a suitable cell line such as a myeloma cell used for hybridoma production
  • Related methods also are described in U.S. Pat. Nos. 5,403,484; 5,571,698; 5,837,500; and 5,702,892.
  • Antibodies can be produced by transgenic mice that are transgenic for specific heavy and light chain immunoglobulin genes. Such methods are known in the art and described in, for example U.S. Pat. Nos. 5,545,806 and 5,569,825, and Janeway et al., supra.
  • Humanized antibodies can also be generated using the antibody resurfacing technology described in U.S. Pat. No. 5,639,641 and Pedersen et al., J. Mol. Biol., 235:959-973 (1994).
  • chimeric antibodies the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used (Morrison et al., Proc. Natl. Acad. Sci. 81: 6851-6855, 1984; Neuberger et al., Nature 312: 604-608, 1984; and Takeda et al., Nature 314: 452-454; 1985).
  • techniques described for the production of single-chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce IL13R ⁇ 2-specific single chain antibodies.
  • a preferred chimeric or humanized antibody has a human constant region, while the variable region, or at least a CDR, of the antibody is derived from a non-human species.
  • Methods for humanizing non-human antibodies are well known in the art. (see U.S. Pat. Nos. 5,585,089, and 5,693,762).
  • a humanized antibody has one or more amino acid residues introduced into a CDR region and/or into its framework region from a source which is non-human. Humanization can be performed, for example, using methods described in Jones et al. ( Nature 321: 522-525, 1986), Riechmann et al., ( Nature, 332: 323-327, 1988) and Verhoeyen et al.
  • CDR complementarity-determining region
  • compositions comprising CDRs may be generated using, at least in part, techniques known in the art to isolate CDRs.
  • Complementarity-determining regions are characterized by six polypeptide loops, three loops for each of the heavy or light chain variable regions.
  • the amino acid position in a CDR is defined by Kabat et al., “Sequences of Proteins of Immunological Interest,” U.S. Department of Health and Human Services, (1983), which is incorporated herein by reference.
  • hypervariable regions of human antibodies are roughly defined to be found at residues 28 to 35, from 49-59 and from residues 92-103 of the heavy and light chain variable regions [Janeway et al., supra].
  • the murine CDRs also are found at approximately these amino acid residues. It is understood in the art that CDR regions may be found within several amino acids of the approximated amino acid positions set forth above.
  • An immunoglobulin variable region also consists of four “framework” regions surrounding the CDRs (FR1-4). The sequences of the framework regions of different light or heavy chains are highly conserved within a species, and are also conserved between human and murine sequences.
  • compositions comprising one, two, and/or three CDRs of a heavy chain variable region or a light chain variable region of a monoclonal antibody are generated.
  • polypeptide compositions comprising these CDRs are generated.
  • Polypeptide compositions comprising one, two, three, four, five and/or six complementarity-determining regions of an antibody are also contemplated.
  • PCR primers complementary to these consensus framework sequences are generated to amplify the CDR sequence located between the primer regions.
  • the amplified CDR sequences are ligated into an appropriate plasmid.
  • the plasmid comprising one, two, three, four, five and/or six cloned CDRs optionally contains additional polypeptide encoding regions linked to the CDR.
  • modified polypeptide compositions comprising one, two, three, four, five, or six CDRs of a heavy or light chain of SEQ ID NOs: 1-6 are generated, wherein a CDR is altered to provide increased specificity or affinity or avidity to the target IL13R ⁇ 2.
  • Sites at locations in the CDRs are typically modified in series, e.g., by substituting first with conservative choices (e.g., hydrophobic amino acid substituted for a non-identical hydrophobic amino acid) and then with more dissimilar choices (e.g., hydrophobic amino acid substituted for a charged amino acid), and then deletions or insertions may be made at the target site.
  • Framework regions (FR) of a murine antibody are humanized by substituting compatible human framework regions chosen from a large database of human antibody variable sequences, including over twelve hundred human V H sequences and over one thousand V L sequences.
  • the database of antibody sequences used for comparison is downloaded from Andrew C. R. Martin's KabatMan web page (http://www.rubic.rdg.ac.uk/abs/).
  • the Kabat method for identifying CDRs provides a means for delineating the approximate CDR and framework regions of any human antibody and comparing the sequence of a murine antibody for similarity to determine the CDRs and FRs.
  • Best matched human V H and V L sequences are chosen on the basis of high overall framework matching, similar CDR length, and minimal mismatching of canonical and V H /V L contact residues.
  • Human framework regions most similar to the murine sequence are inserted between the murine CDRs.
  • the murine framework region may be modified by making amino acid substitutions of all or part of the native framework region that more closely resemble a framework region of a human antibody.
  • Nonpolar (hydrophobic) amino acids include alanine (Ala, A), leucine (Leu, L), isoleucine (Ile, I), valine (Val, V), proline (Pro, P), phenylalanine (Phe, F), tryptophan (Trp, W), and methionine (Met, M); polar neutral amino acids include glycine (Gly, G), serine (Ser, S), threonine (Thr, T), cysteine (Cys, C), tyrosine (Tyr, Y), asparagine (Asn, N), and glutamine (Gln, Q); positively charged (basic) amino acids include arginine (Arg, R), lysine (Lys, K), and histidine
  • “Insertions” or “deletions” are preferably in the range of about 1 to 20 amino acids, more preferably 1 to 10 amino acids. The variation may be introduced by systematically making substitutions of amino acids in a polypeptide molecule using recombinant DNA techniques and assaying the resulting recombinant variants for activity. Nucleic acid alterations can be made at sites that differ in the nucleic acids from different species (variable positions) or in highly conserved regions (constant regions). Methods for expressing polypeptide compositions useful in the invention are described in greater detail below.
  • Another useful technique for generating antibodies for use in the methods of the disclosure may be one which uses a rational design-type approach.
  • the goal of rational design is to produce structural analogs of biologically active polypeptides or compounds with which they interact (agonists, antagonists, inhibitors, peptidomimetics, binding partners, and the like).
  • the active polypeptides comprise the sequences of SEQ ID NOs: 1-6 disclosed herein.
  • By creating such analogs it is possible to fashion additional antibodies which are more immunoreactive than the native or natural molecule.
  • An alternative approach, “alanine scan,” involves the random replacement of residues throughout a molecule with alanine, and the resulting effect on function is determined.
  • Chemically synthesized bispecific antibodies may be prepared by chemically crosslinking heterologous Fab or F(ab′) 2 fragments by means of chemicals such as heterobifunctional reagent succinimidyl-3-(2-pyridyldithiol)-propionate (SPDP, Pierce Chemicals, Rockford, Ill.).
  • the Fab and F(ab′) 2 fragments can be obtained from intact antibody by digesting it with papain or pepsin, respectively (Karpovsky et al., J. Exp. Med. 160:1686-701, 1984; Titus et al., J. Immunol., 138:4018-22, 1987).
  • Methods of testing antibodies for the ability to bind to the epitope of the IL13R ⁇ 2, regardless of how the antibodies are produced, are known in the art and include any antibody-antigen binding assay such as, for example, radioimmunoassay (RIA), ELISA, Western blot, immunoprecipitation, and competitive inhibition assays (see, e.g., Janeway et al., infra, and U.S. Patent Application Publication No. 2002/0197266 A1).
  • RIA radioimmunoassay
  • ELISA ELISA
  • Western blot Western blot
  • immunoprecipitation immunoprecipitation
  • competitive inhibition assays see, e.g., Janeway et al., infra, and U.S. Patent Application Publication No. 2002/0197266 A1.
  • Selection of antibodies from an antibody population for purposes herein also include using blood vessel endothelial cells to “subtract” those antibodies that cross-react with epitopes on such cells other than IL13R ⁇ 2 epitopes.
  • the remaining antibody population is enriched in antibodies preferential for IL13R ⁇ 2 epitopes.
  • a loop structure is often involved with providing the desired binding attributes as in the case of aptamers, which often utilize hairpin loops created from short regions without complementary base pairing, naturally derived antibodies that utilize combinatorial arrangement of looped hyper-variable regions and new phage-display libraries utilizing cyclic peptides that have shown improved results when compared to linear peptide phage display results.
  • aptamers which often utilize hairpin loops created from short regions without complementary base pairing, naturally derived antibodies that utilize combinatorial arrangement of looped hyper-variable regions and new phage-display libraries utilizing cyclic peptides that have shown improved results when compared to linear peptide phage display results.
  • molecular evolution techniques can be used to isolate binding agents specific for the IL13R ⁇ 2 disclosed herein.
  • aptamers see generally, Gold, L., Singer, B., He, Y. Y., Brody.
  • the aptamer is generated by preparing a library of nucleic acids; contacting the library of nucleic acids with a growth factor, wherein nucleic acids having greater binding affinity for the growth factor (relative to other library nucleic acids) are selected and amplified to yield a mixture of nucleic acids enriched for nucleic acids with relatively higher affinity and specificity for binding to the growth factor.
  • the processes may be repeated, and the selected nucleic acids mutated and rescreened, whereby a growth factor aptamer is identified.
  • Nucleic acids may be screened to select for molecules that bind to more than target. Binding more than one target can refer to binding more than one simultaneously or competitively.
  • a binding agent comprises at least one aptamer, wherein a first binding unit binds a first epitope of an IL13R ⁇ 2 and a second binding unit binds a second epitope of the IL13R ⁇ 2.
  • ligand-induced activation of the IL13R ⁇ 2 is reduced upon binding of the binding agent to the IL13R ⁇ 2.
  • the term “reduce” as well as like terms, e.g., “inhibit,” do not necessarily imply 100% or a complete reduction or inhibition. Rather, there are varying degrees of reduction or inhibition of which one of ordinary skill in the art recognizes as having a potential benefit or therapeutic effect. Accordingly, in some embodiments, ligand-induced activation of the IL13R ⁇ 2 is completely abolished.
  • ligand-induced activation is substantially reduced, e.g., reduced by about 10% (e.g., by about 20%, by about 30%, by about 40%, by about 50%, by about 60%, by about 70%, by about 80%, by about 90%) or more, as compared to ligand-induced activation of the IL13R ⁇ 2 when the binding agent is absent or not bound to the IL13R ⁇ 2.
  • Methods of measuring ligand-induced activation of an IL13R ⁇ 2 are known in the art, and include, for example, the assays described in the Examples, below.
  • Conjugates comprising a targeting domain and an effector domain are disclosed herein.
  • the conjugate comprises any one of the binding agents disclosed herein as the targeting domain to localize the conjugate to a cell expressing IL13R ⁇ 2, e.g., a tumor cell expressing the same, and an effector domain.
  • the conjugate is a fusion protein.
  • the conjugate is a chimeric protein.
  • the term “chimeric” refers to a molecule composed of parts of different origins. A chimeric molecule, as a whole, is non-naturally occurring, e.g., synthetic or recombinant, although the parts which comprise the chimeric molecule may be naturally occurring.
  • the term “effector domain” refers to a portion of a conjugate that effects a desired biological function.
  • the effector domain identifies or locates IL13R ⁇ 2-expressing cells.
  • the effector domain may be a diagnostic agent, e.g., a radiolabel, a fluorescent label, an enzyme (e.g., that catalyzes a calorimetric or fluorometric reaction), a substrate, a solid matrix, or a carrier (e.g., biotin or avidin).
  • the diagnostic agent in some aspects is an imaging agent. Many appropriate imaging agents are known in the art, as are methods of attaching the labeling agents to the peptides of the invention (see, e.g., U.S.
  • the imaging agents are administered to a subject in a pharmaceutically acceptable carrier, and allowed to accumulate at a target site having the lymphatic endothelial cells.
  • This imaging agent serves as a contrast reagent for X-ray, magnetic resonance, positron emission tomography, single photon emission computed tomography (SPECT), or sonographic or scintigraphic imaging of the target site.
  • SPECT single photon emission computed tomography
  • Paramagnetic ions useful in the imaging agents of the invention include for example chromium (III), manganese (II), iron (III), iron (II), cobalt (II), nickel (II) copper (II), neodymium (III), samarium (III), ytterbium(III), gadolinium (III), vanadium (II), terbium (III), dysprosium (III), holmium (III) and erbium (III).
  • Ions useful for X-ray imaging include, but are not limited to, lanthanum (III), gold (III), lead (II) and particularly bismuth (III).
  • Radioisotopes for diagnostic applications include for example, 211 astatine, 14 carbon, 51 chromium, 36 chlorine, 57 cobalt, 67 copper, 152 europium, 67 gallium, 3 hydrogen, 123 iodine, 125 iodine, 111 indium, 59 iron, 32 phosphorus, 186 rhenium, 75 selenium, 35 sulphur, 99 mtechnicium, 90 yttrium, and 99 zirconium.
  • the effector domain may be one which alters the physico-chemical characteristics of the conjugate, e.g., an effector which confers increased solubility and/or stability and/or half-life, resistance to proteolytic cleavage, modulation of clearance.
  • the effector domain is a polymer, a carbohydrate, or a lipid.
  • the polymer may be branched or unbranched.
  • the polymer may be of any molecular weight.
  • the polymer in some embodiments has an average molecular weight of between about 2 kDa to about 100 kDa (the term “about” indicating that in preparations of a water-soluble polymer, some molecules will weigh more, some less, than the stated molecular weight).
  • the average molecular weight of the polymer is in some aspects between about 5 kDa and about 50 kDa, between about 12 kDa to about 40 kDa or between about 20 kDa to about 35 kDa.
  • the polymer is modified to have a single reactive group, such as an active ester for acylation or an aldehyde for alkylation, so that the degree of polymerization may be controlled.
  • the polymer in some embodiments is water soluble so that the protein to which it is attached does not precipitate in an aqueous environment, such as a physiological environment.
  • the polymer when, for example, the composition is used for therapeutic use, the polymer is pharmaceutically acceptable.
  • the polymer is a mixture of polymers, e.g., a co-polymer, a block co-polymer.
  • the polymer is selected from the group consisting of: polyamides, polycarbonates, polyalkylenes and derivatives thereof, including polyalkylene glycols, polyalkylene oxides, polyalkylene terepthalates, polymers of acrylic and methacrylic esters, including poly(methyl methacrylate), poly(ethyl methacrylate), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), and poly(octadecyl acrylate), polyvinyl polymers including polyvinyl alcohols, polyvinyl ethers, polyvinyl esters, polyvinyl halides, poly(vinyl acetate), and polyvinylpyr
  • the polymer is a biodegradable polymer, including a synthetic biodegradable polymer (e.g., polymers of lactic acid and glycolic acid, polyanhydrides, poly(ortho)esters, polyurethanes, poly(butic acid), poly(valeric acid), and poly(lactide-cocaprolactone)), and a natural biodegradable polymer (e.g., alginate and other polysaccharides including dextran and cellulose, collagen, chemical derivatives thereof (substitutions, additions of chemical groups, for example, alkyl, alkylene, hydroxylations, oxidations, and other modifications routinely made by those skilled in the art), albumin and other hydrophilic proteins (e.g., zein and other prolamines and hydrophobic proteins)), as well as any copolymer or mixture thereof.
  • a synthetic biodegradable polymer e.g., polymers of lactic acid and glycolic acid, polyanhydrides, poly(ortho)esters
  • the polymer is a bioadhesive polymer, such as a bioerodible hydrogel described by H. S. Sawhney, C. P. Pathak and J. A.
