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WO2011089211A1 - Anticorps anti-cd133 et leurs procédés d'utilisation - Google Patents

Anticorps anti-cd133 et leurs procédés d'utilisation Download PDF

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Publication number
WO2011089211A1
WO2011089211A1 PCT/EP2011/050816 EP2011050816W WO2011089211A1 WO 2011089211 A1 WO2011089211 A1 WO 2011089211A1 EP 2011050816 W EP2011050816 W EP 2011050816W WO 2011089211 A1 WO2011089211 A1 WO 2011089211A1
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Prior art keywords
antibody
amino acid
seq
antibodies
acid sequence
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PCT/EP2011/050816
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English (en)
Inventor
Gundram Jung
Ludger Grosse-Hovest
Hans-Jörg BÜHRING
Steffen Aulwurm
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Synimmune Gmbh
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Publication of WO2011089211A1 publication Critical patent/WO2011089211A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • 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
    • C07K16/2896—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against molecules with a "CD"-designation, not provided for elsewhere
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/72—Increased effector function due to an Fc-modification

Definitions

  • the present invention lies in the field of antibodies and relates to CD 133 specific antibodies with a modified Fc region to enhance antibody-dependent cell cytotoxicity (ADCC) as well as methods of using such antibodies.
  • ADCC antibody-dependent cell cytotoxicity
  • CD133 expressed on the cell surface of somatic stem cells, including hematopoietic, neuronal and glial stem cells, as well as endothelial progenitor cells is associated with membrane microdomains (lipid rafts) and assumed to play an important role in the organization of plasma membrane protrusions. Additionally, it has been found that CD 133 is strongly expressed in many hyperproliferative or malignant cells. In fact, CD133 is considered the most important cancer stem cell (CSC)-associated marker identified so far.
  • CSC cancer stem cell
  • one object of the inventors of the present invention was to provide anti-CD 133 antibodies that can bind to and kill CD 133 -expressing cells in vivo.
  • the present invention is directed to antibodies against human CD 133 and methods of using the same.
  • the antibodies include a variant Fc region.
  • the antibodies are chimeric or humanized antibodies.
  • the present invention is further directed to pharmaceutical compositions comprising these antibodies and methods of using the antibodies in various disease indications.
  • the present invention is directed to an antibody that binds human CD133, wherein said antibody comprises a heavy chain and/or a light chain and has at least one amino acid substitution in the constant region relative to a parent anti-CD 133 antibody, wherein said at least one amino acid substitution includes the amino acid substitutions 239D and 332E, wherein the positional numbering is according to the EU index (Kabat et al., 1983).
  • the substitutions are S239D and I332E.
  • the antibody specifically binds to CD 133. This means that it binds to human CD 133 with significantly higher affinity than to non-target molecules.
  • the affinity of the antibody for its target is at least about 50 nM
  • the anti-CD 133 antibody has cell killing activity, such as, for example, antibody-dependent cell-mediated cytotoxicity (ADCC) effector function. That means that upon contact with CD133-expressing cells, the antibody is capable of facilitating cell death, for example by triggering activation of the complement system, phagocytosis or apoptosis.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • the antibody comprises a heavy and a light chain.
  • the heavy chain may comprise a V H CDR1, a V H CDR2, and a V H CDR3 region and/or the light chain may comprise a VL CDRl, a VL CDR2, and/or a V L CDR3 region.
  • the VL CDRl comprises, consists essentially of or consists of an amino acid sequence selected from the group consisting of the amino acid sequences SEQ ID NO:l and SEQ ID NO:7;
  • the V L CDR2 comprises, consists essentially of or consists of an amino acid sequence selected from the group consisting of the amino acid sequences of SEQ ID NO:2 and SEQ ID NO:8;
  • the VL CDR3 comprises, consists essentially of or consists of an amino acid sequence selected from the group consisting of the amino acid sequences of SEQ ID NO: 3 and SEQ ID NO:9;
  • the VH CDRl comprises, consists essentially of or consists of an amino acid sequence selected from the group consisting of the amino acid sequences of SEQ ID NO:4 and SEQ ID NO: 10;
  • the VH CDR2 comprises, consists essentially of or consists of an amino acid sequence selected from the group consisting of the amino acid sequences of SEQ ID NO: 5 and SEQ ID NO:l 1; and the VH CDR
  • the VL CDRl comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:l;
  • the VL CDR2 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:2;
  • the V L CDR3 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:3;
  • the VH CDRl comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:4;
  • the VH CDR2 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:5;
  • the VH CDR3 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:6.
  • the VL CDRl comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:7; the V L CDR2 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:8; the VL CDR3 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO:9; the VH CDRl comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO: 10; the VH CDR2 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO: 1 1 ; and the V H CDR3 comprises, consists essentially of or consists of the amino acid sequence set forth in SEQ ID NO: 12.
  • the heavy chain of the invented antibody comprises a VH domain comprising, consisting essentially of or consisting of the amino acid sequence set forth in SEQ ID NO: 14 and/or the light chain of the invented antibody comprises a VL domain comprising, consisting essentially of or consisting of the amino acid sequence set forth in SEQ ID NO: 13.
  • the heavy chain of the invented antibody comprises a VH domain comprising, consisting essentially of or consisting of the amino acid sequence set forth in SEQ ID NO:30 and/or the light chain of the invented antibody comprises a VL domain comprising, consisting essentially of or consisting of the amino acid sequence set forth in SEQ ID NO:29.
  • the claimed antibody is a chimeric antibody and comprises a heavy chain having the amino acid sequence set forth in SEQ ID NO:27 and/or a light chain having the amino acid sequence set forth in SEQ ID NO:23.
  • the claimed antibody is a chimeric antibody and comprises a heavy chain having the amino acid sequence set forth in SEQ ID NO: 43 and/or a light chain having the amino acid sequence set forth in SEQ ID O:39.
  • the antibody of the invention comprising amino acid substitutions S239D/I332E binds with enhanced affinity to the FcyRIIIa receptor or has enhanced ADCC effector function as compared to the parent antibody without said substitution.
  • the antibody comprises one or more further amino acid modifications at a position selected from the group consisting of 221, 222, 223, 224, 225, 227, 228, 230, 231 , 232, 233, 234, 235, 236, 237, 238, 240, 241, 243, 244, 245, 246, 247, 249, 255, 258, 260, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271 , 272, 273, 274, 275, 276, 278, 280, 281 , 282, 283, 284, 285, 286, 288, 290, 291 , 292, 293, 294, 295, 296, 297, 298, 299, 300, 301 , 302, 303, 304, 305, 313, 317, 318, 320, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331 , 333, 334, 335, 336, and
  • These one or more further amino acid modifications may be selected from the group of amino acid substitutions consisting of 221K, 221 Y, 222E, 222Y, 223E, 223K, 224E, 224Y, 225E, 225 , 225W, 227E, 227G, 227K, 227Y, 228E, 228G, 228K, 228Y, 230A, 230E, 230G, 230Y, 231E, 231G, 231K, 231P, 231Y, 232E, 232G, 232K, 232Y, 233A, 233D, 233F, 233G, 233H, 2331, 233K, 233L, 233M, 233N, 233Q, 233R, 233S, 233T, 233V, 233W, 233Y, 234A, 234D, 234E, 234F, 234G, 234H, 2341, 234 , 234M, 2
  • the one or more further amino acid modifications are at a position selected from the group consisting of 221, 222, 223, 224, 225, 228, 230, 231, 232, 240, 244, 245, 247, 262, 263, 266, 271, 273, 275, 281 , 284, 291, 299, 302, 304, 313, 323, 325, 328, and 336, wherein the positional numbering is according to the EU index.
  • the one or more further amino acid modifications may be selected from the group of amino acid substitutions consisting of 221K, 221Y, 222E, 222Y, 223E, 223 , 224E, 224Y, 225E, 225 , 225W, 228E, 228G, 228K, 228Y, 230A, 230E, 230G, 230Y, 231 E, 231 G, 231 K, 231 P, 231 Y, 232E, 232G, 232K, 232Y, 240A, 2401, 240M, 240T, 244H, 245A, 247G, 247V, 262A, 262E, 262F, 2621, 262T, 263A, 2631, 263M, 263T, 266A, 2661, 266 , 266T, 271 A, 271 D, 271 E, 271 F, 271G, 271 H, 2711, 271K, 271 L,
  • the present invention features nucleic acid molecules that encode the heavy chain and/or the light chain of an antibody of the invention.
  • These nucleic acid molecules may comprise a nucleotide sequence that encodes the variable domain of the light chain, such as that set forth in SEQ ID NO: 17 or SEQ ID NO:33, or a nucleotide sequence that encodes the variable domain of the heavy chain, such as that set forth in SEQ ID NO: 18 or SEQ ID NO:34.
  • the nucleic acid encoding the light chain of the antibody of the invention has a nucleotide sequence selected from the group consisting of SEQ ID Nos. 24 and 40.
  • the nucleic acid encoding the heavy chain of the antibody of the invention has a nucleotide sequence selected from the group consisting of SEQ ID Nos. 28 and 44.
  • the present invention relates to a method of treating a CD133-related disease or disorder, wherein said method includes administering the antibody of the invention to a subject in need thereof.
  • the subject may, for example, be an animal or human, preferably a mammal, such as a human.
  • said disease or disorder is a cell proliferative disease or disorder.
  • the cell-proliferative disease or disorder may, for example, be cancer.
  • the cancer may be a solid tumor and may be selected from the group consisting of glioma/glioblastoma, melanoma, pancreatic cancer, gastric cancer, colon cancer, colorectal cancer, breast cancer, ovarian cancer, sarcoma, prostate carcinoma, liver cancer and lung cancer, or may be a haematological malignancy, such as a lymphoma or leukemia.
  • the lymphoma or leukemia may be selected from the group consisting of: non-Hodgkin's lymphomas (NHL), chronic lymphocytic leukemia (CLL), B-cell acute lymphoblastic leukemia lymphoma (B-ALL), mantle cell lymphoma ( CL), hairy cell leukemia (HCL), chronic myeloid leukemia (CML), acute myeloid leukemia, and multiple myeloma (MM).
  • the lymphoma is chronic lymphocytic leukemia (CLL).
  • the disease or disorder is myelodysplastic syndrome (MDS).
  • the antibody may be administered in combination with at least one agent selected from the group consisting of a cytotoxic agent, a chemotherapeutic agent, a cytokine, a growth inhibitory agent, an anti-hormonal agent, a kinase inhibitor, an anti-angio genie agent, a cardioprotectant, an immunostimulatory agent, an immunosuppressive agent, an angiogenesis inhibitor, a protein tyrosine kinase inhibitor, and second antibody.
  • a cytotoxic agent a chemotherapeutic agent
  • a cytokine a growth inhibitory agent
  • an anti-hormonal agent a kinase inhibitor
  • an anti-angio genie agent a cardioprotectant
  • an immunostimulatory agent an immunosuppressive agent
  • an angiogenesis inhibitor a protein tyrosine kinase inhibitor
  • second antibody selected from the group consisting of a cytotoxic agent, a chemotherapeutic agent, a cytokine, a growth inhibitory
  • the present invention also encompasses a pharmaceutical composition
  • a pharmaceutical composition comprising an antibody according to the invention and a pharmaceutically acceptable carrier.
  • the present invention is directed to a method of inhibiting proliferation of a cell expressing CD133, wherein said method comprises contacting said cell with an antibody according to the invention.
  • the method may be an in vitro method.
  • the present invention relates to a method of enhancing antibody-dependent cell-mediated cytotoxicity toward a cell expressing CD 133, wherein said method comprises contacting said cell with an antibody according to the invention.
  • a still further aspect of the invention is a method of depleting a mammal of at least one cell expressing CD133, wherein said method comprises administering to the mammal an antibody according to the invention.
  • the present invention also relates to the use of an antibody according to the present invention for treating a CD133-related disease or disorder.
  • the CD 133- related disease or disorder may be a cell proliferative disease or disorder.
  • the cell- proliferative disease or disorder may, for example, be cancer.
  • the cancer may be selected from the group consisting of glioma/glioblastoma, melanoma, pancreatic cancer, gastric cancer, colon cancer, colorectal cancer, breast cancer, ovarian cancer, sarcoma, prostate carcinoma, liver cancer, lung cancer and haematological malignancies, such as lymphomas and leukemias.
  • the lymphoma or leukemia may be selected from the group consisting of: non-Hodgkin's lymphomas (NHL), chronic lymphocytic leukemia (CLL), B-cell acute lymphoblastic leukemia lymphoma (B- ALL), mantle cell lymphoma (MCL), hairy cell leukemia (HCL), chronic myeloid leukemia (CML), acute myeloid leukemia, and multiple myeloma (MM).
  • the lymphoma is chronic lymphocytic leukemia (CLL).
  • the disease or disorder is myelodysplastic syndrome (MDS).
  • the invention relates to the use of an antibody according to the invention for the targeting of a cell expressing CD 133.
  • the targeting may include the use of the antibody to deliver a drug or a toxin to the CD 133 -expressing cell.
  • the invention encompasses the use of an antibody according to the invention for the detection of a cell expressing CD 133 in a biological sample.
  • the antibody may be labeled with a detectable moiety, such as a fluorophore, chromophore, immunogenic tag and the like.
  • the present invention is also directed to a monoclonal antibody against CD 133, wherein the antibody is produced by a transfected producer cell line, such as CHO or Sp2/0.
  • the invention features a transfected cell line producing an antibody according to the invention.
  • the cell line may be a CHO or Sp2/0 cell line
  • Figure 1 shows a schematic representation of the cloning procedure for chimerization of monoclonal antibodies. Boxes represent exons, circle indicate enhancer elements and thin lines UT regions and intron sequences. P, promoter; Li and L 2 , leader sequences encoded by two different exons; E, enhancer; V, variable region; D, diversity region; J, joing region; C ⁇ ) exons of constant region; H, hinge region.
  • Figure 2 shows the parental vector containing the VJ region of the mouse light chain and the C region of human ⁇ gene.
  • the region relevant for the fragment exchange is shown enlarged in Figure 2A.
  • the sequence context generated upon insertion of the VJ region of monoclonal antibodies 293AC1C3B9 or W6B3H10 into the expression vector chimCD133-light is shown by using W6B3H10 as an example in Figure 2B.
  • the cleavage site for secretory signal peptides is indicated by j; and exon- intron boundaries by [, ].
  • Figure 3 shows the original vector containing the human ⁇ isotype Ig heavy chain.
  • the region relevant for cloning the VDJ fragment is shown enlarged (a).
  • the Mlul-Spel fragment to be exchanged (shown enlarged as b) contains the entire constant region of the human ⁇ heavy chain and two amino acid modifications in the CH2 domain as indicated (Ser 23 9-Asp; Iso 332 -Glu).
  • Figure 3B shows the sequence context generated upon insertion of the VDJ region of the heavy chain of monoclonal antibodies 293AC1C3B9 or W6B3H10 into the heavy chain expression vector chimCD 133 -heavy by means of using the sequence of W6B3H10 as an example.
  • the cleavage site for secretory signal peptides is indicated by
  • Figure 4 shows the cell killing effects of the Fc optimized chimeric antibodies chim293AClC3B9-SDIE (A) and chimW6B3H10-SDIE (B) respectively and unstimulated human PBMCs against cultured CD 133 -expressing human WERI-Rbl cells in comparison to the unmodified chimeric antibodies chim293AClC3B9 and chimW6B3H10.
  • Fig. 4 C shows the cell killing effects of chimeric antibodies directed to NG2 that have been Fc optimized in the same positions as the above antibodies on human SKMel63 -melanoma cells. Cytotoxicity was determined using a chromium release assay, duration of the assay and targetreffector ratios are indicated.
  • Figure 5 shows the binding of CD133 antibody 293C3 (293AC1C3B9) to PBMC of 9 patients with chronic lymphatic leukemia (CLL), as determined by flow cytometry.
  • Figure 6 shows an amino acid sequence alignment of the light (A) and heavy (B) chain variable regions of the anti-CD 133 antibody clones 293AC1C3B9 and W6B3H10.
  • ADCC antibody dependent cell-mediated cytotoxicity
  • ADCP' or “antibody dependent cell-mediated phagocytosis” as used herein is meant the cell-mediated reaction wherein nonspecific cytotoxic cells that express FcyRs recognize bound antibody on a target cell and subsequently cause phagocytosis of the target cell.
  • amino acid and “amino acid identity” as used herein is meant one of the 20 naturally occurring amino acids or any non-natural analogues that may be present at a specific, defined position.
  • amino acid as used herein is both naturally occurring and synthetic amino acids.
  • homophenylalanine, citrulline and noreleucine are considered amino acids for the purposes of the invention.
  • amino acid also includes imino acid residues such as proline and hydroxyproline.
