US20180298093A1 - Glycoengineered binding protein compositions - Google Patents

Glycoengineered binding protein compositions Download PDF

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US20180298093A1
US20180298093A1 US15/912,494 US201815912494A US2018298093A1 US 20180298093 A1 US20180298093 A1 US 20180298093A1 US 201815912494 A US201815912494 A US 201815912494A US 2018298093 A1 US2018298093 A1 US 2018298093A1
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domain
population
binding proteins
glycoforms
composition
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Boris Labkovsky
Tariq Ghayur
Georgeen Gaza-Bulseco
Pratibha Mishra
Subramanya Hegde
Sudha Krishnan
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AbbVie Inc
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AbbVie Inc
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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
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • C07K16/241—Tumor Necrosis Factors
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/10—Immunoglobulins specific features characterized by their source of isolation or production
    • C07K2317/14—Specific host cells or culture conditions, e.g. components, pH or temperature
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/21—Immunoglobulins specific features characterized by taxonomic origin from primates, e.g. man
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/40—Immunoglobulins specific features characterized by post-translational modification
    • C07K2317/41—Glycosylation, sialylation, or fucosylation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/52—Constant or Fc region; Isotype
    • 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
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/77—Internalization into the cell
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
    • Y02A50/386—

Definitions

  • the present invention relates to compositions of recombinant Fc binding proteins, e.g., recombinant antibodies, which exhibit improved properties (e.g., a reduced anti-drug immune response) as a result of their optimized glycosylation profile.
  • therapeutic binding proteins have revolutionized the treatment of many diseases, including cancer, inflammatory bowel disease (IBD), ankylosing spondylitis, multiple sclerosis, psoriasis and rheumatoid arthritis (RA).
  • IBD inflammatory bowel disease
  • RA rheumatoid arthritis
  • ADA anti-drug antibodies
  • a 2011 study of rheumatoid arthritis patients treated with adalimumab revealed the development of anti-drug antibodies resulted in significantly lower remission rates.
  • Two-thirds of the anti-adalimumab antibody-positive patients developed antibodies to the drug within the first 28 weeks of treatment.
  • the presence of anti-adalimumab antibodies was further shown to substantially reduce serum adalimumab concentrations.
  • Similar results have been reported for infliximab, adalimumab, and natalizumab (see Bartelds et al., JAMA. 2011; 305(14):1460-1468).
  • Such ADA immune responses therefore, decrease the overall efficacy and utility of therapeutic binding proteins.
  • compositions exhibiting a surprisingly reduced anti-drug antibody (ADA) immune response as a result of their optimized glycoprofile.
  • These compositions generally comprise a population of Fc domain-containing binding proteins that are hypergalactosylated (e.g., enriched for binding proteins with highly galactosylated glycoforms) and/or hypomannosylated (e.g., deficient in binding proteins with highly mannosylated glycoforms) on the Fc glycosylation site of the binding proteins.
  • the compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1.
  • G/M ratio galactose content/mannose content
  • binding protein compositions disclosed herein are particularly advantageous in that they exhibit a longer serum half-life than non-hypergalactosylated and/or non-hypomannosylated Fc domain-containing binding protein compositions and, therefore, require less frequent dosing to be efficacious.
  • the instant disclosure provides a hypergalactosylated population of Fc domain-containing binding proteins, wherein the total percent amount of G1 and G2 glycoforms in the population is more than 50% (e.g., more than 80%, more than 90%, more than 95% or more than 99%). In certain embodiments, the total percent amount of G1 and G2 glycoforms in the population is more than 80%. In certain embodiments, the G1 and G2 glycoforms in the population are fucosylated. In certain embodiments, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%).
  • the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population is more than 80%. In certain embodiments, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population are fucosylated.
  • the binding protein compositions of the invention are also hypomannosylated.
  • the binding protein composition of the inventions may exhibit less than 10% of highly mannosylated glycoforms (oligomannose species, e.g., M3-M9 glycoforms) in population of Fc-domain-containing binding proteins.
  • less than 5% (e.g., less than 1% or less than 0.1%) of the Fc domain-containing binding proteins in the population are highly mannosylated.
  • the binding protein compositions of the invention have a G/M ratio of greater than 1:1 (e.g., at least 2:1, 5:1, 10:1, 80:1 or at least 99:1).
  • the population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the Fc domain-containing binding proteins in the population comprise an antigen-binding portion of an antibody.
  • the antibody is selected from the group consisting of alemtuzumab, bevacizumab, cetuximab, edrecolomab, gemtuzumab ozogamicin, ibritumomab tiuxetan, ofatumumab, panitumumab, rituximab, tositumomab, trastuzumab, arcitumomab, capromab pendetide, nofetumomab, satumomab, basiliximab, daclizumab, muromonab-cd3, infliximab, natalizumab, adalimumab, certolizumab, golimumab, infliximab, tocilizumab, omalizumab, ab
  • the Fc domain-containing binding proteins in the population comprise a non-antibody antigen-binding portion.
  • the hypergalactosylated population is a hypergalactosylated population of dual variable domain immunoglobulins (DVD-Ig).
  • the invention provides compositions wherein the binding proteins in the population bind to tumor necrosis factor alpha (TNFoc).
  • the binding protein is selected from the group consisting of etanercept, infliximab, adalimumab, or golimumab.
  • the binding protein is the anti-TNF antibody adalimumab or a variant thereof.
  • the anti-TNF antibody is an Fc variant of adalimumab (D2E7) comprising the heavy and light chain variable region sequences of adalimumab and a variant Fc region with an amino acid substitution that confers enhanced serum half-life.
  • the variant Fc region is a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence (wherein amino acid numbering is according to the EU numbering convention as in Kabat).
  • the anti-TNF antibody is a variant of adalimumab which exhibits pH-sensitive binding to the TNF antigen.
  • the pH-sensitive variant of adalimumab is a D2E7SS22 comprising the heavy chain of SEQ ID NO: 1 and the light chain of SEQ ID NO: 2.
  • the pH-sensitive variant comprises the heavy and light chain variable regions of D2E7SS2 and a variant Fc region (e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence).
