US20200140565A1 - Novel cd47 monoclonal antibodies and uses thereof - Google Patents

Novel cd47 monoclonal antibodies and uses thereof Download PDF

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US20200140565A1
US20200140565A1 US15/761,309 US201715761309A US2020140565A1 US 20200140565 A1 US20200140565 A1 US 20200140565A1 US 201715761309 A US201715761309 A US 201715761309A US 2020140565 A1 US2020140565 A1 US 2020140565A1
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cancer
antibodies
monoclonal antibody
antibody
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Zhengyi Wang
Lei Fang
Bingshi Guo
Jingwu Zang
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I Mab Biopharma US Ltd
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Definitions

  • CD47 Cluster of Differentiation 47
  • AML acute myeloid leukemia
  • ALL acute lymphoblastic leukemia
  • NHL non-Hodgkin's lymphoma
  • MM multiple myeloma
  • bladder cancer and other solid tumors.
  • High levels of CD47 allow cancer cells to avoid phagocytosis despite having a higher level of calreticulin the dominant pro-phagocytic signal.
  • IAP integrin-associated protein
  • OA3, Rh-related antigen and MER6, CD47 is a multi-spanning transmembrane receptor belonging to the immunoglobulin superfamily. Its expression and activity have been implicated in a number of diseases and disorders. It is a broadly expressed transmembrane glycoprotein with a single Ig-like domain and five membrane spanning regions, which functions as a cellular ligand for SIRP ⁇ with binding mediated through the NH 2 -terminal V-like domain of signal-regulatory-protein ⁇ (SIRP ⁇ ). SIRP ⁇ is expressed primarily on myeloid cells, including macrophages, granulocytes, myeloid dendritic cells (DCs), mast cells, and theft precursors, including hematopoietic stem cells.
  • DCs myeloid dendritic cells
  • Macrophages clear pathogens and damaged or aged cells from the blood stream via phagocytosis.
  • Cell-surface CD47 interacts with its receptor on macrophages, SIRP ⁇ , to inhibit phagocytosis of normal, healthy cells.
  • SIRP ⁇ inhibits the phagocytosis of host cells by macrophages, where the ligation of SIRP ⁇ on macrophages by CD47 expressed on the host target cell generates an inhibitory signal mediated by SHP-1 that negatively regulates phagocytosis.
  • CD47 In keeping with the role of CD47 to inhibit phagocytosis of normal cells, there is evidence that it is transiently up-regulated on hematopoietic stem cells (HSCs) and progenitors just prior to and during their migratory phase, and that the level of CD47 on these cells determines the probability that they are engulfed in vivo.
  • HSCs hematopoietic stem cells
  • CD47 is also constitutively up-regulated on a number of cancers, including myeloid leukemias. Overexpression of CD47 on a myeloid leukemia line increases its pathogenicity by allowing it to evade phagocytosis. It has been concluded that CD47 up-regulation is an important mechanism for providing protection to normal HSCs during inflammation-mediated mobilization, and that leukemic progenitors co-opt this ability in order to evade macrophage killing.
  • CD47 antibodies have been shown to restore phagocytosis and prevent atherosclerosis. See, e.g., Kojima et al., Nature, Vol. 36, 86-90 (Aug. 4, 2016).
  • the present invention provides novel CD47 antibodies or immunologically active fragments thereof that have low immunogenicity in humans and cause low or no level of red blood cell depletion. As well known to a person skilled in the art, such antibodies may be interchangeably called “anti-CD47 antibodies.”
  • the present invention provides isolated monoclonal antibodies and their immunologically active fragments that bind to human CD47.
  • these CD47-binding isolated monoclonal antibodies and their immunologically active fragments are referred to hereinafter as “CD47 antibodies”.
  • the CD47 antibodies of this invention are capable of modulating, e.g., blocking, inhibiting, reducing, antagonizing, neutralizing or otherwise interfering with, CD47 expression, activity and/or signaling, or the interaction between CD47 and SIRP ⁇ .
  • the CD47 antibodies of this invention do not generally cause a significant level of depletion or hemagglutination of human red blood cells, and surprisingly in many cases do not cause any depletion or hemagglutination of human red blood cells at all. Additionally, the CD47 antibodies of this invention have exhibited potent anti-tumor activities.
  • the CD47 antibodies of this invention each include (a) a variable heavy (VH) chain sequence that is at least 90% (e.g., at least 95%) identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO
  • the CD47 antibodies of this invention each include paired VH/VL chain sequences that are at least 90% (e.g., at least 95%, 95%, 96, 97%, 98%, 99%, or 99.5%) identical to a pair of VH and VL amino acid sequences selected from the group consisting of SEQ ID NO: 1 and SEQ ID NO: 2 (i.e., 1A1), SEQ ID NO: 3 and SEQ ID NO: 4 (i.e., 1F8), SEQ ID NO: 5 and SEQ ID NO: 6 (i.e., 2A11), SEQ ID NO: 7 and SEQ ID NO: 8 (i.e., 2C2), SEQ ID NO: 9 and SEQ ID NO: 10 (i.e., 2D7), SEQ ID NO: 11 and SEQ ID NO: 12 (i.e., 2G4), SEQ ID NO: 13 and SEQ ID NO: 14 (i.e., 2G11), SEQ ID NO: 15 and SEQ ID NO:
  • the CD47 antibodies of this invention each include a pair of VH and VL chain sequences selected from the group consisting of SEQ ID NO: 1 and SEQ ID NO: 2 (i.e., 1A1), SEQ ID NO: 3 and SEQ ID NO: 4 (i.e., 1F8), SEQ ID NO: 5 and SEQ ID NO: 6 (i.e., 2A11), SEQ ID NO: 7 and SEQ ID NO: 8 (i.e., 2C2), SEQ ID NO: 9 and SEQ ID NO: 10 (i.e., 2D7), SEQ ID NO: 11 and SEQ ID NO: 12 (i.e., 2G4), SEQ ID NO: 13 and SEQ ID NO: 14 (i.e., 2G11), SEQ ID NO: 15 and SEQ ID NO: 16 (i.e., 6F4), SEQ ID NO: 17 and SEQ ID NO: 18 (i.e., 5H1), SEQ ID NO: 19 and SEQ ID NO: 20 (i.
  • the CD47 antibodies of this invention can be chimeric or humanized. They can prevent or significantly reduce human CD47 from interacting with SIRP ⁇ , or promotes macrophage-mediated phagocytosis of a CD47-expressing cell.
  • the CD47 antibodies of this invention do not cause a significant or noticeable level of hemagglutination or depletion of red blood cells, and in many cases they do not cause hemagglutination or depletion of red blood cells at all.
  • the present invention provides isolated bispecific monoclonal antibodies.
  • Each of such isolated bispecific monoclonal antibodies comprises a first arm and a second arm, wherein the first arm comprises a first monoclonal antibody or immunologically active fragment thereof as described above which binds human CD47, and the second arm comprise a second monoclonal antibody that does not bind human CD47.
  • the second arm in the isolated bispecific monoclonal antibodies binds to a cancer cell.
  • the bispecific monoclonal antibodies inhibit interaction between human CD47 and human SIRP ⁇ .
  • the present invention provides pharmaceutical compositions each containing one of the CD47 antibodies of this invention or an isolated bispecific monoclonal antibody of this invention, and a pharmaceutically acceptable carrier or excipient.