  • the side chain may be in either the (R) or the (S) configuration. In a embodiment, the amino acids are in the (S) or L-configuration. If non-naturally occurring side chains are used, non-amino acid substituents may be used, for example to prevent or retard in vivo degradation.
  • antibody herein is meant a protein consisting of one or more polypeptides substantially encoded by all or part of the recognized immunoglobulin genes.
  • the recognized immunoglobulin genes include the kappa ( ⁇ ), lambda ( ⁇ ), and heavy chain genetic loci, which together comprise the myriad variable region genes, and the constant region genes mu ( ⁇ ), delta ( ⁇ ), gamma ( ⁇ ), epsilon ( ⁇ ), and alpha (a) which encode the IgM, IgD, IgG (IgGl , IgG2, IgG3, and IgG4), IgE, and IgA (IgAl and IgA2) isotypes respectively.
  • Antibody herein is meant to include full length antibodies and antibody fragments, and may refer to a natural antibody from any organism, an engineered antibody, or an antibody generated recombinantly for experimental, therapeutic, or other purposes.
  • B cell or "B lymphocyte” as used herein is meant a type of lymphocyte developed in bone marrow that circulates in the blood and lymph, and provides humoral immunity. B cells recognize free antigen molecules and differentiate or mature into plasma cells that secrete immunoglobulin (antibodies) that inactivate the antigens. Memory cells are also generated that make the specific immunoglobulin (antibody) on subsequent encounters with such antigen.
  • T cell or "T lymphocyte” as used herein is meant a type of lymphocyte developed in bone marrow that circulates in the blood and the lymph, and provides cellular immunity.
  • T cells comprise a T cell receptor that recognizes cell- bound antigen molecules.
  • T cells can mature into helper T cells that secrete cytokines and activate other cell types or cytotoxic T cells that bind to and destroy other cells.
  • CD133 a cholesterol-binding transmembrane glycoprotein.
  • the protein is 846 amino acids long and spans the membrane 5 times and has two large extracellular loops.
  • the N-terminus is located in the extracellular space and the C-terminus is located in the cytoplasma. It is expressed on the cell surface of somatic stem cells, including hematopoietic, neuronal and glial stem cells, as well as endothelial progenitor cells is associated with membrane microdomains (lipid rafts) and assumed to play an important role in the organization of plasma membrane protrusions.
  • CD133 is strongly expressed in many hyperproliferative or malignant cells.
  • CD133 is considered the most important cancer stem cell (CSC)-associated marker identified so far.
  • CSC cancer stem cell
  • the expression of CD133 has been shown for numerous different cancer types, such as glioma/glioblastoma, leukemias, such as chronic lymphatic leukemia, colon cancer, pancreatic cancer, gastric cancer etc.. Based on these results, it is assumed that aberrant CD 133 activity may be involved in the development and progression of cancer.
  • the sequence of human CD133 is provided in SEQ ID NO:71.
  • CDC complement dependent cytotoxicity
  • constant region of an antibody as defined herein is meant the region of the antibody that is encoded by one of the light or heavy chain immunoglobulin constant region genes.
  • constant light chain or “light chain constant region” as used herein is meant the region of an antibody encoded by the kappa (C K ) or lambda (C ⁇ ) light chains
  • the constant light chain typically comprises a single domain, and as defined herein refers to positions 108-214 of C K or lambda Cx, wherein numbering is according to the EU index.
  • constant heavy chain or “heavy chain constant region” as used herein is meant the region of an antibody encoded by the mu, delta, gamma, alpha, or epsilon genes to define the antibody's isotype as IgM, IgD, IgG, IgA, or IgE, respectively
  • the constant heavy chain refers to the N-terminus of the CHI domain to the C-tenninus of the CH3 domain, thus comprising positions 118-447, wherein numbering is according to the EU index.
  • effector function as used herein is meant a biochemical event that results from the interaction of an antibody Fc region with an Fc receptor or ligand. Effector functions include FcyR-mediated effector functions such as ADCC and ADCP, and complement- mediated effector functions such as CDC.
  • effector cell as used herein is meant a cell of the immune system that expresses one or more Fc receptors and mediates one or more effector functions. Effector cells include but are not limited to monocytes, macrophages, neutrophils, dendritic cells, eosinophils, mast cells, platelets, B cells, large granular lymphocytes, Langerhans' cells, natural killer (NK) cells, and T cells and may be from any organism including but not limited to humans, mice, rats rabbits, and monkeys.
  • Fab or "Fab region” as used herein is meant the polypeptides that comprise the VH, CHI, VH, and CL immunoglobulin domains. Fab may refer to this region in isolation, or this region in the context of a full length antibody or antibody fragment.
  • Fc or “Fc region”, as used herein is meant the polypeptide comprising the constant region of an antibody excluding the first constant region immunoglobulin domain
  • Fc refers to the last two constant region immunoglobulin domains of IgA, IgD, and IgG, and the last three constant region immunoglobulin domains of IgE and IgM, and the flexible hinge N-terminal to these domains.
  • Fc may include the J chain.
  • Fc comprises immunoglobulin domains Cy2 and Cy3 and the hinge between C y i and C y2 .
  • the human IgG heavy chain Fc region is usually defined to comprise residues C226 or P230 to its carboxyl-terminus, wherein the numbering is according to the EU index as in Kabat.
  • Fc may refer to this region in isolation, or this region in the context of an Fc polypeptide, for example an antibody.
  • Fc polypeptide as used herein is meant a polypeptide that comprises all or part of an Fc region Fc polypeptides include antibodies Fc fusions, isolated Fes, and Fc fragments.
  • Fc gamma receptor or “FcyR” as used herein is meant any member of the family of proteins that bind the IgG antibody Fc region and are substantially encoded by the FcyR genes. In humans this family includes but is not limited to FcyRI (CD64), including isoforms FcyRIa, FcyRIb, and FcyRIc; FcyRII (CD32), including isoforms FcyRIIa (including allotypes H131 and R131 ), FcyRIIb (including FcyRIIb-1 and FcyRIIb-2), and FcyRIIc; and FcyRIII (CD16), including isoforms FcyRIIIa (including allotypes VI 58 and Fl 58) and FcyRIIIb (including allotypes FcyRIIIb-NAl and FcyRIIIb-NA2) (Jefferis et al., 2002, Immunol Lett 82:57-65
  • Mouse FcyRs include but are not limited to FcyRI (CD64), FcyRII (CD32), FcyRIII (CD 16), and FcyRIII-2 (CD 16-2), as well as any undiscovered mouse FcyRs or FcyR isoforms or allotypes.
  • An FcyR may be from any organism, including but not limited to humans, mice, rats, rabbits, and monkeys.
  • Fc ligand or "Fc receptor” as used herein is meant a molecule, e.g., a polypeptide, from any organism that binds to the Fc region of an antibody to form an Fc- ligand complex.
  • Fc ligands include but are not limited to FcyRs, FcRn, Clq, C3, mannan binding lectin, mannose receptor, staphylococcal protein A, streptococcal protein G, and viral FcyR.
  • Fc ligands also include Fc receptor homologs (FcRH), which are a family of Fc receptors that are homologous to the FcyRs (Davis et al., 2002, Immunological Reviews 190:123-136). Fc ligands may include undiscovered molecules that bind Fc.
  • FcRH Fc receptor homologs
  • IgG as used herein is meant a polypeptide belonging to the class of antibodies that are substantially encoded by a recognized immunoglobulin gamma gene. In humans this class comprises IgGl, IgG2, IgG3, and IgG4. In mice this class comprises IgGl, IgG2a, IgG2b, IgG3.
  • immunoglobulin herein is meant a protein consisting of one or more polypeptides substantially encoded by immunoglobulin genes. Immunoglobulins include but are not limited to antibodies. Immunoglobulins may have a number of structural forms, including but not limited to full length antibodies, antibody fragments, and individual immunoglobulin domains.
  • immunoglobulin (Ig) domain herein is meant a region of an immunoglobulin that exists as a distinct structural entity as ascertained by one skilled in the art of protein structure. Ig domains typically have a characteristic ⁇ -sandwich folding topology. The known Ig domains in the IgG class of antibodies are VH, Cyl, Cy2, Cy3, VL, and CL.
  • amino acid modification herein is meant an amino acid substitution, insertion, and/or deletion in a polypeptide sequence.
  • amino acid substitution or “substitution” herein is meant the replacement of an amino acid at a particular position in a parent polypeptide sequence with another amino acid
  • substitution I332E refers to a variant polypeptide, in this case a constant heavy chain variant, in which the isoleucine at position 332 is replaced with glutamic acid
  • the wildtype residue may or may not be designated.
  • 332E indicates the substitution of position 332 with a glutamic acid.
  • multiple substitutions are typically separated by a slash.
  • 239D/332E refers to a double variant comprising the substitutions 239D and 332E.
  • amino acid insertion or "insertion” as used herein is meant the addition of an amino acid at a particular position in a parent polypeptide sequence.
  • insert -236G designates an insertion of glycine at position 236.
  • amino acid deletion or “deletion” as used herein is meant the removal of an amino acid at a particular position in a parent polypeptide sequence
  • G236- designates the deletion of glycine at position 236.
  • parent polypeptide By “parent polypeptide”, “parent protein”, “precursor polypeptide”, or “precursor protein” as interchangeably used herein is meant a polypeptide that is subsequently modified to generate a variant, e g , any polypeptide which serves as a template and/or basis for at least one amino acid modification described herein.
  • the parent polypeptide may be a naturally occurring polypeptide, or a variant or engineered version of a naturally occurring polypeptide
  • Parent polypeptide may refer to the polypeptide itself, compositions that comprise the parent polypeptide, or the amino acid sequence that encodes it.
  • parent antibody or “parent immunoglobulin” as used herein is meant an antibody or immunoglobulin that is modified to generate a variant (e.g., a parent antibody may include, but is not limited to, a protein comprising the constant region of a naturally occurring Ig).
  • protein or "polypeptide” as used herein is meant at least two covalently attached amino acids, which includes proteins, polypeptides, oligopeptides and peptides
  • the protein may be made up of naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures, i. e. "analogs", such as peptoids.
  • position as used herein is meant a location in the sequence of a protein. Positions may be numbered sequentially, or according to an established format, for example the EU index as in Kabat (Kabat et al., 1983). If not indicated otherwise, all positions mentioned herein are numbered according to the EU index. Corresponding positions are determined as outlined herein, generally through alignment with other parent sequences.
  • residue as used herein is meant a position in a protein and its associated aminoacid identity
  • Serine 239 also referred to as Ser239 and S239
  • Ser239 and S239 is a residue at position 239 in the human antibody IgGl .
  • target antigen or "target” or “antigen” as used herein is meant the molecule that is bound specifically by the variable region of a given antibody.
  • a target antigen may be a protein, carbohydrate, lipid, or other chemical compound.
  • target cell as used herein is meant a cell that expresses a target antigen.
  • variable region as used herein is meant the region of an immunoglobulin that comprises one or more Ig domains substantially encoded by any of the VK, ⁇ , and or VH genes that make up the kappa, lambda, and heavy chain immunoglobulin genetic loci respectively.
  • variant protein a polypeptide sequence that differs from that of a parent polypeptide sequence by virtue of at least one amino acid modification.
  • variant polypeptide may refer to the polypeptide itself, a composition comprising the polypeptide, or the amino sequence that encodes it.
  • the variant polypeptide has at least one amino acid modification compared to the parent polypeptide, e g from about one to about ten amino acid modifications, e.g., from about one to about five amino acid modifications compared to the parent.
  • variant polypeptide sequence herein may possess at least about 80% homology with a parent polypeptide sequence, e g , at least about 90% homology, at least about 95% homology, etc.
  • variant antibody or antibody variant as used herein is meant an antibody sequence that differs from that of a parent antibody sequence by virtue of at least one amino acid modification.
  • variant antibody or antibody variant may refer to the antibody polypeptide itself, compositions comprising the antibody variant polypeptide, or the amino acid sequence that encodes it.
  • constant heavy chain variant or “constant light chain variant” or “Fc variant” as used herein is meant a constant heavy chain, constant light chain, or Fc region polypeptide or sequence, respectively, that differs in sequence from that of a parent sequence by virtue of at least one amino acid modification.
  • wild type or “WT” herein is meant an amino acid sequence or a nucleotide sequence that is found in nature, including allelic variations.
  • a WT protein, polypeptide, antibody, immunoglobulin, IgG, etc. has an amino acid sequence or a nucleotide sequence that has not been intentionally modified.
  • EU index refers to the residue numbering of the human IgGl EU antibody, as described in Edelman et al., 1 69, Biochemistry 63 78-85).
  • Antigens are macromolecules capable of generating an antibody response in an animal and being recognized by the resulting antibody. Both antigens and haptens comprise at least one antigenic determinant or "epitope", which is the region of the antigen or hapten which binds to the antibody. Typically, the epitope on a hapten is the entire molecule.
  • sample refers to an aliquot of material, frequently biological matrices, an aqueous solution or an aqueous suspension derived from biological material.
  • Samples to be assayed for the presence of an analyte by the methods of the present invention include, for example, cells, tissues, homogenates, lysates, extracts, and purified or partially purified proteins and other biological molecules and mixtures thereof.
  • samples typically used in the methods of the invention include human and animal body fluids such as whole blood, serum, plasma, cerebrospinal fluid, sputum, bronchial washing, bronchial aspirates, urine, semen, lymph fluids and various external secretions of the respiratory, intestinal and genitourinary tracts, tears, saliva, milk, white blood cells, myelomas and the like; biological fluids such as cell culture supernatants; tissue specimens which may or may not be fixed; and cell specimens which may or may not be fixed.
  • the samples used in the methods of the present invention will vary based on the assay format and the nature of the tissues, cells, extracts or other materials, especially biological materials, to be assayed. Methods for preparing protein extracts from cells or samples are well known in the art and can be readily adapted in order to obtain a sample that is compatible with the methods of the invention.
  • Specifically binding and “specific binding”, as used herein, mean that an antibody binds to its target (analyte) based on recognition of an epitope on the target molecule.
  • the antibody preferably recognizes and binds to the target molecule with a higher binding affinity than it binds to other compounds that may be present.
  • “specifically binding” may mean that an antibody binds to a. target molecule with at least about a 10 6 -fold greater affinity, preferably at least about a 10 -fold greater affinity, more preferably at least about a 10 -fold greater affinity, and most preferably at least about a 10 9 -fold greater affinity than it binds molecules unrelated to the target molecule.
  • specific binding refers to affinities in the range of about 10 6 -fold to about 10 9 -fold greater than non-specific binding. In some embodiments, specific binding may be characterized by affinities greater than 10 9 -fold over non-specific binding.
  • the binding affinity may be determined by any suitable method. Such methods are known in the art and include, without limitation, surface plasmon resonance and isothermal titration calorimetry. In a specific embodiment, the antibody uniquely recognizes and binds to the target analyte.
  • the term "monoclonal antibody”, as used herein, 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. Furthermore, in contrast to conventional (polyclonal) antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may 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 can include "chimeric" antibodies (U.S. Patent No. 4,816,567; and Morrison et al. (1984) Proc. Natl. Acad. Sci. USA, 81 : 6851-6855) and humanized antibodies (Jones et al. (1986) Nature, 321 : 522-525; Reichmann et al. (1988) Nature, 332: 323- 329; Presta (1992) Curr. Op. Struct. Biol. 2: 593-596).
  • Monoclonal antibodies may be obtained by 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 of Koehler and Milstein (1975), Nature, 256: 495-7; and U. S. Patent No. 4,376,110), the human B-cell hybridoma technique ( osbor, et al. (1983), Immunology Today, 4: 72; Cote, et al. (1983), Proc. Natl. Acad. Sci. USA, 80: 2026-30), and the EBV-hybridoma technique (Cole, et al. (1985), in Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., New York, pp.
  • Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of animals immunized with an antigen, or an antigenic functional derivative thereof.
  • host animals such as rabbits, mice and goats, may be immunized by injection with an antigen or hapten-carrier conjugate optionally supplemented with adjuvants.
  • Antibody fragments that recognize specific epitopes may be generated by known techniques.
  • such fragments include but are not limited to: the F(ab') 2 fragments that can be produced by pepsin digestion of the antibody molecule and the Fab fragments that can be generated by reducing the disulfide bridges of the F(ab') 2 fragments.
  • Fab expression libraries may be constructed (Huse, et al. (1989), Science, 246: 1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.
  • polynucleotide and “nucleic acid (molecule)" are used interchangeably herein to refer to polymeric forms of nucleotides of any length, including naturally occurring and non-naturally occurring nucleic acids.
  • the polynucleotides may contain deoxyribonucleotides, ribonucleotides and/or their analogs.