  • a variant Fc region e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence.
  • the binding compositions of the invention are produced in a cultured mammalian host cell line (e.g., a CHO cell line).
  • the host cell line has been glycoengineered to produce the hypergalactosylated and/or hypomannosylated binding proteins of the invention.
  • the binding proteins of the invention are obtained from a glycoengineered CHO cell.
  • the glycoengineered CHO cell contains a heterologous galactosyltransferase gene (e.g., mouse galactosyltransferase Beta 1,4).
  • the glycoengineered CHO cell contains a knockdown of one of the alleles of the Beta galactosidase gene.
  • exemplary glycoengineered host cells include the GALtr11 CHO cell line and the ZFN-B1 CHO cell line described in Examples 1 and 2 herein, respectively.
  • the instant disclosure provides a method of reducing a subject's anti-drug antibody (ADA) response to a population of Fc domain-containing binding proteins, the method comprising glycoengineering (e.g., hypergalactosylating and/or hypomannosylating) a population of Fc domain-containing binding proteins by increasing the G/M ratio of the population of Fc domain-containing binding proteins, such that the glycoengineered population of Fc domain-containing binding proteins has a greater serum half-life than the non-glycoengineered population of Fc domain-containing binding proteins.
  • glycoengineering e.g., hypergalactosylating and/or hypomannosylating
  • said glycoengineering comprises expressing the Fc domain-containing binding proteins in a glycoengineered host cell (e.g., a CHO cell that has been glycoengineered to express hypergalactosylated and/or hypomannosylated binding proteins), and isolating the hypergalactosylated and/or hypomannosylated binding proteins from the host cell.
  • a glycoengineered host cell e.g., a CHO cell that has been glycoengineered to express hypergalactosylated and/or hypomannosylated binding proteins
  • the population is glycoengineered such that the total percent amount of G1 and G2 glycoforms in the hypergalactosylated population is more than 80%.
  • the G1 and G2 glycoforms in the hypergalactosylated population are fucosylated.
  • the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population is more than 50% (e.g., more than 80%, or more than 99%).
  • the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population is more than 80%. In certain embodiments of the second aspect, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are fucosylated.
  • the methods of the invention comprise glycoengineering a population of Fc domain-containing binding proteins such that population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • the Fc domain-containing binding proteins in the population comprise an antigen-binding portion of an antibody. In certain embodiments of the second aspect, the Fc domain-containing binding proteins in the population comprise a non-antibody antigen-binding portion. In certain embodiments of the second aspect, the Fc domain-containing binding proteins in the hypergalactosylated population comprise a dual variable domain immunoglobulin (DVD-Ig).
  • DVD-Ig dual variable domain immunoglobulin
  • the binding proteins of the invention comprise an antigen-binding portion that binds to tumor necrosis factor alpha (TNF ⁇ ).
  • the binding portion is selected from the group consisting etanercept, infliximab, adalimumab, or golimumab.
  • the binding protein is adalimumab.
  • the binding protein is an Fc variant of adalimumab.
  • the binding protein is D2E7SS22 or an Fc variant thereof.
  • compositions of the invention do not exhibit an increased level of antibody-dependent cellular cytotoxicity (ADCC) activity and/or an increased level of complement-dependent cellular cytotoxicity (CDC) activity as compared to a composition that is not glycoengineered according to the methods of the invention (e.g., a composition that is not hypergalactosylated and/or hypomannosylated).
  • ADCC antibody-dependent cellular cytotoxicity
  • CDC complement-dependent cellular cytotoxicity
  • the instant disclosure provides a glycoengineered host cell (e.g., a CHO cell) that produces a glycoengineered population of Fc domain-containing binding proteins having an enhanced G/M ratio of greater than 10:1 (e.g., greater than 50:1, 90:1 or 99:1).
  • a glycoengineered host cell e.g., a CHO cell
  • Fc domain-containing binding proteins having an enhanced G/M ratio of greater than 10:1 (e.g., greater than 50:1, 90:1 or 99:1).
  • the glycoengineered population of Fc domain-containing binding proteins has one or more of the following properties: the total percent amount of G1 and G2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%); the total percent amount of G1, G2, G1S1, G2S1 or G2S2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%); less than 10% (e.g., less than 1%, or less than 0.1%) of the Fc domain-containing binding proteins in the population comprise highly mannosylated (e.g., M3-M9) glycoforms; a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1): a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1); or a Gtotal:M ratio of at least 10:1 (
  • the instant disclosure provides a method of treating a disorder in a subject in need thereof, comprising administering to the subject an effective amount of the hypergalactosylated population of Fc domain-containing binding proteins described herein.
  • the disorder is a TNFc associated disorder.
  • FIG. 1A is a schematic of the processing and maturation of an N-glycan.
  • the mature Dol-P-P-glycan is transferred to Asn-X-Ser/Thr sequons during protein synthesis as proteins are being translocated into the ER.
  • glucosidases in the ER remove the three glucose residues, and ER mannosidase removes a mannose residue.
  • These reactions are intimately associated with the folding of the glycoprotein assisted by the lectins calnexin and calreticulin, and they determine whether the glycoprotein continues to the Golgi or is degraded.
  • EDEM ER degradation-enhancing ⁇ -mannosidase I-like protein
  • EDEM ER degradation-enhancing ⁇ -mannosidase I-like protein
  • EDEM ER degradation-enhancing ⁇ -mannosidase I-like protein
  • additional mannose residues are removed in the cis compartment of the Golgi until Man 5 GlcNAc 2 Asn is generated.
  • the action of GlcNAcT-1 on Man 5 GlcNAc 2 Asn in the medial-Golgi initiates the first branch of an N-glycan.
  • the action of ⁇ -mannosidase II generates the substrate for GlcNAcT-II.
  • FIG. 1C is a schematic depicting exemplary non-galactosylated glycans imparting immunogenic properties to biologics.
  • FIG. 1D is a schematic depicting exemplary galactosylated glycans imparting non-immunogenic properties to biologics.
  • FIG. 2A shows the cloning of mouse beta1-4 galactosyltransferase into the mammalian expression vector, pCDN3.3.