  • the term “pharmaceutically acceptable carrier or excipient” refers to a carrier or an excipient that is useful for preparing a pharmaceutical composition or formulation that is generally safe, non-toxic, and neither biologically nor otherwise undesirable.
  • a carrier or excipient employed is typically one suitable for administration to human subjects or other mammals.
  • the active ingredient is usually mixed with, diluted by, or enclosed with a carrier or excipient.
  • the carrier or excipient serves as a diluent, it can be a solid, semi-solid, or liquid material, which acts as a vehicle, carrier, or medium for the active ingredient of the antibody.
  • Also within the scope of the present invention is a method for treating a disease in a human subject in need thereof, and the method includes administering to the subject a therapeutically effective amount of a CD47 antibody of this invention, a bispecific monoclonal antibody of this invention, or a pharmaceutical composition of this invention, and the disease is a cancer, a fibrotic disease, or any disease related to inhibition of phagocytosis.
  • the cancer can be selected from the group consisting of ovarian cancer, colon cancer, breast cancer, lung cancer, head and neck cancer, bladder cancer, colorectal cancer, pancreatic cancer, non-Hodgkin's lymphoma, acute lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myelogenous leukemia, hairy cell leukemia (HCL), T-cell prolymphocytic leukemia (T-PLL), large granular lymphocytic leukemia, adult T-cell leukemia, multiple myeloma, melanoma, leiomyoma, leiomyosarcoma, glioma, glioblastoma, myelomas, monocytic leukemias, B-cell derived leukemias, T-cell derived leukemias, B-cell derived lymphomas, T-cell derived lymphomas, endometrial cancer, kidney cancer,
  • solid tumors include, e.g., endometrial cancer, thyroid cancer, cervical cancer, gastric cancer, breast tumors, ovarian tumors, lung tumors, pancreatic tumors, prostate tumors, melanoma tumors, colorectal tumors, lung tumors, head and neck tumors, bladder tumors, esophageal tumors, liver tumors, and kidney tumors, and neuroblastic-derived CNS tumors.
  • the disease related to inhibition of phagocytosis can be a cardiovascular disease (e.g., atherosclerosis, stroke, hypertensive heart disease, rheumatic heart disease, cardiomyopathy, heart arrhythmia, congenital heart disease, valvular heart disease, carditis, aortic aneurysms, peripheral artery disease, or venous thrombosis).
  • a cardiovascular disease e.g., atherosclerosis, stroke, hypertensive heart disease, rheumatic heart disease, cardiomyopathy, heart arrhythmia, congenital heart disease, valvular heart disease, carditis, aortic aneurysms, peripheral artery disease, or venous thrombosis.
  • the term “effective amount” refers to that amount of a CD47 antibody sufficient or required to effect treatment, prognosis or diagnosis of a disease associated with CD47 dependent signaling, as described herein, when administered to a subject.
  • Therapeutically effective amounts of antibodies provided herein, when used alone or in combination, will vary depending upon the relative activity of the antibodies (e.g., promoting macrophage mediated phagocytosis of cancer cells expressing CD47) and depending upon the subject and disease condition being treated, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • the term “isolated” preceding a CD47 antibody of this invention means that the antibody is substantially free of other cellular material.
  • an isolated antibody is substantially free of other proteins from the same species.
  • an isolated antibody is expressed by a cell from a different species and is substantially free of other proteins from the different species.
  • a protein may be rendered substantially free of naturally associated components (or components associated with the cellular expression system used to produce the antibody) by isolation, using protein purification techniques well known in the art.
  • the antibodies, or antigen binding fragments, of the invention are isolated.
  • fusion proteins each comprising a first amino acid sequence and a second amino acid sequence, wherein the first amino acid sequence is SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO: 61, SEQ ID NO: 63, SEQ ID NO: 65,
  • a fusion protein of this invention includes a combination of the first amino acid sequence and the second amino acid sequence, and the combination of these two amino acid sequences is SEQ ID NO: 1 and SEQ ID NO: 2 (i.e., 1A1), SEQ ID NO: 3 and SEQ ID NO: 4 (i.e., 1F8), SEQ ID NO: 5 and SEQ ID NO: 6 (i.e., 2A11), SEQ ID NO: 7 and SEQ ID NO: 8 (i.e., 2C2), SEQ ID NO: 9 and SEQ ID NO: 10 (i.e., 2D7), SEQ ID NO: 11 and SEQ ID NO: 12 (i.e., 2G4), SEQ ID NO: 13 and SEQ ID NO: 14 (i.e., 2G11), SEQ ID NO: 15 and SEQ ID NO: 16 (i.e., 6F4), SEQ ID NO: 17 and SEQ ID NO: 18 (i.e., 5H1), SEQ ID NO: 19 and
  • a fusion protein of this invention includes a combination of the first amino acid sequence and the second amino acid sequence, and the combination of these two amino acid sequences is SEQ ID NO: 1 and SEQ ID NO: 2 (i.e., 1A1), SEQ ID NO: 3 and SEQ ID NO: 4 (i.e., 1F8), SEQ ID NO: 5 and SEQ ID NO: 6 (i.e., 2A11), SEQ ID NO: 7 and SEQ ID NO: 8 (i.e., 2C2), SEQ ID NO: 9 and SEQ ID NO: 10 (i.e., 2D7), SEQ ID NO: 11 and SEQ ID NO: 12 (i.e., 2G4), SEQ ID NO: 13 and SEQ ID NO: 14 (i.e., 2G11), SEQ ID NO: 15 and SEQ ID NO: 16 (i.e., 6F4), SEQ ID NO: 17 and SEQ ID NO: 18 (i.e., 5H1), SEQ ID NO: 19
  • a fusion protein of this invention can further include an additional protein—in addition to the first and second amino acid sequences.
  • the additional protein is an antibody or a cytokine.
  • a fusion protein of this invention can be conjugated with a small-molecule therapeutic agent (e.g., anti-cancer or anti-inflammation agent) or a marker (e.g., a biomarker or fluorescent marker).
  • a small-molecule therapeutic agent e.g., anti-cancer or anti-inflammation agent
  • a marker e.g., a biomarker or fluorescent marker
  • the present invention provides immunodominant epitopes encoded by the CD47 gene comprising a recombinant protein containing conformationally a TNMEAQ loop (residues 26-31), T34, E35, L74, and an LTR hinge (residues 101-103) of CD47.
  • the present invention provides biological molecules that specifically bind to a conformational epitope having an amino acid sequence comprising a TNMEAQ loop (residues 26-31), T34, E35, L74, and an LTR hinge (residues 101-103) of CD47, wherein the antibody can specifically bind to CD47.
  • biomimetic molecules is meant to include synthetic antibodies (monoclonal or bispecific), peptides, and biomimetic molecules.
  • biomimetic molecules refers to molecules which are designed or developed to have structures or properties similar to or resembling those of naturally occurring large compounds such as proteins or nucleotides and which have a molecular weight of, e.g., at least 3,000, at least 5,000, or at least 10,000.
  • FIG. 1 shows dose-dependent response of CD47 antibodies binding to monomeric CD47-ECD.
  • FIG. 2 a and FIG. 2 b show dose-dependent response of CD47 antibodies binding to dimeric CD47-ECD.