  • Methods for selection and preparation of nucleic acids are diverse and well described in standard biomolecular protocols. A typical way would be preparative PCR and chromatographic purification starting from existing template DNAs or stepwise synthesis of artificial nucleic acids.
  • the nucleic acid molecules referred to herein are DNA molecules.
  • amino acid substitutions relate to at least 1, but preferably at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50 or a plurality of amino acid substitutions.
  • contacting or “incubating”, as used interchangeably herein, refer generally to providing access of one component, reagent, analyte or sample to another.
  • detecting refers to any method of verifying the presence of a given molecule.
  • the techniques used to accomplish this may include, but are not limited to, immunoassays, such as ELISA and Immuno PCR (IPCR).
  • Hematological malignancies are cancer types that affect blood, bone marrow, and lymph nodes. Hematological malignancies may derive from either of the two major blood cell lineages: myeloid and lymphoid cell lines.
  • the myeloid cell line normally produces granulocytes, erythrocytes, thrombocytes, macrophages and mast cells; the lymphoid cell line produces B, T, NK and plasma cells.
  • Lymphomas, lymphocytic leukemias, and myeloma are from the lymphoid line, while acute and chronic myelogenous leukemia, myelodysplastic syndromes and myeloproliferative diseases are myeloid in origin.
  • Leukemia is a cancer of the blood or bone marrow and is characterized by an abnormal proliferation of blood cells, usually white blood cells (leukocytes).
  • Leukemia is clinically and pathologically subdivided into a variety of large groups.
  • Acute leukemia is characterized by the rapid increase of immature blood cells. This crowding makes the bone marrow unable to produce healthy blood cells.
  • Immediate treatment is required in acute leukemia due to the rapid progression and accumulation of the malignant cells, which then spill over into the bloodstream and spread to other organs of the body.
  • Acute forms of leukemia are the most common forms of leukemia in children.
  • Chronic leukemia is distinguished by the excessive build up of relatively mature, but still abnormal, white blood cells.
  • lymphoblastic or lymphocytic leukemias In lymphoblastic or lymphocytic leukemias, the cancerous change takes place in a type of marrow cell that normally goes on to form lymphocytes, which are infection-fighting immune system cells.
  • lymphocytic leukemias involve a specific subtype of lymphocyte, the B cell.
  • myeloid or myelogenous leukemias the cancerous change takes place in a type of marrow cell that normally goes on to form red blood cells, some other types of white cells, and platelets.
  • B-cell chronic lymphocytic leukemia also known as chronic lymphoid leukemia (CLL)
  • CLL chronic lymphoid leukemia
  • immature B cells proliferate in an uncontrolled way and accumulate in the bone marrow and blood.
  • CLL occurs mainly in adults, but in rare cases can also occur in teenagers and occasionally in children (inherited).
  • Most (>75%) people newly diagnosed with CLL are over the age of 50, and the majority are men.
  • Most people are diagnosed without symptoms as the result of a routine blood test that returns a high white blood cell count, but as it advances CLL results in swollen lymph nodes, spleen, and liver, and eventually anemia and infections.
  • CLL is treated with chemotherapy and monoclonal antibodies, for example alemtuzumab (directed against CD 52) and rituximab (directed against CD20).
  • Monoclonal antibodies are a class of therapeutic proteins that may be used to treat cell-proliferative diseases and disorders, in particular those affecting the hematopoietic system.
  • a number of favorable properties of antibodies including but not limited to specificity for target, ability to mediate immune effector mechanisms, and long half-life in serum, make antibodies powerful therapeutics.
  • the present invention describes antibodies against CD 133.
  • CD133 has been found to be expressed among others on acute leukemia cells.
  • antibodies can mediate anti-tumor mechanism via growth inhibitory or apoptotic signaling that may occur when an antibody binds to its target on tumor cells. Such signaling may be potentiated when antibodies are presented to tumor cells bound to immune cells via FcyR. Therefore increased affinity of antibodies to FcyRs may result in enhanced antiproliferative effects.
  • Antibodies are immunological proteins that bind a specific antigen
  • antibodies are constructed from paired heavy and light polypeptide chains
  • the light and heavy chain variable regions show significant sequence diversity between antibodies, and are responsible for binding the target antigen
  • Each chain is made up of individual immunoglobulin (Ig) domains, and thus the generic term immunoglobulin is used for such proteins.
  • Natural antibody structural units typically comprise a tetramer.
  • Each tetramer is typically composed of two identical pairs of polypeptide chains, each pair having one "light” chain (typically having a molecular weight of about 25 kDa) and one "heavy” chain (typically having a molecular weight of about 50-70 kDa).
  • Each of the light and heavy chains are made up of two distinct regions, referred to as the variable and constant regions.
  • the heavy chain is composed of four immunoglobulin domains linked from N- to C-terminus in the order VH-CH1-CH2-CH3, referring to the heavy chain variable domain, heavy chain constant domain 1 , heavy chain constant domain 2, and heavy chain constant domain 3 respectively (also referred to as VH-Cyl-Cy2-Cy3, referring to the heavy chain variable domain, constant gamma 1 domain, constant gamma 2 domain, and constant gamma 3 domain respectively).
  • the IgG light chain is composed of two immunoglobulin domains linked from N- to C-terminus in the order VL-CL, referring to the light chain variable domain and the light chain constant domain, respectively.
  • the constant regions show less sequence diversity, and are responsible for binding a number of natural proteins to elicit important biochemical events.
  • variable region of an antibody contains the antigen binding determinants of the molecule, and thus determines the specificity of an antibody for its target antigen
  • the variable region is so named because it is the most distinct in sequence from other antibodies within the same class
  • three loops are gathered for each of the V domains of the heavy chain and light chain to form an antigen-binding site
  • Each of the loops is referred to as a complementarity-determining region (hereinafter referred to as a "CDR"), in which the variation in the amino acid sequence is most significant
  • CDRs complementarity-determining region
  • variable region outside of the CDRs is referred to as the framework (FR) region
  • FR region The variable region outside of the CDRs.
  • sequence variability does occur in the FR region between different antibodies
  • this characteristic architecture of antibodies provides a stable scaffold (the FR region) upon which substantial antigen binding diversity (the CDRs) can be explored by the immune system to obtain specificity for a broad array of antigens.
  • a number of high-resolution structures are available for a variety of variable region fragments from different organisms, some unbound and some in complex with antigen. Sequence and structural features of antibody variable regions are disclosed, for example, in Morea et al.
  • Antibodies are grouped into classes, also referred to as isotypes, as determined genetically by the constant region.
  • Human constant light chains are classified as kappa (CK) and lambda ⁇ ) light chains.
  • Human heavy chains are classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
  • the IgG class is the most commonly used for therapeutic purposes.
  • IgG as used herein is meant a polypeptide belonging to the class of antibodies that are substantially encoded by a recognized immunoglobulin gamma gene. In humans this class comprises subclasses IgGl, IgG2, IgG3, and IgG4. In mice this class comprises subclasses IgGl, IgG2a, IgG2b and IgG3. IgM has subclasses, including, but not limited to, IgMl and IgM2. IgA has several subclasses, including but not limited to IgAl and IgA2.
  • isotype as used herein is meant any of the classes or subclasses of immunoglobulins defined by the chemical and antigenic characteristics of their constant regions.
  • the known human immunoglobulin isotypes are IgGl, IgG2, IgG3, IgG4, IgAl, IgA2, IgMl, IgM2, IgD, and IgE.
  • IgGs that are hybrid compositions of the natural human IgG isotypes. Effector functions such as ADCC, ADCP, CDC, and serum half-life differ significantly between the different classes of antibodies, including for example human IgGl, IgG2, IgG3, IgG4, IgAl, IgA2, IgD, IgE, IgG, and IgM (Michaelsen et al., 1992, Molecular Immunology, 29(3): 319-326). A number of studies have explored IgGl, IgG2, IgG3, and IgG4 variants in order to investigate the determinants of the effector function differences between them. See for example Canfield & Morrison, 1991 , J.
  • IgG Immunoglobulin Variants with Optimized Effector Function As described in USSN 11/256,060, filed Oct. 21, 2005, entitled “IgG Immunoglobulin Variants with Optimized Effector Function", it is possible to engineer amino acid modifications in an antibody that comprise constant regions from other immunoglobulin classes.
  • Such engineered hybrid IgG compositions may provide improved effector function properties, including improved ADCC, phagocytosis, CDC, and serum half-life.
  • Gm polymorphism is determined by the IGHG1 , IGHG2 and IGHG3 genes which have alleles encoding allotypic antigenic determinants referred to as Glm, G2m, and G3m allotypes for markers of the human IgGl, IgG2 and IgG3 molecules (no Gm allotypes have been found on the gamma 4 chain). Markers may be classified into "allotypes" and "iso allotypes". These are distinguished on different serological bases dependent upon the strong sequence homologies between isotypes.
  • Allotypes are antigenic determinants specified by allelic forms of the Ig genes. Allotypes represent slight differences in the amino acid sequences of heavy or light chains of different individuals. Even a single amino acid difference can give rise to an allotypic determinant, although in many cases there are several amino acid substitutions that have occurred.
  • Allotypes are sequence differences between alleles of a subclass whereby the antisera recognize only the allelic differences
  • An isoallotype is an allele in one isotype which produces an epitope which is shared with a non- polymorphic homologous region of one or more other isotypes and because of this the antisera will react with both the relevant allotypes and the relevant homologous isotypes (Clark, 1997, IgG effector mechanisms, Chem. Immunol. 65-88-110, Gorman & Clark, 1990, Semin. Immunol. 2(6):457-66).
  • the antibodies of the present invention may be substantially encoded by any allotype, isoallotype, or haplotype of any immunoglobulin gene
  • Antibodies of the present invention may be substantially encoded by genes from any organism, e , mammals, including but not limited to humans, rodents including but not limited to mice and rats, lagomorpha including but not limited to rabbits and hares, camelidae including but not limited to camels, llamas, and dromedaries, and non-human primates, including but not limited to Prosimians, Platyrrhini (New World monkeys), Cercopithecoidea (Old World monkeys), and Hominoidea including the Gibbons and Lesser and Great Apes.
  • the antibodies of the present invention are substantially human.
  • the antibodies of the present invention may be substantially encoded by immunoglobulin genes belonging to any of the antibody classes.
  • the antibodies of the present invention comprise sequences belonging to the IgG class of antibodies, including human subclasses IgGl, IgG2, IgG3, and IgG4.
  • the antibodies of the present invention comprise sequences belonging to the IgA (including human subclasses IgAI and lgA2), IgD, IgE, IgG, or IgM classes of antibodies.
  • the antibodies of the present invention may comprise more than one protein chain. That is, the present invention may find use in an antibody that is a monomer or an oligomer, including a homo- or hetero-oligomer.
  • the antibodies of the invention are based on human IgG sequences, and thus human IgG sequences are used as the "base" sequences against which other sequences are compared, including but not limited to sequences from other organisms, for example rodent and primate sequences, as well as sequences from other immunoglobulin classes such as IgA, IgE, IgD, IgM, and the like. It is contemplated that, although the antibodies of the present invention are engineered in the context of one parent antibody, the variants may be engineered in or "transferred' to the context of another, second parent antibody.
  • the amino acid sequence of a first antibody outlined herein is directly compared to the sequence of a second antibody. After aligning the sequences, using one or more of the homology alignment programs known in the art (for example using conserved residues as between species), allowing for necessary insertions and deletions in order to maintain alignment (i.e., avoiding the elimination of conserved residues through arbitrary deletion and insertion), the residues equivalent to particular amino acids in the primary sequence of the first antibody are defined. Alignment of conserved residues may conserve 100% of such residues.
  • Equivalent residues may also be defined by determining structural homology between a first and second antibody that is at the level of tertiary structure for antibodies whose structures have been determined. In this case, equivalent residues are defined as those for which the atomic coordinates of two or more of the main chain atoms of a particular amino acid residue of the parent or precursor (N on N, CA on CA, C on C and O on O) are within 0.13 nm, e g , 0.1 nm, after alignment.
  • the antibodies discovered by the present invention may be engineered into any second parent antibody that has significant sequence or structural homology with the antibody
  • the parent antibody is human IgGl
  • the variant antibody may be engineered in a human IgG2 parent antibody, a human IgA parent antibody, a mouse IgG2a or IgG2b parent antibody, and the like
  • the context of the parent antibody does not affect the ability to transfer the antibodies of the present invention to other parent antibodies
  • the variant antibodies that are engineered in a human IgGl antibody that targets one antigen epitope may be transferred into a human IgGl antibody that targets one antigen epitope
  • immunoglobulin domains there are several immunoglobulin domains in the heavy chain.
  • immunoglobulin (Ig) domain herein is meant a region of an immunoglobulin having a distinct tertiary structure.
  • the domains of the constant heavy chain including, the constant heavy (CH) domains and the hinge.
  • the IgG isotypes each have three CH regions: “CHI " refers to positions 118-220, “CH2” refers to positions 237-340, and “CH3” refers to positions 341 -447 according to the EU index as in Kabat.
  • hinge or “hinge region” or “antibody hinge region” or “immunoglobulin hinge region” herein is meant the flexible polypeptide comprising the amino acids between the first and second constant domains of an antibody.
  • the IgG CHI domain ends at EU position 220, and the IgG CH2 domain begins at residue EU position 237.
  • the hinge is herein defined to include positions 221 (D221 in IgGl) to 236 (G236 in IgGl ), wherein the numbering is according to the EU index as in Kabat.
  • the lower hinge is included, with the “lower hinge” generally referring to positions 226 or 230.
  • the constant heavy chain refers to the N- terminus of the CHI domain to the C-terminus of the CH3 domain, thus comprising positions 1 18-447, wherein numbering is according to the EU index.
  • the constant light chain comprises a single domain, and as defined herein refers to positions 108-214 of CK or C , wherein numbering is according to the EU index.
  • full-length antibodies Specifically included within the definition of “antibody” are full-length antibodies.
  • full length antibody herein is meant the structure that constitutes the natural biological form of an antibody, including variable and constant regions.
  • the full length antibody of the IgG class is a tetramer and consists of two identical pairs of two immunoglobulin chains, each pair having one light and one heavy chain, each light chain comprising immunoglobulin domains VL and CL, and each heavy chain comprising immunoglobulin domains VH, CHI (Oyl), CH2 (Cy2), and CH3 (Cy3).
  • IgG antibodies may consist of only two heavy chains, each heavy chain comprising a variable domain attached to the Fc region.
  • the antibodies can be a variety of structures, including, but not limited to antibody fragments.
  • Antibody fragments include but are not limited to bispecific antibodies, minibodies, domain antibodies, synthetic antibodies, antibody mimetics, chimeric antibodies, antibody fusions (sometimes referred to as "antibody conjugates"), and fragments of each, respectively.
  • Specific antibody fragments include, but are not limited to, (i) the Fab fragment consisting of VL, VH, CL and CHI domains, (ii) the Fd fragment consisting of the VH and CHI domains, (iii) the Fv fragment consisting of the VL and VH domains of a single antibody; (iv) the dAb fragment, which consists of a single variable region, (v) isolated CDR regions, (vi) F(ab') 2 fragments, a bivalent fragment comprising two linked Fab fragments (vii) single chain Fv molecules (scFv), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form an antigen binding site (viii) bispecific single chain Fv dimers and (ix) "diabodies” or "triabodies", multivalent or multispecific fragments constructed by gene fusion.
  • the antibody fragments may be modified.
  • the molecules may be stabilized by the incorporation of disulfide bridges linking the VH and VL domains.
  • disulfide bridges linking the VH and VL domains. Examples of antibody formats and architectures are described in Holliger & Hudson, 2006, Nature Biotechnology 23(9):1126- 1136, and Carter 2006, Nature Reviews Immunology 6:343-357 and references cited therein.
  • Antibodies of the invention may include multispecific antibodies, notably bispecific antibodies, also sometimes referred to as "diabodies". These are antibodies that bind to two (or more) different antigens. Diabodies can be manufactured in a variety of ways known in the art, e.g., prepared chemically or from hybrid hybridomas. In one embodiment, the antibody is a minibody. Minibodies are minimized antibodylike proteins comprising a scFv joined to a CH3 domain. In some cases, the scFv can be joined to the Fc region, and may include some or all of the hinge region. For a description of multispecific antibodies see Holliger & Hudson, 2006, Nature Biotechnology 23(9): 1126-1136 and references cited therein.
  • the antibody of the invention is an antibody fragment.
  • Antibodies of the present invention may comprise Fc fragments
  • An Fc fragment of the present invention may comprise from 1 - 90% of the Fc region, e.g , 10 - 90%, 30 - 90%, etc
  • an Fc fragment of the present invention may comprise an IgGl Cy2 domain, an IgGl Cy2 domain and hinge region, an IgGl Cy3 domain, and so forth.