  • FIG. 2B shows the DNA sequence (SEQ ID NO: 1) and corresponding amino acid sequence (SEQ ID NO: 2) of the mouse beta1-4 galactosyltransferase.
  • FIG. 2D shows a mass spectrometry (MALDI-TOF) analysis of the glycoengineered Galtr-11 adalimumab preparation in FIG. 2C .
  • Prominent peaks indicate the presence of the G1F (50,800 Da) and G2F (50,962 Da) glycoforms.
  • FIG. 2E shows a mass spectrometry (MALDI-TOF) analysis of the glycoengineered SA-D2E7 adalimumab preparation of FIG. 2C before (bottom panel) and after (top panel) treatment with sialyltransferase.
  • Prominent peaks indicate the presence of GIF (50,800 Da), G2F (50,962 Da), G2S1F (A1F; 51,253 Da), and G2S2F (51,544 Da) glycoforms.
  • FIG. 3A shows the pinocytosis by human dendritic cells of non-glycoengineered adalimumab (D2E7/Humira®) and glycoengineered adalimumab (ZFN-B1) produced in a CHO cell line with a knockout of one of the alleles of the beta galactosidase gene.
  • D2E7/Humira® non-glycoengineered adalimumab
  • ZFN-B1 glycoengineered adalimumab
  • FIG. 3C shows the pinocytosis by human dendritic cells of non-glycoengineered adalimumab (D2E7/Humira®) and glycoengineered adalimumab (Ga188-D2E7 and SA-D2E7).
  • FIG. 5B shows the pharmacokinetic (PK) profile of a non-glycoengineered preparation of anti-TNF ⁇ mAb D2E7 (HUMIRA®; lot 2158962) Serum Concentrations after 5 mg/kg IV dosing in CD-1 Mice (W14-0203).
  • PK pharmacokinetic
  • FIG. 5C shows the pharmacokinetic (PK) parameters of the glycoengineered anti-TNF ⁇ High Galactose mAb ZFN-B-1 (lot 2168407) after 5 mg/kg IV Dosing in CD-1 Mice.
  • FIG. 6 is a schematic depicting exemplary naturally-occurring N-glycan glycoforms.
  • Mammalian cells have a more diverse range of modifications than any of the other organisms.
  • Certain motifs extending the N-glycan arms lactosamine chains, terminal GalNAc, terminal sialylation, fucosylation are also found in mammalian O-glycans.
  • FIG. 7A depicts an exemplary 2-AB HPLC quantitative analysis of glycoengineered binding compositions of the invention.
  • Cell line 236 is a galactosyl transferase transfected CHO cell line producing Adalimumab (D2E7).
  • ZFN-B 1 is a CHO cell line producing Adalimumab and containing a knockdown of the Beta galactosidase gene.
  • ABT-122 is an IL17xTNF DVD-Ig.
  • FIG. 7B depicts an exemplary 2-AB HPLC quantitative analysis of the Galtr-11 (pink trace, second from top) and SA-D2E7 (blue trace, second from bottom) glycoengineered binding compositions of the invention as compared to a non-glycoengineered form of adalimumab (Humira®; top trace).
  • the bottom trace corresponds to sialylated glycan standards.
  • FIG. 7C depicts an exemplary ion exchange chromatogram (WCX-10 HPLC) of the Galtr-11 (blue trace, second from top) and SA-D2E7 (bottom green trace) glycoengineered binding compositions of the invention, as compared to a non-glycoengineered form of adalimumab (Humira®; top red trace).
  • the addition of sialic acid imparts a charge to the glycan resulting in earlier elution from the ion-exchange column
  • compositions exhibiting a surprisingly reduced anti-drug antibody (ADA) immune response as a result of their optimized glycoprofile.
  • These compositions generally comprise a population of Fc domain-containing binding proteins that are hypergalactosylated (e.g., enriched for binding proteins with highly galactosylated glycoforms) and/or hypomannosylated (e.g., deficient in binding proteins with highly mannosylated glycoforms) on the Fc glycosylation site of the binding proteins.
  • hypergalactosylated e.g., enriched for binding proteins with highly galactosylated glycoforms
  • hypomannosylated e.g., deficient in binding proteins with highly mannosylated glycoforms
  • compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1. Also provided are methods of treating a disorder using these compositions, and methods and host cells for making such compositions.
  • G/M ratio galactose content/mannose content
  • glycoengineered binding protein compositions disclosed herein are particularly advantageous in that they exhibit a longer serum half-life than non-glycoengineered Fc domain-containing binding protein compositions and, therefore, require less frequent dosing to be efficacious.
  • the term “Fc domain-containing binding protein” refers to a protein that specifically binds to an antigen, wherein the protein comprises an Fc domain, or an Fc-receptor binding fragment thereof, comprising an N-glycan.
  • the N-glycan is an N-linked biantennary glycans present in the CH2 domain of an immunoglobulin constant (Fc) region (e.g., at EU position 297).
  • Fc immunoglobulin constant
  • “N-glycans” are attached at an amide nitrogen of an asparagine or an arginine residue in a protein via an N-acetylglucosamine residue.
  • N-linked glycosylation sites occur in the peptide primary structure containing, for example, the amino acid sequence asparagine-X-serine/threonine, where X is any amino acid residue except proline and aspartic acid.
  • N-Glycans are fully described in, for example, Drickamer K, Taylor M E (2006). Introduction to Glycobiology, 2nd ed., which is incorporated herein by reference in its entirety.
  • N glycan refers to the Asn-297 N-linked biantennary glycans present in the CH2 domain of an immunoglobulin constant (Fc) region. These oligosaccharides may contain terminal mannose, N-acetyl-glucosamine, Galactose or Sialic acid (see FIGS. 1C and 1D ).
  • glycoengineering refers to any art-recognized method for altering the glycoform profile of a binding protein composition. Such methods include expressing a binding protein composition in a genetically engineered host cell (e.g., a CHO cell) that has been genetically engineered to express a heterologous glycosyltransferase or glycosidase. In other embodiments, the glycoengineering methods comprise culturing a host cell under conditions that bias for particular glycoform profiles.