  • FIG. 3 a , FIG. 3 b , and FIG. 3 c dose-dependent response of CD47 antibodies blocking the binding of CD47 to SIRP ⁇ .
  • FIG. 4 a and FIG. 4 b show dose-dependent response of CD47 antibodies binding to CD47+ Raji cells; and FIG. 4 c , FIG. 4 d and FIG. 4 e show binding kinetics and data of CD47 antibodies as measured by Biocore analysis.
  • FIG. 5 a and FIG. 5 b show phagocytosis of tumor cells by human M ⁇ with CD47 antibodies.
  • FIGS. 6 a -6 c show macrophage-mediated phagocytosis of various human blood cancer cell lines triggered by CD47 antibodies.
  • FIGS. 7 a and 7 b show red blood cells (RBC)-sparing properties in RBC agglutination assay with CD47 antibodies.
  • FIGS. 8 a , 8 b , 8 c , and 8 d show activities to bind RBC and induce RBC agglutination by CD antibodies at different and higher doses.
  • FIGS. 9 a , 9 b , 9 c , and 9 d show RBC-binding activities of CD47 antibodies.
  • FIG. 10 shows results of red blood cell agglutination across multiple human blood samples induced by CD47 antibodies.
  • FIG. 11 shows the human platelet binding activities of CD47 antibodies and SIRPa-Ig fusion, with CD61 stained as a surface marker for platelets.
  • FIG. 12 shows the test results of cyno red blood cell agglutination induced by CD47 antibodies and SIRPa-Ig fusion in vitro.
  • FIG. 13 shows the test results of phagocytosis and AML cells binding by CD47 antibodies and control.
  • FIG. 14 a and FIG. 14 b show the efficacy of treatments with CD47 antibodies and control on luciferase-Raji xenograft mice.
  • FIG. 15 shows the polarization of macrophage in tumor-bearing mice induced by CD47 antibodies and control.
  • FIG. 16 shows the CD47 expression profiles using PDX samples of various human cancer types.
  • FIG. 17 shows results of safety pharm study (hematology) in cynomolgus monkeys.
  • FIG. 18 shows completion in binding of CD47 between antibodies 1F8 and 5F9, and between antibodies 1F8 and 2A1, due to their different epitopes, and structures of the 5F9/CD47 complex and the 1F8/CD47 complex.
  • FIGS. 19 a , 19 b , 19 c , 19 d , 19 e , 19 f , 19 g , and 19 h show the effects of the CD47 antibody 13H3 on RBC congregation, hemoglobin, platelets, and lymphocytes, respectively.
  • FIG. 20 shows strong binding affinity of 34C5 to recombinant CD47-ECD.
  • FIG. 21 shows strong binding affinity of 34C5 to CD47-bearing Raji cells.
  • FIG. 22 shows that 34C5 was able to effectively block CD47 binding to SIRP ⁇ , with an EC 50 of 0.30 nM.
  • FIG. 23 shows that the antibody 34C5 promoted phagocystosis of tumor cells by human M ⁇ .
  • FIG. 24 shows the antibody 34C5 did not cause in vitro RBC agglutination.
  • FIG. 25 shows the antibody 34C5 decrease its binding to RBC with the decreasing concentration of this antibody.
  • FIG. 26 shows amino acid sequences of some CD47 antibodies of this invention and their respective nucleotide sequences.
  • FIG. 27 shows the amino acid sequence for CD47 Immunoglobulin-like domain (Ig-V) 19-141.
  • the present invention provides novel isolated monoclonal CD47 antibodies that can prevent human CD47 from interacting with SIRP ⁇ , or promote macrophage-mediated phagocytosis of a CD47-expressing cell. These CD47 antibodies do not cause a significant or noticeable level of hemagglutination or depletion of red blood cells, and in many cases they do not cause hemagglutination or depletion of red blood cells at all.
  • a CD47 antibodies of this invention would include (a) a variable heavy (VH) chain sequence that is at least 90% (e.g., at least 95%) identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 59, SEQ ID NO:
  • a CD47 antibodies of this invention would include a combined VH/VL chain sequence that is at least 90% (e.g., at least 95%) identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1 and SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6, SEQ ID NO: 7 and SEQ ID NO: 8, SEQ ID NO: 9 and SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID NO: 12, SEQ ID NO: 13 and SEQ ID NO: 14, SEQ ID NO: 15 and SEQ ID NO: 16, SEQ ID NO: 17 and SEQ ID NO: 18, SEQ ID NO: 19 and SEQ ID NO: 20, SEQ ID NO: 21 and SEQ ID NO: 22, SEQ ID NO: 23 and SEQ ID NO: 24, SEQ ID NO: 25 and SEQ ID NO: 26, SEQ ID NO: 27 and SEQ ID NO: 28, SEQ ID NO: 29 and SEQ ID NO: 30, SEQ ID NO: 31 and
  • antibody is used in the broadest sense and specifically covers monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, mufti-specific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired biological activity.
  • Antibodies or “Abs”
  • immunoglobulins or “Igs” are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas.
  • epitopic determinants means any antigenic determinant on an antigen to which the paratope of an antibody binds.
  • Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or sugar side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.
  • the term “native antibodies and immunoglobulins” are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond (also termed a “VH/VL pair”), while the number of disulfide linkages varies between the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (VH) followed by a number of constant domains.
  • VH variable domain
  • Each light chain has a variable domain at one end (VL) and a constant domain at its other end; the constant domain of the light chain is aligned with the first constant domain of the heavy chain, and the light chain variable domain is aligned with the variable domain of the heavy chain.
  • Particular amino acid residues are believed to form an interface between the light- and heavy-chain variable domains. See, e.g., Clothia et al., J. Mol. Biol., 186:651 (1985); Novotny and Haber, Proc. Natl. Acad. Sci. U.S.A., 82:4592 (1985).
  • variable refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR).
  • CDRs complementarity-determining regions
  • FR framework
  • the variable domains of native heavy and light chains each comprise four FR regions, largely adopting a ⁇ -sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the ⁇ -sheet structure.
  • the CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies. See, e.g., Kabat et al., Sequences of Proteins of Immunological Interest , Fifth Edition, National Institute of Health, Bethesda, Md. (1991).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.
  • Variable region sequences of interest include the provided humanized variable region sequences for CD47 antibodies.
  • 1A1 includes SEQ ID NO: 1 (heavy) and SEQ ID NO: 2 (light)
  • 1F8 includes SEQ ID NO: 3 (heavy) and SEQ ID NO: 4 (light)
  • 2A11 includes SEQ ID NO: 5 (heavy) and SEQ ID NO: 6 (light).
  • Papain digestion of antibodies produces two identical antigen-binding fragments, called “Fab” fragments, each with a single antigen-binding site, and a residual “Fc” fragment, whose name reflects its ability to crystallize readily.
  • Pepsin treatment yields an F(ab′)2 fragment that has two antigen-combining sites and is still capable of cross-linking antigen.
  • Fv is the minimum antibody fragment which contains a complete antigen-recognition and -binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association.
  • one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a “dimeric” structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site. See, e.g., Pluckthun, in The Pharmacology of Monoclonal Antibodies , Vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994).
  • the Fab fragment also contains the constant domain of the light chain and the first constant domain (CH 1 ) of the heavy chain.