  • polyhyaluronic acids casein, gelatin, glutin, polyanhydrides, polyacrylic acid, alginate, chitosan, poly(methyl methacrylates), poly(ethyl methacrylates), poly(butylmethacrylate), poly(isobutyl methacrylate), poly(hexylmethacrylate), poly(isodecyl methacrylate), poly(lauryl methacrylate), poly(phenyl methacrylate), poly(methyl acrylate), poly(isopropyl acrylate), poly(isobutyl acrylate), and poly(octadecyl acrylate).
  • the polymer is a water-soluble polymer or a hydrophilic polymer.
  • Suitable water-soluble polymers are known in the art and include, for example, polyvinylpyrrolidone, hydroxypropyl cellulose (HPC; Klucel), hydroxypropyl methylcellulose (HPMC; Methocel), nitrocellulose, hydroxypropyl ethylcellulose, hydroxypropyl butylcellulose, hydroxypropyl pentylcellulose, methyl cellulose, ethylcellulose (Ethocel), hydroxyethyl cellulose, various alkyl celluloses and hydroxyalkyl celluloses, various cellulose ethers, cellulose acetate, carboxymethyl cellulose, sodium carboxymethyl cellulose, calcium carboxymethyl cellulose, vinyl acetate/crotonic acid copolymers, poly-hydroxyalkyl methacrylate, hydroxymethyl methacrylate, methacrylic acid copolymers, polymethacrylic acid, polymethylmethacrylate, male
  • the water-soluble polymers or mixtures thereof include, but are not limited to, N-linked or O-linked carbohydrates, sugars, phosphates, carbohydrates; sugars; phosphates; polyethylene glycol (PEG) (including the forms of PEG that have been used to derivatize proteins, including mono-(C1-C 10) alkoxy- or aryloxy-polyethylene glycol); monomethoxy-polyethylene glycol; dextran (such as low molecular weight dextran of, for example, about 6 kD), cellulose; other carbohydrate-based polymers, poly-(N-vinyl pyrrolidone), polyethylene glycol, propylene glycol homopolymers, a polypropylene oxide/ethylene oxide co-polymer, polyoxyethylated polyols (e.g., glycerol) and polyvinyl alcohol.
  • PEG polyethylene glycol
  • dextran such as low molecular weight dextran of, for example, about 6 kD
  • polyethylene glycol PEG
  • PEG polyethylene glycol
  • PEG polyethylene glycol
  • PEG polyethylene glycol
  • PEG is a linear or branched neutral polyether, available in a broad range of molecular weights, and is soluble in water and most organic solvents.
  • PEG is effective at excluding other polymers or peptides when present in water, primarily through its high dynamic chain mobility and hydrophobic nature, thus creating a water shell or hydration sphere when attached to other proteins or polymer surfaces.
  • PEG is nontoxic, non-immunogenic, and approved by the Food and Drug Administration for internal consumption. Proteins or enzymes when conjugated to PEG have demonstrated bioactivity, non-antigenic properties, and decreased clearance rates when administered in animals.
  • Hydrophobic polymer surfaces such as polyurethanes and polystyrene, can be modified by the grafting of PEG (MW 3,400) and employed as nonthrombogenic surfaces.
  • Surface properties can be more consistent with hydrophilic surfaces, due to the hydrating effect of PEG. More importantly, protein (albumin and other plasma proteins) adsorption can be greatly reduced, resulting from the high chain motility, hydration sphere, and protein exclusion properties of PEG.
  • PEG (MW 3,400) was determined as an optimal size in surface immobilization studies, Park et al., J. Biomed. Mat. Res. 26:739-45, 1992, while PEG (MW 5,000) was most beneficial in decreasing protein antigenicity. F. M.
  • Methods for preparing pegylated binding agent polypeptides may comprise the steps of (a) reacting the polypeptide with polyethylene glycol (such as a reactive ester or aldehyde derivative of PEG) under conditions whereby the binding agent polypeptide becomes attached to one or more PEG groups, and (b) obtaining the reaction product(s).
  • polyethylene glycol such as a reactive ester or aldehyde derivative of PEG
  • the optimal reaction conditions for the acylation reactions will be determined based on known parameters and the desired result. For example, the larger the ratio of PEG:protein, the greater the percentage of poly-pegylated product.
  • the binding agent will have a single PEG moiety at the N-terminus. See U.S. Pat. No. 8,234,784, incorporated by reference herein.
  • the effector domain is a carbohydrate.
  • the carbohydrate is a monosaccharide (e.g., glucose, galactose, fructose), a disaccharide (e.g., sucrose, lactose, maltose), an oligosaccharide (e.g., raffinose, stachyose), a polysaccharide (e.g., a starch, amylase, amylopectin, cellulose, chitin, callose, laminarin, xylan, mannan, fucoidan, or galactomannan).
  • a monosaccharide e.g., glucose, galactose, fructose
  • a disaccharide e.g., sucrose, lactose, maltose
  • an oligosaccharide e.g., raffinose, stachyose
  • a polysaccharide
  • the effector domain is a lipid.
  • the lipid in some embodiments, is a fatty acid, eicosanoid, prostaglandin, leukotriene, thromboxane, N-acyl ethanolamine, glycerolipid (e.g., mono-, di-, tri-substituted glycerols), glycerophospholipid (e.g., phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine, phosphatidylserine), sphingolipid (e.g., sphingosine, ceramide), sterol lipid (e.g., steroid, cholesterol), prenol lipid, saccharolipid, or a polyketide, oil, wax, cholesterol, sterol, fat-soluble vitamin, monoglyceride, diglyceride, triglyceride, or a phospholipid.
  • glycerolipid e
  • the effector domain is a lethal domain that confers lethality, such that when the conjugate is localized to a cell expressing IL13R ⁇ 2, e.g., a tumor cell expressing the same.
  • the effector domain confers upon the conjugate the ability to kill an IL13R ⁇ 2-expressing cell once the binding agent has found and bound to its IL13R ⁇ 2 target.
  • the effector domain is a cytotoxin (also referred to herein as a “cytotoxic agent”).
  • the cytotoxic agent is any molecule (chemical or biochemical) which is toxic to a cell.
  • the cytotoxic agent is a chemotherapeutic agent.
  • Chemotherapeutic agents are known in the art and include, but are not limited to, platinum coordination compounds, topoisomerase inhibitors, antibiotics, antimitotic alkaloids and difluoronucleosides, as described in U.S. Pat. No. 6,630,124.
  • the chemotherapeutic agent is a platinum coordination compound.
  • platinum coordination compound refers to any tumor cell growth-inhibiting platinum coordination compound that provides the platinum in the form of an ion.
  • the platinum coordination compound is cis-diamminediaquoplatinum (II)-ion; chloro(diethylenetriamine)-platinum(II)chloride; dichloro(ethylenediamine)-platinum(II), diammine(1,1-cyclobutanedicarboxylato) platinum(II) (carboplatin); spiroplatin; iproplatin; diammine(2-ethylmalonato)-platinum(II); ethylenediaminemalonatoplatinum(II); aqua(1,2-diaminodyclohexane)-sulfatoplatinum(II); (1,2-diaminocyclohexane)malonatoplatinum(II); (4-caroxyphthalato)(1,2-diaminocyclohex
  • cisplatin is the platinum coordination compound employed in the compositions and methods of the present invention.
  • Cisplatin is commercially available under the name PLATINOLTM from Bristol Myers-Squibb Corporation and is available as a powder for constitution with water, sterile saline or other suitable vehicle.
  • Other platinum coordination compounds suitable for use in the present invention are known and are available commercially and/or can be prepared by conventional techniques.
  • Cisplatin, or cis-dichlorodiammineplatinum II has been used successfully for many years as a chemotherapeutic agent in the treatment of various human solid malignant tumors.
  • diamino-platinum complexes have also shown efficacy as chemotherapeutic agents in the treatment of various human, solid, malignant tumors.
  • Such diamino-platinum complexes include, but are not limited to, spiroplatinum and carboplatinum.
  • cisplatin and other diamino-platinum complexes have been widely used as chemotherapeutic agents in humans, they have had to be delivered at high dosage levels that can lead to toxicity problems such as kidney damage.
  • the chemotherapeutic agent is a topoisomerase inhibitor.
  • Topoisomerases are enzymes that are capable of altering DNA topology in eukaryotic cells. They are critical for cellular functions and cell proliferation. Generally, there are two classes of topoisomerases in eukaryotic cells, type I and type II. Topoisomerase I is a monomeric enzyme of approximately 100,000 molecular weight. The enzyme binds to DNA and introduces a transient single-strand break, unwinds the double helix (or allows it to unwind), and subsequently reseals the break before dissociating from the DNA strand.
  • the topoisomerase inhibitor is camptothecin or a camptothecin analog.
  • Camptothecin is a water-insoluble, cytotoxic alkaloid produced by Camptotheca accuminata trees indigenous to China and Nothapodytes foetida trees indigenous to India. Camptothecin exhibits tumor cell growth-inhibiting activity against a number of tumor cells.
  • Compounds of the camptothecin analog class are typically specific inhibitors of DNA topoisomerase I.
  • the cytotoxic agent is any tumor cell growth-inhibiting camptothecin analog claimed or described in U.S. Pat. No. 5,004,758; European Patent Application Number 88311366.4 (Publication Number EP 0 321 122); U.S. Pat. No. 4,604,463; European Patent Application Publication Number EP 0 137 145; U.S. Pat. No.
  • CPT-11 is a camptothecin analog with a 4-(piperidino)-piperidine side chain joined through a carbamate linkage at C-10 of 10-hydroxy-7-ethyl camptothecin.
  • CPT-11 is currently undergoing human clinical trials and is also referred to as irinotecan; Wani et al, J. Med. Chem., 23, 554 (1980); Wani et al., J. Med. Chem., 30, 1774 (1987); U.S. Pat. No. 4,342,776; European Patent Application Publication Number EP 418 099; U.S. Pat. No. 4,513,138; European Patent Application Publication Number EP 0 074 770; U.S. Pat. No.
  • the topoisomerase inhibitor may be selected from the group consisting of topotecan, irinotecan and 9-aminocamptothecin.
  • the chemotherapeutic agent is an antibiotic compound. Suitable antibiotics include, but are not limited to, doxorubicin, mitomycin, bleomycin, daunorubicin and streptozocin.
  • the chemotherapeutic agent is an antimitotic alkaloid.
  • antimitotic alkaloids can be extracted from Cantharanthus roseus , and have been shown to be efficacious as anticancer chemotherapy agents.
  • a great number of semi-synthetic derivatives have been studied both chemically and pharmacologically (see, O. Van Tellingen et al, Anticancer Research, 12, 1699-1716 (1992)).
  • the antimitotic alkaloids of the present invention include, but are not limited to, vinblastine, vincristine, vindesine, Taxol and vinorelbine.
  • the latter two antimitotic alkaloids are commercially available from Eli Lilly and Company, and Pierre Fabre Laboratories, respectively (see, U.S. Pat. No. 5,620,985).
  • the antimitotic alkaloid is vinorelbine.
  • the chemotherapeutic agent is a difluoronucleoside.
  • 2′-deoxy-2′,2′-difluoronucleosides are known in the art as having antiviral activity. Such compounds are disclosed and taught in U.S. Pat. Nos. 4,526,988 and 4,808,614. European Patent Application Publication 184,365 discloses that these same difluoronucleosides have oncolytic activity.
  • the 2′-deoxy-2′,2′-difluoronucleoside used in the compositions and methods of the disclosure is 2′-deoxy-2′,2′-difluorocytidine hydrochloride, also known as gemcitabine hydrochloride.
  • Gemcitabine is commercially available or can be synthesized in a multi-step process as disclosed in U.S. Pat. Nos. 4,526,988, 4,808,614 and 5,223,608, the teachings of each of which are incorporated herein by reference in its entirety.
  • the effector domain is an apoptosis tag which causes the IL13R ⁇ 2-expressing cell to apoptose.
  • the apoptosis tag is a TRAIL protein, or a portion thereof.
  • the apoptosis tag comprises the amino acid sequence of SEQ ID NO: 27.
  • the conjugate comprises the amino acid sequence of SEQ ID NO: 25.
  • the effector domain is an Fc domain of IgG or other immunoglobulin.
  • the fusion can be fused directly to a binding agent or fused through an intervening sequence.
  • a human IgG hinge, CH2 and CH3 region may be fused at either the N-terminus or C-terminus of a binding agent to attach the Fc region.
  • the resulting Fc-fusion agent enables purification via a Protein A affinity column (Pierce, Rockford, Ill.). Peptide and proteins fused to an Fc region can exhibit a substantially greater half-life in vivo than the unfused counterpart.
  • a fusion to an Fc region allows for dimerization/multimerization of the fusion polypeptide.
  • the Fc region may be a naturally occurring Fc region, or may be modified for superior characteristics, e.g., therapeutic qualities, circulation time, reduced aggregation.
  • the binding agent are conjugated, e.g., fused to an immunoglobulin or portion thereof (e.g., variable region, CDR, or Fc region).
  • immunoglobulins include IgG, IgA, IgE, IgD or IgM.
  • the Fc region is a C-terminal region of an Ig heavy chain, which is responsible for binding to Fc receptors that carry out activities such as recycling (which results in prolonged half-life), antibody dependent cell-mediated cytotoxicity (ADCC), and complement dependent cytotoxicity (CDC).
  • ADCC antibody dependent cell-mediated cytotoxicity
  • CDC complement dependent cytotoxicity
  • the human IgG heavy chain Fc region stretches from Cys226 to the C-terminus of the heavy chain.
  • the “hinge region” generally extends from Glu216 to Pro230 of human IgG1 (hinge regions of other IgG isotypes may be aligned with the IgG1 sequence by aligning the cysteines involved in cysteine bonding).
  • the Fc region of an IgG includes two constant domains, CH2 and CH3.
  • the CH2 domain of a human IgG Fc region usually extends from amino acids 231 to amino acid 341.
  • the CH3 domain of a human IgG Fc region usually extends from amino acids 342 to 447.
  • the Fc region may comprise one or more native or modified constant regions from an immunoglobulin heavy chain, other than CH1, for example, the CH2 and CH3 regions of IgG and IgA, or the CH3 and CH4 regions of IgE.
  • Suitable conjugate moieties include portions of immunoglobulin sequence that include the FcRn binding site.
  • FcRn a salvage receptor, is responsible for recycling immunoglobulins and returning them to circulation in the blood.
  • the region of the Fc portion of IgG that binds to the FcRn receptor has been described based on X-ray crystallography (Burmeister et al. 1994, Nature 372:379).
  • the major contact area of the Fc with the FcRn is near the junction of the CH2 and CH3 domains.
  • Fc-FcRn contacts are all within a single Ig heavy chain.
  • the major contact sites include amino acid residues 248, 250-257, 272, 285, 288, 290-291, 308-311, and 314 of the CH2 domain and amino acid residues 385-387, 428, and 433-436 of the CH3 domain.
  • Fc ⁇ R are responsible for antibody-dependent cell-mediated cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC).
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • CDC complement-dependent cytotoxicity
  • positions within the Fc region that make a direct contact with Fc ⁇ R are amino acids 234-239 (lower hinge region), amino acids 265-269 (B/C loop), amino acids 297-299 (C/E loop), and amino acids 327-332 (F/G) loop (Sondermann et al., Nature 406: 267-273, 2000).
