# US 2010/0166741 A1 · Altered br-3 binding polypeptides > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2010/0166741 A1 - Document ID: US20100166741A1 - Status: Published application - Kind: A1 - Application number: 12/373,662 - Filed: 2007-07-12 - Published: 2010-07-01 - Earliest claimed: 2006-07-13 - Assignees: Genentech, Inc.; Biogen Idec MA Inc. - Inventors: Robert F. Kelley; Amy Yijuan Shen; Dorothea Reilly; Mark S. Dennis; Germaine Fuh; Chingwei V. Lee; Christine M. Ambrose; Jeffrey S. Thompson - Web page: https://patentgrep.com/patent/US20100166741A1 ## CPC - C07K 16/2878: {against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95} - A61P 35/00: Antineoplastic agents - A61P 35/04: specific for metastasis - A61P 37/00: Drugs for immunological or allergic disorders - A61K 2039/505: {comprising antibodies} - C07K 2317/24: containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered - C07K 2317/34: Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues - C07K 2317/41: Glycosylation, sialylation, or fucosylation - C07K 2317/52: Constant or Fc region; Isotype - C07K 2317/72: Increased effector function due to an Fc-modification - C07K 2317/73: Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation - C07K 2317/732: Antibody-dependent cellular cytotoxicity [ADCC] - C07K 2317/76: Antagonist effect on antigen, e.g. neutralization or inhibition of binding - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) ## Abstract The present invention relates to novel BR3 binding antibodies having altered Fc effector function and/or having a mature core carbohydrate structure in the Fc region which lacks fiicose. The present invention also relates to the use of those BR3 binding antibodies and polypeptides in, e.g., methods of treatment, screening methods, diagnostic methods, assays and protein purification methods. ## Claims ### Claim at position 1 1-35. (canceled) ### Claim 36 An anti-BR3 antibody having an Fc region wherein said anti-BR3 antibody is afucosylated. ### Claim 37 (depends on 36) An anti-BR3 antibody composition comprising an afucosylated anti-BR3 antibody of claim 36. ### Claim 38 (depends on 37) The anti-BR3 antibody composition of claim 37, wherein said composition comprises at least 2% afucosylated anti-BR3 antibodies. ### Claim 39 (depends on 39) The anti-BR3 antibody composition of claim 39, wherein said composition comprises at least 4% afucosylated-anti-BR3 antibodies. ### Claim 40 (depends on 39) The anti-BR3 antibody composition of claim 39, wherein said composition comprises at least 10% afucosylated anti-BR3 antibodies. ### Claim 41 (depends on 40) The anti-BR3 antibody composition of claim 40, wherein said composition comprises at least 19% afucosylated-anti-BR3 antibodies. ### Claim 42 (depends on 41) The anti-BR3 antibody composition of claim 41, wherein said composition comprises 100% afucosylated anti-BR3 antibodies. ### Claim 43 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, further comprising a variant Fc sequence, wherein the Fc sequence has a substitution at any one or any combination of positions selected from the group consisting of 268D, 326D, 333A/334A, 298A/333A, 298A/334A, 239D/332E, 239D/298A/332E, 239D/268D/298A/332E, 239D/268D/298A/326A/332A, 239D/268D/298A/326A/332E, 239D/268D/283L/298A/332E, 239D/268D/283L/298A/326A/332E, 239D/330L/332E, 272Y/254T/256E, T250Q/M428L, D265A, and N297A, wherein the D265A substitution is in the absence of N297A and the N297A substitution is in the absence of D265A. ### Claim 44 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, further comprising a variant Fc sequence, wherein the antibody comprises an Fc region that has been altered to change the ADCC, CDC and/or pharmacokinetic property of the antibody compared to a wild type IgG Fc sequence by substituting an amino acid at any one or any combination of positions selected from the group consisting of: 238, 239, 246, 248, 249, 250, 252, 254, 255, 256, 258, 265, 267, 268, 269, 270, 272, 276, 278, 280, 283, 285, 286, 289, 290, 292, 293, 