  • Fab′ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH 1 domain including one or more cysteines from the antibody hinge region.
  • Fab′-SH is the designation herein for Fab′ in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab′) 2 antibody fragments originally were produced as pairs of Fab′ fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • immunoglobulins There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these can be further divided into subclasses (isotypes), e.g., IgG1, IgG2, IgG3, IgG4, IgA1, IgA2.
  • the heavy-chain constant domains that correspond to the different classes of immunoglobulins are called ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • the subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.
  • antibody fragment and all grammatical variants thereof, are defined as a portion of an intact antibody comprising the antigen binding site or variable region of the intact antibody, wherein the portion is free of the constant heavy chain domains (i.e. CH2, CH3, and CH4, depending on antibody isotype) of the Fc region of the intact antibody.
  • constant heavy chain domains i.e. CH2, CH3, and CH4, depending on antibody isotype
  • antibody fragments include Fab, Fab′, Fab′-SH, F(ab′) 2 , and Fv fragments; diabodies; any antibody fragment that is a polypeptide having a primary structure consisting of one uninterrupted sequence of contiguous amino acid residues (referred to herein as a “single-chain antibody fragment” or “single chain polypeptide.”), including without limitation (1) single-chain Fv (scFv) molecules, (2) single chain polypeptides containing only one light chain variable domain, or a fragment thereof that contains the three CDRs of the light chain variable domain, without an associated heavy chain moiety, and (3) single chain polypeptides containing only one heavy chain variable region, or a fragment thereof containing the three CDRs of the heavy chain variable region, without an associated light chain moiety; and mufti-specific or multivalent structures formed from antibody fragments.
  • scFv single-chain Fv
  • the heavy chain(s) can contain any constant domain sequence (e.g. CH1 in the IgG isotype) found in a non-Fc region of an intact antibody, and/or can contain any hinge region sequence found in an intact antibody, and/or can contain a leucine zipper sequence fused to or situated in the hinge region sequence or the constant domain sequence of the heavy chain(s).
  • any constant domain sequence e.g. CH1 in the IgG isotype
  • conjugate used herein is defined as a heterogeneous molecule formed by the covalent attachment of one or more antibody fragment(s) to one or more polymer molecule(s), wherein the heterogeneous molecule is water soluble, i.e. soluble in physiological fluids such as blood, and wherein the heterogeneous molecule is free of any structured aggregate.
  • a conjugate of interest is polyethylenglycol (PEG).
  • structured aggregate refers to (1) any aggregate of molecules in aqueous solution having a spheroid or spheroid shell structure, such that the heterogeneous molecule is not in a micelle or other emulsion structure, and is not anchored to a lipid bilayer, vesicle or liposome; and (2) any aggregate of molecules in solid or insolubilized form, such as a chromatography bead matrix, that does not release the heterogeneous molecule into solution upon contact with an aqueous phase.
  • conjugate encompasses the aforementioned heterogeneous molecule in a precipitate, sediment, bioerodible matrix or other solid capable of releasing the heterogeneous molecule into aqueous solution upon hydration of the solid.
  • the term “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Each mAb is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they can be synthesized by hybridoma culture, uncontaminated by other immunoglobulins.
  • the modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present invention may be made in an immortalized B cell or hybridoma thereof, or may be made by recombinant DNA methods.
  • the monoclonal antibodies herein include hybrid and recombinant antibodies produced by splicing a variable (including hypervariable) domain of an CD47 antibody with a constant domain (e.g. “humanized” antibodies), or a light chain with a heavy chain, or a chain from one species with a chain from another species, or fusions with heterologous proteins, regardless of species of origin or immunoglobulin class or subclass designation, as well as antibody fragments (e.g., Fab, F(ab′) 2 , and Fv), so long as they exhibit the desired biological activity.
  • Fab fragment antigen binding
  • the monoclonal antibodies herein specifically include “chimeric” antibodies (immunoglobulins) in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.
  • chimeric antibodies immunoglobulins in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.
  • an “isolated” antibody is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1) to greater than 75% by weight of antibody as determined by the Lowry method, and most preferably more than 80%, 90% or 99% by weight, or (2) to homogeneity by SOS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • epitope tagged refers to a CD47 antibody fused to an “epitope tag”.
  • the epitope tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the CD47 antibody.
  • the epitope tag preferably is sufficiently unique so that the antibody specific for the epitope does not substantially cross-react with other epitopes.
  • Suitable tag polypeptides generally have at least 6 amino acid residues and usually between about 8-50 amino acid residues (preferably between about 9-30 residues).
  • Examples include the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10 antibodies thereto (see, e.g., Evan et al., Mol. Cell. Biol., 5 (12):3610-3616 (1985)); and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody (see, e.g., Paborsky et al., Protein Engineering, 3 (6):547-553 (1990)).
  • gD Herpes Simplex virus glycoprotein D
  • label refers to a detectable compound or composition which is conjugated directly or indirectly to the antibody.
  • the label may itself be detectable by itself (e.g., radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable.
  • solid phase refers to a non-aqueous matrix to which the antibody of the present invention can adhere.
  • solid phases encompassed herein include those formed partially or entirely of glass (e.g. controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones.
  • the solid phase can comprise the well of an assay plate; in others it is a purification column (e.g., an affinity chromatography column). This term also includes a discontinuous solid phase of discrete particles. See, e.g., U.S. Pat. No. 4,275,149.
  • the present invention also provides pharmaceutical compositions containing these CD47 antibodies and methods for treating diseases in a subject with these CD47 antibodies or pharmaceutical compositions.
  • treatment refers to both therapeutic treatment and prophylactic or preventative measures of a disease (such as cancer or a fibrotic disease).
  • a disease such as cancer or a fibrotic disease.
  • Those in need of treatment include those already with the disease as well as those in which the disease is to be prevented.
  • cancer examples include, but are not limited to, ovarian cancer, colon cancer, breast cancer, lung cancer, head and neck cancer, bladder cancer, colorectal cancer, pancreatic cancer, non-Hodgkin's lymphoma, acute lymphocytic leukemia, chronic lymphocytic leukemia, acute myeloid leukemia, chronic myelogenous leukemia, multiple myeloma, melanoma, leiomyoma, leiomyosarcoma, glioma, glioblastoma, myelomas, monocytic leukemias, B-cell derived leukemias, T-cell derived leukemias, B-cell derived lymphomas, T-cell derived lymphomas, and solid tumors.
  • the fibrotic disease can be, e.g., myocardial infarction, angina, osteoarthritis, pulmonary fibrosis, asthma, cystic fibrosis, bronchitis, or asthma.
  • the term “subject” for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc.
  • the mammal is human.
  • the CD47 antibodies of this invention can also be used in vitro and in vivo to monitor the course of CD47 disease therapy.
  • a particular therapeutic regimen aimed at ameliorating disease is effective.
  • the CD47 antibodies of this invention may be used in vitro in immunoassays in which they can be utilized in liquid phase or bound to a solid phase carrier.
  • the CD47 antibodies in these immunoassays can be detectably labeled in various ways.
  • types of immunoassays which can utilize monoclonal antibodies of the invention are flow cytometry, e.g. FACS, MACS, immunohistochemistry, competitive and non-competitive immunoassays in either a direct or indirect format.