  • an Fc fragment of the present invention additionally comprises a fusion partner, effectively making it an Fc fragment fusion.
  • Fc fragments may or may not contain extra polypeptide sequence.
  • Immunogenicity is the result of a complex series of responses to a substance that is perceived as foreign, and may include production of neutralizing and non-neutralizing antibodies, formation of immune complexes, complement activation, mast cell activation, inflammation, hypersensitivity responses, and anaphylaxis.
  • Several factors can contribute to protein immunogenicity, including but not limited to protein sequence, route and frequency of administration, and patient population. Immunogenicity may limit the efficacy and safety of a protein therapeutic in multiple ways. Efficacy can be reduced directly by the formation of neutralizing antibodies Efficacy may also be reduced indirectly, as binding to either neutralizing or non- neutralizing antibodies typically leads to rapid clearance from serum Severe side effects and even death may occur when an immune reaction is raised.
  • protein engineering is used to reduce the immunogenicity of the antibodies of the present invention.
  • the scaffold components can be a mixture from different species.
  • Such antibody may be a chimeric antibody and/or a humanized antibody.
  • both “chimeric antibodies” and “humanized antibodies' refer to antibodies that combine regions from more than one species.
  • “Chimeric antibodies” traditionally comprise variable region(s) from a mouse (or rat, in some cases) and the constant region(s) from a human (Morrison et al , 1984, Proc Natl Acad Sci USA 81 6851-6855).
  • humanized antibody as used herein is meant an antibody comprising a human framework region (FR) and one or more complementarity determining regions (CDRs) from a non-human (usually mouse or rat) antibody.
  • the non-human antibody providing the CDRs is called the “donor” and the human immunoglobulin providing the framework is called the “acceptor”.
  • Humanization relies principally on the grafting of donor CDRs onto acceptor (human) VL and VH frameworks (Winter US 5,225,539). This strategy is referred to as “CDR grafting". "Backmutation" of selected acceptor framework residues to the corresponding donor residues is often required to regain affinity that is lost in the initial grafted construct (US 5,693,762).
  • the humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region, typically that of a human immunoglobulin, and thus will typically comprise a human Fc region.
  • an immunoglobulin constant region typically that of a human immunoglobulin
  • human Fc region typically comprise a human Fc region.
  • a variety of techniques and methods for humanizing and reshaping non-human antibodies are well known in the art (See Tsurushita & Vasquez, 2004, Humanization of Monoclonal Antibodies, Molecular Biology of B Cells, 533-545, Elsevier Science (USA), and references cited therein). Humanization or other methods of reducing the immunogenicity of nonhuman antibody variable regions may include resurfacing methods, as described for example in Roguska et al., 1 94, Proc Natl Acad Sci USA 91 969-973).
  • selection based methods may be employed to humanize and/or affinity mature antibody variable regions, that is, to increase the affinity of the variable region for its target antigen.
  • Other humanization methods may involve the grafting of only parts of the CDRs, including but not limited to methods described in USSN 09/810,502, Tan et al , 2002, J Immunol 169 1119-1125, De Pascalis et al , 2002, J Immunol 169 3076-3084.
  • Structure-based methods may be employed for humanization and affinity maturation, for example as described in USSN 10/153,159 and related applications.
  • the immunogenicity of the antibody is reduced using a method described in USSN 11/004,590, entitled “Methods of Generating Variant Proteins with Increased Host String Content and Compositions Thereof, filed on December 3, 2004.
  • Modifications to reduce immunogenicity may include modifications that reduce binding of processed peptides derived from the parent sequence to MHC proteins.
  • amino acid modifications would be engineered such that there are no or a minimal number of immune epitopes that are predicted to bind, with high affinity, to any prevalent MHC alleles.
  • Several methods of identifying MHC-binding epitopes in protein sequences are known in the art and may be used to score epitopes in an antibody of the present invention. See for example USSN 09/903,378, USSN 10/754,296, USSN 1 1/249,692, and references cited therein.
  • the antibodies of the present invention may be fully human, that is the sequences of the antibodies are completely or substantially human.
  • Fully human antibody or “complete human antibody” refers to a human antibody having the gene sequence of an antibody derived from a human chromosome with the modifications outlined herein.
  • a number of methods are known in the art for generating fully human antibodies, including the use of transgenic mice (Bruggemann et al., 1997, Curr Opin Biotechnol 8:455- 458,) or human antibody libraries coupled with selection methods (Griffiths et al., 1998, Curr Opin Biotechnol 9:102-108).
  • the antibodies of the present invention target CD133 and may comprise the variable regions (e.g., the CDRs) of any known or undiscovered anti-CD 133 antibody.
  • Antibodies of the invention may display selectivity for CD 133. Examples include full-length versus splice variants, cell-surface vs. soluble forms, selectivity for various polymorphic variants, or selectivity for specific conformational forms of a target.
  • An antibody of the present invention may bind any epitope or region on CD 133 and may be specific for fragments, mutant forms, splice forms, or aberrant forms of the antigens. A number of useful antibodies have been discovered that target CD 133 that may find use in the present invention.
  • the antibodies of the present invention may find use in a wide range of products.
  • the antibody of the invention is a therapeutic, a diagnostic, or a research reagent.
  • an antibody of the invention is a therapeutic.
  • An antibody of the present invention may find use in an antibody composition that is monoclonal or polyclonal.
  • the antibodies of the present invention are used to kill target cells that bear the target antigen, for example cancer cells.
  • the antibodies of the present invention are used to block, antagonize, or agonize the target antigen.
  • the antibodies of the present invention are used to block, antagonize, or agonize the target antigen and kill the target cells that bear the target antigen.
  • sequences of the variable domains including the CDRs identified herein can be combined in any combination in an antibody. Further, these sequences may be independently modified by adding all or part of an Fc region or Fc variant as disclosed herein. The modified sequences can also be combined in any combination in an antibody.
  • the present invention is directed to antibodies comprising modifications, wherein the modifications alter affinity to one or more Fc receptors, and/or alter the ability of the antibody to mediate one or more effector functions.
  • Modifications of the invention include amino acid modifications.
  • the inventors of the present invention have surprisingly found that by introducing the amino acid substitutions 23 D and 332E in the CH2 domain of the Fc part of known anti-CD 133 antibodies, such as W6B3 und 293 -C3, the cell killing activity of these antibodies can be significantly increased.
  • the amino acid substitutions are S239D and I332E. This is surprising, as it has been experimentally shown that the same modifications do not generally increase cell killing activity. In other words, in different antibodies directed to a different target antigen, the introduction of these substitutions had no measurable effect on cell killing.
  • modified antibodies can comprise further amino acid modifications at heavy chain constant region positions 221 , 222, 223, 224, 225, 227, 228, 230, 231 , 232, 233, 234, 235, 236, 237, 238, 240, 241 , 243, 244, 245, 246, 247, 249, 255, 258, 260, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 278, 280, 281 , 282, 283, 284, 285, 286, 288, 290, 291 , 292, 293, 294, 295, 296, 297, 298, 299, 300, 301 , 302, 303, 304, 305, 313, 317, 318, 320, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 333, 334, 335, 336, and 337, which have been found to
  • additional variants that alter binding to one or more human Fc receptors may comprise an amino acid modification in the heavy chain constant region, as described herein, selected from the group consisting of 22 IK, 221Y, 222E, 222Y, 223E, 223K, 224E, 224Y, 225E, 225K, 225W, 227E, 227G, 227K, 227Y, 228E, 228G, 228K, 228Y, 230A, 230E, 230G, 230Y, 231 E, 231 G, 231 K, 231 P, 231 Y, 232E, 232G, 232K, 232Y, 233A, 233D, 233F, 233G, 233H, 2331, 233K, 233L, 233M, 233N, 233Q, 233R, 233S, 233T, 233V, 233W, 233Y, 234A, 234D, 234E
  • the invented antibodies can comprise further amino acid modifications outside the Fc region, such as those described in USSN 11/090,981 , filed March 24, 2005, entitled “Immunoglobulin variants outside the Fc region", including amino acid modifications at heavy chain constant region positions 118, 119, 120, 121 , 122, 124, 126, 129, 131 , 132, 133, 135, 136, 137, 138, 139, 147, 148, 150, 151 , 152, 153, 155, 157, 159, 160, 161 , 162, 163, 164, 165, 166, 167, 168, 169, 171 , 172, 173, 174, 175, 176, 177, 178, 179, 180, 183, 187, 188, 189, 190, 191 , 192, 193, 194, 195, 196, 197, 198, 199, 201 , 203, 205, 206,
  • variants that alter binding to one or more human Fc receptors may comprise an amino acid modification in the heavy chain constant region, as described herein, selected from the group consisting of 118K, 118E, 118Y, 119R, 119E, 119Y, 120R, 120E, 1201, 121 E, 121Y, 121 H, 122E, 122R, 124K, 124E, 124Y, 126K, 126D, 129L, 129D, 131G, 131T, 132D, 132R, 132L, 133R, 133E, 133L, 1351, 135E, 135K, 136E, 136K, 1361, 137E, 138S, 138R, 138D, 1391, 139E, 139K, 147A, 147E, 148Y, 148 , 150L, 150 , 150 , 150
  • variants that alter binding to one or more human Fc receptors may comprise an amino acid modification in the light chain constant region, as described herein, selected from the group consisting of 108D, 1081, 108Q, 109D, 109P, 109R, 110E, 1 101, 11 OK, 111 E, 1 1 1 K, 1 11 LI 1 12E, 1 12R, 112Y1 1 14D, 1 141, 1 14K, 116T, 121 Dl 122R, 122S, 122Y, 123L, 123R, 124E, 125E, 125K, 126D, 126L, 126Q, 127A, 127D, 127K, 128N, 129E, 1291, 129K, 131T, 137K, 137S, 138D, 138K, 138L, 140E1 140H, 140K, 141 El 141 K, 142D, 142G, 142L, 143A, 143L, 143
  • substitutions that may also be used in the present invention include other substitutions that modulate Fc receptor affinity, FcyR-mediated effector function, and/or complement mediated effector function include but are not limited to 298A, 298T, 326A, 326D, 326E, 326W, 326Y, 333A, 333S, 334L, and 334A (US 6,737,056; Shields et a/, Journal of Biological Chemistry, 2001 , 276(9):6591-6604; US 6,528,624; ldusogie et al, 2001 , J.
  • antibodies of the present invention may be combined with constant heavy chain variants that alter FcRn binding.
  • constant heavy chain variants that alter FcRn binding include modifications that modify FcRn affinity in a pH-specific manner.
  • variants that increase Fc binding to FcRn include but are not limited to: 250E, 250Q, 428L, 428F, 250Q/428L (Hinton et al., 2004, J. Biol. Chem. 279(8): 6213-6216, Hinton et al.
  • antibodies may comprise isotypic modifications, that is modifications in a parent IgG to the amino acid type in an alternate IgG.
  • the present invention provides variant antibodies that are optimized for a number of therapeutically relevant properties.
  • a variant antibody comprises one or more amino acid modifications relative to a parent antibody, wherein the amino acid modification(s) provide one or more optimized properties.
  • the antibodies of the present invention are variant antibodies.
  • An antibody of the present invention differs in amino acid sequence from its parent antibody by virtue of at least the two amino acid modifications 239D and 332E.
  • the variant antibodies of the present invention may comprise more than the two afore-mentioned amino acid modifications as compared to the parent, for example from about three to fifty amino acid modifications, e.g., from about three to ten amino acid modifications, from about three to about five amino acid modifications, etc., compared to the parent.
  • sequences of the variant antibodies and those of the parent antibodies are substantially homologous.
  • the variant antibody sequences herein will possess about 80% homology with the parent antibody sequence, e.g., at least about 90% homology, e at least about 95% homology, etc.
  • the antibodies of the present invention may comprise amino acid modifications that provide optimized effector function properties relative to the parent. Substitutions and optimized effector function properties are described in USSN 10/672,280, PCT US03/30249, and USSN 10/822,231 , and USSN 60/627,774, filed 11/12/2004 and entitled "Optimized Fc Variants". Properties that may be optimized include but are not limited to enhanced or reduced affinity for an FcyR. In one embodiment, the antibodies of the present invention are optimized to possess enhanced affinity for a human activating FcyR, e.g., FcyRI, FcyRIIa, FcyRIIc, FcyRIIIa, and FcyRIIIb.
  • an antibody of the invention is optimized to possess enhanced affinity for a human FcyRIIIa.
  • the antibodies are optimized to possess reduced affinity for the human inhibitory receptor FcyRIIb.
  • antibodies of the present invention provide enhanced affinity for one or more FcyRs, yet reduced affinity for one or more other FcyRs.
  • an antibody of the present invention may have enhanced binding to FcyRIIIa, yet reduced binding to FcyRIIb.
  • an antibody of the present invention may have enhanced binding to FcyRIIa and FcyRI, yet reduced binding to FcyRIIb.
  • the modifications of the invention may enhance binding affinity for one or more FcyRs.
  • greater affinity or 'improved affinity” or “enhanced affinity” or “better affinity” than a parent immunoglobulin, as used herein is meant that an Fc variant binds to an Fc receptor with a significantly higher equilibrium constant of association (Ka) or lower equilibrium constant of dissociation (Kd) than the parent polypeptide when the amounts of variant and parent polypeptide in the binding assay are essentially the same.
  • the Fc variant with improved FcyR binding affinity may display f om about 5 fold to about 1000 fold, e g from about 10 fold to about 500 fold improvement in Fc receptor binding affinity compared to the parent polypeptide, where Fc receptor binding affinity is determined by methods known in the art. Accordingly, by “reduced affinity" as compared to a parent Fc polypeptide as used herein is meant that an Fc variant binds an Fc receptor with significantly lower Ka or higher Kd than the parent polypeptide.
  • Embodiments comprise optimization of Fc binding to a human FcyR, however in alternate embodiments the antibodies of the present invention possess enhanced or reduced affinity for FcyRs from nonhuman organisms, including but not limited to rodents and non- human primates.
  • Antibodies that are optimized for binding to a nonhuman FcyR may find use in experimentation.
  • mouse models are available for a variety of diseases that enable testing of properties such as efficacy, toxicity, and pharmacokinetics for a given drug candidate.
  • cancer cells can be grafted or injected into mice to mimic a human cancer, a process referred to as xenografting.
  • the antibodies of the present invention may provide valuable information with regard to the efficacy of the protein, its mechanism of action, and the like.
  • the antibodies of the present invention may also be optimized for enhanced functionality and/or solution properties in aglycosylated form.
  • the aglycosylated antibodies of the present invention bind an Fc ligand with greater affinity than the aglycosylated form of the parent antibody.
  • the Fc ligands include but are not limited to FcyRs, Clq, FcRn, and proteins A and G, and may be from any source including but not limited to human, mouse, rat, rabbit, or monkey.
  • the antibodies are optimized to be more stable and/or more soluble than the aglycosylated form of the parent antibody.
  • Antibodies of the invention may comprise modifications that modulate interaction with Fc ligands other than FcyRs, including but not limited to complement proteins, FcRn, and Fc receptor homologs (FcRHs).
  • FcRHs include but are not limited to FcRHl, FcRH2, FcRH3, FcRH4, FcRH5, and FcRH6 (Davis et ai, 2002, Immunol. Reviews 190:123-136).
  • Antibodies of the present invention may comprise one or more modifications that provide optimized properties that are not specifically related to effector function per se.
  • the modifications may be amino acid modifications, or may be modifications that are made enzymatically or chemically. Such modification(s) likely provide some improvement in the antibody, for example an enhancement in its stability, solubility, function, or clinical use.
  • the present invention contemplates a variety of improvements that may be made by coupling the antibodies of the present invention with additional modifications.
  • the variable region of an antibody of the present invention may be affinity matured, that is to say that amino acid modifications have been made in the VH and/or VL domains of the antibody to enhance binding of the antibody to its target antigen.
  • Such types of modifications may improve the association and/or the dissociation kinetics for binding to the target antigen.
  • Other modifications include those that improve selectivity for target antigen vs. alternative targets. These include modifications that improve selectivity for antigen expressed on target vs non- target cells.
  • Other improvements to the target recognition properties may be provided by additional modifications.
  • Such properties may include, but are not limited to, specific kinetic properties (i.e. association and dissociation kinetics), selectivity for the particular target versus alternative targets, and selectivity for a specific form of target versus alternative forms. Examples include full-length versus splice variants, cell- surface vs. soluble forms, selectivity for various polymorphic variants, or selectivity for specific conformational forms of the target antigen.
  • Antibodies of the invention may comprise one or more modifications that provide reduced or enhanced internalization of an antibody.