  • the lower hinge region of IgE has also been implicated in the FcRI binding (Henry, et al., Biochemistry 36, 15568-15578, 1997).
  • Amino acid modifications may be made to the Fc region of an immunoglobulin.
  • Such variant Fc regions comprise at least one amino acid modification in the CH3 domain of the Fc region (residues 342-447) and/or at least one amino acid modification in the CH2 domain of the Fc region (residues 231-341).
  • Mutations believed to impart an increased affinity for FcRn include T256A, T307A, E380A, and N434A (Shields et al. 2001, J. Biol. Chem. 276:6591).
  • Other mutations may reduce binding of the Fc region to Fc ⁇ RI, Fc ⁇ RIIA, Fc ⁇ RIIB, and/or Fc ⁇ RIIIA without significantly reducing affinity for FcRn.
  • substitution of the Asn at position 297 of the Fc region with Ala or another amino acid removes a highly conserved N-glycosylation site and may result in reduced immunogenicity with concomitant prolonged half-life of the Fc region, as well as reduced binding to Fc ⁇ Rs (Routledge et al. 1995, Transplantation 60:847; Friend et al. 1999, Transplantation 68:1632; Shields et al. 1995, J. Biol. Chem. 276:6591).
  • Amino acid modifications at positions 233-236 of IgG1 have been made that reduce binding to Fc ⁇ Rs (Ward and Ghetie 1995, Therapeutic Immunology 2:77 and Armour et al. 1999, Eur. J. Immunol. 29:2613).
  • Some exemplary amino acid substitutions are described in U.S. Pat. Nos. 7,355,008 and 7,381,408, each of which is incorporated by reference herein in its entirety.
  • the binding agent is fused to alkaline phosphatase (AP).
  • AP alkaline phosphatase
  • the effector domain is a T-cell signaling domain.
  • the conjugate is a chimeric antigen receptor (CAR).
  • Chimeric antigen receptors are engineered transmembrane proteins that combine the specificity of an antigen-specific antibody with a T-cell receptor's function.
  • CARs comprise an ectodomain, a spacer region, a transmembrane domain, and an endodomain.
  • the ectodomain of a CAR in exemplary aspects comprises an antigen recognition region, which may be an scFV of an antigen-specific antibody.
  • the ectodomain also in some embodiments comprises a signal peptide which directs the nascent protein into the endoplasmic reticulum.
  • the ectodomain comprises a spacer which links the antigen recognition region to the transmembrane domain.
  • the transmembrane (TM) domain is the portion of the CAR which traverses the cell membrane.
  • the TM domain comprises a hydrophobic alpha helix.
  • the TM domain comprises all or a portion of the TM domain of CD28.
  • the TM domain comprises all or a portion of the TM domain of CD8 ⁇ .
  • the endodomain of a CAR comprises one or more signaling domains.
  • the endodomain comprises the zeta chain of CD3, which comprises three copies of the Immunoreceptor Tyrosine-based Activation Motif (ITAM).
  • ITAM generally comprises a Tyr residue separated by two amino acids from a Leu or Ile.
  • the ITAMs occur in multiples (at least two) and each ITAM is separated from another by 6-8 amino acids.
  • the endodomain of CARs may also comprises additional signaling domains, e.g., portions of proteins that are important for downstream signal transduction.
  • the endodomain comprises signaling domains from one or more of CD28, 41BB or 4-1BB (CD137), ICOS, CD27, CD40, OX40 (CD134), or Myd88. Sequences encoding signaling domains of such proteins are provided herein as SEQ ID NOs: 39-42, 68-79, 81, and 83. Methods of making CARs, expressing them in cells, e.g., T-cells, and utilizing the CAR-expressing T-cells in therapy, are known in the art. See, e.g., International Patent Application Publication Nos.
  • the conjugate of the disclosure is an IL13R ⁇ 2-specific chimeric antigen receptor (CAR) comprising a binding agent described herein, a hinge region, and an endodomain comprising a signaling domain of a CD3 zeta chain and a signaling domain of CD28, CD134, and/or CD137.
  • CAR chimeric antigen receptor
  • the CAR comprises (A) each of the amino acid sequence of: NYLMN (SEQ ID NO: 1); RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); GYGTAYGVDY (SEQ ID NO: 3); RASESVDNYGISFMN (SEQ ID NO: 4); AASRQGSG (SEQ ID NO: 5); and QQSKEVPWT (SEQ ID NO: 6), (B) a hinge region; and (C) an endodomain comprising a signaling domain of a CD3 zeta chain and a signaling domain of CD28, CD134, and/or CD137.
  • NYLMN SEQ ID NO: 1
  • RIDPYDGDIDYNQNFKD SEQ ID NO: 2
  • GYGTAYGVDY SEQ ID NO: 3
  • RASESVDNYGISFMN SEQ ID NO: 4
  • AASRQGSG SEQ ID NO: 5
  • QQSKEVPWT SEQ ID NO: 6
  • the CD3 zeta chain signaling domain comprises the amino acid sequence of SEQ ID NO: 41.
  • the CAR further comprises a transmembrane (TM) domain based on the TM domain of CD28.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 47.
  • the CAR further comprises a transmembrane (TM) domain based on the TM domain of CD8 ⁇ .
  • the CAR comprises the amino acid sequence of SEQ ID NO: 85.
  • the hinge region comprises the amino acid sequence of SEQ ID NO: 35 or SEQ ID NO: 37.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 49 or SEQ ID NO: 51.
  • the endodomain of the CAR of the disclosures comprises the amino acid sequence of SEQ ID NO: 53 or SEQ ID NO: 55. In exemplary aspects, the endodomain of the CAR of the disclosure comprises the amino acid sequence of SEQ ID NO: 87 or SEQ ID NO: 89. In exemplary aspects, the endodomain of the CAR of the disclosure comprises the amino acid sequence of SEQ ID NO: 91, SEQ ID NO: 93 or SEQ ID NO: 95. In exemplary aspects, the endodomain of the CAR of the disclosure comprises the amino acid sequence of SEQ ID NO: 97, SEQ ID NO: 99 or SEQ ID NO: 101.
  • the endodomain further comprises a signaling domain of one or more of: CD137, CD134, CD27, CD40, ICOS, and Myd88.
  • the endodomain comprises one or more of the amino acid sequences of SEQ ID NOs: 68, 70, 72, 74, 76, and 78, which provide a sequence comprising a CD27 signaling domain, a sequence comprising a CD40 signaling domain, a sequence comprising a CD134 signaling domain, a sequence comprising a CD137 signaling domain, a sequence comprising an ICOS signaling domain, and a sequence comprising a Myd88 signaling domain, respectively.
  • the CAR comprises (A) each of the amino acid sequence of: NYLMN (SEQ ID NO: 1); RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); GYGTAYGVDY (SEQ ID NO: 3); RASESVDNYGISFMN (SEQ ID NO: 4); AASRQGSG (SEQ ID NO: 5); and QQSKEVPWT (SEQ ID NO: 6), (B) a hinge region; (C) an endodomain comprising a signaling domain of a CD3 zeta chain and a signaling domain of CD28 and at least one other signaling domain.
  • the CAR comprises an endodomain comprising a signaling domain of 41BB (CD137).
  • the CAR comprises an endodomain comprising an amino acid sequence of SEQ ID NO: 81.
  • the CD137 signaling is N-terminal to a CD3 zeta chain signaling chain.
  • the endodomain comprises the amino acid sequence of SEQ ID NO: 87.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 91.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 97.
  • the CAR comprises an endodomain comprising a signaling domain of OX40 (CD134). In exemplary aspects the CAR comprises an endodomain comprising an amino acid sequence of SEQ ID NO: 83. In exemplary aspects, the CD137 signaling is N-terminal to a CD3 zeta chain signaling chain. In exemplary aspects, the endodomain comprises the amino acid sequence of SEQ ID NO: 89. In exemplary aspects, the CAR comprises the amino acid sequence of SEQ ID NO: 95. In exemplary aspects, the CAR comprises the amino acid sequence of SEQ ID NO: 99.
  • the CAR comprises (A) each of the amino acid sequence of: NYLMN (SEQ ID NO: 1); RIDPYDGDIDYNQNFKD (SEQ ID NO: 2); GYGTAYGVDY (SEQ ID NO: 3); RASESVDNYGISFMN (SEQ ID NO: 4); AASRQGSG (SEQ ID NO: 5); and QQSKEVPWT (SEQ ID NO: 6), (B) a hinge region; (C) a transmembrane domain of CD8a chain, and (D) an endodomain comprising a signaling domain of a CD3 zeta chain, and, optionally, at least one other signaling domain.
  • NYLMN SEQ ID NO: 1
  • RIDPYDGDIDYNQNFKD SEQ ID NO: 2
  • GYGTAYGVDY SEQ ID NO: 3
  • RASESVDNYGISFMN SEQ ID NO: 4
  • AASRQGSG SEQ ID NO: 5
  • the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 85.
  • the CAR further comprises a CD137 signaling domain and a CD3 zeta chain signaling domain.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 93.
  • the CAR comprises the amino acid sequence of SEQ ID NO: 101.
  • sequences of three additional IL13R ⁇ 2-specific CARs are provided.
  • One CAR contains a CD8 ⁇ TM domain, and a 41BB.zeta signaling domain (SEQ ID NO:93 encoded by SEQ ID NO:94).
  • the other two CARs contain a CD28 TM domain and either a CD28.CD134.zeta (SEQ ID NO:99 encoded by SEQ ID NO:100) or CD28.CD137.zeta (SEQ ID NO:101 encoded by SEQ ID NO:102) signaling domain.
  • nucleic acid comprising a nucleotide sequence encoding any of the binding agents and conjugates (e.g., chimeric proteins, fusion proteins, CARs) described herein.
  • the nucleic acid may comprise any nucleotide sequence which encodes any of the binding agents and conjugates described herein.
  • the nucleic acid comprises a nucleotide sequence encoding each of the CDRs of SEQ ID NOs: 1-6.
  • nucleic acid of the disclosures comprises a nucleic acid sequence which encodes a SEQ ID NO: 7 and/or SEQ ID NO: 8.
  • the nucleic acid of the disclosures comprises a nucleic acid sequence which encodes SEQ ID NO: 13 or SEQ ID NO: 14.
  • the nucleic acid provided herein comprises the sequence of SEQ ID NO: 15 and/or SEQ ID NO: 16.
  • the nucleic acid comprises a nucleotide sequence of SEQ ID NO: 66 or 67.
  • the nucleic acid comprises a nucleotide sequence which encodes the sequence of SEQ ID NO: 25.
  • the nucleic acid comprises a nucleotide sequence of SEQ ID NO: 26.
  • the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes SEQ ID NO: 28 or 30. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes an amino acid sequence which is at least 90% identical to SEQ ID NO: 28 or 30. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 29 or 31. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes SEQ ID NO: 33.
  • the nucleic acid comprises a nucleotide sequence of SEQ ID NO: 34. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes SEQ ID NO: 35 or 37. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 36 or 38. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes SEQ ID NO: 39 or 41.
  • the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 40 or 42. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes SEQ ID NO: 47. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 48. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes SEQ ID NO: 49 or 51.
  • the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 50 or 52. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes SEQ ID NO: 53 or 55. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises SEQ ID NO: 54 or 56. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and encodes one or more of SEQ ID NOs: 68, 70, 72, 74, 76, and 78.
  • the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises one or more of SEQ ID NOs: 69, 71, 73, 75, 77, and 79. In exemplary aspects, the nucleic acid comprises a nucleotide sequence which encodes each of SEQ ID NOs: 1-6 and comprises one or more of SEQ ID NOs: 82, 84, 86, 88, 90, 92, 94, 96. In exemplary aspects, the nucleic acid comprises a nucleotide sequence comprising one of SEQ ID NOs: 98, 100, and 102.
  • nucleic acid includes “polynucleotide,” “oligonucleotide,” and “nucleic acid molecule,” and generally means a polymer of DNA or RNA, which may be single-stranded or double-stranded, synthesized or obtained (e.g., isolated and/or purified) from natural sources, which may contain natural, non-natural or altered nucleotides, and which may 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 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 disclosures 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 may replicate in a living cell, or (ii) molecules that result from the replication of those described in (i) above.
  • the replication may be in vitro replication or in vivo replication.
  • nucleic acids in exemplary aspects are constructed based on chemical synthesis and/or enzymatic ligation reactions using procedures known in the art. See, for example, Sambrook et al., supra, and Ausubel et al., supra.
  • a nucleic acid may 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 may 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-thiouridme, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N-substituted adenine, 7-methylguanine, 5-methylammomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueo
  • the disclosures provides recombinant expression vectors comprising any of the nucleic acids of the disclosures.
  • 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 disclosures are not naturally-occurring as a whole. However, parts of the vectors may be naturally-occurring.
  • the inventive recombinant expression vectors may comprise any type of nucleotides, including, but not limited to DNA and RNA, which may be single-stranded or double-stranded, synthesized or obtained in part from natural sources, and which may contain natural, non-natural or altered nucleotides.
  • the recombinant expression vectors may comprise naturally-occurring or non-naturally occurring internucleotide linkages, or both types of linkages. In exemplary aspects, the altered nucleotides or non-naturally occurring internucleotide linkages do not hinder the transcription or replication of the vector.
  • the recombinant expression vector of the disclosures may be any suitable recombinant expression vector, and may be used to transform or transfect any suitable host.
  • Suitable vectors include those designed for propagation and expansion or for expression or both, such as plasmids and viruses.
  • the vector may be selected from the group consisting of the pUC series (Fermentas Life Sciences), the pBluescript series (Stratagene, LaJolla, Calif.), the pET series (Novagen, Madison, Wis.), the pGEX series (Pharmacia Biotech, Uppsala, Sweden), and the pEX series (Clontech, Palo Alto, Calif.).
  • Bacteriophage vectors such as ⁇ GTIO, ⁇ GT1 1, ⁇ ZapII (Stratagene), ⁇ EMBL4, and ⁇ NM1 149, also may be used.
  • plant expression vectors include pBIO1, pBI101.2, pBI101.3, pBI121 and pBIN19 (Clontech).
  • animal expression vectors include pEUK-Cl, pMAM and pMAMneo (Clontech).
  • the recombinant expression vector is a viral vector, e.g., a retroviral vector.
  • the recombinant expression vectors of the disclosures may be prepared using standard recombinant DNA techniques described in, for example, Sambrook et al., supra, and Ausubel et al., supra.
  • Constructs of expression vectors, which are circular or linear, may be prepared to contain a replication system functional in a prokaryotic or eukaryotic host cell.
  • Replication systems may be derived, e.g., from CoIE1, 2 ⁇ plasmid, ⁇ , SV40, bovine papilloma virus, 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 (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 (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 may include one or more marker genes, which allow for selection of transformed or transfected hosts.
  • Marker genes include biocide resistance, e.g., resistance to antibiotics, heavy metals, etc., complementation in an auxotrophic host 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 may comprise a native or normative promoter operably linked to the nucleotide sequence encoding the binding agent or conjugate or to the nucleotide sequence which is complementary to or which hybridizes to the nucleotide sequence encoding the binding agent or conjugate.