294, 295, 296, 297, 298, 301, 303, 305, 307, 309, 312, 314, 315, 320, 322, 324, 326, 327, 329, 330, 331, 332, 333, 334, 335, 337, 338, 340, 360, 373, 376, 378, 382, 388, 389, 398, 414, 416, 419, 428, 430, 434, 435, 437, 438 and 439 of the Fc region. ### Claim 45 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody has ADCC activity in the presence of human effector cells or has increased ADCC in the presence of human effector cells compared to an anti-BR3 antibody comprising a human wildtype IgG1 Fc. ### Claim 46 (canceled) ### Claim 47 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody can block BAFF (SEQ ID NO:143) from binding to the extracellular domain of BR3 (SEQ ID NO:151). ### Claim 48 (canceled) ### Claim 49 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody binds an FcγRIII. ### Claim 50 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody binds the FcγRIII with better affinity, or mediates antibody-dependent cell-mediated cytotoxicity (ADCC) more effectively, than the glycoprotein with a mature core carbohydrate structure including fucose attached to the Fc region of the glycoprotein. ### Claim at position 17 51-53. (canceled) ### Claim 54 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the fucosyltransferase gene is the FUT8 gene. ### Claim 55 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody is essentially free of bisecting N-acetylglucosamine (GlcNAc) attached to the mature core carbohydrate structure. ### Claim 56 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody has bisecting N-acetylglucosamine (GlcNAc) attached to the mature core carbohydrate structure. ### Claim 57 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody has one or more galactose residues attached to the mature core carbohydrate structure. ### Claim 58 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody is essentially free of one or more galactose residues attached to the mature core carbohydrate structure. ### Claim 59 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody has one or more sialic acid residues attached to the mature core carbohydrate structure. ### Claim 60 (depends on 36) The afucosylated anti-BR3 antibody of claim 36, wherein the antibody is essentially free of one or more sialic acid residues attached to the mature core carbohydrate structure. ### Claim 61 (depends on 37) A pharmaceutical composition comprising the antibody composition of claim 37. ### Claim at position 26 62-63. (canceled) ### Claim 64 (depends on 36) The anti-BR3 antibody of claim 36, wherein the anti-BR3 antibody is a humanized or human antibody that binds to a human BR3 extracellular domain sequence and has an H1, H2 and H3 region with at least 70% homology to the H1, H2 and H3 region, respectively, of any one of the antibodies of Table 2 and has an L1, L2 and L3 region with at least 70% homology to the L1, L2 and L3 region, respectively, of any one of the antibodies of Table 2. ### Claim 65 (depends on 36) The anti-BR3 antibody of claim 36, wherein the anti-BR3 antibody is a human or humanized antibody that binds to a human BR3 extracellular domain sequence and has at least 70% homology to a VH domain of any one of the antibodies of Table 2. ### Claim 66 (depends on 36) The anti-BR3 antibody of claim 36, wherein the anti-BR3 antibody is a humanized antibody that binds to a human BR3 extracellular domain sequence, the antibody comprising an H3 sequence of any one of SEQ ID NOs. 4-13, 15, 16-18, 20, 22, 24, 26, 28-73, 75-76, 78, 80-85, 87-96, 98, 100, 102, 104, 106, 107, 109-110, 112, 116, 118, 120, 122, 124-127 and 129-131 and further comprising the H1 and H2 sequences and the L1, L2, and L3 sequences from any one of the antibodies disclosed in Table 2. ### Claim at position 30 67-69. (canceled) ### Claim 70 (depends on 36) The anti-BR3 antibody of claim 36, wherein the anti-BR3 antibody has been conjugated to a cytotoxic agent or a chemotherapeutic agent. ### Claim 71 (depends on 70) The anti-BR3 antibody of claim 70, wherein the cytotoxic agent is a