  • Detection of the antigens using the CD47 antibodies of this invention can be done utilizing immunoassays which are run in either the forward, reverse, or simultaneous modes, including immunohistochemical assays on physiological samples.
  • Those of skill in the art will know, or can readily discern, other immunoassay formats without undue experimentation.
  • the CD47 antibodies of the invention can be bound to many different carriers and used to detect the presence of CD47 expressing cells.
  • Examples of well-known carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, agaroses and magnetite.
  • the nature of the carrier can be either soluble or insoluble for purposes of the invention. Those skilled in the art will know of other suitable carriers for binding monoclonal antibodies, or will be able to ascertain such, using routine experimentation.
  • a label may be covalently or non-covalently attached to an antibody of the invention or a fragment thereof, including fragments consisting or comprising of CDR sequences.
  • Examples of the types of labels which can be used in the present invention include enzymes, radioisotopes, fluorescent compounds, colloidal metals, chemiluminescent compounds, and bioluminescent compounds.
  • Those of ordinary skill in the art will know of other suitable labels for binding to the monoclonal antibodies of the invention, or will be able to ascertain such, using routine experimentation.
  • the binding of these labels to the monoclonal antibodies of the invention can be done using standard techniques common to those of ordinary skill in the art.
  • a CD47 antibody of this invention is attached to a nanoparticle, e.g. for use in imaging.
  • Useful nanoparticles are those known in the art, for example including without limitation, Raman-silica-gold-nanoparticle (R—Si—Au—NP).
  • the R—Si—Au—NPs consist of a Raman organic molecule, with a narrow-band spectral signature, adsorbed onto a gold core. Because the Raman organic molecule can be changed, each nanoparticles can carry its own signature, thereby allowing multiple nanoparticles to be independently detected simultaneously by multiplexing.
  • the entire nanoparticle is encapsulated in a silica shell to hold the Raman organic molecule on the gold nanocore.
  • Optional polyethylene glycol (PEG)-ylation of R—Si—Au—NPs increases their bioavailability and provides functional “handles”' for attaching targeting moieties. See, e.g., Thakor et al (2011), Sci. Transl. Med., 3 (79):79ra33; Jokerst et al. (2011) Small., 7 (5):625-33; Gao et al. (2011) Biomaterials, 32 (8):2141-8.
  • CD47 may be detected by the CD47 antibodies of this invention when present in biological fluids and on tissues, in vivo or in vitro. Any sample containing a detectable amount of CD47 can be used.
  • a sample can be a liquid such as urine, saliva, cerebrospinal fluid, blood, serum and the like, or a solid or semi-solid such as tissues, feces, and the like, or, alternatively, a solid tissue such as those commonly used in histological diagnosis.
  • Another labeling technique which may result in greater sensitivity consists of coupling the antibodies to low molecular weight haptens. These haptens can then be specifically detected by means of a second reaction. For example, it is common to use haptens such as biotin, which reacts with avidin, or dinitrophenol, pyridoxal, or fluorescein, which can react with specific anti-hapten antibodies.
  • a CD47 antibody of this invention can be provided in a kit, i.e., a packaged combination of reagents in predetermined amounts with instructions for performing the diagnostic assay.
  • the kit will include substrates and cofactors required by the enzyme (e.g., a substrate precursor which provides the detectable chromophore or fluorophore).
  • substrates and cofactors required by the enzyme e.g., a substrate precursor which provides the detectable chromophore or fluorophore.
  • other additives may be included such as stabilizers, buffers (e.g., a block buffer or lysis buffer) and the like.
  • the relative amounts of the various reagents may be varied widely to provide for concentrations in solution of the reagents which substantially optimize the sensitivity of the assay.
  • the reagents may be provided as dry powders, usually lyophilized, including excipients which on dissolution will provide a reagent solution having the appropriate concentration.
  • Therapeutic formulations comprising one or more antibodies of the invention are prepared for storage by mixing the antibody having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers (see, e.g., Remington's Pharmaceutical Sciences, 16th edition, Osol, A. Ed. (1980)), in the form of lyophilized formulations or aqueous solutions.
  • the antibody composition will be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners.
  • the “therapeutically effective amount” of the antibody to be administered will be governed by such considerations, and is the minimum amount necessary to prevent the CD47 associated disease.
  • the therapeutic dose may be at least about 0.01 ⁇ g/kg body weight, at least about 0.05 ⁇ g/kg body weight; at least about 0.1 ⁇ g/kg body weight, at least about 0.5 ⁇ g/kg body weight, at least about 1 ⁇ g/kg body weight, at least about 2.5 ⁇ g/kg body weight, at least about 5 ⁇ g/kg body weight, and not more than about 100 ⁇ g/kg body weight. It will be understood by one of skill in the art that such guidelines will be adjusted for the molecular weight of the active agent, e.g. in the use of antibody fragments, or in the use of antibody conjugates.
  • the dosage may also be varied for localized administration, e.g.
  • intranasal, inhalation, etc. or for systemic administration, e.g., intraperitoneal (I.P.), intravenous (I.V.), intradermal (I.D.), intramuscular (I.M.), and the like.
  • I.P. intraperitoneal
  • I.V. intravenous
  • I.D. intradermal
  • I.M. intramuscular
  • a CD47 antibody of this invention needs not be, but is optionally formulated with one or more agents that potentiate activity, or that otherwise increase the therapeutic effect. These are generally used in the same dosages and with administration routes as used hereinbefore or about from 1 to 99% of the heretofore employed dosages.
  • Acceptable carriers, excipients, or stabilizers are non-toxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutarnine, asparagine, hist
  • the active ingredients containing CD47 antibodies may also be entrapped in microcapsule prepared, e.g., by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • a CD47 antibody or pharmaceutical composition of this invention can be administered by any suitable means, including parenteral, subcutaneous, intraperitoneal, intrapulmonary, and intranasal.
  • Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration.
  • the anti-CD47 antibody is suitably administered by pulse infusion, particularly with declining doses of the antibody.
  • the appropriate dosage of antibody will depend on the type of disease to be treated, as defined above, the severity and course of the disease, whether the antibody is administered for preventive purposes, previous therapy, the patient's clinical history and response to the antibody, and the discretion of the attending physician.
  • the antibody is suitably administered to the patient at one time or over a series of treatments.
  • an article of manufacture containing materials useful for the treatment of the disorders described above comprises a container and a label.
  • Suitable containers include, for example, bottles, vials, syringes, and test tubes.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition which is effective for treating the condition and may have a sterile access port (e.g., the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the active agent in the composition is the anti-CD47 antibody.
  • the label on, or associated with, the container indicates that the composition is used for treating the condition of choice.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
  • a pharmaceutically-acceptable buffer such as phosphate-buffered saline, Ringer's solution and dextrose solution.
  • It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
  • CD47 is a 50 kDa membrane receptor that has extracellular N-terminal IgV domain, five transmembrane domains, and a short C-terminal intracellular tail.
  • Human CD47-IgV domain protein conjugated with human Fc or Biotinylated human CD47-IgV domain protein (ACROBiosystems) was used as antigen for phage library panning.
  • the phage library was constructed using phagemid vectors which consisted of the antibody gene fragments that were amplified from spleens or bone marrows of >50 healthy human subjects.
  • the antibody format is single chain variable fragment (VH+linker+VL).