  • promoters e.g., strong, weak, inducible, tissue-specific and developmental-specific, is within the ordinary skill of the artisan.
  • the promoter may 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
  • the inventive recombinant expression vectors may be designed for either transient expression, for stable expression, or for both. Also, the recombinant expression vectors may be made for constitutive expression or for inducible expression. Further, the recombinant expression vectors may 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 may 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.
  • agent e.g., a drug
  • HSV Herpes Simplex Virus
  • TK thymidine kinase
  • the disclosures further provides a host cell comprising any of the nucleic acids or vectors described herein.
  • the term “host cell” refers to any type of cell that may contain the nucleic acid or vector described herein.
  • the host cell is a eukaryotic cell, e.g., plant, animal, fungi, or algae, or may be a prokaryotic cell, e.g., bacteria or protozoa.
  • the host cells is a cell originating or obtained from a subject, as described herein.
  • the host cell originates from or is obtained from a 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). 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.
  • the host cell is a cultured cell or a primary cell, i.e., isolated directly from an organism, e.g., a human.
  • the host cell in exemplary aspects is 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 (CHO) cells, monkey VERO cells, T293 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 in some aspects a mammalian cell.
  • the host cell is a human cell. While the host cell may be of any cell type, the host cell may originate from any type of tissue, and may be of any developmental stage.
  • the host cell is a hematopoietic stem cell or progenitor cell. See, e.g, Nakamura De Oliveira et al., Human Gene Therapy 24:824-839 (2013).
  • the host cell in exemplary aspects is a peripheral blood lymphocyte (PBL).
  • the host cell is a natural killer cell.
  • the host cell is a T cell.
  • the T cell may 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 may be obtained from numerous sources, including but not limited to blood, bone marrow, lymph node, the thymus, or other tissues or fluids. T cells may also be enriched for or purified. The T cell may be obtained by maturing hematopoietic stem cells, either in vitro or in vivo, into T cells. In exemplary aspects, the T cell is a human T cell.
  • the T cell is a T cell isolated from a human.
  • the T cell may be any type of T cell, including NKT cell, and may be of any developmental stage, including but not limited to, CD4+/CD8+ double positive T cells, CDA+ helper T cells, e.g., Th1 and Th2 cells, CD8+ T cells (e.g., cytotoxic T cells), peripheral blood mononuclear cells (PBMCs), peripheral blood leukocytes (PBLs), tumor infiltrating cells (TILs), memory T cells, naive T cells, and the like.
  • the T cell is a CD8+ T cell or a CD4+ T cell.
  • the population of cells may 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 cells, 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 cells, a muscle cell, a brain cell, etc.
  • the population of cells may 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 may 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 expressing a nucleic acid or a vector described herein.
  • the binding agents, conjugates, nucleic acids, vectors, host cells, or populations of cells are admixed with a pharmaceutically acceptable carrier. Accordingly, pharmaceutical compositions comprising any of the binding agents, conjugates, nucleic acids, vectors, host cells, or populations of cells described herein and comprising a pharmaceutically acceptable carrier, diluent, or excipient are contemplated.
  • the pharmaceutically acceptable carrier is any of those conventionally used and is limited only by physico-chemical considerations, such as solubility and lack of reactivity with the active binding agent(s), and by the route of administration.
  • the pharmaceutically acceptable carriers described herein, for example, vehicles, adjuvants, excipients, and diluents, are well-known to those skilled in the art and are readily available to the public.
  • the pharmaceutically acceptable carrier is one that is chemically inert to the active ingredient(s) of the pharmaceutical composition, e.g., the first binding agent and the second binding agent, and one which has no detrimental side effects or toxicity under the conditions of use.
  • the carrier in some embodiments does not produce adverse, allergic, or other untoward reactions when administered to an animal or a human.
  • the pharmaceutical composition in some aspects is free of pyrogens, as well as other impurities that could be harmful to humans or animals.
  • Pharmaceutically acceptable carriers include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like; the use of which are well known in the art.
  • Acceptable carriers, excipients or stabilizers are nontoxic to recipients and are preferably inert at the dosages and concentrations employed, and include buffers such as phosphate, citrate, or other organic acids; antioxidants such as ascorbic acid; low molecular weight polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as Tween, Pluronics or polyethylene glycol (PEG).
  • buffers such as phosphate, citrate, or other organic acids
  • antioxidants such as ascorbic acid
  • compositions useful for practicing the methods disclosed herein may be prepared for storage by mixing the selected composition having the desired degree of purity with optional physiologically pharmaceutically-acceptable carriers, excipients, or stabilizers (Remington's Pharmaceutical Sciences, 18th edition, A. R. Gennaro, ed., Mack Publishing Company (1990)) in the form of a lyophilized cake or an aqueous solution.
  • Pharmaceutical compositions may be produced by admixing with one or more suitable carriers or adjuvants such as water, mineral oil, polyethylene glycol, starch, talcum, lactose, thickeners, stabilizers, suspending agents, and the like.
  • suitable carriers or adjuvants such as water, mineral oil, polyethylene glycol, starch, talcum, lactose, thickeners, stabilizers, suspending agents, and the like.
  • Such compositions may be in the form of solutions, suspensions, tablets, capsules, creams, salves, ointments, or other conventional forms.
  • compositions to be used for in vivo administration should be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution.
  • Therapeutic compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
  • the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • the form should be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and should be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the composition for parenteral administration ordinarily will be stored in lyophilized form or in solution.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and by the use of surfactants.
  • the prevention of the action of microorganisms can be brought about by various antibacterial and/or antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by the inclusion in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • the choice of carrier will be determined in part by the particular type of binding agents of the pharmaceutical composition, as well as by the particular route used to administer the pharmaceutical composition. Accordingly, there are a variety of suitable formulations of the pharmaceutical composition.
  • composition of the present disclosures can comprise any pharmaceutically acceptable ingredient including, for example, acidifying agents, additives, adsorbents, aerosol propellants, air displacement agents, alkalizing agents, anticaking agents, anticoagulants, antimicrobial preservatives, antioxidants, antiseptics, bases, binders, buffering agents, chelating agents, coating agents, coloring agents, desiccants, detergents, diluents, disinfectants, disintegrants, dispersing agents, dissolution-enhancing agents, dyes, emollients, emulsifying agents, emulsion stabilizers, fillers, film-forming agents, flavor enhancers, flavoring agents, flow enhancers, gelling agents, granulating agents, humectants, lubricants, mucoadhesives, ointment bases, ointments, oleaginous vehicles, organic bases, pastille bases, pigments, plasticizers, polishing agents, preservatives, sequestering agents,
  • the pharmaceutical compositions may be formulated to achieve a physiologically compatible pH.
  • the pH of the pharmaceutical composition may be at least 5, at least 5.5, at least 6, at least 6.5, at least 7, at least 7.5, at least 8, at least 8.5, at least 9, at least 9.5, at least 10, or at least 10.5 up to and including pH 11, depending on the formulation and route of administration.
  • the pharmaceutical compositions may comprise buffering agents to achieve a physiologically compatible pH.
  • the buffering agents may include any compounds capable of buffering at the desired pH such as, for example, phosphate buffers (e.g., PBS), triethanolamine, Tris, bicine, TAPS, tricine, HEPES, TES, MOPS, PIPES, cacodylate, MES, and others known in the art.
  • the pharmaceutical composition comprising the binding agents described herein is formulated for parenteral administration, subcutaneous administration, intravenous administration, intramuscular administration, intraarterial administration, intrathecal administration, or interperitoneal administration.
  • the pharmaceutical composition is administered via nasal, spray, oral, aerosol, rectal, or vaginal administration.
  • the compositions may be administered by infusion, bolus injection or by implantation device.
  • Formulations suitable for oral administration can consist of (a) liquid solutions, such as an effective amount of the composition of the present disclosure dissolved in diluents, such as water, saline, or orange juice; (b) capsules, sachets, tablets, lozenges, and troches, each containing a predetermined amount of the active ingredient, as solids or granules; (c) powders; (d) suspensions in an appropriate liquid; and (e) suitable emulsions.
  • Liquid formulations may include diluents, such as water and alcohols, for example, ethanol, benzyl alcohol, and the polyethylene alcohols, either with or without the addition of a pharmaceutically acceptable surfactant.
  • Capsule forms can be of the ordinary hard- or soft-shelled gelatin type containing, for example, surfactants, lubricants, and inert fillers, such as lactose, sucrose, calcium phosphate, and corn starch.
  • Tablet forms can include one or more of lactose, sucrose, mannitol, corn starch, potato starch, alginic acid, microcrystalline cellulose, acacia, gelatin, guar gum, colloidal silicon dioxide, croscarmellose sodium, talc, magnesium stearate, calcium stearate, zinc stearate, stearic acid, and other excipients, colorants, diluents, buffering agents, disintegrating agents, moistening agents, preservatives, flavoring agents, and other pharmacologically compatible excipients.
  • Lozenge forms can comprise a composition of the disclosure in a flavor, usually sucrose and acacia or tragacanth, as well as pastilles comprising a composition of the disclosure in an inert base, such as gelatin and glycerin, or sucrose and acacia, emulsions, gels, and the like, optionally also containing such excipients as are known in the art.
  • a flavor usually sucrose and acacia or tragacanth
  • pastilles comprising a composition of the disclosure in an inert base, such as gelatin and glycerin, or sucrose and acacia, emulsions, gels, and the like, optionally also containing such excipients as are known in the art.
  • compositions of the disclosure can be delivered via pulmonary administration and can be made into aerosol formulations to be administered via inhalation.
  • aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen, and the like. They also may be formulated as pharmaceuticals for non-pressured preparations, such as in a nebulizer or an atomizer. Such spray formulations also may be used to spray mucosa.
  • the composition is formulated into a powder blend or into microparticles or nanoparticles. Suitable pulmonary formulations are known in the art.
  • Topical formulations are well-known to those of skill in the art. Such formulations are particularly suitable in the context of the invention for application to the skin.
  • parenteral administration includes, but is not limited to, intravenous, intraarterial, intramuscular, intracerebral, intracerebroventricular, intracardiac, subcutaneous, intraosseous, intradermal, intrathecal, intraperitoneal, retrobulbar, intrapulmonary, intravesical, and intracavernosal injections or infusions. Administration by surgical implantation at a particular site is contemplated as well.
  • Formulations suitable for parenteral administration include aqueous and non-aqueous, isotonic sterile injection solutions, which can contain anti-oxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives.
  • parenteral means not through the alimentary canal but by some other route such as subcutaneous, intramuscular, intraspinal, or intravenous.
  • composition of the present disclosure can be administered with a physiologically acceptable diluent in a pharmaceutical carrier, such as a sterile liquid or mixture of liquids, including water, saline, aqueous dextrose and related sugar solutions, an alcohol, such as ethanol or hexadecyl alcohol, a glycol, such as propylene glycol or polyethylene glycol, dimethylsulfoxide, glycerol, ketals such as 2,2-dimethyl-1,5,3-dioxolane-4-methanol, ethers, poly(ethyleneglycol) 400, oils, fatty acids, fatty acid esters or glycerides, or acetylated fatty acid glycerides with or without the addition of a pharmaceutically acceptable surfactant, such as a soap or a detergent, a suspending agent, such as pectin, carbomers, methylcellulose, hydroxypropylmethylcellulose, or carboxymethylcellulose, or emulsifying agents and other pharmaceutical adjuvant
  • Oils which can be used in parenteral formulations include petroleum, animal, vegetable, or synthetic oils. Specific examples of oils include peanut, soybean, sesame, cottonseed, corn, olive, petrolatum, and mineral. Suitable fatty acids for use in parenteral formulations include oleic acid, stearic acid, and isostearic acid. Ethyl oleate and isopropyl myristate are examples of suitable fatty acid esters.
  • the parenteral formulations in some embodiments contain preservatives or buffers.
  • such compositions optionally contain one or more nonionic surfactants having a hydrophile-lipophile balance (HLB) of from about 12 to about 17.
  • HLB hydrophile-lipophile balance
  • the quantity of surfactant in such formulations will typically range from about 5% to about 15% by weight.
  • Suitable surfactants include polyethylene glycol sorbitan fatty acid esters, such as sorbitan monooleate and the high molecular weight adducts of ethylene oxide with a hydrophobic base, formed by the condensation of propylene oxide with propylene glycol.
  • parenteral formulations can be presented in unit-dose or multi-dose sealed containers, such as ampoules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid excipient, for example, water, for injections, immediately prior to use.
  • sterile liquid excipient for example, water
  • Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described and known in the art.
  • Injectable formulations are in accordance with the invention.
  • the requirements for effective pharmaceutical carriers for injectable compositions are well-known to those of ordinary skill in the art (see, e.g., Pharmaceutics and Pharmacy Practice , J. B. Lippincott Company, Philadelphia, Pa., Banker and Chalmers, eds., pages 238-250 (1982), and ASHP Handbook on Injectable Drugs , Toissel, 4th ed., pages 622-630 (1986)).
  • composition of the disclosure can be formulated as inclusion complexes, such as cyclodextrin inclusion complexes, or liposomes.
  • the amount or dose of the pharmaceutical composition administered is sufficient to effect, e.g., a therapeutic or prophylactic response, in the subject or animal over a reasonable time frame.
  • the dose of the pharmaceutical composition is sufficient to treat or prevent a disease or medical condition in a period of from about 12 hours, about 18 hours, about 1 to 4 days or longer, e.g., 5 days, 6 days, 1 week, 10 days, 2 weeks, 16 to 20 days, or more, from the time of administration. In certain embodiments, the time period is even longer.
  • the dose is determined by the efficacy of the particular pharmaceutical composition and the condition of the animal (e.g., human), as well as the body weight of the animal (e.g., human) to be treated.
  • an assay which comprises comparing the extent to which the binding agents block IL13R ⁇ 2-mediated cell growth upon administration of a given dose to a mammal among a set of mammals each of which is given a different dose of binding agents is used to determine a starting dose to be administered to a mammal.
  • the extent to which the binding agents block IL13R ⁇ 2 mediated cell growth upon administration of a certain dose can be assayed by methods known in the art.
  • the dose of the pharmaceutical composition also will be determined by the existence, nature and extent of any adverse side effects that might accompany the administration of a particular pharmaceutical composition. Typically, the attending physician will decide the dosage of the pharmaceutical composition with which to treat each individual patient, taking into consideration a variety of factors, such as age, body weight, general health, diet, sex, binding agents of the pharmaceutical composition to be administered, route of administration, and the severity of the condition being treated.
  • the dose of the binding agent of the present disclosure can be about 0.0001 to about 1 g/kg body weight of the subject being treated/day, from about 0.0001 to about 0.001 g/kg body weight/day, or about 0.01 mg to about 1 g/kg body weight/day.
  • the pharmaceutical composition in some aspects comprise the binding agent of the present disclosure at a concentration of at least A, wherein A is about 0.001 mg/ml, about 0.01 mg/ml, 0 about 1 mg/ml, about 0.5 mg/ml, about 1 mg/ml, about 2 mg/ml, about 3 mg/ml, about 4 mg/ml, about 5 mg/ml, about 6 mg/ml, about 7 mg/ml, about 8 mg/ml, about 9 mg/ml, about 10 mg/ml, about 11 mg/ml, about 12 mg/ml, about 13 mg/ml, about 14 mg/ml, about 15 mg/ml, about 16 mg/ml, about 17 mg/ml, about 18 mg/ml, about 19 mg/ml, about 20 mg/ml, about 21 mg/ml, about 22 mg/ml, about 23 mg/ml, about 24 mg/ml, about 25 mg/ml or higher.