  • antibodies of the present invention can be utilized or combined with additional modifications in order to reduce the cellular internalization of an antibody that occurs via interaction with one or more Fc ligands. This property might be expected to enhance effector function, and potentially reduce immunogenicity of the antibodies of the invention.
  • antibodies of the present invention can be utilized directly or combined with additional modifications in order to enhance the cellular internalization of an antibody that occurs via interaction with one or more Fc ligands.
  • modifications are made to improve biophysical properties of the antibodies of the present invention, including but not limited to stability, solubility, and oligomeric state. Modifications can include, for example, substitutions that provide more favorable intramolecular interactions in the antibody such as to provide greater stability, or substitution of exposed nonpolar amino acids with polar amino acids for higher solubility
  • modifications can also be combined with additional modifications that reduce oligomeric state or size, such that tumor penetration is enhanced, or in vivo clearance rates are increased as desired.
  • modifications to the antibodies of the present invention include those that enable the specific formation or homodimeric or homomultimeric molecules.
  • modifications include but are not limited to engineered disulfides, as well as chemical modifications or aggregation methods which may provide a mechanism for generating covalent homodimeric or homomultimers
  • methods of engineering and compositions of such molecules are described in Kan et al., 2001 , J. Immunol., 2001 , 166: 1320-1326; Stevenson et al., 2002, Recent Results Cancer Res. 159 104-12; US 5,681 ,566; Caron et al, 1992, J. Exp. Med. 176:1191-1195, and Shopes, 1992, J. Immunol.
  • Additional modifications to the variants of the present invention include those that enable the specific formation or heterodimeric, heteromultimeric, bifunctional, and/or multifunctional molecules. Such modifications include, but are not limited to, one or more amino acid substitutions in the CH3 domain, in which the substitutions reduce homodimer formation and increase heterodimer formation. For example, methods of engineering and compositions of such molecules are described in Atwell et al., 1997, J. Mol. Biol. 270(l):26-35, and Carter et al., 2001 , J. Immunol. Methods 248:7-15, each incorporated herein it its entirety by reference. Additional modifications include modifications in the hinge and CH3 domains, in which the modifications reduce the propensity to form dimers.
  • the antibodies of the present invention comprise modifications that remove proteolytic degradation sites. These may include, for example, protease sites that reduce production yields, as well as protease sites that degrade the administered protein in vivo. In one embodiment, additional modifications are made to remove covalent degradation sites such as deamidation (i.e. deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues), oxidation, and proteolytic degradation sites.
  • deamidation i.e. deamidation of glutaminyl and asparaginyl residues to the corresponding glutamyl and aspartyl residues
  • oxidation oxidation
  • Deamidation sites that are particularly useful to remove are those that have enhance propensity for deamidation, including, but not limited to asparaginyl and glutamyl residues followed by glycines (NG and QG motifs, respectively). In such cases, substitution of either residue can significantly reduce the tendency for deamidation. Common oxidation sites include methionine and cysteine residues. Other covalent modifications, that can either be introduced or removed, include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the "-amino groups of lysine, arginine, and histidine side chains (T.E.
  • Modifications may include those that improve expression and/or purification yields from hosts or host cells commonly used for production of biologies. These include, but are not limited to various mammalian cell lines (e.g. CHO), yeast cell lines, bacterial cell lines, and plants. Additional modifications include modifications that remove or reduce the ability of heavy chains to form inter-chain disulfide linkages. Additional modifications include modifications that remove or reduce the ability of heavy chains to form intra-chain disulfide linkages.
  • the antibodies of the present invention may comprise modifications that include the use of unnatural amino acids incorporated using, for example, the technologies developed by Schultz and colleagues, including but not limited to methods described by Cropp & Shuitz, 2004, Trends Genet. 20(12):625-30, Anderson et al., 2004, Proc. Natl. Acad. Sci. U.S.A. 101 (2):7566-71, Zhang et al., 2003, 303(5656):371-3, and Chin et al., 2003, Science 301(5635):964-7.
  • these modifications enable manipulation of various functional, biophysical, immunological, or manufacturing properties discussed above.
  • these modifications enable additional chemical modification for other purposes.
  • the antibody may be linked to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, polyoxyalkylenes, or copolymers of polyethylene glycol and polypropylene glycol.
  • Additional amino acid modifications may be made to enable specific or non-specific chemical or posttranslational modification of the antibodies.
  • Such modifications include, but are not limited to PEGylation and glycosylation.
  • Specific substitutions that can be utilized to enable PEGylation include, but are not limited to, introduction of novel cysteine residues or unnatural amino acids such that efficient and specific coupling chemistries can be used to attach a PEG or otherwise polymeric moiety.
  • Introduction of specific glycosylation sites can be achieved by introducing novel N-X-T/S sequences into the antibodies of the present invention.
  • Covalent modifications of antibodies are included within the scope of this invention, and are generally, but not always, done post-translationally.
  • several types of covalent modifications of the antibody are introduced into the molecule by reacting specific amino acid residues of the antibody with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues.
  • the covalent modification of the antibodies of the invention comprises the addition of one or more labels.
  • labeling group is any detectable label.
  • the labeling group is coupled to the antibody via spacer arms of various lengths to reduce potential steric hindrance.
  • Various methods for labeling proteins are known in the art and may be used in performing the present invention. In general, labels fall into a variety of classes, depending on the assay in which they are to be detected: a) isotopic labels, which may be radioactive or heavy isotopes; b) magnetic labels (e.g., magnetic particles); c) redox active moieties; d) optical dyes; enzymatic groups (e.g.
  • the labeling group is coupled to the antibody via spacer arms of various lengths to reduce potential steric hindrance.
  • Various methods for labeling proteins are known in the art and may be used in performing the present invention.
  • Fluorophores can be either "small molecule” fluores, or proteinaceous fluores.
  • fluorescent label is meant any molecule that may be detected via its inherent fluorescent properties.
  • the antibodies of the invention are antibody "fusion proteins", sometimes referred to herein as "antibody conjugates".
  • the fusion partner or conjugate partner can be proteinaceous or non-proteinaceous; the latter generally being generated using functional groups on the antibody and on the conjugate partner.
  • Conjugate and fusion partners may be any molecule, including small molecule chemical compounds and polypeptides. For example, a variety of antibody conjugates and methods are described in Trail et al., 1999, Curr. Opin. Immunol. 1 1 :584-588.
  • conjugate partners include but are not limited to cytokines, cytotoxic agents, toxins, radioisotopes, chemotherapeutic agent, anti-angiogenic agents, a tyrosine kinase inhibitors, and other therapeutically active agents.
  • conjugate partners may be thought of more as payloads, that is to say that the goal of a conjugate is targeted delivery of the conjugate partner to a targeted cell, for example a cancer cell or immune cell, by the antibody.
  • the conjugation of a toxin to an antibody targets the delivery of the toxin to cells expressing the target antigen.
  • the concepts and definitions of fusion and conjugate are overlapping.
  • an antibody as a fusion or conjugate is not meant to constrain it to any particular embodiment of the present invention. Rather, these terms are used loosely to convey the broad concept that any antibody of the present invention may be linked genetically, chemically, or otherwise, to one or more polypeptides or molecules to provide some desirable property.
  • Suitable conjugates include, but are not limited to, labels as described below, drugs and cytotoxic agents including, but not limited to, cytotoxic drugs (e.g., chemotherapeutic agents) or toxins or active fragments of such toxins.
  • cytotoxic drugs e.g., chemotherapeutic agents
  • Suitable toxins and their corresponding fragments include diptheria A chain, exotoxin A chain, ricin A chain, abrin A chain, curcin, crotin, phenomycin, enomycin and the like.
  • Cytotoxic agents also include radiochemicals made by conjugating radioisotopes to antibodies, or binding of a radionuclide to a chelating agent that has been covalently attached to the antibody. Additional embodiments utilize calicheamicin, aunstatins, geldanamycin, maytansine, and duocarmycins and analogs; for the latter, see U.S. 2003/0050331.
  • the antibodies of the present invention are fused or conjugated to a cytokine.
  • cytokine as used herein is meant a generic term for proteins released by one cell population that act on another cell as intercellular mediators.
  • cytokines may be fused to antibody to provide an array of desirable properties Examples of such cytokines are lymphokines, monokines, and traditional polypeptide hormones.
  • cytokines include growth hormone such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone, thyroxine; insulin; proinsulin; relaxin, prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); hepatic growth factor; fibroblast growth factor, prolactin, placental lactogen; tumor necrosis factor-alpha and -beta; mullerian-inhibiting substance, mouse gonadotropin-associated peptide; inhibin; activin, vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF-beta; platelet-growth factor, transforming growth factors (TGFs) such as TGF-alpha and TGF-beta; insulin-like growth factor-1 and -II; erythropoietin (EPO);
  • the antibodies of the present invention are fused, conjugated, or operably linked to a toxin, including but not limited to small molecule toxins and enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof
  • a toxin including but not limited to small molecule toxins and enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof
  • small molecule toxins include but are not limited to calicheamicin, maytansine (US 5,208,020), trichothene, and CC1065.
  • the antibody is conjugated to one or more maytansine molecules (e g about 1 to about 10 maytansine molecules per antibody molecule).
  • Maytansine may, for example, be converted to May-SS-Me which may be reduced to May-SH3 and reacted with modified antibody (Chan et al. 5 1992, Cancer Research 52 127-131) to generate a maytansinoid-antibody conjugate
  • Another conjugate of interest comprises an antibody conjugated to one or more calicheamicin molecules.
  • the calicheamicin family of antibiotics are capable of producing double-stranded DNA breaks at sub-picomolar concentrations.
  • Structural analogues of calicheamicin that may be used include are, for example, disclosed in Hinman et al., 1993, Cancer Research 53 3336-3342, Lode et al , 1998, Cancer Research 58 2925-2928, US 5,714,586; US 5,712,374, US 5,264,586; and US 5,773,001.
  • Dolastatin 10 analogs such as auristatin E (AE) and monomethylauristatin E (MMAE) may find use as conjugates for the antibodies of the present invention (Doronina et al., 2003, Nat Biotechnol 21(7):778-84; Francisco et al., 2003 Blood 102(4): 1458-65).
  • Useful enzymatically active toxins include but are not limited to diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes.
  • the present invention further contemplates a conjugate between an antibody of the present invention and a compound with nucleolytic activity, for example a ribonuclease or DNA endonuclease such as a deoxyribonuclease (Dnase).
  • a compound with nucleolytic activity for example a ribonuclease or DNA endonuclease such as a deoxyribonuclease (Dnase).
  • an antibody of the present invention may be fused, conjugated, or operably linked to a radioisotope to form a radioconjugate.
  • a radioactive isotope are available for the production of radioconjugate antibodies. Examples include, but are not limited to, At211, 1131, 1125, Y90, Rel86, Rel88, Sml53, Bi212, P32, and radioactive isotopes of Lu.
  • an antibody of the present invention may be conjugated to a "receptor” (such as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand” (e.g. avidin) which is conjugated to a cytotoxic agent (e.g. a radionucleotide).
  • a "ligand” e.g. avidin
  • cytotoxic agent e.g. a radionucleotide
  • the antibody is conjugated or operably linked to an enzyme in order to employ Antibody Dependent Enzyme Mediated Prodrug Therapy (ADEPT).
  • ADPT Antibody Dependent Enzyme Mediated Prodrug Therapy
  • ADEPT may be used by conjugating or operably linking the antibody to a prodrug-activating enzyme that converts a prodrug (e.g. a peptidyl chemotherapeutic agent, see PCT WO 81/01145, incorporated herein it its entirety by reference) to an active anti-cancer drug.
  • a prodrug e.g. a peptidyl chemotherapeutic agent, see PCT WO 81/01145, incorporated herein it its entirety by reference
  • the enzyme component of the immunoconjugate useful for ADEPT includes any enzyme capable of acting on a prodrug in such a way so as to covert it into its more active, cytotoxic form.
  • Enzymes that are useful in the method of this invention include but are not limited to alkaline phosphatase useful for converting phosphate-containing prodrugs into free drugs; arylsulfatase useful for converting sulfate-containing prodrugs into free drugs; cytosine deaminase useful for converting non-toxic 5-fluorocytosine into the anti-cancer drug, 5- fluorouracil; proteases, such as serratia protease, thermolysin, subtilisin, carboxypeptidases and cathepsins (such as cathepsins B and L), that are useful for converting peptide-containing prodrugs into free drugs; D-alanylcarboxypeptidases, useful for converting prodrugs that contain D- amino acid substituents, carbohydrate- cleaving enzymes such as beta-galactosidase and neuramimidase useful for converting glycosylated prodrugs into free drugs, beta-lactamase useful for
  • antibodies with enzymatic activity can be used to convert the prodrugs of the invention into free active drugs (see, for example, Massey, 1987, Nature 328. 457-458, incorporated herein it its entirety by reference)
  • Antibody-abzyme conjugates can be prepared for delivery of the abzyme to a tumor cell population.
  • additional conjugates are contemplated for the antibodies of the present invention.
  • a variety of chemotherapeutic agents, anti- angiogenic agents, tyrosine kinase inhibitors, and other therapeutic agents are described below, which may find use as antibody conjugates.
  • Fc polypeptides are also contemplated as fusion and conjugate partners.
  • an antibody may be a multimeric Fc polypeptide, comprising two or more Fc regions.
  • Fc regions may be linked using a chemical engineering approach
  • Fab's and Fc's may be linked by thioether bonds originating at cysteine residues in the hinges, generating molecules such as FabFc 2 .
  • Fc regions may be linked using disulfide engineering and/or chemical cross-linking
  • Fc regions may be linked genetically.
  • Fc regions in an antibody are linked genetically to generated tandemly linked Fc regions as described in USSN 1 1/022,289, filed 12/21/2004, entitled "Fc polypeptides with novel Fc ligand binding sites ".Tandemly linked Fc polypeptides may comprise two or more Fc regions, e g , one to three, two, etc , Fc regions. It may be advantageous to explore a number of engineering constructs in order to obtain homo- or hetero- tandemly linked antibodies with the most favorable structural and functional properties. Tandemly linked antibodies may be homo-tandemly linked antibodies, that is an antibody of one isotype is fused genetically to another antibody of the same isotype.
  • FcyR, Clq, and/or FcRn binding sites on tandemly linked Fc polypeptides effector functions and/or pharmacokinetics may be enhanced.
  • antibodies from different isotypes may be tandemly linked, referred to as hetero- tandemly linked antibodies
  • an antibody that binds both FcyRs and FcyRI may provide a significant clinical improvement.
  • Fusion and conjugate partners may be linked to any region of an antibody of the present invention, including at the N- or C- termini, or at some residue in- between the termini.
  • a fusion or conjugate partner is linked at the N- or C-terminus of the antibody, e g , the N-terminus.
  • linkers may find use in the present invention to covalently link antibodies to a fusion or conjugate partner.
  • linker sequence By “linker”, “linker sequence” , “spacer”, “tethering sequence” or grammatical equivalents thereof, herein is meant a molecule or group of molecules (such as a monomer or polymer) that connects two molecules and often serves to place the two molecules in a desirable configuration.
  • Linkers are known in the art, for example, homo-or hetero-bifunctional linkers as are well known (see, 1994 Pierce Chemical Company catalog, technical section on cross-linkers, pages 155-200).
  • a number of strategies may be used to covalently link molecules together. These include, but are not limited to polypeptide linkages between N- and C-termini of proteins or protein domains, linkage via disulfide bonds, and linkage via chemical cross-linking reagents.
  • the linker is a peptide bond, generated by recombinant techniques or peptide synthesis.
  • the linker may contain amino acid residues that provide flexibility.
  • the linker peptide may predominantly include the following amino acid residues Gly, Ser, Ala, or Thr.
  • the linker peptide should have a length that is adequate to link two molecules in such a way that they assume the correct conformation relative to one another so that they retain the desired activity. Suitable lengths for this purpose include at least one and not more than 50 amino acid residues. In one embodiment, the linker is from about 1 to 30 amino acids in length, with linkers of 1 to 20 amino acids in length being desirable.
  • Useful linkers include glycine-serine polymers (including, for example, (GS)n, (GSGGS)n, (GGGGS)n and (GGGS)n, where n is an integer of at least one), glycine-alanine polymers, alanine-serine polymers, and other flexible linkers, as will be appreciated by those in the art.
  • nonproteinaceous polymers including but not limited to polyethylene glycol (PEG), polypropylene glycol, polyoxyalkylenes, or copolymers of polyethylene glycol and polypropylene glycol, may find use as linkers, that is may find use to link the antibodies of the present invention to a fusion or conjugate partner, or to link the antibodies of the present invention to a conjugate
  • PEG polyethylene glycol
  • polypropylene glycol polyoxyalkylenes
  • copolymers of polyethylene glycol and polypropylene glycol may find use as linkers, that is may find use to link the antibodies of the present invention to a fusion or conjugate partner, or to link the antibodies of the present invention to a conjugate
  • the present invention provides methods for producing and experimentally testing antibodies.