  • the library size was 1.1 ⁇ 1010 and the sequence diversity was analyzed as follows. For the 62 clones picked up from the library and further sequenced, 16 sequences have truncation, frameshift or amber codon; 46 sequences have full length scFv of which all the HCDR3 sequences are unique. In the 46 full length scFv, 13 sequences have lambda light chain and 33 sequences have kappa light chain.
  • phage panning To obtain phage clones that specifically bind to the human CD47-IgV domain, two methods for phage panning were used.
  • the phage libraries developed as described above were first incubated in casein-coated immunotube for 2 hours.
  • the human CD47-IgV-Fc fusion protein was used for first round of panning. Unbound phages were removed by washing with PBST for 5-20 times. The bound phages were eluted with freshly prepared 100 mM Triethylamine solution and neutralized by addition a Tris-HCl buffer, to become the first output phage pools. This first output phage pool was rescued through infection of E. Coli TG-1 cells for amplification, followed by the second round of panning using biotinylated human CD47-IgV as antigen.
  • the bound phages were eluted in the same process and became the second output phage pool which was then rescued and then again followed by the third round of panning using human CD47-IgV-Fc fusion protein as antigen.
  • the bound phages then became the third output phage pool and underwent the fourth round of panning using biotinylated human CD47-IgV.
  • the phage libraries were first incubated in casein-blocked 100 ⁇ l streptavdin-magnetic beads to deplete streptavdin beads binders.
  • the streptavidin-magnetic beads and AG0084-huIgG1/k were used for negative depletion.
  • the depleted library was rescued, which was followed by the second round of panning using biotinylated human CD47-IgV as antigens and further underwent negative depletion with casein blocked streptavdin-magnetic beads.
  • the unbound phages were removed by washing with PBST for 5-20 times.
  • the bound phages were eluted with a freshly prepared 100 mM Triethylamine solution, neutralized by addition of a Tris-HCl buffer, and then rescued, which was followed by the third round of panning using human CD47-IgV-Fc fusion protein and depleted with AG0084-huIgG1/k.
  • the bound phages then become the third output phage pool and underwent the fourth round of panning using biotinylated human CD47-IgV and negative depletion with casein blocked streptavdin-magnetic beads.
  • phage clones that specifically bound to the human CD47-IgV domain were obtained and enriched. They were then diluted and plated to grow at 37° C. for 8 hours and captured by anti-kappa antibody-coated filter overnight. Biotinylated human CD47-IgV (50 nM) and NeutrAvidin-AP conjugate (1:1000 dilution) were applied to the filter to detect the positively bound phage clones. Positive phage plaques were picked and eluted into 100 ⁇ L of phage elution buffer.
  • eluted phages were used to infect 1 mL XL1 blue cells to make high titer phage (HT) for Phage single point ELISA (SPE).
  • the positive single clones picked from the filer lift were subjected to the binding of human CD47-IgV-Fc fusion protein and biotinylated human CD47-IgV domain protein. These positive single clones were also sequenced for their VH and VL genes. All the positive hits with unique VH and VL genes were cloned into expression vectors pFUSE2ss-CLIg-hk (light chain, InvivoGen, Cat No.
  • pfuse2ss-hclk and pFUSEss-CHIg-hG1 (heavy chain, InvivoGen, Cat No. pfusess-hchg1).
  • the antibodies were expressed in HEK293 cells and purified by Protein A Plus Agarose.
  • Binding affinity of the CD-47 antibodies of this invention can be improved by in vitro affinity maturation, e.g., by site-specific randomized mutation, which resulted in mutated sequences that are also within the scope of this invention.
  • BiaCore analysis of 1F8, a CD47 antibody of this invention showed a binding affinity (KD) of 2.8 nM with a high dissociation rate of 1.04E-03 1/s, which could be improved by in vitro affinity maturation.
  • KD binding affinity
  • An extensive analysis of the CDR sequence of heavy chain and light chain of 1F8 identified several residues in HCDR1 and LCDR1 regions that could be randomized mutated. Therefore, the random mutagenesis libraries can be constructed and introduced into the specific residues to generate a variety of new sequences.
  • the CDR mutagenesis libraries are panned using biotinylated soluble CD47 ECD in solution phase under the equilibrium condition.
  • enriched output binders are selected for the binding ELISA test and subsequent converted into full IgGs which are subjected to the BiaCore analysis to specifically select for the off-rate improved sequence.
  • BiaCore analysis to specifically select for the off-rate improved sequence.
  • Recombinant human CD47-Fc fusion protein (Acrobiosystems) was coated at 2 ug/mL in phosphate buffer saline (PBS) onto microtiter plates for 2 hours at the room temperature (RT). After coating of antigen, the wells were blocked with PBS/0.05% Tween (PBST) with 1% BSA for 1 hour at the room temperature (RT). After washing of the wells with PBST, purified phages from single clones were added to the wells and incubated for 1 hour at RT. For detection of the binding phage clones, the HRP conjugated secondary antibodies against M13 (Jackson Immuno Research) were added, followed by the addition of fluorogenic substrates (Roche).
  • PBS phosphate buffer saline
  • Recombinant human CD47/mouse Fc fusion protein or biotinylated CD47 protein was coated at 1 ug/mL in PBS onto microtiter plates for 2 hours at RT. After coating of antigen the wells were blocked with PBS/0.05% Tween (PBST) with 1% BSA for 1 hour at RT. After washing of the wells with PBST, the antibodies diluted in PBS were added to the wells (5 ug/mL) and incubated for 1 hour at RT. For detection of the binding antibodies, the HRP conjugated secondary antibodies against human Fc (Jackson Immuno Research) were added, followed by the addition of fluorogenic substrates (Roche). Between all incubation steps, the wells of the plate were washed with PBST three times. Fluorescence was measured in a TECAN Spectrafluor plate reader.
  • CD47 antibodies of this invention showed good binding activities for recombinant human CD47-Fc fusion protein and biotinylated CD47 protein.
  • CD47-Fc fusion protein (Acrobiosystems) was coated at 1 ug/mL in PBS onto microtiter plates for 16 hours at 4° C. After blocking for 1 hour with 1% BSA in PBST at RT, 1 ug/ml of SIRPa-His protein was added either in the absence or presence of CD47 antibodies (10 ug/mL) at RT for 1 hour. Plates were subsequently washed three times and incubated with an HRP-conjugated anti-His secondary antibody for 1 hour at RT. After washing, the TMB solution was added to each well for 30 minutes and the reaction was stopped with 2.0 M H 2 SO 4 , and OD was measured at 490 nm.
  • a CD47 antibody of this invention 1F8 was selected for this test, in comparison with two existing reference antibodies.
  • Biotinylated CD47 protein (Acrobiosystems) was coated at 1 ug/mL in PBS onto microtiter plates for 2 hours at RT. After coating of antigen, the wells were blocked with PBS/0.05% Tween (PBST) with 1% BSA for 1 hour at RT. After washing of the wells with PBST, different concentrations of CD47 antibodies were added to the well and incubated for 1 hour at RT. For detection of the binding antibodies, the HRP conjugated secondary antibodies against human Fc (Jackson Immuno Research) were added followed by the addition of fluorogenic substrates (Roche). Between all incubation steps, the wells of the plate were washed with PBST three times. Fluorescence was measured in a TECAN Spectrafluor plate reader.