  • A is about 0.001 mg/ml, about 0.01
  • the pharmaceutical composition comprises the binding agent at a concentration of at most B, wherein B is about 30 mg/ml, about 25 mg/ml, about 24 mg/ml, about 23, mg/ml, about 22 mg/ml, about 21 mg/ml, about 20 mg/ml, about 19 mg/ml, about 18 mg/ml, about 17 mg/ml, about 16 mg/ml, about 15 mg/ml, about 14 mg/ml, about 13 mg/ml, about 12 mg/ml, about 11 mg/ml, about 10 mg/ml, about 9 mg/ml, about 8 mg/ml, about 7 mg/ml, about 6 mg/ml, about 5 mg/ml, about 4 mg/ml, about 3 mg/ml, about 2 mg/ml, about 1 mg/ml, or about 0.1 mg/ml.
  • the compositions may contain an analog at a concentration range of A to B mg/ml, for example, about 0.001 to about 30.0 mg/
  • Additional dosing guidance can be gauged from other antibody therapeutics, such as bevacizumab (AvastinTM Genentech); Cetuximab (ExbituxTM Imclone), Panitumumab (VectibixTM Amgen), and Trastuzumab (HerceptinTM Genentech).
  • bevacizumab AvastinTM Genentech
  • Cetuximab ExbituxTM Imclone
  • Panitumumab VectibixTM Amgen
  • Trastuzumab HerceptinTM Genentech
  • the disclosed pharmaceutical formulations may be administered according to any regimen including, for example, daily (1 time per day, 2 times per day, 3 times per day, 4 times per day, 5 times per day, 6 times per day), every two days, every three days, every four days, every five days, every six days, weekly, bi-weekly, every three weeks, monthly, or bi-monthly.
  • Timing like dosing can be fine-tuned based on dose-response studies, efficacy, and toxicity data, and initially gauged based on timing used for other antibody therapeutics.
  • the pharmaceutical composition is in certain aspects modified into a depot form, such that the manner in which the active ingredients of the pharmaceutical composition (e.g., the binding agents) is released into the body to which it is administered is controlled with respect to time and location within the body (see, for example, U.S. Pat. No. 4,450,150).
  • Depot forms in various aspects, include, for example, an implantable composition comprising a porous or non-porous material, such as a polymer, wherein the binding agents are encapsulated by or diffused throughout the material and/or degradation of the non-porous material.
  • the depot is then implanted into the desired location within the body and the binding agents are released from the implant at a predetermined rate.
  • the pharmaceutical composition in certain aspects is modified to have any type of in vivo release profile.
  • the pharmaceutical composition is an immediate release, controlled release, sustained release, extended release, delayed release, or bi-phasic release formulation.
  • Methods of formulating peptides (e.g., peptide binding agents) for controlled release are known in the art. See, for example, Qian et al., J Pharm 374: 46-52 (2009) and International Patent Application Publication Nos. WO 2008/130158, WO2004/033036; WO2000/032218; and WO 1999/040942.
  • sustained-release preparations include semipermeable polymer matrices in the form of shaped articles, e.g., films, or microcapsules.
  • Sustained release matrices include polyesters, hydrogels, polylactides (U.S. Pat. No. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman, et al., Biopolymers, 22: 547-556 (1983)), poly (2-hydroxyethyl-methacrylate) (Langer, et al., J. Biomed. Mater. Res., 15:167-277 (1981) and Langer, Chem.
  • Sustained-release compositions also may include liposomes, which can be prepared by any of several methods known in the art (e.g., DE 3,218,121; Epstein, et al., Proc. Natl. Acad. Sci. USA, 82:3688-3692 (1985); Hwang, et al., Proc. Natl. Acad. Sci. USA, 77:4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949).
  • compositions of the disclosures may be employed alone, or in combination with other agents.
  • more than one type of binding agent are administered.
  • the administered composition e.g., pharmaceutical composition
  • the compositions of the disclosure are administered together with another therapeutic agent or diagnostic agent, including any of those described herein.
  • Certain diseases, e.g., cancers, or patients may lend themselves to a treatment of combined agents to achieve an additive or even a synergistic effect compared to the use of any one therapy alone.
  • the binding agents, conjugates, host cells, populations of cells, and pharmaceutical compositions are useful for treating a neoplasm, tumor, or a cancer.
  • the term “treat” and “prevent” as well as words stemming therefrom, as used herein, do not necessarily imply 100% or complete treatment (e.g., cure) or prevention. Rather, there are varying degrees of treatment or prevention of which one of ordinary skill hi the art recognizes as having a potential benefit or therapeutic effect.
  • the methods of the present disclosures can provide any amount or any level of treatment or prevention of a cancer in a patient, e.g., a human.
  • the treatment or prevention provided by the method disclosed herein can include treatment or prevention of one or more conditions or symptoms of the disease, e.g., cancer, being treated or prevented.
  • “prevention” can encompass delaying the onset of the disease, or a symptom or condition thereof.
  • the materials and methods described herein are especially useful for inhibiting neoplastic cell growth or spread; particularly neoplastic cell growth for which the IL13R ⁇ 2 targeted by the binding agents plays a role.
  • Neoplasms treatable by the binding agents, conjugates, host cells, populations of cells, and pharmaceutical compositions of the disclosures include solid tumors, for example, carcinomas and sarcomas.
  • Carcinomas include malignant neoplasms derived from epithelial cells which infiltrate, for example, invade, surrounding tissues and give rise to metastases.
  • Adenocarcinomas are carcinomas derived from glandular tissue, or from tissues that form recognizable glandular structures.
  • Another broad category of cancers includes sarcomas and fibrosarcomas, which are tumors whose cells are embedded in a fibrillar or homogeneous substance, such as embryonic connective tissue.
  • the invention also provides methods of treatment of cancers of myeloid or lymphoid systems, including leukemias, lymphomas, and other cancers that typically are not present as a tumor mass, but are distributed in the vascular or lymphoreticular systems. Further contemplated are methods for treatment of adult and pediatric oncology, growth of solid tumors/malignancies, myxoid and round cell carcinoma, locally advanced tumors, cancer metastases, including lymphatic metastases.
  • the cancers listed herein are not intended to be limiting. Both age (child and adult), sex (male and female), primary and secondary, pre- and post-metastatic, acute and chronic, benign and malignant, anatomical location cancer embodiments and variations are contemplated targets.
  • Cancers are grouped by embryonic origin (e.g., carcinoma, lymphomas, and sarcomas), by organ or physiological system, and by miscellaneous grouping. Particular cancers may overlap in their classification, and their listing in one group does not exclude them from another.
  • Carcinomas that may be targeted include adrenocortical, acinar, acinic cell, acinous, adenocystic, adenoid cystic, adenoid squamous cell, cancer adenomatosum, adenosquamous, adnexel, cancer of adrenal cortex, adrenocortical, aldosterone-producing, aldosterone-secreting, alveolar, alveolar cell, ameloblastic, ampullary, anaplastic cancer of thyroid gland, apocrine, basal cell, basal cell, alveolar, comedo basal cell, cystic basal cell, morphea-like basal cell, multicentric basal cell, nodulo-ulcerative basal cell, pigmented basal cell, sclerosing basal cell, superficial basal cell, basaloid, basosquamous cell, bile duct, extrahepatic bile duct, intrahepatic bil
  • Sarcomas that may be targeted include adipose, alveolar soft part, ameloblastic, avian, botryoid, sarcoma botryoides, chicken, chloromatous, chondroblastic, clear cell sarcoma of kidney, embryonal, endometrial stromal, epithelioid, Ewing's, fascial, fibroblastic, fowl, giant cell, granulocytic, hemangioendothelial, Hodgkin's, idiopathic multiple pigmented hemorrhagic, immunoblastic sarcoma of B cells, immunoblastic sarcoma of T cells, Jensen's, Kaposi's, Kupffer cell, leukocytic, lymphatic, melanotic, mixed cell, multiple, lymphangio, idiopathic hemorrhagic, multipotential primary sarcoma of bone, osteoblastic, osteogenic, parosteal, polymorphous, pseudo-
  • Lymphomas that may targeted include AIDS-related, non-Hodgkin's, Hodgkin's, T-cell, T-cell leukemia/lymphoma, African, B-cell, B-cell monocytoid, bovine malignant, Burkitt's, centrocytic, lymphoma cutis, diffuse, diffuse, large cell, diffuse, mixed small and large cell, diffuse, small cleaved cell, follicular, follicular center cell, follicular, mixed small cleaved and large cell, follicular, predominantly large cell, follicular, predominantly small cleaved cell, giant follicle, giant follicular, granulomatous, histiocytic, large cell, immunoblastic, large cleaved cell, large noncleaved cell, Lennert's, lymphoblastic, lymphocytic, intermediate; lymphocytic, intermediately differentiated, plasmacytoid; poorly differentiated lymphocytic, small lymph
  • Leukemias and other blood cell malignancies that may be targeted include acute lymphoblastic, acute myeloid, lymphocytic, chronic myelogenous, hairy cell, lymphoblastic, myeloid, lymphocytic, myelogenous, leukemia, hairy cell, T-cell, monocytic, myeloblastic, granulocytic, gross, hand mirror-cell, basophilic, hemoblastic, histiocytic, leukopenic, lymphatic, Schilling's, stem cell, myelomonocytic, prolymphocytic, micromyeloblastic, megakaryoblastic, megakaryocytic, Rieder cell, bovine, aleukemic, mast cell, myelocytic, plasma cell, subleukemic, multiple myeloma, nonlymphocytic, and chronic myelocytic leukemias.
  • Brain and central nervous system (CNS) cancers and tumors that may be targeted include astrocytomas (including cerebellar and cerebral), gliomas (including malignant gliomas, glioblastomas, brain stem gliomas, visual pathway and hypothalamic gliomas), brain tumors, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumors, primary central nervous system lymphoma, extracranial germ cell tumor, myelodysplastic syndromes, oligodendroglioma, myelodysplastic/myeloproliferative diseases, myelogenous leukemia, myeloid leukemia, multiple myeloma, myeloproliferative disorders, neuroblastoma, plasma cell neoplasm/multiple myeloma, central nervous system lymphoma, intrinsic brain tumors, astrocytic brain tumors, and metastatic tumor cell invasion in the central nervous system.
  • Gastrointestinal cancers that may be targeted include extrahepatic bile duct cancer, colon cancer, colon and rectum cancer, colorectal cancer, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal carcinoid tumors, gastrointestinal stromal tumors, bladder cancers, islet cell carcinoma (endocrine pancreas), pancreatic cancer, islet cell pancreatic cancer, prostate cancer rectal cancer, salivary gland cancer, small intestine cancer, colon cancer, and polyps associated with colorectal neoplasia.
  • gastric (stomach) cancer gastric (stomach) cancer
  • gastrointestinal carcinoid tumor gastrointestinal carcinoid tumors
  • gastrointestinal stromal tumors gastrointestinal stromal tumors
  • bladder cancers islet cell carcinoma (endocrine pancreas), pancreatic cancer, islet cell pancreatic cancer, prostate cancer rectal cancer, salivary gland cancer, small intestine cancer, colon cancer, and polyps associated with
  • Bone cancers that may be targeted include osteosarcoma and malignant fibrous histiocytomas, bone marrow cancers, bone metastases, osteosarcoma/malignant fibrous histiocytoma of bone, and osteomas and osteosarcomas.
  • Breast cancers that may be targeted include small cell carcinoma and ductal carcinoma.
  • Lung and respiratory cancers that may be targeted include bronchial adenomas/carcinoids, esophagus cancer esophageal cancer, esophageal cancer, hypopharyngeal cancer, laryngeal cancer, hypopharyngeal cancer, lung carcinoid tumor, non-small cell lung cancer, small cell lung cancer, small cell carcinoma of the lungs, mesothelioma, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, nasopharyngeal cancer, oral cancer, oral cavity and lip cancer, oropharyngeal cancer; paranasal sinus and nasal cavity cancer, and pleuropulmonary blastoma.
  • bronchial adenomas/carcinoids esophagus cancer esophageal cancer, esophageal cancer, hypopharyngeal cancer, laryngeal cancer, hypopharyngeal cancer, lung carcinoid tumor, non-small cell lung cancer
  • Urinary tract and reproductive cancers that may be targeted include cervical cancer, endometrial cancer, ovarian epithelial cancer, extragonadal germ cell tumor, extracranial germ cell tumor, extragonadal germ cell tumor, ovarian germ cell tumor, gestational trophoblastic tumor, spleen, kidney cancer, ovarian cancer, ovarian epithelial cancer, ovarian germ cell tumor, ovarian low malignant potential tumor, penile cancer, renal cell cancer (including carcinomas), renal cell cancer, renal pelvis and ureter (transitional cell cancer), transitional cell cancer of the renal pelvis, and ureter, gestational trophoblastic tumor, testicular cancer, ureter and renal pelvis, transitional cell cancer, urethral cancer, endometrial uterine cancer, uterine sarcoma, vaginal cancer, vulvar cancer, ovarian carcinoma, primary peritoneal epithelial neoplasms, cervical carcinoma, uterine cancer and solid tumors in the ovarian
  • Skin cancers and melanomas (as well as non-melanomas) that may be targeted include cutaneous t-cell lymphoma, intraocular melanoma, tumor progression of human skin keratinocytes, basal cell carcinoma, and squamous cell cancer.
  • Liver cancers that may be targeted include extrahepatic bile duct cancer, and hepatocellular cancers.
  • Eye cancers that may be targeted include intraocular melanoma, retinoblastoma, and intraocular melanoma
  • Hormonal cancers that may be targeted include: parathyroid cancer, pineal and supratentorial primitive neuroectodermal tumors, pituitary tumor, thymoma and thymic carcinoma, thymoma, thymus cancer, thyroid cancer, cancer of the adrenal cortex, and ACTH-producing tumors.
  • Miscellaneous other cancers that may be targeted include advanced cancers, AIDS-related, anal cancer, adrenal, cortical, aplastic anemia, aniline, betel or buyo cheek, cerebriform, chimney-sweeps, clay pipe, colloid, contact, cystic, dendritic, cancer avers, duct, dye workers, encephaloid, cancer en cuirasse, endometrial, endothelial, epithelial, glandular, cancer in situ, kang, kangri, latent, medullary, melanotic, mule-spinners′, non-small cell lung, occult cancer, paraffin, pitch workers′, scar, schistosomal bladder, scirrhous, lymph node, small cell lung, soft, soot, spindle cell, swamp, tar, and tubular cancers.
  • Miscellaneous other cancers that may be targeted also include carcinoid (gastrointestinal and bronchial) Castleman's disease chronic myeloproliferative disorders, clear cell sarcoma of tendon sheaths, Ewing's family of tumors, head and neck cancer, lip and oral cavity cancer, Waldenstrom's macroglobulinemia, metastatic squamous neck cancer with occult primary, multiple endocrine neoplasia syndrome, multiple myeloma/plasma cell neoplasm, Wilms' tumor, mycosis fungoides, pheochromocytoma, sezary syndrome, supratentorial primitive neuroectodermal tumors, unknown primary site, peritoneal effusion, malignant pleural effusion, trophoblastic neo-plasms, and hemangiopericytoma.