  • the described methods are not meant to constrain the present invention to any particular application or theory of operation. Rather, the provided methods are meant to illustrate generally that one or more antibodies may be produced and experimentally tested to obtain variant antibodies.
  • General methods for antibody molecular biology, expression, purification, and screening are described in Antibody Engineering, edited by Duebel & Kontermann, Springer- Verlag, Heidelberg, 2001 , and Hayhurst & Georgiou, 2001 , Curr Opin Chem Biol 5 683-689; Maynard & Georgiou, 2000, Annu Rev Biomed Eng 2 339-76, Antibodies. A Laboratory Manual by Harlow & Lane, New York: Cold Spring Harbor Laboratory Press, 1988.
  • nucleic acids are created that encode the antibodies, and that may then be cloned into host cells, expressed and assayed, if desired.
  • nucleic acids, and particularly DNA may be made that encode each protein sequence.
  • These practices are carried out using well-known procedures. For example, a variety of methods that may find use in the present invention are described in Molecular Cloning - A Laboratory Manual, 3 rd Ed. (Maniatis, Cold Spring Harbor Laboratory Press, New York, 2001), and Current Protocols in Molecular Biology (John Wiley & Sons).
  • the generation of exact sequences for a library comprising a large number of sequences is potentially expensive and time consuming.
  • library herein is meant a set of variants in any form, including but not limited to a list of nucleic acid or amino acid sequences, a list of nucleic acid or amino acid substitutions at variable positions, a physical library comprising nucleic acids that encode the library sequences, or a physical library comprising the variant proteins, either in purified or unpurified form. Accordingly, there are a variety of techniques that may be used to efficiently generate libraries of the present invention. Such methods that may find use in the present invention are described or referenced in US 6,403,312; USSN 09/782,004, USSN 09/927,790; USSN 10/218,102; PCT WO 01/40091 ; and PCT WO 02/25588.
  • Such methods include but are not limited to gene assembly methods, PCR-based method and methods which use variations of PCR, ligase chain reaction-based methods, pooled oligo methods such as those used in synthetic shuffling, error-prone amplification methods and methods which use oligos with random mutations, classical site-directed mutagenesis methods, cassette mutagenesis, and other amplification and gene synthesis methods.
  • gene assembly methods PCR-based method and methods which use variations of PCR
  • ligase chain reaction-based methods pooled oligo methods such as those used in synthetic shuffling
  • error-prone amplification methods and methods which use oligos with random mutations
  • classical site-directed mutagenesis methods cassette mutagenesis
  • cassette mutagenesis cassette mutagenesis
  • other amplification and gene synthesis methods include but are not limited to gene assembly methods, PCR-based method and methods which use variations of PCR, ligase chain reaction-based methods, pooled oligo methods such as those used in synthetic shuff
  • the antibodies of the present invention may be produced by culturing a host cell transformed with nucleic acid, e.g., an expression vector, containing nucleic acid encoding the antibodies, under the appropriate conditions to induce or cause expression of the protein.
  • nucleic acid e.g., an expression vector, containing nucleic acid encoding the antibodies
  • the conditions appropriate for expression will vary with the choice of the expression vector and the host cell, and will be easily ascertained by one skilled in the art through routine experimentation.
  • a wide variety of appropriate host cells may be used, including but not limited to mammalian cells, bacteria, insect cells, and yeast.
  • a variety of cell lines that may find use in the present invention are described in the ATCC cell line catalog, available from the American Type Culture Collection.
  • the antibodies are expressed in mammalian expression systems, including systems in which the expression constructs are introduced into the mammalian cells using virus such as retrovirus or adenovirus.
  • virus such as retrovirus or adenovirus.
  • Any mammalian cells may be used, e.g., human, mouse, rat, hamster, primate cells, etc.. Suitable cells also include known research cells, including but not limited to Jurkat T cells, NIH3T3, CHO, BHK, COS, HEK293, PER C.6, HeLa, Sp2/0, NSO cells and variants thereof.
  • library proteins are expressed in bacterial cells.
  • Bacterial expression systems are well known in the art, and include Escherichia coli (E. coli).
  • antibodies are produced in insect cells (e g Sf21/Sf9) or yeast cells (e.g. S. cerevisiae, Pichia, etc.).
  • antibodies are expressed in vitro using cell free translation systems.
  • In vitro translation systems derived from both prokaryotic (e.g. E. coli) and eukaryotic (e.g. wheat germ, rabbit reticulocytes) cells are available and may be chosen based on the expression levels and functional properties of the protein of interest. For example, as appreciated by those skilled in the art, in vitro translation is required for some display technologies, for example ribosome display.
  • the antibodies may be produced by chemical synthesis methods.
  • transgenic expression systems both animal (e.g. cow, sheep or goat milk, embryonated hen's eggs, whole insect larvae, etc.) and plant (e.g. corn, tobacco, duckweed, etc.).
  • the nucleic acids that encode the antibodies of the present invention may be incorporated into an expression vector in order to express the protein.
  • a variety of expression vectors may be utilized for protein expression.
  • Expression vectors may comprise self- replicating extra-chromosomal vectors or vectors which integrate into a host genome. Expression vectors are constructed to be compatible with the host cell type.
  • expression vectors which find use in the present invention include but are not limited to those which enable protein expression in mammalian cells, bacteria, insect cells, yeast, and in in vitro systems. As is known in the art, a variety of expression vectors are available, commercially or otherwise, that may find use in the present invention for expressing antibodies.
  • Expression vectors typically comprise a protein operably linked with control or regulatory sequences, selectable markers, any fusion partners, and/or additional elements.
  • operably linked herein is meant that the nucleic acid is placed into a functional relationship with another nucleic acid sequence.
  • these expression vectors include transcriptional and translational regulatory nucleic acid operably linked to the nucleic acid encoding the antibody, and are typically appropriate to the host cell used to express the protein, hi general, the transcriptional and translational regulatory sequences may include promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences.
  • expression vectors typically contain a selection gene or marker to allow the selection of transformed host cells containing the expression vector. Selection genes are well known in the art and will vary with the host cell used.
  • Antibodies may be operably linked to a fusion partner to enable targeting of the expressed protein, purification, screening, display, and the like. Fusion partners may be linked to the antibody sequence via a linker sequence.
  • the linker sequence will generally comprise a small number of amino acids, typically less than ten, although longer linkers may also be used. Typically, linker sequences are selected to be flexible and resistant to degradation. As will be appreciated by those skilled in the art, any of a wide variety of sequences may be used as linkers.
  • a common linker sequence comprises the amino acid sequence GGGGS.
  • a fusion partner may be a targeting or signal sequence that directs antibody and any associated fusion partners to a desired cellular location or to the extracellular media.
  • certain signaling sequences may target a protein to be either secreted into the growth media, or into the periplasmic space, located between the inner and outer membrane of the cell.
  • a fusion partner may also be a sequence that encodes a peptide or protein that enables purification and/or screening.
  • Such fusion partners include but are not limited to polyhistidine tags (His-tags) (for example H6 and H10 or other tags for use with Immobilized Metal Affinity Chromatography (IMAC) systems (e.g Ni affinity columns)), GST fusions, MBP fusions, Strep-tag, the BSP biotinylation target sequence of the bacterial enzyme BirA, and epitope tags which are targeted by antibodies (for example c-myc tags, flag-tags, and the like). As will be appreciated by those skilled in the art, such tags may be useful for purification, for screening, or both.
  • His-tags polyhistidine tags
  • IMAC Immobilized Metal Affinity Chromatography
  • an antibody may be purified using a His-tag by immobilizing it to a Ni affinity column, and then after purification the same His-tag may be used to immobilize the antibody to a Ni 2+ coated plate to perform an ELISA or other binding assay (as described below).
  • a fusion partner may enable the use of a selection method to screen antibodies (see below). Fusion partners that enable a variety of selection methods are well-known in the art, and all of these find use in the present invention.
  • phage display can be employed (Kay et ah, Phage display of peptides and proteins: a laboratory manual, Academic Press, San Diego, CA, 1996; Lowman et al., 1991, Biochemistry 30: 10832-10838; Smith, 1985, Science 228: 1315-1317).
  • Fusion partners may enable antibodies to be labeled.
  • a fusion partner may bind to a specific sequence on the expression vector, enabling the fusion partner and associated antibody to be linked covalently or noncovalently with the nucleic acid that encodes them.
  • antibodies are purified or isolated after expression.
  • Proteins may be isolated or purified in a variety of ways known to those skilled in the art. Standard purification methods include chromatographic techniques, including ion exchange, hydrophobic interaction, affinity, sizing or gel filtration, and reversed-phase, carried out at atmospheric pressure or at high pressure using systems such as FPLC and HPLC. Purification methods also include electrophoretic, immunological, precipitation, dialysis, and chromatofocusing techniques. Ultrafiltration and diafiltration techniques, in conjunction with protein concentration, are also useful. As is well known in the art, a variety of natural proteins bind Fc and antibodies, and these proteins can find use in the present invention for purification of antibodies.
  • the bacterial proteins A and G bind to the Fc region.
  • the bacterial protein L binds to the Fab region of some antibodies, as of course does the antibody's target antigen.
  • Purification can often be enabled by a particular fusion partner.
  • antibodies may be purified using glutathione resin if a GST fusion is employed, Ni 2+ affinity chromatography if a His-tag is employed, or immobilized anti-flag antibody if a flag- tag is used.
  • suitable purification techniques see, e.g. Protein Purification: Principles and Practice, 3 rd Ed., Scopes, Springer-Verlag, NY, 1994. The degree of purification necessary will vary depending on the screen or use of the antibodies.
  • no purification is necessary.
  • screening may take place directly from the media.
  • some methods of selection do not involve purification of proteins.
  • protein purification may not be performed.
  • Antibodies may be screened using a variety of methods, including but not limited to those that use in vitro assays, in vivo and cell-based assays, and selection technologies. Automation and high-throughput screening technologies may be utilized in the screening procedures. Screening may employ the use of a fusion partner or label. The use of fusion partners has been discussed above.
  • label herein is meant that the antibodies of the invention have one or more elements, isotopes, or chemical compounds attached to enable the detection in a screen.
  • labels fall into three classes: a) immune labels, which maybe an epitope incorporated as a fusion partner that is recognized by an antibody, b) isotopic labels, which may be radioactive or heavy isotopes, and c) small molecule labels, which may include fluorescent and colorimetric dyes, or molecules such as biotin that enable other labeling methods. Labels may be incorporated into the compound at any position and may be incorporated in vitro or in vivo during protein expression.
  • the functional and/or biophysical properties of antibodies are screened in an in vitro assay.
  • In vitro assays may allow a broad dynamic range for screening properties of interest.
  • Properties of antibodies that may be screened include but are not limited to stability, solubility, and affinity for Fc ligands, for example FcyRs. Multiple properties may be screened simultaneously or individually. Proteins may be purified or unpurified, depending on the requirements of the assay.
  • the screen is a qualitative or quantitative binding assay for binding of antibodies to a protein or nonprotein molecule that is known or thought to bind the antibody.
  • the screen is a binding assay for measuring binding to the target antigen.
  • the screen is an assay for binding of antibodies to an Fc ligand, including but not limited to the family of FcyRs, the neonatal receptor FcRn, the complement protein Clq, and the bacterial proteins A and G.
  • the Fc ligands may be from any organism, e.g., humans, mice, rats, rabbits, monkeys, etc..
  • Binding assays can be carried out using a variety of methods known in the art, including but not limited to FRET (Fluorescence Resonance Energy Transfer) and BRET (Bioluminescence Resonance Energy Transfer)-based assays, AlphaScreen(TM) (Amplified Luminescent Proximity Homogeneous Assay), Scintillation Proximity Assay, ELISA (Enzyme-Linked Immunosorbent Assay), SPR (Surface Plasmon Resonance, also known as Biacore(TM)), isothermal titration calorimetry, differential scanning calorimetry, gel electrophoresis, and chromatography including gel filtration. These and other methods may take advantage of some fusion partner or label of the antibody. Assays may employ a variety of detection methods including but not limited to chromogenic, fluorescent, luminescent, or isotopic labels.
  • proteins for example stability and solubility
  • Protein stability may be determined by measuring the thermodynamic equilibrium between folded and unfolded states.
  • antibodies of the present invention may be unfolded using chemical denaturant, heat, or pH, and this transition may be monitored using methods including, but not limited to, circular dichroism spectroscopy, fluorescence spectroscopy, absorbance spectroscopy, NMR spectroscopy, calorimetry, and proteolysis.
  • the kinetic parameters of the folding and unfolding transitions may also be monitored using these and other techniques.
  • the solubility and overall structural integrity of an antibody may be quantitatively or qualitatively determined using a wide range of methods that are known in the art.
  • Methods which may find use in the present invention for characterizing the biophysical properties of antibodies include gel electrophoresis, isoelectric focusing, capillary electrophoresis, chromatography such as size exclusion chromatography, ion- exchange chromatography, and reversed-phase high performance liquid chromatography, peptide mapping, oligosaccharide mapping, mass spectrometry, ultraviolet absorbance spectroscopy, fluorescence spectroscopy, circular dichroism spectroscopy, isothermal titration calorimetry, differential scanning calorimetry, analytical ultra-centrifugation, dynamic light scattering, proteolysis, and cross-linking, turbidity measurement, filter retardation assays, immunological assays, fluorescent dye binding assays, protein-staining assays, microscopy, and detection of aggregates via ELISA or other binding assay.
  • Structural analysis employing X-ray crystallographic techniques and NMR spectroscopy may also find use.
  • stability and/or solubility may be measured by determining the amount of protein solution after some defined period of time.
  • the protein may or may not be exposed to some extreme condition, for example elevated temperature, low pH, or the presence of denaturant.
  • the aforementioned functional and binding assays also provide ways to perform such a measurement. For example, a solution comprising an antibody could be assayed for its ability to bind target antigen, then exposed to elevated temperature for one or more defined periods of time, then assayed for antigen binding again. Because unfolded and aggregated protein is not expected to be capable of binding antigen, the amount of activity remaining provides a measure of the antibody's stability and solubility.
  • the biological properties of the antibodies of the present invention may be characterized in cell, tissue, and whole organism experiments.
  • drugs are often tested in animals, including but not limited to mice, rats, rabbits, dogs, cats, pigs, and monkeys, in order to measure a drug's efficacy for treatment against a disease or disease model, or to measure a drug's pharmacokinetics, toxicity, and other properties.
  • the animals may be referred to as disease models.
  • Therapeutics are often tested in mice, including but not limited to nude mice, SCID mice, xenograft mice, and transgenic mice (including knockins and knockouts).
  • an antibody of the present invention that is intended as an anti-cancer therapeutic may be tested in a mouse cancer model, for example a xenograft mouse.
  • a tumor or tumor cell line is grafted onto or injected into a mouse, and subsequently the mouse is treated with the therapeutic to determine the ability of the antibody to reduce or inhibit cancer growth and metastasis.
  • An alternative approach is the use of a SCID murine model in which immune-deficient mice are injected with human Peripheral Blood Lymphocytes (PBLs), conferring a semi-functional and human immune system - with an appropriate array of human FcRs - to the mice that have subsequently been injected with antibodies or Fc-polypeptides that target injected human tumor cells.
  • PBLs Peripheral Blood Lymphocytes
  • the Fc-polypeptides that target the desired antigen interact with human PBLs within the mice to engage tumoricidal effector functions.
  • Such experimentation may provide meaningful data for determination of the potential of the antibody to be used as a therapeutic. Any organism, e.g., mammals, may be used for testing.
  • monkeys can be suitable therapeutic models, and thus may be used to test the efficacy, toxicity, pharmacokinetics, or other property of the antibodies of the present invention.
  • Tests of the antibodies of the present invention in humans are ultimately required for approval as drugs, and thus of course these experiments are contemplated.
  • the antibodies of the present invention may be tested in humans to determine their therapeutic efficacy, toxicity, pharmacokinetics, and/or other clinical properties.
  • Toxicity studies are performed to determine the antibody or Fc-fusion related- effects that cannot be evaluated in standard pharmacology profile or occur only after repeated administration of the agent. Most toxicity tests are performed in two species - a rodent and a non-rodent - to ensure that any unexpected adverse effects are not overlooked before new therapeutic entities are introduced into man. In general, these models may measure a variety of toxicities including genotoxicity, chronic toxicity, immunogenicity, reproductive/developmental toxicity, and carcinogenicity. Included within the aforementioned parameters are standard measurement of food consumption, bodyweight, antibody formation, clinical chemistry, and macro- and microscopic examination of standard organs/tissues (e g cardiotoxicity).