  • a genetically engineered host cell e.g., a CHO cell
  • the glycoengineering methods comprise culturing a host cell under conditions that bias for particular glycoform profiles.
  • hypergalactosylated population refers to a population of Fc domain-containing binding proteins in which the galactose content of the N glycan is increased as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence.
  • a hypergalactosylated population can be expressed as having an increased number of G1 and G2 glycoforms as compared to the reference population of Fc domain-containing binding proteins.
  • hypomannosylated population refers to a population of Fc domain-containing binding proteins in which the mannose content of the N glycan is decreased as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence.
  • a hypomannosylated population can be expressed as having a decreased number of oligomannose glycoforms (e.g., M3-M9 glycoforms) as compared to the reference population of Fc domain-containing binding proteins.
  • the mannose content is determined by measuring the content of one or more of oligomannose glycoforms selected from the group consisting of Man3, Man4, Man5, Man6, Man7, Man 8 and Man 9.
  • the oligomannose content is determined by measuring at least Man 5, Man 6, and Man 7.
  • the oligomannose content is determined by measuring all M3-M9 glycoforms.
  • G0 glycoform As used herein the terms “G0 glycoform,” “G1 glycoform,” and “G2 glycoform” refer to N-Glycan glycoforms that have zero, one or two terminal galactose residues respectively, as depicted in FIGS. 1C and 1D herein. These terms include G0, G1, and G2 glycoforms that are fucosylated (shown as G0F, G1F and G2F respectively in FIGS. 1C and 1D ) or comprise a bisecting N-acetylglucosamine residue.
  • the G1 and G2 glycoforms further comprise sialic acid residues linked to one or both of the terminal galactose residues to form G1S1, G2S1 and G2S2 glycoforms.
  • G1S1 glycoform As used herein the terms “G1S1 glycoform,” “G2S1 glycoform,” and “G252 glycoform” refer to N-Glycan glycoforms that have a sialic acid residue linked to the sole terminal galactose residue in a G1 glycoform, one of the terminal galactose residue in a G2 glycoform, or both of the terminal galactose residue in a G2 glycoform, respectively (see FIG. 1D herein).
  • G1S1, G2S1 and G2S2 glycoforms that are fucosylated or comprise a bisecting N-acetylglucosamine residue.
  • the sialic residues of G1S1, G2S1 and G2S2 glycoforms are linked by alpha-2,6-sialic acid linkages to the terminal galactose residue of each glycoform in order to enhance the anti-inflammatory activity of the binding molecule (see e.g., Anthony et al., PNAS 105: 19571-19578, 2008).
  • G1F glycoform As used herein the terms “G1F glycoform,” “G2F glycoform,” “G1S1F glycoform,” “G2S1F glycoform,” and “G2S2F glycoform” refer to “G1 glycoform,” and “G2 glycoform” “G1S1 glycoform,” “G2S1 glycoform,” and “G252 glycoform” that are fucosylated.
  • M3-M9 glycoforms refers to the mannosylated glycoforms depicted in FIG. 1C .
  • G/M ratio refers to the ratio of the total percent amount of all galactose containing glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of oligomannose (e.g., M3-M9) glycoforms.
  • G1/2:M ratio refers to the ratio of the total percent amount of G1 and G2 glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of M3-M8 glycoforms.
  • GS:M ratio refers to the ratio of the total percent amount G1S1, G2S1 and G2S2 glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of M3-M9 glycoforms.
  • the term “reference binding composition” or “reference antibody” refers to a binding composition having the substantially the same amino acid sequence as (e.g., having about 90-100% identical amino acid sequence) of a glycoengineered antibody composition of the invention disclosed herein, e.g., a binding composition to which it is compared.
  • the reference composition is a FDA approved therapeutic Fc-domain containing binding protein (e.g., antibody) or a biosimilar thereof.
  • the reference binding composition comprises a non-hypergalactosylated population of Fc-domain containing binding proteins.
  • non-hypergalactosylated population refers a population of Fc domain-containing binding proteins in which the amount of G1 and/or G2 glycoforms are not enriched relative to the G0 glycoforms, as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence.
  • infliximab refers to the anti-TNF antibody marketed as REMICADETM, having Chemical Abstracts Service (CAS) designation 170277-31-3.
  • the term “golimumab” refers to the anti-TNF antibody marketed as SIMPONITM, having Chemical Abstracts Service (CAS) designation 476181-74-5.
  • infliximab refers to the anti-TNF immunoadhesin marketed as ENBRELTM, having Chemical Abstracts Service (CAS) designation 1094-08-2.
  • human TNF-alpha is intended to refer to a human cytokine that exists as a 17 kD secreted form and a 26 kD membrane associated form, the biologically active form of which is composed of a trimer of noncovalently bound 17 kD molecules.
  • the structure of human TNF-alpha is described further in, for example, Pennica, D., et al. (1984) Nature 312:724-729; Davis, J. M., et al. (1987) Biochemistry 26:1322-1326; and Jones, E. Y., et al. (1989) Nature 338:225-228.
  • human TNF-alpha is intended to include recombinant human TNF-alpha, which can be prepared by standard recombinant expression methods or purchased commercially (R & D Systems, Catalog No. 210-TA, Minneapolis, Minn.)
  • antibody broadly refers to any immunoglobulin (Ig) molecule comprised of four polypeptide chains, two heavy (H) chains and two light (L) chains, or any functional fragment, mutant, variant, or derivation thereof, which retains the essential epitope binding features of an Ig molecule.
  • Ig immunoglobulin
  • Such mutant, variant, or derivative antibody formats are known in the art. Non-limiting embodiments of which are discussed below.
  • each heavy chain is comprised of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region.
  • the heavy chain constant region is comprised of three domains, CH1, CH2 and CH3.
  • Each light chain is comprised of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region.
  • the light chain constant region is comprised of one domain, CL.
  • the VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, 1-R3, CDR3, FR4
  • Immunoglobulin molecules can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass.