  • carcinoid gastrointestinal and bronchial
  • Castleman's disease chronic myeloproliferative disorders clear cell sarcoma
  • the cancer is any one of the foregoing described in which IL13R ⁇ 2 is expressed on the cells of the cancer.
  • the cancer is colon cancer.
  • the cancer is Glioblastoma Multiforme.
  • the method of treating cancer in a subject in need thereof comprises administering to the subject any of the binding agents, conjugates, nucleic acids, vectors, host cells, cell populations, or pharmaceutical compositions described herein, in an amount effective to treat the cancer.
  • the method comprises administering a conjugate described herein.
  • the method comprises administering host cells of the disclosures and the host cells are autologous cells in relation to the subject being treated.
  • the method comprises administering host cells of the disclosures and the host cells are cells obtained from the subject being treated.
  • the cells are T-lymphocytes.
  • the cells are natural killer cells.
  • Lipofectamine 2000 and the pEF6/Myc-His vector were obtained from Invitrogen.
  • Monoclonal antibodies to IL13R ⁇ 2 (clones YY-23Z and B-D13) and the IsoStrip mouse monoclonal antibody isotyping kit were purchased from Santa Cruz Biotechnology (Santa Cruz, Calif.).
  • the mAb to IL13R ⁇ 2 (clone 83807) and recombinant human and mouse IL13R ⁇ 2hFc and IL13R ⁇ 1hFc chimeras were purchased from R&D Systems (Minneapolis, Minn.).
  • Biotinylated horse anti-mouse antibodies and the Elite kit were obtained from Vector Laboratories (Burlingame, Calif.).
  • 3,3′-Diaminobenzidine substrate was purchased from Dako (Carpinteria, Calif.). Goat anti-mouse antibody conjugated with peroxidase was purchased from Chemicon International (Temicula, Calif.), and Pngase F was purchased from New England Biolabs (Ipswich, Mass.).
  • the QuikChange LightningTM site-directed mutagenesis kit was purchased from Agilent Technologies, Inc. (Santa Clara, Calif.), and the RNeasy PlusTM kit was received from Qiagen (Valencia, Calif.).
  • the cDNA iScriptTM kit, 7.5% Tris-HCl gel, and ImmunStarTM WesternCTM developing reagent and protein marker were purchased from Bio-Rad.
  • the human IL-13 ELISA kit was purchased from eBioscience (San Diego, Calif.). GBM12 and GBM43 were kindly provided by Dr. David C. James (University of California-San Francisco), and the cDNA encoding human wild-type IL13R ⁇ 2 was obtained from Dr. Waldemar Debinski (Wake Forest University). Obtaining the cDNA encoding the human wild-type IL13R ⁇ 2 or most other proteins involves the use of well-known techniques and readily available reagents.
  • U373 (GBM), 293T (human embryonic kidney), and Raji (Burkitt's lymphoma) cell line were purchased from the American Type Culture Collection (ATCC; Manassas, Va.).
  • U373 cells expressing enhanced green fluorescent protein and firefly luciferase U373.eGFP.ffLuc
  • 293T cells expressing green fluorescent protein 293T.GFP
  • IL13R ⁇ 2 and GFP 293T.IL13R ⁇ 2.GFP
  • the human recombinant IL13R ⁇ 2hFc fusion was used for immunization of animals and in all screening assays.
  • Two 6-week-old female BALB/c mice were immunized with intraperitoneal injection of 10 ⁇ g of rhIL13R ⁇ 2hFc protein in complete Freund's adjuvant followed by intraperitoneal injection of 10 ⁇ g of rhIL13R ⁇ 2hFc protein in incomplete Freund's adjuvant at a 2-week interval for 2 months.
  • mice spleen cells were fusions with the mouse myeloma cell line X63.Ag8.653 subclone P3O1 by using a procedure described by Köhler and Milstein (27). Hybridoma supernatants were assayed for the presence of IL13R ⁇ 2 antibodies using an enzyme-linked immunosorbent assay (ELISA). Selected populations were cloned, and supernatants were assayed to identify the clones with strongest binding.
  • ELISA enzyme-linked immunosorbent assay
  • the cDNA encoding human wild-type IL13R ⁇ 2 was amplified with the following primer pair: forward, 5′-GCTTGGTACCGAATGGCTTTCGTTTGCTTGGC-3′ (SEQ ID NO: 17) and reverse, 5′-GTTTTTGTTCGAATGTATCACAGAAAAATTCTGG-3′ (SEQ ID NO: 18).
  • the purified PCR product was restricted with KpnI and BstBI enzymes, agarose gel-purified, and subsequently cloned into the pEF6/Myc-His vector in a reading frame with Myc and His6 tags.
  • CHO cells were plated at 80% confluence and transfected with a plasmid encoding the IL13R ⁇ 2 using Lipofectamine 2000. The following day, 4 ⁇ g/ml blasticidin was added for selection of cells that had stably incorporated and expressed the IL13R ⁇ 2 transcript. A stable population of cells was further subcloned in 96-well plates at a density of one cell/well. Ten days later, single clones were screened by flow cytometry for cell surface expression of IL13R ⁇ 2 using an antibody to IL13R ⁇ 2 (clone B-D13). The clone with the highest level of IL13R ⁇ 2 expression was selected and expanded for subsequent screening of hybridomas secreting IL13R ⁇ 2 antibodies.
  • 96-well plates were coated with 50 ⁇ l of human or mouse recombinant IL13R ⁇ 2hFc or IL13R ⁇ 1hFc or human control IgG at a concentration of 1 ⁇ g/ml overnight at 4° C. Following washes with TBS-Tween 20 buffer and blocking with 1% nonfat dry milk, 50 ⁇ l of purified antibodies, serum, or hybridoma supernatants at various dilutions were applied to the plate and incubated for 1 hour at room temperature. Bound antibodies were detected with goat anti-mouse antibodies conjugated to alkaline phosphatase following the development with alkaline phosphatase substrate. Plates were read at A405 using a UniRead 800 plate reader (BioTek).
  • CHO or HEK cells expressing IL13R ⁇ 2; the glioma cell lines A172, N10, U251, U87, and U118; patient-derived GBM12 and GBM43, and primary human astrocytes were stained with IL13R ⁇ 2 (clone 47) monoclonal antibody at 1 ⁇ g/ml followed by goat anti-mouse Alexa Fluor 647 (1:500). All staining procedures were performed on ice. Samples were analyzed using the BD FACSCanto flow cytometer and FACSDiVaTM software.
  • a FACSCalibur instrument (BD Bioscience, Mountain View, Calif.) was used to acquire immunofluorescence data that were analyzed with CellQuest (BD) or FCS Express software (De Novo Software, Los Angeles, Calif.).
  • Isotype controls were immunoglobulin G1-fluorescein isothiocyanate (IgG1-FITC; BD Bioscience) and IgG1-phycoerythrin (IgG1-PE; BD Bioscience).
  • SSR 47-CAR expression was detected by staining T cells with an IL13R ⁇ 2 chimera followed by Fc-FITC (Milipore) or Fc-PE (SouthernBiotech).
  • LSR 47-CARs were detected using Fc-FITC or Fc-PE.
  • U373 cells were analyzed for PD-L1 expression using a CD271 PE antibody (BD Bioscience). Forward- and side-scatter gating were used to discriminate live cells from dead cells. Cells were collected and washed once with phosphate-buffered saline (PBS) containing 1% FBS (Sigma; FACS buffer) prior to the addition of antibodies. Cell were incubated for 30 minutes on ice in the dark, washed once, and fixed in 0.5% paraformaldehyde/FACS buffer prior to analysis.
  • PBS phosphate-buffered saline
  • FACS buffer 1% FBS
  • RNA was generated from the cell pellets using the RNeasy Plus kit. 200 ng of total RNA was then converted into cDNA using the cDNA iScript kit. The cDNA was further amplified by PCR for IL13R ⁇ 2 and GAPDH for 30 cycles using IL13R ⁇ 2 and GAPDH primers and visualized on a 1% agarose gel.
  • IL13R ⁇ 2 (clone 47) monoclonal antibody
  • commercially available IL13R ⁇ 2 monoclonal antibodies (clones 83807 and B-D13)
  • target rhIL13R ⁇ 2
  • SPR surface plasmon resonance
  • the monoclonal antibodies were immobilized (covalently) to the dextran matrix of the sensor chip (CMS) using the amino coupling kit.
  • CMS sensor chip
  • the carboxyl groups on the sensor surfaces were activated with an injection of a solution containing 0.2M N-ethyl-N′-(3-diethylamino-propyl)-carbodiimide and 0.05M N-hydroxysuccinimide.
  • the immobilization procedure was completed by the injection of 1Methanolamine hydrochloride to block the remaining ester groups. All steps of the immobilization process were carried out at a flow rate of 10 ⁇ l/minute.
  • the control surface was prepared similarly with the exception that running buffer was injected rather than monoclonal antibodies. Binding reactions were performed at 25° C. in HBS-P buffer (20 mM HEPES, pH 7.4, 150 mM NaCl, and 0.005% (v/v) surfactant P20) using a flow rate of 20 ⁇ l/minute.
  • Target (rhIL13R ⁇ 2) was added at various concentrations in the flow during the binding phase. The amount of protein bound to the sensor chip was monitored by the change in refractive index (represented by response units (RU)).
  • the instrument was programmed to perform a series of binding measurements with increasing concentrations of target over the same surface. Triplicate injections of each concentration of target were performed. Sensorgrams (plots of changes in RU on the surface as a function of time) were analyzed using BIAevaluation v4.1. Affinity constants were estimated by curve fitting using a 1:1 binding model.
  • the estimation of kinetic parameters was performed by repetitive injections of a range of target concentrations over the immobilized mAbs. Data were prepared by the method of “double referencing.” This method utilizes parallel injections of each target sample over a control dextran surface as well as running buffer injections over both the immobilized mAbs and control dextran surfaces. Subtraction of these sensorgrams yielded the control; this was subtracted from the experimental sensorgram. Each data set (consisting of sensorgrams of increasing target concentrations over the same level of immobilized mAbs) was analyzed using various kinetic models. The BIAevaluation v 4.1 software was then used for data analysis. Affinity constants were estimated by curve fitting using a 1:1 binding model.
  • a 96-well plate was coated with 50 ⁇ l of affinity-purified hrIL13R ⁇ 2hFc at 1 ⁇ g/ml in carbonate buffer, pH 9.6 and stored overnight at 4° C. After washing with PBS containing 0.05% Tween 20, mAbs to IL13R ⁇ 2 (10 ⁇ g/ml) or control mIgG were added for 30 minutes at room temperature. After washing, 50 ⁇ l of purified rhIL-13 in PBS and 0.1% BSA at 10 ng/ml were added for a 1-hour incubation at room temperature and assayed for bound rhIL-13 using detection reagents from a human IL-13 ELISA kit.
  • HEK cells expressing wild-type IL13R ⁇ 2 or 4-amino-acid mutants (see Example 10) in the IL13R ⁇ 2 sequence were pretreated with either rhIL-13 or mAb IL13R ⁇ 2 (clone 47) at 2 ⁇ g/ml for 30 minutes on ice followed by a 1-hour incubation with IL13R ⁇ 2 (clone 47) mAb or rhIL-13 at 100 ng/ml, respectively.
  • Binding of rhIL-13 to IL13R ⁇ 2 alone or in the presence of competitor was detected with human IL-13 mAb-FITC.
  • Binding of IL13R ⁇ 2 (clone 47) mAb to rhIL13R ⁇ 2 alone or in the presence of competitor was detected with anti-mouse antibody conjugated to Alexa Fluor 649 and analyzed by flow cytometry.
  • Tyr 207 , Asp 271 , Tyr 315 , and Asp 318 of the human IL13R ⁇ 2 were identified as residues crucial for interaction with human IL-13 (28).
  • the Tyr 207 , Asp 271 , Tyr 315 , and Asp 318 residues were mutated to Ala separately or at the same time (4-amino-acid mutant) using the QuikChange Lightning site-directed mutagenesis kit according to the manufacturer's recommendations. Sequencing of selected clones was performed using conventional techniques, which confirmed the presence of the selected mutation.
  • HEK cells were transfected with wild-type or mutated variants of IL13R ⁇ 2 cDNA in the pEF6 Myc-His vector using Lipofectamine Plus transfection reagent. 48 hours after transfection, the cells were collected and analyzed for binding to IL13R ⁇ 2 (clone 47) mAb via flow cytometry.
  • the rhIL13R ⁇ 2 was applied to a 7.5% Tris-HCl gel (Bio-Rad) at 200 ng/lane and resolved under reducing conditions. After the transfer of proteins to a PVDF membrane (Bio-Rad) and blocking with 2% nonfat dry milk, the membrane was stained with anti-IL13R ⁇ 2 mAb (clones YY-23Z and B-D13) at 2 ⁇ g/ml or with supernatant collected from hybridoma clones (diluted 10 times), followed by goat anti-mouse antibody conjugated to peroxidase. ImmunStarTM WesternCTM was used to develop reactions. Images were captured using a Bio-Rad ChemiDoc imaging system.
  • cells were dissociated with PBS+3 mM EDTA and lysed in a buffer containing 50 mM Tris, 150 mM NaCl, 5 mM EDTA, 1% Triton X-100 (all from Sigma, St. Louis, Mo.), and protease inhibitors (Thermo Scientific, Waltham, Mass.). Protein concentrations were determined using a Bio-Rad protein assay (Bio-Rad, Hercules, Calif.) with bovine serum albumin (BSA) as the standard. Samples were denatured in Laemmli buffer (Bio-Rad) at 95° C. for 5 minutes.
  • BSA bovine serum albumin
  • the GBM tissues were collected in accordance with a protocol approved by the Institutional Review Board at the University of Chicago. Flash-frozen brain-tumor tissues were cut to a thickness of 10 ⁇ m. Tissue sections were fixed with ⁇ 20° C. methanol and stained for human IL13R ⁇ 2 using mouse IL13R ⁇ 2 (clone 47) mAb at a concentration of 3 ⁇ g/ml or isotype control mIgG1. The bound antibodies were detected with biotinylated horse anti-mouse antibodies (1:100). The antigen-antibody binding was detected by the Elite kit with 3,3′-diaminobenzidine substrate. Slides were analyzed using the CRI Panoramic Scan Whole Slide Scanner and Panoramic Viewer software.
  • mice All animals were maintained and cared for in accordance with the Institutional Animal Care and Use Committee protocol and according to National Institutes of Health guidelines.
  • the animals used in the experiments were 6- to 7-week-old male athymic nu/nu mice.
  • Mice were anesthetized with an intraperitoneal injection of ketamine hydrochloride/xylazine (25 mg/ml/2.5 mg/ml) mixture.
  • ketamine hydrochloride/xylazine 25 mg/ml/2.5 mg/ml
  • a midline cranial incision was made, and a right-sided burr hole was placed 2 mm lateral to the sagittal suture and about 2 mm superior to ⁇ .
  • Animals were positioned in a stereotactic frame, and a Hamilton needle was inserted through the burr hole and advanced 3 mm.