  • PK pharmacokinetics
  • the pharmacokinetics (PK) of the antibodies of the invention can be studied in a variety of animal systems, with the most relevant being non-human primates such as the cynomolgous and rhesus monkeys.
  • Single or repeated i.v./s.c. administrations over a dose range of 6000-fold (0.05-300 mg/kg) can be evaluated for the half-life (days to weeks) using plasma concentration and clearance as well as volume of distribution at a steady state and level of systemic absorbance can be measured.
  • Examples of such parameters of measurement generally include maximum observed plasma concentration (Cmax), the time to reach Cmax (Tmax), the area under the plasma concentration-time curve from time 0 to infinity [AUCo-inf] and apparent elimination half-life (T[/ 2 ). Additional measured parameters could include compartmental analysis of concentration-time data obtained following i.v. administration and bioavailability. Examples of pharmacological/toxicological studies using cynomolgus have been established for Rituxan® and Zevalm® in which monoclonal antibodies to CD20 are cross-reactive. Biodistribution, dosimetry (for radiolabled antibodies), and PK studies can also be done in rodent models.
  • the antibodies of the present invention may confer superior pharmacokinetics in animal systems or in humans. For example, increased binding to FcRn may increase the half-life and exposure of the therapeutic antibody. Alternatively, decreased binding to FcRn may decrease the half-life and exposure of the Fc-containing drug in cases where reduced exposure is favorable such as when such drug has side effects. It is known in the art that the array of Fc receptors is differentially expressed on various immune cell types, as well as in different tissues.
  • Differential tissue distribution of Fc receptors may ultimately have an impact on the pharmacodynamic (PD) and pharmacokinetic (PK) properties of antibodies of the present invention.
  • PD pharmacodynamic
  • PK pharmacokinetic
  • Pharmacodynamic studies may include, but are not limited to, targeting specific tumor cells or blocking signaling mechanisms, measuring depletion of target antigen expressing cells or signals, etc.. Such pharmacodynamic effects may be demonstrated in animal models or in humans.
  • the antibodies of the present invention may be used for therapeutic purposes. As will be appreciated by those in the art, the antibodies of the present invention may be used for any therapeutic purpose that uses antibodies and the like. In one embodiment, the antibodies are administered to a patient to treat disorders including but not limited to cancer.
  • a "patient' for the purposes of the present invention includes both humans and other animals, e.g., mammals, e.g., humans.
  • the antibodies of the present invention have both human therapy and veterinary applications.
  • treatment or “treating” in the present invention is meant to include therapeutic treatment, as well as prophylactic, or suppressive measures for a disease or disorder
  • successful administration of an antibody prior to onset of the disease results in treatment of the disease.
  • successful administration of an optimized antibody after clinical manifestation of the disease to combat the symptoms of the disease comprises treatment of the disease.
  • Treatment” and “treating” also encompasses administration of an optimized antibody after the appearance of the disease in order to eradicate the disease.
  • Successful administration of an agent after onset and after clinical symptoms have developed, with possible abatement of clinical symptoms and perhaps amelioration of the disease, comprises treatment of the disease.
  • Those "in need of treatment” include mammals already having the disease or disorder, as well as those prone to having the disease or disorder, including those in which the disease or disorder is to be prevented.
  • an antibody of the present invention is administered to a patient having a disease involving inappropriate expression of a protein or other molecule, such as CD133.
  • a disease involving inappropriate expression of a protein or other molecule such as CD133.
  • this is meant to include diseases and disorders characterized by aberrant proteins, due for example to alterations in the amount of a protein present, protein localization, posttranslational modification, conformational state, the presence of a mutant protein, etc..
  • An overabundance may be due to any cause, including but not limited to overexpression at the molecular level, prolonged or accumulated appearance at the site of action, or increased activity of a protein relative to normal. Included within this definition are diseases and disorders characterized by a reduction of a protein.
  • This reduction may be due to any cause, including but not limited to reduced expression at the molecular level, shortened or reduced appearance at the site of action, mutant forms of a protein, or decreased activity of a protein relative to normal.
  • Such an overabundance or reduction of a protein can be measured relative to normal expression, appearance, or activity of a protein, and the measurement may play an important role in the development and/or clinical testing of the antibodies of the present invention.
  • cancer and “cancerous” herein refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth.
  • examples of cancer include but are not limited to carcinoma, lymphoma, blastoma, sarcoma (including liposarcoma), neuroendocrine tumors, mesothelioma, schwanoma, meningioma, adenocarcinoma, melanoma, and leukemia or lymphoid malignancies.
  • cancers include hematologic malignancies, such as non-Hodgkin's lymphomas (NHL), B- cell acute lymphoblastic leukemia/lymphoma (B-ALL), and T-cell acute lymphoblastic leukemia/lymphoma (T- ALL), thymoma, Langerhans cell histocytosis, multiple myeloma (MM), myeloid neoplasias such as acute myelogenous leukemias (AML), including AML with maturation, AML without differentiation, acute promyelocytic leukemia, acute myelomonocytic leukemia, and acute monocytic leukemias, myelodysplastic syndromes, and chronic myeloproliferative disorders (MDS), including chronic myelogenous leukemia (CML).
  • NHL non-Hodgkin's lymphomas
  • B-ALL B- cell acute lymphoblastic leukemia/lymphoma
  • T- ALL T-
  • the target of the antibodies of the present invention may be polymorphic in the human population.
  • the efficacy of the antibodies of the present invention may thus be affected by the presence or absence of specific polymorphisms in proteins.
  • FcyRIIIA is polymorphic at position 158, which is commonly either V (high affinity) or F (low affinity).
  • V high affinity
  • F low affinity
  • Patients with the V/V homozygous genotype are observed to have a better clinical response to treatment with the anti-CD20 antibody Rituxan® (rituximab), likely because these patients mount a stronger NK response (Dall'Ozzo et al. (2004) Cancer Res. 64-4664-9).
  • Additional polymorphisms include but are not limited to FcyRIIA R131 or H131, and such polymorphisms are known to either increase or decrease Fc binding and subsequent biological activity, depending on the polymorphism.
  • Antibodies of the present invention may bind to a particular polymorphic form of a receptor, for example FcyRIIIA 158 V, or to bind with equivalent affinity to all of the polymorphisms at a particular position in the receptor, for example both the 158V and 158F polymorphisms of FcyRIIIA.
  • antibodies of the present invention may have equivalent binding to polymorphisms that may be used in an antibody to eliminate the differential efficacy seen in patients with different polymorphisms.
  • Such a property may give greater consistency in therapeutic response and reduce non-responding patient populations.
  • Such variant Fc with identical binding to receptor polymorphisms may have increased biological activity, such as ADCC, CDC or circulating half-life, or alternatively decreased activity, via modulation of the binding to the relevant Fc receptors.
  • antibodies of the present invention may bind with higher or lower affinity to one of the polymorphisms of a receptor, either accentuating the existing difference in binding or reversing the difference.
  • Such a property may allow creation of therapeutics particularly tailored for efficacy with a patient population possessing such polymorphism.
  • a patient population possessing a polymorphism with a higher affinity for an inhibitory receptor such as FcyRIIb could receive a drug containing an antibody with reduced binding to such polymorphic form of the receptor, creating a more efficacious drug.
  • patients are screened for one or more polymorphisms in order to predict the efficacy of the antibodies of the present invention.
  • This information may be used, for example, to select patients to include or exclude from clinical trials or, post-approval, to provide guidance to physicians and patients regarding appropriate dosages and treatment options.
  • patients are selected for inclusion in clinical trials for an antibody of the present invention if their genotype indicates that they are likely to respond significantly better to an antibody of the present invention as compared to one or more currently used antibody therapeutics.
  • appropriate dosages and treatment regimens are determined using such genotype information.
  • patients are selected for inclusion in a clinical trial or for receipt of therapy post- approval based on their polymorphism genotype, where such therapy contains an antibody engineered to be specifically efficacious for such population, or alternatively where such therapy contains an antibody that does not show differential activity to the different forms of the polymorphism.
  • the present invention comprises prognostic tests performed on clinical samples such as blood and tissue samples.
  • tests may assay for effector function activity, including but not limited to ADCC, CDC, phagocytosis, and opsonization, or for killing, regardless of mechanism, of cancerous or otherwise pathogenic cells.
  • ADCC assays such as those described previously, are used to predict, for a specific patient, the efficacy of a given antibody of the present invention.
  • Such information may be used to identify patients for inclusion or exclusion in clinical trials, or to inform decisions regarding appropriate dosages and treatment regimens.
  • Such information may also be used to select a drug that contains a particular antibody that shows superior activity in such assay.
  • compositions are contemplated wherein an antibody of the present invention and one or more therapeutically active agents are formulated.
  • Formulations of the antibodies of the present invention are prepared for storage by mixing the antibody having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed., 1980), in the form of lyophilized formulations or aqueous solutions.
  • Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, acetate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl orbenzyl 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, glutamine, asparagine, hist
  • the pharmaceutical composition that comprises the antibody of the present invention may be in a water-soluble form, such as being present as pharmaceutically acceptable salts, which is meant to include both acid and base addition salts.
  • “Pharmaceutically acceptable acid addition salt” refers to those salts that retain the biological effectiveness of the free bases and that are not biologically or otherwise undesirable, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like, and organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesuifonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid and the like.
  • inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like
  • organic acids such as acetic acid, propionic acid, glycolic acid, pyruvic acid,
  • “Pharmaceutically acceptable base addition salts” include those derived from inorganic bases such as sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum salts and the like. Particularly useful are the ammonium, potassium, sodium, calcium, and magnesium salts.
  • Salts derived from pharmaceutically acceptable organic nontoxic bases include salts of primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines and basic ion exchange resins, such as isopropylamine, trimethylamine, diethylamine, triethylamine, tripropylamine, and ethanolamine.
  • the formulations to be used for in vivo administration should be sterile. This is readily accomplished by filtration through sterile filtration membranes or other methods.
  • a liposome is a small vesicle comprising various types of lipids, phospholipids and/or surfactant that is useful for delivery of a therapeutic agent to a mammal.
  • Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al., 1985, Proc Natl Acad Sci USA, 82:3688; Hwang et al., 1980, Proc Natl Acad Sci USA, 77:4030; US 4,485,045; US 4,544,545; and PCT WO 97/38731. Liposomes with enhanced circulation time are disclosed in US 5,013,556.
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.
  • Particularly useful liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE).
  • PEG-PE PEG-derivatized phosphatidylethanolamine
  • Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter.
  • a chemotherapeutic agent or other therapeutically active agent is optionally contained within the liposome (Gabizon et al., 1989, J National Cancer Inst 81 :1484).
  • the antibody and other therapeutically active agents may also be entrapped in microcapsules prepared by methods including but not limited to coacervation techniques, interfacial polymerization (for example using hydroxymethylcellulose or gelatin- microcapsules, or poly-(methylmethacylate) microcapsules), colloidal drug delivery systems (for example, liposomes, albumin microspheres, micro emulsions, nano-particles and nano capsules), and macroemulsions.
  • coacervation techniques for example using hydroxymethylcellulose or gelatin- microcapsules, or poly-(methylmethacylate) microcapsules
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, micro emulsions, nano-particles and nano capsules
  • macroemulsions for example, liposomes, albumin microspheres, micro emulsions, nano-particles and nano capsules
  • Sustained-release preparations may be prepared.
  • sustained-release preparations include semipermeable matrices of solid hydrophobic polymer, which matrices are in the form of shaped articles, e.g. films, or microcapsules.
  • sustained-release matrices include polyesters, hydrogels (for example poly(2- hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (US 3,773,919), copolymers of L-glutamic acid and gamma ethyl-L- glutamate, non- degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the Lupron Depot® (which are injectable microspheres composed of lactic acid- glycolic acid copolymer and leuprolide acetate), poly-D-(-)-3-hydroxybutyric acid, and ProLease® (commercially available from Alkermes), which is a microsphere-based delivery system composed of the desired bioactive molecule
  • Administration of the pharmaceutical composition comprising an antibody of the present invention may be done in a variety of ways, including, but not limited to orally, subcutaneously, intravenously, intranasally, intraotically, transdermally, topically (e.g., gels, salves, lotions, creams, etc.), intraperitoneally, intramuscularly, intrapulmonary, vaginally, parenterally, rectally, or intraocularly.
  • the pharmaceutical composition may be formulated accordingly depending upon the manner of introduction.
  • protein therapeutics are often delivered by IV infusion or bolus.
  • the antibodies of the present invention may also be delivered using such methods.
  • administration may be by intravenous infusion with 0.9% sodium chloride as an infusion vehicle.
  • any of a number of delivery systems are known in the art and may be used to administer the antibodies of the present invention. Examples include, but are not limited to, encapsulation in liposomes, microparticles, microspheres (eg. PLA/PGA microspheres), and the like.
  • an implant of a porous, non- porous, or gelatinous material, including membranes or fibers, may be used.
  • Sustained release systems may comprise a polymeric material or matrix such as polyesters, hydrogels, poly(vinylalcohol), polylactides, copolymers of L-glutamic acid and ethyl-L- glutamate, ethylene-vinyl acetate, lactic acid-glycolic acid copolymers such as the Lupron Depot®, and poly-D-(-)-3-hydroxyburyric acid. It is also possible to administer a nucleic acid encoding the antibody of the current invention, for example by retroviral infection, direct injection, or coating with lipids, cell surface receptors, or other transfection agents. In all cases, controlled release systems may be used to release the antibody at or close to the desired location of action.
  • a polymeric material or matrix such as polyesters, hydrogels, poly(vinylalcohol), polylactides, copolymers of L-glutamic acid and ethyl-L- glutamate, ethylene-vinyl acetate, lactic acid-g
  • the dosing amounts and frequencies of administration are, in one embodiment, selected to be therapeutically or prophylactically effective.
  • adjustments for protein degradation, systemic versus localized delivery, and rate of new protease synthesis, as well as the age, body weight, general health, sex, diet, time of administration, drug interaction and the severity of the condition may be necessary, and will be ascertainable with routine experimentation by those skilled in the art.
  • the concentration of the therapeutically active antibody in the formulation may vary from about 0.1 to 100 weight %. In one embodiment, the concentration of the antibody is in the range of 0.003 ⁇ to 1.0 molar.
  • a therapeutically effective dose of the antibody of the present invention may be administered.
  • therapeutically effective dose herein is meant a dose that produces the effects for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques. Dosages may range from 0.0001 to 100 mg/kg of body weight or greater, for example 0.1, 1, 10, or 50 mg/kg of body weight, e.g., 1 to lOmg/kg of body weight.
  • only a single dose of the antibody is used. In other embodiments, multiple doses of the antibody are administered.
  • the elapsed time between administrations may be less than 1 hour, about 1 hour, about 1-2 hours, about 2-3 hours, about 3-4 hours, about 6 hours, about 12 hours, about 24 hours, about 48 hours, about 2-4 days, about 4-6 days, about 1 week, about 2 weeks, or more than 2 weeks.
  • the antibodies of the present invention are administered in metronomic dosing regimes, either by continuous infusion or frequent administration without extended rest periods.
  • Such metronomic administration may involve dosing at constant intervals without rest periods.
  • Such regimens encompass chronic low-dose or continuous infusion for an extended period of time, for example 1-2 days, 1-2 weeks, 1-2 months, or up to 6 months or more.
  • the use of lower doses may minimize side effects and the need for rest periods.
  • the antibody of the present invention and one or more other prophylactic or therapeutic agents are cyclically administered to the patient.
  • Cycling therapy involves administration of a first agent at one time, a second agent at a second time, optionally additional agents at additional times, optionally a rest period, and then repeating this sequence of administration one or more times.
  • the number of cycles is typically from 2 - 10. Cycling therapy may reduce the development of resistance to one or more agents, may minimize side effects, or may improve treatment efficacy.
  • the antibodies of the present invention may be administered concomitantly with one or more other therapeutic regimens or agents.
  • the additional therapeutic regimes or agents may be used to improve the efficacy or safety of the antibody.
  • the additional therapeutic regimes or agents may be used to treat the same disease or a comorbidity rather than to alter the action of the antibody.
  • an antibody of the present invention may be administered to the patient along with chemotherapy, radiation therapy, or both chemotherapy and radiation therapy.
  • the antibody of the present invention may be administered in combination with one or more other prophylactic or therapeutic agents, including but not limited to cytotoxic agents, chemotherapeutic agents, cytokines, growth inhibitory agents, anti-hormonal agents, kinase inhibitors, anti-angiogenic agents, cardioprotectants, immuno stimulatory agents, immunosuppressive agents, agents that promote proliferation of hematological cells, angiogenesis inhibitors, protein tyrosine kinase (PT ) inhibitors, additional antibodies, FcyRIIb or other Fc receptor inhibitors, or other therapeutic agents.