  • the term “Fc domain” is used to define the C-terminal region of an immunoglobulin heavy chain, which may be generated by papain digestion of an intact antibody.
  • the Fc domain may be a native sequence Fc domain or a variant Fc domain.
  • the Fc domain of an immunoglobulin generally comprises two constant domains, a CH2 domain and a CH3 domain, and optionally comprises a CH4 domain Replacements of amino acid residues in the Fc portion to alter antibody effector function are known in the art (Winter, et al. U.S. Pat. Nos. 5,648,260; 5,624,821).
  • the Fc domain of an antibody mediates several important effector functions e.g.
  • At least one amino acid residue is altered (e.g., deleted, inserted, or replaced) in the Fc domain of an Fc domain-containing binding protein such that effector functions of the binding protein are altered.
  • antibody portion refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen. It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Such antibody embodiments may also be bispecific, dual specific, or multi-specific formats; specifically binding to two or more different antigens.
  • binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) an F(ab′).sub.2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CH1 domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546, Winter et al., PCT publication WO 90/05144 A1 herein incorporated by reference), which comprises a single variable domain; and (vi) an isolated complementarity determining region (CDR).
  • CDR complementarity determining region
  • the two domains of the Fv fragment, VL and VH are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883).
  • single chain Fv single chain Fv
  • Such single chain antibodies are also intended to be encompassed within the term “antigen-binding portion” of an antibody.
  • Other forms of single chain antibodies, such as diabodies are also encompassed.
  • Diabodies are bivalent, bispecific antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger, P., et al. (1993) Proc. Natl. Acad. Sci. USA 90:6444-6448; Poljak, R. J., et al. (1994) Structure 2:1121-1123).
  • Such antibody binding portions are known in the art (Kontermann and Dubel eds., Antibody Engineering (2001) Springer-Verlag. New York. 790 pp.
  • single chain antibodies also include “linear antibodies” comprising a pair of tandem Fv segments (VH-CH1-VH-CH1) which, together with complementary light chain polypeptides, form a pair of antigen binding regions (Zapata et al. Protein Eng. 8(10):1057-1062 (1995); and U.S. Pat. No. 5,641,870).
  • VH domain and VL domain refer to single antibody variable heavy and light domains, respectively, comprising FR (Framework Regions) 1, 2, 3 and 4 and CDR (Complementary Determinant Regions) 1, 2 and 3 (see Kabat et al. (1991) Sequences of Proteins of Immunological Interest. (NIH Publication No. 91-3242, Bethesda).
  • CDR or “complementarity determining region” means the noncontiguous antigen combining sites found within the variable region of both heavy and light chain polypeptides. These particular regions have been described by Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat et al., Sequences of protein of immunological interest. (1991), and by Chothia et al., J. Mol. Biol. 196:901-917 (1987) and by MacCallum et al., J. Mol. Biol. 262:732-745 (1996) where the definitions include overlapping or subsets of amino acid residues when compared against each other. The amino acid residues which encompass the CDRs as defined by each of the above cited references are set forth for comparison.
  • the term “CDR” is a CDR as defined by Kabat, based on sequence comparisons.
  • framework (FR) amino acid residues refers to those amino acids in the framework region of an immunoglobulin chain.
  • framework region or “PR region” as used herein, includes the amino acid residues that are part of the variable region, but are not part of the CDRs (e.g., using the Kabat definition of CDRs).
  • the term “specifically binds to” refers to the ability of a binding protein to bind to an antigen with an K d of at least about 1 ⁇ 10 ⁇ 6 M, 1 ⁇ 10 ⁇ 7 M, 1 ⁇ 10 ⁇ 8 M, 1 ⁇ 10 ⁇ 9 M, 1 ⁇ 10 ⁇ 10 M, 1 ⁇ 10 ⁇ 11 M, 1 ⁇ 10 ⁇ 12 M, or more, and/or bind to an antigen with an affinity that is at least two-fold greater than its affinity for a nonspecific antigen. It shall be understood, however, that the binding protein are capable of specifically binding to two or more antigens which are related in sequence.
  • the binding polypeptides of the invention can specifically bind to both human and a non-human (e.g., mouse or non-human primate) orthologs of an antigen.
  • polypeptide refers to any polymeric chain of amino acids.
  • peptide and protein are used interchangeably with the term polypeptide and also refer to a polymeric chain of amino acids.
  • polypeptide encompasses native or artificial proteins, protein fragments and polypeptide analogs of a protein sequence.
  • a polypeptide may be monomeric or polymeric.
  • PK pharmacokinetic
  • host cell is intended to refer to a cell into which exogenous DNA has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell, but, to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein.
  • host cells include prokaryotic and eukaryotic cells selected from any of the Kingdoms of life. Preferred eukaryotic cells include protist, fungal, plant and animal cells.
  • host cells include but are not limited to the prokaryotic cell line E. Coli; mammalian cell lines CHO, HEK 293 and COS; the insect cell line Sf9; and the fungal cell Saccharomyces cerevisiae.
  • the host cell is an engineered CHO cell, e.g., a CHO cell transformed with a heterologous galactosyltransferase and/or a heterologous sialyltransferase.
  • the invention provides a composition comprising a population of Fc-domain containing binding proteins that are hypergalactosylated and/or hypomannosylated.
  • the population of Fc domain-containing binding proteins employed in the compositions and methods disclosed herein has an increased amount of G1 and/or G2 glycoforms relative to the G0 glycoforms, as compared to a reference population comprising a reference Fc domain-containing binding protein with the same amino acid sequence.
  • all of the Fc-domain binding polypeptides in the population may be directed to the same antigen or epitope.
  • all of the Fc-domain binding polypeptides in the population are encoded by the same nucleic acid sequence.