  • Intracranial penetration was followed by (i) injection of 2.5 ⁇ 10 4 U251 glioma cells in 2.5 ⁇ l of sterile PBS in combination with 200 ng of mIgG or IL13R ⁇ 2 (clone 47) mAb or (ii) 3 days post-intracranial injection of glioma cells with PBS or 10 ⁇ g of IL13R ⁇ 2 (clone 47 or B-D13) mAb as described previously (29, incorporated herein by reference). All mice were monitored for survival. Three animals from each group were sacrificed at day 17, and brains were harvested and frozen for sectioning, hematoxylin and eosin (H&E) staining, and microscopic analysis.
  • H&E hematoxylin and eosin
  • ICR-SCID mice were purchased from Taconic (IcrTac:ICR-Prkdcscid; Fox Chase C.B-17 SCIDTM ICR; Taconic, Hudson, N.Y.).
  • mice Male 7- to 9-week-old mice were anesthetized, head were shaved and the mice were immobilized in a CunninghamTM Mouse/Neonatal Rat Adaptor (Stoelting, Wood Dale, Ill.) stereotactic apparatus fitted into an E15600 Lab Standard Stereotaxic Instrument (Stoelting), and then scrubbed with 1% povidone-iodine. A 10 mm skin incision was made along the midline. The tip of a 30G 1 ⁇ 2 inch needle mounted on a Hamilton syringe (Hamilton, Reno, Nev.) served as the reference point. A 1 mm burr-hole was drilled into the skull 1 mm anterior and 2 mm to the right of the bregma.
  • a codon-optimized gene was synthesized by GeneArt (Invitrogen, Carlsbad, Calif.) containing the immunoglobulin heavy-chain leader peptide37, and scFv47 flanked by 5′ NcoI and 3′ BamHI sites.
  • This mini gene was subcloned into SFG retroviral vector containing IL13R ⁇ 2-specific CARs (47-CARs) with short or long spacer regions (SSRs, LSRs) and CD28. ⁇ , CD28.OX40. ⁇ , CD28.41BB. ⁇ , or 41BB. ⁇ endodomains.5,38,39 All CARs contained a CD28 transmembrane domain except for 47.SSR.CAR.41BB. ⁇ , which had a CD8 ⁇ transmembrane domain. 47.SSR.CAR and 47.LSR.CAR without an endodomain (47.SSR.CAR. ⁇ and 47.LSR.CAR. ⁇ ) were generated by PCR cloning.
  • RD114-pseudotyped retroviral particles were generated by transient transfection of 293T cells as previously described in Johnson et al., Sci. Transl. Med. 7:275ra22 (2015), incorporated herein by reference.
  • PBMCs Human peripheral blood mononuclear cells from healthy donors were obtained under a Baylor College of Medicine IRB-approved protocol, after informed consent was obtained in accordance with the Declaration of Helsinki.
  • Lymphoprep Regener Bio-One, Monroe, N.C.
  • OKT3 CRL-8001, ATCC
  • CD28 BD Bioscience, Mountain View, Calif.
  • IL7 human interleukin-7
  • IL15 IL15, 5 ng/mL; Proleukin; Chiron, Emeryville, Calif.
  • OKT3/CD28-stimulated T cells 2.5 ⁇ 10 5 cells/well
  • RetroNectin® RetroNectin® (Clontech, Mountainview, Calif.)-coated plates in the presence of IL7 and IL15.
  • T cells were transferred into new wells and subsequently expanded with IL-7 and IL15.
  • Non-transduced (NT) T cells were activated with OKT3/CD28 and expanded in parallel with IL-7 and IL15. 47-CAR expression was determined 3 to 4 days post-transduction.
  • Non-tissue culture 24-well plates were precoated with recombinant human IL13R ⁇ 1, IL13R ⁇ 2, or IL4R protein, (R&D Systems, Minneapolis, Minn.) at a final concentration of 500 ng/well. Plates were washed once using RPMI, and CAR or NT T cells were plated. After 24 hours, supernatants were harvested and interferon ⁇ (IFN ⁇ ) and Interleukin 2 (IL2) release were measured by ELISA according to the manufacturer's instructions (R&D Systems, Minneapolis, Minn.).
  • IFN ⁇ interferon ⁇
  • IL2 Interleukin 2
  • CAR T cells were co-cultured with target cells at a 1:2 effector to target (E:T) ratio in a 24-well plate.
  • NT T cells served as controls. After 24 hours, culture supernatants were harvested, and the presence of IFN ⁇ and IL2 was determined by ELISA according to the manufacturer's instructions (R&D Systems, Minneapolis, Minn.).
  • Standard chromium ( 51 Cr) release assays were performed as described in Gottschalk et al., Blood 101:1905-1912 (2003), incorporated herein by reference. Briefly, 1 ⁇ 10 6 target cells were labeled with 0.1 mCi (3.7MBq) 51 Cr and mixed with decreasing numbers of effector cells to give effector to target ratios of 40:1, 20:1, 10:1, and 5:1. Target cells incubated in complete medium alone or in 1% Triton X-100 were used to determine spontaneous and maximum 51 Cr release, respectively. After 4 hours, supernatants were collected and radioactivity was measured in a gamma counter (Cobra Quantum; PerkinElmer; Wellesley; MA). The mean percentage of specific lysis of triplicate wells was calculated according to the following formula: [test release ⁇ spontaneous release]/[maximal release ⁇ spontaneous release] ⁇ 100.
  • Isofluorane anesthetized animals were imaged using the IVIS® system (IVIS, Xenogen Corp., Alameda, Calif.) 10-15 minutes after 150 mg/kg D-luciferin (Xenogen) per mouse was injected intraperitoneally.
  • the photons emitted from the luciferase-expressing tumor cells were quantified using Living Image software (Caliper Life Sciences, Hopkinton, Mass.).
  • a pseudo-color image representing light intensity (blue least intense and red most intense) was generated and superimposed over the grayscale reference image.
  • mice were euthanized when the tumor radiance was greater than 1 ⁇ 10 9 on two occasions or when they met euthanasia criteria (neurological deficits, weight loss, signs of distress) in accordance with the Center for Comparative Medicine at Baylor College of Medicine.
  • the primary goal of this study was to generate a high affinity monoclonal antibody suitable for targeting of the IL13R ⁇ 2 expressed on the surface of tumor cells.
  • the concentration of rhIL13R ⁇ 2 absorbed to the plastic at 1 ⁇ g/ml was found to be suitable for the detection of antibody binding ( FIG. 1A ).
  • the rhIL13R ⁇ 2hFc was characterized for its “nativity” by utilizing a pair of commercially available antibodies recognizing only the native (found on the cell surface) and denatured (using Western blotting under reducing conditions) forms of IL13R ⁇ 2 and for its binding properties to rhIL13R ⁇ 2 in ELISA with antibody clones B-D13 and YY-23Z, respectively. Both clones B-D13 and YY-23Z were able to recognize the rhIL13R ⁇ 2hFc in a plate-bound ELISA ( FIG. 1B ). Denaturation of antigen at 95° C.
  • the rhIL13R ⁇ 2hFc absorbed to the plastic of ELISA plates containing both native and denatured forms of the protein.
  • Analysis of serum from animals immunized with a fusion of rhIL13R ⁇ 2 and hFc revealed the presence of antibodies against both rhIL13R ⁇ 2 and human Fc fragment.
  • human IgG was included as an additional negative control for the screening of hybridoma populations.
  • clone 47 strongly binds to the antigen in plate-bound ELISA but not by Western blotting, indicating the ability of clone 47 to recognize a native conformation of the antigen. Therefore, clone 47 was selected for further characterization and for further experiments. Clone 47 was found to be of the IgG1 isotype, possessing a ⁇ chain.
  • FIG. 2A shows strong and specific binding of clone 47 to rhIL13R ⁇ 2 when compared with clones 83807 and B-D13.
  • Clone 47 reached the plateau of binding at the low concentration of 0.05 ⁇ g/ml. None of the antibodies showed binding to human IgG utilized as an additional negative control in these experiments.
  • a clonal line of CHO cells expressing the full size wild-type human IL13R ⁇ 2 (clone 6) was generated. Binding of the antibody to control CHO cells transfected with an empty vector was compared with that of CHO cells expressing IL13R ⁇ 2. Again, the IL13R ⁇ 2 (clone 47) mAb demonstrated strong and specific binding to IL13R ⁇ 2 expressed on the cell surface but not to control CHO cells, indicating that this antibody specifically recognizes a native conformation of the IL13R ⁇ 2 ( FIG. 2B ). Clone 47 demonstrated the strongest affinity for IL13R ⁇ 2 at the lowest tested concentration of 0.25 ⁇ g/ml.
  • FIG. 3 , A and B show the flow charts of the comparative staining of glioma cells, human astrocytes, and HEK cells expressing recombinant human IL13R ⁇ 2 on the cell surface with the IL13R ⁇ 2 (clones 47, 83807, and B-D13) mAb.
  • FIG. 3 , A and B reveal (i) various levels of IL13R ⁇ 2 expression on the cell surface and (ii) superior binding of the clone 47 versus clones B-D13 (1.2-4.6-fold difference between the cell lines) and 83807 to the surface of analyzed cell lines.
  • N10 glioma cells were incubated with either the IL13R ⁇ 2 (clone 47) mAb at 1 ⁇ g/ml or the IL13R ⁇ 2 (clone 47) mAb preincubated with a 10-fold excess of rhIL13R ⁇ 2 ( FIG. 10 ) and analyzed by flow cytometry.
  • a significant ablation of interaction between the IL13R ⁇ 2 (clone 47) mAb in the presence of a 10-fold excess of rhIL13R ⁇ 2 was found when compared with clone 47 alone.
  • IL13R ⁇ 2 (clone 47) mAb possessed the ability to bind IL13R ⁇ 2 on the surface of glioma cells in situ
  • intracranial glioma xenografts of U251 cells expressing green fluorescent protein (GFP) were established in nude mice. Three weeks later, animals were sacrificed, and cells were obtained and placed into in vitro culture conditions. After 48 hours, the cells were collected and stained with control mIgG or IL13R ⁇ 2 (clone 47) mAb. Cultured GFP-expressing U251 cells served as a positive control. GFP-positive U251 cells represented about 56% of the total cells ( FIG.
  • FIG. 4 shows the sensorgrams for each antibody. The measurements are summarized in Table 1.
  • FIG. 4A shows that clone 47 demonstrates a prolonged and stable association with rhIL13R ⁇ 2 measured over a 30-minute time frame, whereas clones 83807 ( FIG. 4B ) and B-D13 ( FIG. 4C ) dissociate relatively quickly.
  • the affinity of binding for the IL13R ⁇ 2 (clone 47) mAb to rhIL13R ⁇ 2 was calculated at 1.39 ⁇ 10 ⁇ 9 M. This value exceeded the affinity of the commercially available antibody clones 83807 and B-D13 to rhIL13R ⁇ 2 by 75-fold and 33-fold, respectively.
  • Clone 47 demonstrated the highest binding affinity (R max ) to rhIL13R ⁇ 2 at 390 RU when compared with 250 and 8-16 RU for clones 83807 and B-D13, respectively. These data indicate that the IL13R ⁇ 2 (clone 47) mAb possesses properties superior to clones 83807 and B-D13 as well as demonstrates a higher affinity toward rhIL13R ⁇ 2.
  • IL13R ⁇ 2 (clone 47) mAb possesses inhibitory properties
  • competitive binding assays utilizing a rhIL13R ⁇ 2hFc chimera and HEK cells transiently expressing the human IL13R ⁇ 2 were performed.
  • the competitive binding assay was set up in a plate-bound ELISA format.
  • the rhIL13R ⁇ 2hFc absorbed to the plate served as the target antigen.
  • FIG. 5A shows that the IL13R ⁇ 2 (clone 47) mAb significantly abolished the binding of rhIL-13 to rhIL13R ⁇ 2, whereas the IL13R ⁇ 2 mAb clones B-D13 and 83807 exhibited significantly less competition for binding of human IL-13.
  • HEK 293T cells were transfected with an agent encoding wild-type or a 4-amino-acid mutant form of IL13R ⁇ 2 cDNA in which Tyr207, Asp271, Tyr315, and Asp318 residues were substituted with Ala.
  • these residues of the human IL13R ⁇ 2 were identified as amino acids required for the interaction with the cognate ligand, IL-13.
  • the presence of all four mutations in one molecule has been shown to result in near complete loss of the binding of IL-13 to the mutated form of IL13R ⁇ 2 (28).
  • FIG. 5B shows about 50% binding inhibition of IL13R ⁇ 2 (clone 47) mAb by a 20-fold excess of rhIL-13 to wild-type (WT) IL13R ⁇ 2 but not to the 4-amino-acid mutant form of IL13R ⁇ 2.
  • WT wild-type
  • IL-13 and the IL13R ⁇ 2 (clone 47) monoclonal antibody can significantly compete with one other for binding of IL13R ⁇ 2
  • residues Tyr207, Asp271, Tyr315, and Asp318 contributing to the interaction of IL-13 with IL13R ⁇ 2 (28) were also important for binding of the IL13R ⁇ 2 (clone 47) mAb to IL13R ⁇ 2.
  • the plasmids encoding cDNA for IL13R ⁇ 2 carrying individual mutations of Tyr207, Asp271, Tyr315, or Asp318 residues to Ala or a combination of all four mutations in one molecule were generated and transiently expressed in HEK cells.
  • IL13R ⁇ 2 (clone 47) mAb to wild-type and mutant forms of IL13R ⁇ 2 was analyzed by flow cytometry.
  • the IL13R ⁇ 2 mAbs 83807 and B-D13 were used as reference antibodies to exclude a possible influence of variations in the level of expression of wild-type or mutated variants of IL13R ⁇ 2 on the surface of HEK cells ( FIG. 6A ).
  • Data were calculated as a ratio of IL13R ⁇ 2 (clone 47) binding to IL13R ⁇ 2 when compared with both antibody clones 83807 and B-D13.
  • FIG. 6A demonstrates that the binding of IL13R ⁇ 2 (clone 47) mAb was not significantly affected by either the individual mutations or the 4-amino-acid mutant form of IL13R ⁇ 2 when compared with wild-type receptor. In contrast, binding of IL-13 to the 4-amino-acid mutant form of IL13R ⁇ 2 was nearly abolished ( FIG. 6B ). These data indicate that the Tyr207, Asp271, Tyr315, and Asp318 residues are not crucial for the interaction of IL13R ⁇ 2 (clone 47) mAb with IL13R ⁇ 2 but are necessary for binding to IL-13.
  • N-Linked Glycosylation Affects the Affinity of the IL13R ⁇ 2 mAb for IL13R ⁇ 2
  • N-Linked glycosylation has previously been demonstrated to be important for efficient binding of IL-13 to the cognate receptor, IL13R ⁇ 2 (30). Taking into consideration the significant overlap in epitope recognition between the IL13R ⁇ 2 (clone 47) mAb and IL-13, we expected N-linked glycosylation of IL13R ⁇ 2 to contribute to binding of the IL13R ⁇ 2 (clone 47) mAb. To confirm this expectation, rhIL13R ⁇ 2hFc was treated with Pngase F to remove N-linked glycosylation from the protein. The binding of the IL13R ⁇ 2 (clone 47) mAb to control and deglycosylated target protein was investigated.