  • cytotoxic agents including but not limited to cytotoxic agents, chemotherapeutic agents, cytokines, growth inhibitory agents, anti-hormonal agents, kinase inhibitors, anti-angiogenic agents, cardioprotectants, immuno stimulatory agents, immunosuppressive agents, agents that promote proliferation of hematological cells, angiogenesis inhibitors, protein tyrosine kinase (PT ) inhibitors, additional antibodies, FcyRI
  • the terms "in combination with” and “co-administration” are not limited to the administration of the prophylactic or therapeutic agents at exactly the same time. Instead, it is meant that the antibody of the present invention and the other agent or agents are administered in a sequence and within a time interval such that they may act together to provide a benefit that is increased versus treatment with only either the antibody of the present invention or the other agent or agents. In one embodiment, that the antibody and the other agent or agents act additively, e.g., they act synergistically. Such molecules are suitably present in combination in amounts that are effective for the purpose intended. The skilled medical practitioner can determine empirically, or by considering the pharmacokinetics and modes of action of the agents, the appropriate dose or doses of each therapeutic agent, as well as the appropriate timings and methods of administration.
  • the antibodies of the present invention are administered with one or more additional molecules comprising antibodies or Fc.
  • the antibodies of the present invention may be co -administered with one or more other antibodies that have efficacy in treating the same disease or an additional comorbidity, for example two antibodies may be administered that recognize two antigens that are overexpressed in a given type of cancer.
  • the antibodies of the present invention are administered with a chemotherapeutic agent.
  • chemotherapeutic agent as used herein is meant a chemical compound useful in the treatment of cancer.
  • examples of chemotherapeutic agents include but are not limited to alkylating agents such as thiotepa and cyclophosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan, androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone, anti-adrenals such as aminoglutethimide, mitotane, trilostane, anti- androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; antibiotics such as aclacinomysins, actinomycin, authramycin, azasenne, bleomycin
  • paclitaxel (TAXOL®, Bristol-Myers Squibb Oncology, Princeton, N.J.) and docetaxel (TAXOTERE®, Rhne-Poulenc Rorer, Antony, France); topoisomerase inhibitor RFS 2000; thymidylate synthase inhibitor (such as Tomudex); additional chemotherapeutics including aceglatone; aldophosphamide glycoside; aminolevulinic acid; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; difluoromethylornithine (DMFO); elformithine; elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol; nitracrine; pentostatin; phenamet;
  • a chemotherapeutic or other cytotoxic agent may be administered as a prodrug.
  • prodrug as used herein is meant a precursor or derivative form of a pharmaceutically active substance that is less cytotoxic to tumor cells compared to the parent drug and is capable of being enzymatically activated or converted into the more active parent form. See, for example Wilman, 1986, Biochemical Society Transactions, 615th Meeting Harbor, 14:375- 382; Stella et al., "Prodrugs: A Chemical Approach to Targeted Drug Delivery,” Directed Drug Delivery; and Borchardt eet al., (ed.): 247-267, Humana Press, 1985.
  • the prodrugs that may find use with the present invention include but are not limited to phosphate-containing prodrugs, thiophosphate-containing prodrugs, sulfate-containing prodrugs, peptide-containing prodrugs, D-amino acid- modified prodrugs, glycosylated prodrugs, beta-lactam-containing prodrugs, optionally substituted phenoxyacetamide-containing prodrugs or optionally substituted phenylacetamide-containing prodrugs, 5-fluorocytosine and other 5-fluorouridine prodrugs which can be converted into the more active cytotoxic free drug.
  • cytotoxic drugs that can be derivatized into a prodrug form for use with the antibodies of the present invention include but are not limited to any of the aforementioned chemotherapeutic agents.
  • the antibody is administered with one or more immunomodulatory agents.
  • immunomodulatory agents may increase or decrease production of one or more cytokines, up- or down-regulate self-antigen presentation, mask MHC antigens, or promote the proliferation, differentiation, migration, or activation state of one or more types of immune cells.
  • Immunomodulatory agents include but are not limited to non- steroidal anti-inflammatory drugs (NSAIDs) such as aspirin, ibuprofen, celecoxib, diclofenac, etodolac, fenoprofen, indomethacin, ketoralac, oxaprozin, nabumentone, sulindac, tolmentin, rofecoxib, naproxen, ketoprofen, and nabumetone, steroids (e.g.
  • NSAIDs non- steroidal anti-inflammatory drugs
  • glucocorticoids dexamethasone, cortisone, hydroxycortisone, methylprednisolone, prednisone, prednisolone, trimcinolone, azulfidineicosanoids such as prostaglandins, thromboxanes, and leukotrienes, as well as topical steroids such as anthrahn, calcipotriene, clobetasol, and tazarotene), cytokines such as TGFb, IFN , IFNp, IFNy, IL-2, IL-4, IL-10, cytokine, chemokine, or receptor antagonists including antibodies, soluble receptors, and receptor-Fc fusions against BAFF, B7, CCR2, CCR5, CD2, CD3, CD4, CD6, CD7, CD8, CD11 , CD14, CD15, CD17, CD18, CD20, CD23, CD28, CD40, CD40L, CD44, CD45, CD402, CD
  • antibodies of the present invention are administered with a cytokine.
  • cytokine as used herein is meant a generic term for proteins released by one cell population that act on another cell as intercellular mediators. Examples of such cytokines are lymphokines, monokines, and traditional polypeptide hormones.
  • cytokines include growth hormones such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone, thyroxine; insulin; proinsulin, relaxin, prorelaxin, glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH), hepatic growth factor, fibroblast growth factor; prolactin, placental lactogen, tumor necrosis factor- alpha and -beta; mullerian- inhibiting substance, mouse gonadotropin-associated peptide, inhibin; activin, vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF-beta; platelet- growth factor, transforming growth factors (TGFs) such as TGF- alpha and TGF-beta, insulin-like growth factor-1 and -II; erythropoietin (EPO),
  • cytokines or other agents that stimulate cells of the immune system are co-administered with the antibody of the present invention.
  • a mode of treatment may enhance desired effector function.
  • agents that stimulate NK cells including but not limited to IL-2 may be co-administered.
  • agents that stimulate macrophages including but not limited to C5a, formyl peptides such as N-formyl-methionyl-leucyl-phenylalanine (Beigier-Bompadre et al. (2003) Scand J. Immunol. 57.
  • agents that stimulate neutrophils including but not limited to G-CSF, GM-CSF, and the like may be administered Furthermore, agents that promote migration of such immunostimulatory cytokines may be used. Also additional agents including but not limited to interferon gamma, IL-3 and IL-7 may promote one or more effector functions.
  • cytokines or other agents that inhibit effector cell function are co-administered with the antibody of the present invention Such a mode of treatment may limit unwanted effector function
  • the patient to be treated with an antibody of the present invention may also receive radiation therapy.
  • Radiation therapy can be administered according to protocols commonly employed in the art and known to the skilled artisan. Such therapy includes but is not limited to cesium, iridium, iodine, or cobalt radiation.
  • the radiation therapy may be whole body irradiation, or may be directed locally to a specific site or tissue in or on the body, such as the lung, bladder, or prostate.
  • radiation therapy is administered in pulses over a period of time from about 1 to 2 weeks. The radiation therapy may, however, be administered over longer periods of time.
  • radiation therapy may be administered to patients having head and neck cancer for about 6 to about 7 weeks.
  • the radiation therapy may be administered as a single dose or as multiple, sequential doses.
  • the skilled medical practitioner can determine empirically the appropriate dose or doses of radiation therapy useful herein.
  • the antibody of the present invention and one or more other anti-cancer therapies are employed to treat cancer cells ex vivo. It is contemplated that such ex vivo treatment may be useful in bone marrow transplantation and particularly, autologous bone marrow transplantation.
  • treatment of cells or tissue(s) containing cancer cells with antibody and one or more other anti-cancer therapies, such as described above can be employed to deplete or substantially deplete the cancer cells prior to transplantation in a recipient patient.
  • the antibodies of the invention may employ in combination with still other therapeutic techniques such as surgery or phototherapy.
  • Escherichia coli DH5a (Invitrogen, Düsseldorf, Germany) was used for the amplification of plasmids and cloning.
  • Mouse myeloma cell line Sp2/0-Agl4 (ATCC, American Type Culture Collection, Manassas,VA, USA) used for production of recombinant hum-CD 133 (Prominin) specific antibody derivatives was cultured in IMDM (PAN-Biotech, Aidenbach, Germany) supplemented with 10% fetal calf serum (PAN-Biotech, Aidenbach, Germany), 1% penicillin and streptomycin (Lonza, Basel, Switzerland). Stable transfectants were selected with 1 mg/ml G418 (Invitrogen, Düsseldorf, Germany).
  • Hybridoma cell line 293AC1C3H9 secreting mouse IgG2b/K and hybridoma cell line W6B3H10 secreting mouse IgGl/ ⁇ anti human CD 133 (Prominin) specific antibodies were grown in IMDM-medium supplemented with 10% fetal calf serum (PAN-Biotech, Aidenbach, Germany), 1% penicillin and streptomycin (Lonza, Basel, Switzerland).
  • Cytoplasmatic RNAs were prepared from the hybridoma cell lines 293AC1C3H9 and W6B3H10 using the RNeasy Kit (Qiagen, Hilden, Germany) applying a modified protocol for the isolation of cytoplasmatic RNA only.
  • double-stranded cDNA (ds-cDNA) was prepared from 0,3-2 ⁇ g of mRNA using the cDNA Synthesis System (Roche, Mannheim, Germany). To permit blunt-end formation on the DNA strands the ds-cDNA was incubated with T4-DNA polymerase. The reaction mixture was extracted once with an equal volume phenol-chloroform-isoamylalcohol (25:24:1) and precipitated with ethanol. The dissolved ds-cDNA pellet was incubated with T4 DNA ligase (Roche, Mannheim, Germany) to circularize the cDNA (Uematsu Y.
  • T4 DNA ligase (Roche, Mannheim, Germany)
  • primers for the vector system and immunoglobulin constant region specific primers were used (summarized in Table 1).
  • hybridoma cell line 293AC1C3H9 (light chain amino acid sequence set forth in SEQ ID NO: 15 including the variable domain (SEQ ID NO: 13), the variable domain including CD 1 (SEQ ID NO:l), CDR2 (SEQ ID NO:2) and CDR3 (SEQ ID NO:3); heavy chain amino acid sequence set forth in SEQ ID NO: 16, including the variable domain (SEQ ID NO: 14), the variable domain including CDR1 (SEQ ID NO:4), CDR2 (SEQ ID NO:5) and CDR3 (SEQ ID NO:6)) and hybridoma cell line W6B3H10 (light chain amino acid sequence set forth in SEQ ID NO:31 including the variable domain (SEQ ID NO:29), the variable domain including CDR1 (SEQ ID NO:7), CDR2 (SEQ ID NO:8) and CDR3 (SEQ ID NO:9); heavy chain amino acid sequence set forth in SEQ ID NO:32 including the variable
  • the light chain of murine antibody 293AC1C3H9 is encoded by the nucleotide sequence set forth in SEQ ID NO: 19 (complete cDNA sequence set forth in SEQ ID NO:20), wherein the variable domain is encoded by the nucleotide sequence set forth in SED ID NO: 17.
  • the heavy chain of antibody 293AC1C3H9 is encoded by the nucleotide sequence set forth in SEQ ID NO:21 (complete cDNA sequence set forth in SEQ ID NO:22), wherein the variable domain is encoded by the nucleotide sequence set forth in SEQ ID NO: 18.
  • the light chain of murine antibody W6B3H10 is encoded by the nucleotide sequence set forth in SEQ ID NO:35 (complete cDNA sequence set forth in SEQ ID NO:3 ), wherein the variable domain is encoded by the nucleotide sequence set forth in SED ID NO:33.
  • the heavy chain of antibody W6B3H10 is encoded by the nucleotide sequence set forth in SEQ ID NO:37 (complete cDNA sequence set forth in SEQ ID NO:38), wherein the variable domain is encoded by the nucleotide sequence set forth in SEQ ID NO:34.
  • the cloned V regions were combined with the desired C regions in an expression vector.
  • the cloning procedure performed here allows the introduction of complete Ig V regions and their expression in lymphoid cells without any alterations of their amino acid sequence.
  • the nucleotide sequence of the amplicon obtained in Example 1 was determined after subcloning by sequencing (primer in Table 1) and used for design of primer pairs (C C; D D'; Table 2).
  • the reamplified DNA fragments of the V segments is cut with appropriate restriction nucleases (summarized in Table 2) and then ligated into the expression vectors.
  • the vectors ( Figure 2 and 3) contain human light and heavy constant region genes.
  • the parental vector for the light chain contains the VJ region of the mouse light chain and the C region of human ⁇ gene. Restriction sites were introduced at the required locations (Xhol and Spel) in order to substitute the light chain Xhol-Spel fragment with the appropriate VJ fragment of the light chain of monoclonal antibodies 293AC1C3H9 or W6B3H10 or any other monoclonal antibody.
  • the region relevant for the fragment exchange is shown enlarged in Figure 2.
  • the fragment to be exchanged contains part of the second exon of the leader sequence, an appropriate site (Xhol) for in frame fusion, the VJ region and part of the second intron with restriction site Spel.
  • the original vector for the heavy chain contains the human ⁇ isotype Ig heavy chain. Restriction sites were introduced at the required positions in intron I and II for exchange of the Aatll-Clal fragment with the VDJ fragment of the heavy chain of monoclonal antibodies 293AC1C3H9 or W6B3H10 or any other monoclonal antibody.
  • the region relevant for cloning the VDJ fragment is shown enlarged in Figure 3 a.
  • the fragment to be exchanged contains parts of the first intron with an Aatll restriction site, the second exon of the leader sequence, the VDJ region and part of the second intron with the restriction site Clal.
  • Mlul-Spel fragment to be exchanged contains the entire constant region of the human ⁇ heavy chain and two amino acid modifications in the CH2 domain as indicated (Ser 2 39-Asp; Ile 3 32-Glu)
  • chimeric antibodies 293AC1C3H9 or W6B3H10 and the Fc optimized variants SDIE 293 and SDIE W6B3 were obtained. These comprise the following amino acid and nucleotide sequences:
  • Chimeric antibody 293AC1C3H9 light chain amino acid sequence as set forth in SEQ ID NO:23 and as encoded by the nucleotide sequence set forth in SEQ ID NO:24, heavy chain amino acid sequence as set forth in SEQ ID NO:25 and as encoded by the nucleotide sequence set forth in SEQ ID NO:26,
  • SDIE 293 (chimeric, Fc optimized antibody): light chain amino acid sequence set forth in SEQ ID NO:23 and encoded by the nucleotide sequence set forth in SEQ ID NO:24, heavy chain amino acid sequence set forth in SEQ ID NO:27 and encoded by the nucleotide sequence set forth in SEQ ID NO:28.
  • Chimeric antibody W6B3H10 light chain amino acid sequence as set forth in SEQ ID NO:39 and as encoded by the nucleotide sequence set forth in SEQ ID NO:40, heavy chain amino acid sequence as set forth in SEQ ID NO:41 and as encoded by the nucleotide sequence set forth in SEQ ID NO:42.
  • SDIE W6B3 (chimeric, Fc optimized antibody): light chain amino acid sequence set forth in SEQ ID NO:39 and encoded by the nucleotide sequence set forth in SEQ ID NO:40, heavy chain amino acid sequence set forth in SEQ ID NO:43 and encoded by the nucleotide sequence set forth in SEQ ID NO:44.
  • WERI-Rbl Cells were originally described by McFall RC et al., Cancer Res 37,1003-1010 (1977) and provided by Dr. H.-J. Buhring, Department of Internal Medicine II, University of Tubingen.
  • S -Mel63 Human melanoma cell line, original supplier: Dr. A. Knuth, Nordwestkrankenhaus Frankfurt/Main, Germany.
  • the effector cells used were peripheral blood mononuclear cells isolated from the blood of normal healthy donors.
  • Example 5 Binding of two different ant-CD 133 antibodies to PBMCs of chronic lymphatic leukemia (CLL) patients

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Abstract

L'invention concerne des anticorps ayant une région Fc modifiée comprenant les substitutions d'acides aminés 239D et 332E pour améliorer la cytotoxicité cellulaire dépendant d'un anticorps (ADCC) de ces anticorps. L'invention concerne également des compositions pharmaceutiques contenant ces anticorps, des acides nucléiques codant pour ces anticorps ainsi que des procédés d'utilisation de tels anticorps.
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