  • the population of Fc domain-containing binding proteins comprises less than 70%, less than 69%, less than 68%, less than 67%, less than 66%, less than 65%, less than 64%, less than 63%, less than 62%, less than 61%, less than 60%, less than 59%, less than 58%, less than 57%, less than 56%, less than 55%, less than 54%, less than 53%, less than 52%, less than 51%, less than 50%, less than 49%, less than 48%, less than 47%, less than 46%, less than 45%, less than 44%, less than 43%, less than 42%, less than 41%, less than 40%, less than 39%, less than 38%, less than 37%, less than 36%, less than 35%, less than 34%, less than 33%, less than 32%, less than 31%, less than 30%, less than 29%, less than 28%, less than 27%, less than 26%, less than 25%, less than 24%, less than 23%, less than 22%,
  • the population of Fc domain-containing binding proteins comprises 70%, 69%, 68%, 67%, 66%, 65%, 64%, 63%, 62%, 61%, 60%, 59%, 58%, 57%, 56%, 55%, 54%, 53%, 52%, 51%, 50%, 49%, 48%, 47%, 46%, 45%, 44%, 43%, 42%, 41%, 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% of the G0 glycoform.
  • the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 6
  • the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60%, more than 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 59%
  • the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30,31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2 glycoform.
  • the total percent amount of G1 and G2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and 99%, between 52% and 99%, between 53%
  • the total percent amount of G1 and G2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%, between 20% and 63%, between 20% and 62%
  • the population of Fc domain-containing binding proteins employed in the compositions and methods disclosed herein has an increased amount of G1S1, G2S1 and G2S2 glycoforms relative to the G0 glycoforms, as compared to a reference population comprising a reference Fc domain-containing binding protein with the same amino acid sequence.
  • the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 6
  • the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G1S1 glycoform.
  • the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 6
  • the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2S1 glycoform.
  • the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 6
  • the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2S2 glycoform.
  • the total percent amount of G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and 99%, between 5
  • the total percent amount of G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%, between 20% and
  • the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and
  • the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%
  • the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are G1F, G2F, G1S1F, G2S1F and G2S2F glycoforms.
  • the sialylated glycoforms e.g., G1S1, G2S1 and G2S2 glycoforms
  • the sialylated glycoforms in the population of Fc domain-containing binding proteins have increased levels of terminal alpha 2,6-sialic acid linkages on their Fc glycans.
  • the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are G1F, G2F, G1S1F, G2S1F and G2S2F glycoforms.
  • the compositions of the invention are obtained from host cells (e.g., CHO cells or other mammalian host cells) capable of expressing a population of hyperglycosylated and/or hypomannosylated Fc domain-containing binding proteins when grown in culture.
  • the composition is obtained from host cells that are genetically engineered for the production of a hyperglycosylated and/or hypomannosylated binding proteins.
  • the host cell e.g., a CHO cell
  • the host cell may be genetically engineered to overexpress a heterologous galactosyltransferase such as human (3 1, 4-galactosyltransferase (E.C.
  • the host cell is a CHO cell having a knock out at least one of the alleles of the beta galactosidase gene ( Cricetulus griseus Glb1 (Gene ID: 100767446); mRNA sequence: NCBI Reference Sequence: XM_007630176.1; genomic sequence NW_003613697.1 from 2278553 to 2336708).
  • the binding protein composition is obtained from a host cell that is cultured under conditions such that hypergalactosylated and/or hypomannosylated binding proteins are produced.
  • the binding protein is expressed in a host cell with one or more sialyltransferase enzymes, e.g., an a 2,6 sialyltransferase (e.g., ST6Gal-1).
  • Exemplary binding protein compositions of the invention may be obtained from cultured mammalian (e.g., CHO) host cells have a “high Gal/low Man” glycoform profile which provides for unexpectedly improved properties (e.g., reduced ADA activity and/or prolonged half-life). Notably, this glycoform profile differs from the highly mannosylated glycoprofile of binding proteins produced in the milk of transgenic animals (see, e.g., US 2014/0296490). Accordingly, in certain embodiments, the glycoengineered binding protein compositions disclosed herein are not obtained from the milk of transgenic animals e.g., transgenic goats. Antibody compositions with high oligomannose content are thought to promote the ADA response and/or reduce serum half-life.
  • binding protein compositions of the invention exhibit a low degree of terminally mannosylated glycoforms (e.g., M3-M9 glycoforms).
  • binding protein compositions of the invention comprise a population of Fc domain-containing binding proteins comprising less than 10%, less than 9%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2% or less than 1% of oligomannose (e.g., M3-M9) glycoforms.
  • compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1.
  • the population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1,
  • the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:
  • the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80
  • Glycoengineered binding compositions of the invention may exhibit improvement in at least one biological activity as compared to a reference binding composition.
  • Biological activity of the preparation can be analyzed by any known method.
  • a binding activity of the binding composition is improved (e.g., binding to a ligand or receptor).
  • a therapeutic activity of the glycoengineered binding composition is improved (e.g., an activity in decreasing severity or symptom of a disease or condition, or in delaying appearance of a symptom of a disease or condition).
  • a pharmacologic activity of the glycoengineered binding composition is improved (e.g., bioavailability, pharmacokinetics, pharmacodynamics). Methods of analyzing bioavailability, pharmacokinetics, and pharmacodynamics of glycoprotein therapeutics are well known in the art.
  • Glycoengineered binding protein compositions of the invention may exhibit reduced ADA activity and/or enhanced half-life without also exhibiting enhanced complement dependent cytotoxicity (CDC) activity and/or enhanced antibody-dependent cellular cytotoxicity (ADCC) activity.
  • the glycoengineered binding protein composition of the invention exhibit reduced ADCC and/or CDC activity relative to a reference binding protein composition comprising the same polypeptide sequence but is not glycoengineered (e.g., hypergalactosylated and/or hypomannosylated) according to the methods of the invention.
  • the reference binding protein composition is not hypergalactosylated and hypomannosylated.
  • the reference composition is transgenically produced in mammary gland epithelial cells.
  • the glycoengineered binding protein compositions of the invention do not induce B-cell depletion. In other embodiments, the glycoengineered binding protein compositions of the invention are not produced in mammary gland epithelial cells.
  • the hypergalactosylated compositions of the invention exhibit reduced ADA activity and/or enhanced half-life relative to the reference antibody composition.