  • Reference antibodies 5F9 and 2A1 was produced according to the sequence of Hu5F9 and CC-90002 as disclosed by researchers at Stanford University, Inhibrx LLC, and Celgene Corp. (see, e.g., U.S. Pat. Nos. 9,017,675 B2, 9,382,320, 9,221,908, US Pat. Application Pub. No. 2014/0140989 and WO 2016/109415) and used for the same study.
  • the three CD47 antibodies used in Example 4 i.e., 1F8, 5F9, and 2A1 were also used in this study.
  • CD47/mouse Fc fusion protein (Acrobiosystems) was coated at 1 ug/ml in PBS onto microtiter plates for 2 hours at RT. After coating of antigen the wells were blocked with PBS/0.05% Tween (PBST) with 1% BSA for 1 hour at RT. After washing of the wells with PBST, different concentrations of anti-CD47 antibodies were added to the well and incubated for 1 at RT. For detection of the binding antibodies, the HRP conjugated secondary antibodies against human Fc (Jackson Immuno Research) were added followed by the addition of fluorogenic substrates (Roche). Between all incubation steps, the wells of the plate were washed with PBST three times. Fluorescence was measured in a TECAN Spectrafluor plate reader.
  • CD47 antibodies i.e., 1F8, 5F9, and 2A1 were also used in this study.
  • Recombinant CD47-Fc fusion protein (Acrobiosystems) was coated at 1 ug/ml in PBS onto microtiter plates for 16 hours at 4° C. After blocking for 1 h with 1% BSA in PBST at RT, 1 ug/mL of SIRPa-His protein was added either in the absence or presence of different concentrations of anti-CD47 antibodies at RT for 1 h. Plates were subsequently washed three times and incubated with an HRP-conjugated anti-His secondary antibody for 1 h at RT. After washing, the TMB solution was added to each well for 30 min and the reaction was stopped with 2M H 2 SO 4 , and OD was measured at 490 nm.
  • CD47 antibodies i.e., 1F8, 5F9, and 2A1 were also used in this study.
  • Raji cells which endogenously express human CD47 on the surface were stained with different concentrations of 1F8, 5F9 and 2A1 antibodies at 4° C. for 30 minutes. Then, the cells were washed with PBS three times, followed by incubation with APC-labeled anti-human Fc specific antibody (Invitrogen) at 4° C. for 30 minutes. Binding was measured using a FACSCanto (Becton-Dickinson).
  • FIG. 4 c and FIG. 4 d show the binding kinetics of 1F8 and 13H3, respectively, as measured by Biocore analysis; and FIG. 4 e shows the data.
  • CD47 antibodies i.e., 1F8, 5F9, and 2A1 were also used in this study.
  • PBMCs peripheral blood cells were isolated from human blood, and the monocytes were differentiated into macrophages for 6 days.
  • the monocyte derived macrophages (MDMs) were scraped and re-plated in 24-well dishes and allowed to adhere for 24 hours.
  • the human tumor cell line Raji which endogenously expressed CD47 were chosen as target cells and labeled with 1 uM CFSE for 10 minutes, then added to MDMs at a ratio of 5:1 tumor cells per phagocyte and CD47 antibodies was added at various doses. After incubation for 3 hours, non-phagocytosed target cells were washed away with PBS and the remaining phagocytes were scraped off, stained with macrophage marker CD14 antibody, and analyzed by flow cytometry. Phagocytosis was measured by gating on CD14 + cells and then assessing the percent of CFSE + cells.
  • FIGS. 6 a , 6 b , and 6 c show the macrophage-mediated phagocytosis of three different human blood cancer cell lines, triggered by the three CD47 antibodies.
  • CD47 antibody 5F9 already showed significant RBC agglutination at a concentration of or higher than 0.1 ug/uL
  • CD47 antibodies 1F8 and 2A1 resulted in essentially no RBC agglutination at the tested concentrations up to 30 ug/uL ( FIGS. 7 a and 7 b ) or even up to 150 ug/mL ( FIGS. 8 a and 8 b ).
  • FIGS. 8 c and 8 d show that CD47 antibodies of this invention (i.e., 1F8 and 13H3) resulted in essentially no RBC agglutination at the tested concentrations up to 150 ug/mL, whereas CD47 antibody 5F9 already showed significant RBC agglutination at a concentration of or higher than 0.1 ug/uL.
  • CD47 antibodies against human RBCs Binding of CD47 antibodies against human RBCs was examined by flow cytometry. Human RBCs were incubated with CD47 antibodies (10 ug/mL) at 4° C. for 1 hour, followed by the addition of APC-conjugated secondary antibody at 4° C. for 30 minutes.
  • CD47 antibody of this invention 1F8 did not bind to RBC while reference CD47 antibodies 5F9 and 2A1 did at the tested concentrations.
  • FIGS. 9 c and 9 d show that while 1F8 resulted in no RBC binding at the tested concentrations, 13H3 only resulted in very low RBC binding at the tested concentrations.
  • FIGS. 10 a and 10 b show the titration results of the hemagglutination assay, which is denoted “agglutination index” as determined by measuring the area of the RBC pellets in the presence of the antibody, normalized to that of IgG control or reference antibody.
  • CD47 antibodies of this invention binding of CD47 antibodies of this invention against human platelets was examined by flow cytometry. Human peripheral whole blood was incubated with test CD47 antibodies of this invention (at 10 ug/mL) or SIRP ⁇ -Ig fusion and CD61 was stained as a surface marker for platelets. The binding of CD47 antibodies or SIRP ⁇ -Ig fusion was measured by gating on the CD61 positive population (platelet) and further examining the percentages of CD47 or SIRP ⁇ -Ig fusion binding.
  • tested CD47 antibodies of this invention did not appreciably bind to human platelets whereas SIRP ⁇ proteins did.
  • FIG. 12 b shows the titration results of the hemagglutination assay, which is denoted “agglutination index” as determined by measuring the area of the RBC pellets in the presence of the antibody, normalized to that of IgG control.
  • AML-PB003F Primary PBMCs from AML patient (AML-PB003F) were labeled with 1 uM CFSE for 10 minutes, then added to MDMs at a ratio of 5:1 tumor cells per phagocyte and the indicated CD47 antibodies was added at various concentrations. After 3-hr incubation, non-phagocytosed target cells were washed away with PBS and the remaining phagocytes were scraped off, stained with a CD14 antibody, and analyzed by flow cytometry. Phagocytosis was measured by gating on CD14+ cells and then assessing the percentage of CFSE+ cells. Phagocytosis was measured as previously mentioned.
  • the tested CD47 antibodies of this invention all showed significant AML binding capabilities (greater than 75%) and phagocytosis capabilities (at least 36%), all of which are much higher than the reference CD47 antibody used in the same essay.
  • NSG mice were engrafted with Raji Luc-EGFP at a concentration of 1 million cells/mouse via tail vein injection. They were imaged in vivo to determine the level of engraftment five days post engraftment.
  • Treatment of CD47 antibodies i.e., 1F8, 5F9, and 2A1 started from the same day at a dose of 10 mg/kg. All mice were injected every other day via intraperitoneal injection. Mice were imaged in vivo via IVIS Lumina III imaging system at the following time points: Day 0 of antibody treatment, Day 2 of treatment, Day 6 of treatment, and Day 9 of treatment. The tumor growth in the mice was measured by the analysis of bioluminescent radiance through in vivo live imaging system.