radioactive isotope or a toxin. ### Claim 72 (depends on 36) The anti-BR3 antibody of claim 36, wherein the antibody is a monoclonal antibody. ### Claim 73 (depends on 36) The anti-BR3 antibody of claim 36, wherein the antibody is a humanized antibody. ### Claim 74 (depends on 36) The anti-BR3 antibody of claim 36, wherein the antibody is derived from a human antibody sequence. ### Claim 75 (depends on 36) The anti-BR3 antibody of claim 36, wherein the antibody is a multi-specific antibody. ### Claim 76 (depends on 36) An isolated nucleic acid molecule that encodes the antibody of claim 36. ### Claim 77 (depends on 36) An expression vector encoding the antibody of claim 36. ### Claim 78 (depends on 76) A host cell comprising a nucleic acid molecule of claim 76. ### Claim 79 (depends on 36, 78) The host cell of claim 78, that produces the antibody of claim 36. ### Claim 80 (depends on 78) The host cell of claim 78, which is a mammalian cell, a yeast cell, or a plant cell. ### Claim 81 (depends on 37) A method of treating a BR3 positive cancer, comprising administering to a patient suffering from the cancer a therapeutically effective amount of a composition of claim 37. ### Claim 82 (depends on 37) A method of treating a B cell neoplasm, comprising administering to a patient suffering from the neoplasm a therapeutically effective amount of a composition of claim 37. ### Claim 83 (depends on 37) A method of treating an autoimmune disease, comprising administering to a patient suffering from the autoimmune disease a therapeutically effective amount of a composition of claim 37. ### Claim 84 (depends on 37) A method of treating a cancer, comprising administering to a patient suffering from the cancer a therapeutically effective amount of a composition of claim 37. ### Claim 85 (depends on 37) A method of depleting B cells from a mixed population of cells comprising contacting the mixed population of cells with a composition of claim 37. ### Claim 86 (depends on 83) The method according to claim 83 further comprising the step of administering a therapeutically effective amount of an anti-CD20 antibody sequentially or concurrently with the anti-BR3 antibody. ### Claim 87 (depends on 86) The method according to claim 86, further comprising the step of contacting the mixed population with an anti-CD20 antibody sequentially or simultaneously with the anti-BR3 antibody. ### Claim 88 (depends on 86) The method of claim 86, wherein the CD20 binding antibody is the rituximab antibody. ### Claim 89 (depends on 83) The method of claim 83, further comprising the sequential or concurrent administration of a therapeutically effective amount of at least one of the group consisting of: a BAFF antagonist, a biologic response modifier, a B cell depletion agent, a cytotoxic agent, a chemotherapeutic agent and an immunosuppressive agent. ### Claim 90 (depends on 89) The method of according to claim 89, wherein the BAFF antagonist is selected from the group consisting of BR3-Fc, TACI-Fc, BCMA-Fc, an anti-BAFF peptibody, an anti-BAFF antibody and an anti-BR3 antibody. ### Claim at position 52 91-92. (canceled) ### Claim 93 (depends on 83) The method of claim 83, wherein the autoimmune disease is selected from the group consisting of rheumatoid arthritis, juvenile rheumatoid arthritis, systemic lupus erythematosus (SLE), Wegener's disease, inflammatory bowel disease, idiopathic thrombocytopenic purpura (ITP), thrombotic thrombocytopenic purpura (TTP), autoimmune thrombocytopenia, multiple sclerosis, psoriasis, IgA nephropathy, IgM polyneuropathies, myasthenia gravis, vasculitis, diabetes mellitus, Reynaud's syndrome, Sjörgen's syndrome and glomerulonephritis. ### Claim 94 (depends on 93) The method of claim 93, wherein the autoimmune disease is rheumatoid arthritis. ### Claim 95 (depends on 89) The method of claim 89, wherein the immunosuppressive agent is methotrexate. ### Claim 96 (depends on 37) The composition of claim 37, wherein about 20-100% of the anti-BR3 antibodies in the composition are afucosylated.