  • the ADA activity of the glycoengineered composition of the invention is at least 1.1 times lower, at least 1.2 times lower, at least 1.3 times lower, at least 1.4 times lower, at least 1.5 times lower, at least 1.6 times lower, at least 1.7 times lower, at least 1.8 times lower, at least 10 times lower, at least 20 times lower, at least 50 times lower or up to 100 times lower when compared to the reference composition.
  • the glycoengineered binding protein compositions of the invention exhibit decreased internalization by dendritic cells in a dendritic cell internalization (DCI) assay, as compared to a reference binding protein composition.
  • DCI dendritic cell internalization
  • the glycoengineered binding protein compositions may be fluorescently labelled with a pH-sensitive fluorophore (e.g., pH rodo Red) and combined with dendritic cells and an immunostimulant (e.g., LPS). Internalization of the fluorescently labelled antibodies may be quantified by measuring (e.g., via FACS cell sorting) the fluorescence which occurs upon uptake and exposure of the fluorophore-labelled antibody to the acidic pH in the endosomal compartments of the dendritic cell.
  • a pH-sensitive fluorophore e.g., pH rodo Red
  • an immunostimulant e.g., LPS
  • the glycoengineered binding protein compositions of the invention exhibit at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% reduction in fluorescent intensity as compared to a reference antibody composition comprising the same binding polypeptide sequence.
  • the glycoengineered binding protein composition is a hypergalactosylated and/or hypomannosylated preparation of adalimumab and the reference binding protein composition is a commercially available or non-glycoengineered preparation of adalimumab (e.g.., Humira®).
  • the reference binding protein composition is a binding protein composition (e.g., an adalimumab composition) obtained from the milk of a transgenic animal.
  • glycan structure and composition as described herein are analyzed, for example, by one or more enzymatic methods, chromatographic methods, mass spectrometry (MS) methods, electrophoretic methods, nuclear magnetic resonance (NMR) methods, and combinations thereof.
  • exemplary enzymatic methods include contacting a composition with one or more enzymes under conditions and for a time sufficient to release one or more glycan(s) (e.g., one or more exposed glycan(s)).
  • the one or more enzymes include(s) PNGase F.
  • MS mass spectrometry
  • MALDI-MS matrix assisted laser desorption ionisation mass spectrometry
  • FTMS Fourier transform mass spectrometry
  • IMS-MS ion mobility separation with mass spectrometry
  • ETD-MS electron transfer dissociation
  • Exemplary electrophoretic methods include, but are not limited to, capillary electrophoresis (CE), CE-MS, gel electrophoresis, agarose gel electrophoresis, acrylamide gel electrophoresis, SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blotting using antibodies that recognize specific glycan structures, and combinations thereof.
  • CE capillary electrophoresis
  • CE-MS gel electrophoresis
  • agarose gel electrophoresis agarose gel electrophoresis
  • acrylamide gel electrophoresis acrylamide gel electrophoresis
  • SDS-PAGE SDS-polyacrylamide gel electrophoresis
  • glycans are characterized using one or more of chromatographic methods, electrophoretic methods, nuclear magnetic resonance methods, and combinations thereof.
  • the percent content of each labeled glycoform can be quantified using art-recognized methods.
  • the glycoforms can be quantified based on the N-glycan peaks of a chromatogram, such as a NP HPLC spectrum.
  • Exemplary chromatograms of binding protein composition of the invention are depicted in FIG. 7 .
  • the glycoform profile in a population of Fc-containing binding proteins can be determined by releasing the N-glycans from the binding proteins, resolving the N-glycans on a chromatogram, identifying the N-glycan that corresponds to a specific peak, determining the peak intensity and applying the data to a quantitative formula.
  • ⁇ f 1 n ⁇ ⁇ ( number ⁇ ⁇ of ⁇ ⁇ Gal ) * ( % ⁇ ⁇ relative ⁇ ⁇ Area )
  • ⁇ f 1 n ⁇ ⁇ ( number ⁇ ⁇ of ⁇ ⁇ A ) * ( % ⁇ ⁇ relative ⁇ ⁇ Area ) * 100
  • “number of Gal” represents the number of Galactose motifs on the antennae of the glycan corresponding to the peak;
  • number of A corresponds to the number of antennae of the glycan form corresponding to the peak; and “% relative Area” corresponds to % of the Area under the corresponding peak.
  • mannosylation state of a particular binding protein composition can be determined according to the same formula, but where the “number of Gal” is substituted for “number of Man”. “Number of Man” represents that number of Mannose motifs on the antennae of the glycan corresponding to the peak.
  • the invention provides a population of Fc domain-containing binding proteins (e.g., TNF binding proteins) with a reduced anti-drug immune response.
  • Fc domain-containing binding proteins e.g., TNF binding proteins
  • the variant Fc region is a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence (wherein amino acid numbering is according to the EU numbering convention as in Kabat).
  • the anti-TNF antibody is a variant of adalimumab which exhibits pH-sensitive binding to the TNF antigen.
  • PH-sensitive variants may exhibit reduced binding of the TNF-antigen at an acidic pH, thereby promoting release from the endosomal compartment and prolonging serum half-life.
  • pH-sensitive variants comprise histidine mutations within the CDRs of heavy or light chain variable regions of adalimumab.
  • Exemplary pH-sensitive variants of Adalimumab include D2E7SS22.
  • the heavy chain of D2E7SS22 is provided in SEQ ID NO: 1 (variant Histidine bolded and underlined; C-terminal lysine in parentheses may be present or absent):
  • the light chain of D2E7SS22 is provided in SEQ ID NO:2 (variant Histidine bolded and underlined):
  • the pH-sensitive variant comprises the heavy and light chain variable regions of D2E7SS22 and a variant Fc region (e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence).
  • a variant Fc region e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence.
  • the binding proteins comprise an antigen binding fragment of an antibody.
  • the binding protein comprises a single chain variable region sequence (ScFv).
  • Single chain variable region sequences comprise a single polypeptide having one or more antigen binding sites, e.g., a VL domain linked by a flexible linker to a VH domain.
  • ScFv molecules can be constructed in a VH-linker-VL orientation or VL-linker-VH orientation.