  • the analysis of bioluminescent radiance shows that the tumors in the mice barely grew within the first three days after the treatments with the tested CD47 antibody of this invention (i.e., 1F8) and the tumors reduced from day 6 after the treatments. By comparison, the tumors in the mice treated with reference CD47 antibody continued to grow during the same treatment period.
  • FIG. 14 b shows that the CD47 antibody 13H3 was also effective in vivo in Raji xenograph model at different test concentrations.
  • mice were euthanized by the use of CO 2 for rodent euthanasia.
  • the splenocytes from four groups of mice were isolated and analyzed for the percentage of M1 macrophages (% of CD80 positive in F4/80 positive macrophages) and M2 macrohpages (% of CD206 positive in F4/80 positive macrophages) by flow cytometry analysis.
  • FIGS. 16 a , 16 b and 16 c show the different expression levels of CD47 after the treatments with CD47 antibodies.
  • CBC Hematology
  • Na ⁇ ve cyno monkeys were intravenously infused with single dose or repeat dose (weekly dosing) of the anitibody 13H3 (20 mg/kg).
  • Hematology (CBC) parameters were examined including Erythrocyte count (RBC), Hemoglobin (HGB), Platelet Counts and Lymphocyte Counts at the indicated time points following the antibody administration.
  • FIGS. 19 a , 19 b , 19 c , 19 d , 19 e , 19 f , 19 g , and 19 h show the effects of the CD47 antibody 13H3 on RBC congregation, hemoglobin, platelets, and lymphocytes.
  • CD47 ECD protein and first anti-CD47 antibody were pre-incubated and added to a biotinylated second anti-CD47 antibody detected by a Strptavidin-HRP antibody. If the first anti-CD47 antibody competed against the binding of CD47 ECD to the second antibody, both antibodies were placed in same or overlapping epitope bins. If not, they were placed in non-overlapping epitope bins.
  • FIGS. 18 a and 18 b show that CD47 antibody of this invention 1F8 has a different epitope than those of reference antibodies 5F9 and 2A1.
  • FIG. 18 c shows the crystal structure of reference Ab 5F9 (upper part) in complex with human CD47-ECD (green) as reported in the literature (See, e.g., J. Clin. Investigation, 126, 7: 2610-2620).
  • FIG. 18 d shows the crystal structure of 1F8-Fab (upper part) in complex with human CD47-ECD (green).
  • the complex structure of CD47-1F8 Fab adopts straighter head to head orientation, unlike the complex structures of CD47-SIRP ⁇ and CD47-5F9 diabody presenting tilted head to head orientation.
  • the 1F8 epitope on CD47 is discontinuous and extensive which includes residues L3, V25, T26, N27, M28, E29, A30, Q31, T34, E35, Y37, A53, L54, L74, K75, G76, T99, E100, L101, T102 and R103, of which L3, N27, E29, Q31, T34, E35, Y37, A53, T99, E100, L101, T102 and R103 are involved in the interactions with SIRP ⁇ , explaining the antagonistic properties of 1F8.
  • the complex structure also reveals VH domain of 1F8 forms 8 hydrogen bonds and 4 salt bridges to CD47 and VL domain of 1F8 forms 8 hydrogen bonds to CD47 as well.
  • the 1F8 antibody binds mostly different epitopes of the target although all are binding in the similar head-to-head orientation.
  • the 1F8 epitope on CD47 is conformationally discontinuous and includes a TNMEAQ loop (residues 26-31), T34, E35, L74, and an LTR hinge (residues 101 -103) of CD47.
  • Many hydrogen bond interactions are formed between side chains of antibody residues and CD47 main chain oxygen atoms.
  • a salt bridge is also formed between R103 of 1F8 and E35 of CD47. Several Van der Waals contacts are also observed which are critical to keep appropriate orientation.
  • the VH domain of antibody 1F8 is primarily involved in binding to the T34, E35 and the LTR hinge (residues 101-103) of CD47, while the VK domain interact with the TNMEAQ loop (residues 26-31) and L74. These epitopes on CD47 are different from that in 5F9 antibody and SIRPa. Structural analysis suggest that two long loops (residues 26-38 and 52-59) of the 1F8 antibody help it bind to CD47 in a nearly vertical orientation which may lead to the antibody to be separated in such a way that CD47 on adjacent cells could not be bridged by the antibody, thereby preventing most of blood cell hemaglutination.
  • FIG. 18 e shows the comparison of interaction of 5F9 and 1F8 with CD47.
  • antibody 5F9's residue Tyr101 point towards N-term of CD47 through a van der Waals contact and Arg102 forms a hydrogen bond with Glu104 of CD47.
  • Antibody 1F8's loop residues Asn31, Trp33, and hinge residues Arg53 and Asp56 form inter-domain hydrogen bonds net, then Asn31 and Arg53 form hydrogen bonds with main chain of Leu101 and Thr34 in CD47.
  • 5F9 does not appear to make interaction, except residue Tyr 52 forms a van der Waals contact with Leu3 on CD47.
  • the hinge (residue 52-56) is 3 residues shorted than that of 1F8 (residues 52-59).
  • both Fab 1F8 and 5F9 have several important hydrogen bond interactions with CD47 from the loop (V29 -Y38 in 1F8 and V152-Y158 in 5F9).
  • Residues Y97 and Y98 in 1F8 “push” the loop (residues 26-38) away, and the latter formed 2 hydrogen bonds between 1F8 and CD47, namely between Arg34 of 1F8 and main chain of Leu74 on CD47, and between Arg36 of 1F8 and main chain of Thr26 on CD47.
  • 5F9's residues Gly218 and Ser219 cause the loop (residues 149-158) in 5F9 to form 3 hydrogen bonds with CD47 (at Asn157-Lys39, Tyr159-G1u104 and Lys177-Thr99,).
  • the loop (residues 149-158) in 5F9 is about 3 residues shorter than that in 1F8 (residues 26-38).
  • mice To generate anti-human CD47 antibodies, different strains of 6-8-week mice including BALB/C, C57/BL6 or SJL mice were immunized with recombinant human CD47 extracellular domain protein for several rounds. After immunization, mice with sufficient titres of anti-CD47 IgG were boosted with the same antigen followed by fusion. The hybridoma supernatants were tested for direct binding with human CD47 ECD protein and competition of SIRP ⁇ binding to CD47 by ELISA screening. Through a series of screening assays, 34C5 was selected for the humanization and further in vitro characterization according to the assays described above.
  • FIG. 20 and FIG. 21 show strong binding affinity of 34C5 to recombinant CD47-ECD (with an EC 50 of 0.27 nM) and to CD47-bearing Raji cells (with an EC 50 of 0.83 nM), respectively.
  • FIG. 22 shows that 34C5 was able to effectively block CD47 binding to SIRP ⁇ , with an EC 50 of 0.30 nM.
  • FIG. 23 shows that the antibody 34C5 promoted phagocystosis of tumor cells by human M ⁇ .
  • FIG. 24 shows the antibody 34C5 did not cause in vitro RBC agglutination.
  • FIG. 25 shows the antibody 34C5 decrease its binding to RBC with the decreasing concentration of this antibody.

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EP3411071A4 (en) 2019-08-28
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