  • FIG. 8 shows positive (brown) staining in the two human GBM samples, albeit with different frequency of positive cells in the sample as well as a U251 glioma cell-based glioma xenograft. Positive staining was detected in two of the three GBM samples analyzed, which is consistent with the expectation that fewer than 50% of primary GBM express IL13R ⁇ 2 (3).
  • the IL13R ⁇ 2 Monoclonal Antibody Prolongs the Survival of Animals with an Intracranial Glioma Xenograft
  • mice were inoculated in the brains of mice and 3 days later injected through the same burr hole with either PBS or the IL13R ⁇ 2 (clone 47 or B-D13) mAb as described previously (29).
  • IL13R ⁇ 2 (clone 47) mAb shows promise in promoting tumor rejection of IL13R ⁇ 2-expressing U251 glioma cells in the mouse brain. This finding leads to the expectation that antibody agent incorporating the IL13R ⁇ 2-binding domain of the IL13R ⁇ 2 (clone 47) mAb will be efficacious in treating a variety of human and non-human cancers characterized by the presentation of IL13R ⁇ 2, such as IL13R ⁇ 2-expressing glioma cells and other malignant cell types.
  • IL13R ⁇ 2 is overexpressed in a majority of high-grade astrocytomas and other malignancies, and has been validated as a target for therapeutic applications in various preclinical models.
  • current IL13-based therapeutic agents lack specificity due to interaction with the IL13Ra1 receptor, which is widely expressed by normal or healthy cells.
  • the generation of a targeting agent that strictly binds to IL13R ⁇ 2 would significantly expand the therapeutic potential for the treatment of IL13R ⁇ 2-expressing cancers.
  • mAb47 monoclonal antibody 47
  • the mAb47 exclusively binds to a native form of human IL13R ⁇ 2.
  • scFv single-chain antibody fragment
  • the single-chain antibody (scFv) fragment was tested for its targeting properties as a soluble agent, and an adenovirus (Ad) with a modified fiber incorporating scFv47 as a targeting motif was agented.
  • the phage-display approach was utilized for selection of a functional combination of variable heavy (VH) and light (VL) chains from established hybridoma cells producing mAb47.
  • VH variable heavy
  • VL light
  • Purified phages displaying scFv47 were tested for their interaction with IL13R ⁇ 2hFc recombinant protein, i.e., a fusion of IL13R ⁇ 2 and the Fc region of an antibody.
  • a competitive ELISA was utilized to verify that the parental mAb47 and the scFv47 fragment bind to the same epitope.
  • the soluble form of scFv47 expressed in E. coli and CHO cells was analyzed by SDS-PAGE, and tested for stability and targeting properties.
  • IL13R ⁇ 2-specific Ad the fiber of a replication-deficient Ad5 encoding green fluorescent protein was replaced with a chimeric fiber gene composed of a T4 fibritin trimerization domain linked at its C-terminal to scFV47 (AdFFscFv47-CMV-GFP).
  • AdFFscFv47-CMV-GFP a chimeric fiber gene composed of a T4 fibritin trimerization domain linked at its C-terminal to scFV47
  • AdFFscFv47-CMV-GFP an agent encoding the adenoviral genome was rescued in HEK293F28 cells, propagated, and purified.
  • IL13R ⁇ 2 + and IL13R ⁇ 2 ⁇ U251 cell lines were established via stable transfection with either control or IL13R ⁇ 2-specific shRNAs (U251-IL13R ⁇ 2.KO), respectively.
  • the AdFFscFv47-CMV-GFP virus was tested for targeting properties in
  • an IL13R ⁇ 2-specific chimeric antigen receptor (CAR) was initially constructed.
  • a codon-optimized minigene was synthesized that contained the immunoglobulin heavy-chain leader peptide and the heavy and light chains of the IL13R ⁇ 2-specific single-chain variable fragment (scFv) separated by a linker (the scFv was derived from hybridoma 47, Balyasnikova et al. J Biol. Chem. 2012; 287(36):30215-30277).
  • the minigene was subcloned into an SFG retroviral vector containing the human IgG1-CH2CH3 domain, a CD28 transmembrane domain, and costimulatory domains derived from CD28 and the CD3 ⁇ -chain.
  • CD3/CD28-activated human T cells were transduced with RD114-pseudotyped retroviral particles and subsequently expanded using IL2.
  • Functional analysis revealed that T cells expressing IL13R ⁇ 2-specific CARs (IL13R ⁇ 2-CAR T cells) recognized recombinant IL13R ⁇ 2 protein as judged by cytokine production (IFN ⁇ and IL2; FIGS. 19 and 20 ), and killed IL13R ⁇ 2-positive cells in a cytotoxicity assay ( FIG. 18 ).
  • Non-transduced (NT) T cells did not produce cytokines and had no cytolytic activity.
  • IL13R ⁇ 2 is aberrantly expressed in Glioblastoma Multiforme and is, therefore, a promising target for CAR T-cell immunotherapy.
  • the antigen recognition domain of CARs normally consists of a single-chain variable fragment (scFv), but current IL13R ⁇ 2-specific CARs use IL13 muteins as an antigen recognition domain.
  • IL13 mutein-based CARs however, have been shown to also recognize IL13R ⁇ 1, raising significant safety concerns. To overcome this obstacle, a high affinity IL13R ⁇ 2-specific scFv has been agented.
  • This scFv is used in developing a scFv-based IL13R ⁇ 2-specific CAR (IL13R ⁇ 2-CAR), which, when expressed in T cells, will provide IL13R ⁇ 2-CAR T cells having cytotoxic effector function.
  • IL13R ⁇ 2-CAR scFv-based IL13R ⁇ 2-specific CAR
  • Antigen-specific T cells were incorporated into an effective immunotherapy for diffuse intrinsic pontine glioma (DIPG) and glioblastoma (GBM), which are the most aggressive, uniformly fatal, primary human brain tumors in children.
  • IL13R ⁇ 2 is expressed at a high frequency in both DIPG and GBM, but not in normal brain, making it a promising target for T-cell immunotherapy, including scFv-based therapy, scFv-CAR T-cell-based therapy, and scFv fusions to other frameworks providing effector function, such as BiTEs and scFv-CAR-NKs.
  • IL13-binding CARs have been generated using mutated forms of IL13 as CAR binding domains, but these CARs also recognize IL13R ⁇ 1, raising significant toxicity concerns.
  • IL13R ⁇ 2-specific scFv that does not recognize IL13R ⁇ 1 was generated.
  • a panel of IL13R ⁇ 2-CARs were agented that contain the IL13R ⁇ 2-specific scFv as an ectodomain, a short hinge (SH) or a long hinge (LH), a CD28 transmembrane domain, and endodomains that contain signaling domains derived from CD3 ⁇ and co-stimulatory molecules (e.g., CD28. ⁇ , CD137. ⁇ , CD28.CD137. ⁇ , CD28.CD134. ⁇ ).
  • IL13R ⁇ 2-CAR T cells were generated by retroviral transduction, and effector function was determined in vitro, using co-culture and cytotoxicity assays, and in vivo, using the U373 brain xenograft model ( FIG. 21 ).
  • T cells expressing IL13R ⁇ 2-CARs with a deleted endodomain secreted no cytokines, confirming that cytokine production depends on the presence of a functional IL13R ⁇ 2-CAR.
  • injection of IL13R ⁇ 2.SH.CD28. ⁇ -CAR T cells into U373-bearing mice resulted in regression of glioma xenografts, as judged by bioluminescence imaging ( FIG. 21 ).
  • IL13R ⁇ 2.LH.CD28. ⁇ - or IL13R ⁇ 2. ⁇ -CAR T cells had no antitumor effects.
  • Two retroviral vectors encoding CARs based on scFv47 (47-CARs; FIG. 31A ) 24,25 were initially generated. Both CARs contained an N-terminal leader sequence, a codon-optimized synthetic gene encoding scFv47, a spacer region, a CD28 transmembrane domain, and signaling domains derived from CD28 and CD3. ⁇ ( FIG. 31A ).
  • the spacer region was either the IgG1 hinge (16 amino acids; short spacer region (SSR); 47-CAR.SSR.CD28. ⁇ ) or the IgG1-CH2CH3 domain (293 amino acids; long spacer region (LSR); 47-CAR.LSR.CD28. ⁇ ).
  • LSR and SSR 47-CARs without signaling domains were constructed (47-CAR.SSR. ⁇ , 47-CAR.LSR. ⁇ ; FIG. 31A ).
  • CD3/CD28-activated T cells from healthy donors were transduced with RD114-pseudotyped retroviral particles, and 4 to 5 days post-transduction, T-cell phenotype and CAR expression was determined by FACS analysis. CARs were expressed on the cell surface, and the transduction efficiency ranged from 69.2%-98.5% with no significant differences between constructs ( FIG. 31B , C).
  • T cells expressing 47-CAR.SSR.CD28. ⁇ , 47-CAR.LSR.CD28. ⁇ , M47-CAR.SSR. ⁇ , or M47-CAR.LSR. ⁇ were cultured on tissue culture plates that were uncoated or coated with recombinant proteins encoding IL13R ⁇ 1, IL13R ⁇ 2, or IL4R.
  • T cells expressing 47-CAR.SSR.CD28. ⁇ or 47-CAR.LSR.CD28. ⁇ produced significant levels of IFN ⁇ (p ⁇ 0.001) when stimulated with recombinant IL13R ⁇ 2 proteins in comparison to IL13R ⁇ 1- or IL4R-stimulated T cells ( FIG. 33A ).
  • T cells expressing 47-CAR.SSR. ⁇ or 47-CAR.LSR. ⁇ produced no IFN ⁇ in response to all three proteins, indicating that IFN ⁇ production depends on an intact 47-CAR signaling domain.
  • 47-CAR.LSR.CD28. ⁇ T cells also produced low levels of IFN ⁇ without activation, indicating baseline T-cell activation, which was confirmed by intracellular staining for phosphorylated CD3. ⁇ ( FIG. 34 ).
  • IL13mutein-CAR.LSR.CD28. ⁇ T cells produced significant levels of IFN ⁇ in the presence of IL13R ⁇ 1 (p ⁇ 0.001) and IL13R ⁇ 2 (p ⁇ 0.05) in comparison to NT T cells.
  • 47-CAR T cells were then confirmed using cell lines that were negative for IL13R ⁇ 1 and IL13R ⁇ 2 (Raji), positive for IL13R ⁇ 1 (293T-GFP cells), or positive for IL13R ⁇ 1 and IL13R ⁇ 2 (U373, 293T-GFP/IL13R ⁇ 2; FIG. 35 ).
  • T cells expressing 47-CAR.SSR.CD28. ⁇ , 47-CAR.LSR.CD28. ⁇ , 47-CAR.SSR. ⁇ , or 47-CAR.LSR. ⁇ were co-cultured with Raji, 293T-GFP, or 293T-GFP/IL13R ⁇ 2 cells.
  • NT T cells served as controls.
  • 47-CAR.SSR.CD28. ⁇ and 47-CAR.LSR.CD28. ⁇ T cells produced significant amounts of IFN ⁇ only in the presence of U373 or 293T-GFP/IL13R ⁇ 2 cells ( FIG. 33B ) with SSR.CAR T cells producing significantly more IFN ⁇ than LSR.CAR T cells (p ⁇ 0.001).
  • 47-CAR.SSR.CD28. ⁇ T cells produced also significant amounts of IL2 in the presence of 293T-GFP/IL13R ⁇ 2 and U373 cells, while 47-CAR.LSR.CD28. ⁇ T cells did not ( FIG. 33C ).
  • NT-T cells and T cells expressing 47-CAR.SSR. ⁇ or 47-CAR.LSR. ⁇ produced no IFN ⁇ or IL2 in response to any target cells.
  • SSR Short Spacer Region
  • 47-CAR.SSR.CD28. ⁇ T cells produced the highest amount of IL2, followed by 47-CAR.SSR.41BB. ⁇ and 47-CAR.SSR.CD28.OX40. ⁇ T cells.
  • cytotoxicity assays no significant difference was observed between all three constructs using Raji, 293T-GFP, 293T-GFP/IL13R ⁇ 2, and U373 cells as targets ( FIG. 37B ).
  • mice On day 0, U373.eGFP.ffLuc cells were injected stereotactically into brains of SCID mice and, on day 7, T cells expressing 47-CAR.SSR.CD28. ⁇ , 47-CAR.SSR.41BB. ⁇ , 47-CAR.SSR.CD28.OX40. ⁇ or 47-CAR.SSR. ⁇ were injected intratumorally. While mice treated with 47-CAR.SSR. ⁇ T cells showed continuous tumor growth within 4 days of T-cell injection, mice treated with 47-CAR.SSR T cells that had functional endodomains did not ( FIG. 38A , B).
  • 47-CAR.SSR.CD28. ⁇ T-cell-treated mice had the longest median survival (84 days). There was no statistical difference, however, in comparison to the median survival of 47-CAR.SSR.41BB. ⁇ (63 days) or 47-CAR.SSR.CD28.OX40. ⁇ (56 days) T-cell-treated mice.
  • mice While 47-CAR T cells had potent anti-glioma activity, mice developed recurrent gliomas.
  • U373 cells were isolated from two tumor-bearing mice that had been treated either with 47-CAR.SSR.CD28. ⁇ or 47-CAR.SSR.CD28.OX40. ⁇ T cells. FACS analysis after short-term culture revealed cell surface expression of IL13R ⁇ 2, and these cells were readily killed by 47-CAR T cells in cytotoxicity assays ( FIG. 39 ).
  • T-cells were determined by genetically modifying T cells with 47-CAR.SSR.CD28. ⁇ and eGFP.ffLuc (Luc/47-CAR T cells), and injecting them into U373 tumor-bearing mice. T cells persisted for less than 7 days. Without wishing to be bound by theory, limited persistence appears to be the most likely explanation for tumor recurrence ( FIG. 40 ).
  • IL13R ⁇ 2-CAR.CD28. ⁇ T cells expressing IL15 were generated by double transducing T cells with retroviruses containing expression cassettes encoding i) IL13R ⁇ 2-CAR.CD28. ⁇ or ii) IL15, ⁇ Nerve Growth Factor Receptor ( ⁇ NGFR), and inducible Caspase 9 (iC9) separated by 2A sequences.
  • Suitable 2A sequences include any 2A sequence known in the art, as exemplified by the 2A amino acid sequence from porcine teschovirus-1 (SEQ ID NO:109) encoded by the polynucleotide sequence set forth as SEQ ID NO:110, the 2A amino acid sequence from Thoseaasigna virus (SEQ ID NO:111) encoded by the polynucleotide sequence set forth as SEQ ID NO:112, the 2A amino acid sequence from Equine rhinitis A virus (ERAV) (SEQ ID NO:113) encoded by the polynucleotide sequence set forth as SEQ ID NO:114, or the 2A amino acid sequence from Foot and Mouth Disease Virus (FMDV) (SEQ ID NO:115) encoded by the polynucleotide sequence set forth as SEQ ID NO:116.
  • porcine teschovirus-1 SEQ ID NO:109
  • SEQ ID NO:110 the 2A amino acid sequence from Thoseaasigna virus encoded by the polynu

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