  • the flexible hinge that links the VL and VH domains that make up the antigen binding site preferably comprises from about 10 to about 50 amino acid residues. Connecting peptides are known in the art.
  • Binding proteins of the invention may comprise at least one scFv and/or at least one constant region.
  • the binding proteins are multivalent (e.g., tetravalent) antibodies which are produced by fusing a DNA sequence encoding an antibody with a ScFv molecule (e.g., an altered ScFv molecule).
  • these sequences are combined such that the ScFv molecule (e.g., an altered ScFv molecule) is linked at its N-terminus or C-terminus to an Fc fragment of an antibody via a flexible linker (e.g., a gly/ser linker).
  • a tetravalent antibody of the current disclosure can be made by fusing an ScFv molecule to a connecting peptide, which is fused to a CH1 domain.
  • the binding proteins comprise an altered minibody.
  • Altered minibodies of the current disclosure are dimeric molecules made up of two polypeptide chains each comprising an ScFv molecule (e.g., an altered ScFv molecule comprising an altered VH domain described supra) which is fused to a CII3 domain or portion thereof via a connecting peptide.
  • Minibodies can be made by constructing an ScFv component and connecting peptide-CH3 component using methods described in the art (see, e.g., U.S. Pat. No. 5,837,821 or WO 94/09817A1).
  • a tetravalent minibody can be constructed. Tetravalent minibodies can be constructed in the same manner as minibodies, except that two ScFv molecules are linked using a flexible linker. The linked scFv-scFv construct is then joined to a CH3 domain.
  • the binding proteins comprise multispecific or multivalent antibodies comprising one or more variable domain in series on the same polypeptide chain, e.g., tandem variable domain (TVD) polypeptides.
  • TVD polypeptides include the “double head” or “Dual-Fv” configuration described in U.S. Pat. No. 5,989,830.
  • variable domains of two different antibodies are expressed in a tandem orientation on two separate chains (one heavy chain and one light chain), wherein one polypeptide chain has two times a VH in series separated by a peptide linker (VH1-linker-VH2) and the other polypeptide chain consists of complementary VL domains connected in series by a peptide linker (VL1-linker-VL2).
  • variable domains of two different antibodies are expressed in a tandem orientation on two separate polypeptide chains (one heavy chain and one light chain), wherein one polypeptide chain has two VH in series separated by a peptide linker (VH1-linker-VH2) and the other polypeptide chain consists of complementary VL domains connected in series by a peptide linker in the opposite orientation (VL2-linker-VL1).
  • Additional antibody variants based on the “Dual-Fv” format include the Dual-Variable-Domain IgG (DVD-IgG) bispecific antibody (see U.S. Pat. No. 7,612,181 and the TBTI format (see US 2010/0226923 A1).
  • the binding proteins comprise a cross-over dual variable domain IgG (CODV-IgG) bispecific antibody based on a “double head” configuration (see US20120251541 A1, which is incorporated by reference herein in its entirety).
  • CODV-IgG antibody variants generally have one polypeptide chain with VL domains connected in series to a CL domain (VL1-L1-VL2-L2-CL) and a second polypeptide chain with complementary VH domains connected in series in the opposite orientation to a CH1 domain (VH2-L3-VH1-L4-CH1), where the polypeptide chains form a cross-over light chain-heavy chain pair.
  • the second polypeptide may be further connected to an Fc domain (VH2-L3-VH1-L4-CH1-Fc).
  • the binding proteins comprise an immunoadhesin molecule comprising a non-antibody binding region (e.g., a receptor, ligand, or cell-adhesion molecule) fused to an antibody constant region (see e.g., Ashkenazi et al., Methods, 1995 8(2), 104-115, which is incorporated by reference herein in its entirety).
  • a non-antibody binding region e.g., a receptor, ligand, or cell-adhesion molecule
  • the binding proteins comprise an immunoglobulin-like domain.
  • Suitable immunoglobulin-like domains include, without limitation, fibronectin domains (see, for example, Koide et al. (2007), Methods Mol. Biol. 352: 95-109, which is incorporated by reference herein in its entirety), DARPin (see, for example, Stumpp et al. (2008) Drug Discov. Today 13 (15-16): 695-701, which is incorporated by reference herein in its entirety), Z domains of protein A (see, Nygren et al. (2008) FEBS J. 275 (11): 2668-76, which is incorporated by reference herein in its entirety), lipocalins (see, for example, Skerra et al.
  • the Fc domain-containing binding proteins of the invention are capable of binding one or more targets selected from the group consisting of ABCF1; ACVR1; ACVR1B; ACVR2; ACVR2B; ACVRL1; ADORA2A; Aggrecan; AGR2; AICDA; AIF1; AIG1; AKAP1; AKAP2; AMH; AMHR2; ANGPT1; ANGPT2; ANGPTL3; ANGPTL4; ANPEP; APC; APOC1; AR; AZGP1 (zinc-a-glycoprotein); B7.1; B7.2; BAD; BAFF; BAG1; BAI1; BCL2; BCL6; BDNF; BLNK; BLR1 (MDR15); BlyS; BMP1; BMP2; BMP3B (GDF10); BMP4; BMP6; BMP8; BMPRIA; BMPR1B; BMPR2; BPAG1 (plectin); BRCA
  • the binding proteins produced using the methods and compositions disclosed herein exhibit improved properties (e.g., affinity or stability) with respect to a corresponding parental reference binding protein.
  • the engineered binding protein may dissociate from its target antigen with a k off rate constant of about 0.1 s ⁇ 1 or less, as determined by surface plasmon resonance, or inhibit the activity of the target antigen with an IC 50 of about 1 ⁇ 10 ⁇ 6 M or less.
  • the binding protein may dissociate from the target antigen with a k off rate constant of about 1 ⁇ 10 ⁇ 2 5 ⁇ 1 or less, as determined by surface plasmon resonance, or may inhibit activity of the target antigen with an IC 50 of about 1 ⁇ 10 ⁇ 7 M or less.
  • the binding protein may dissociate from the target with a k off rate constant of about 1 ⁇ 10 ⁇ 3 s ⁇ 1 or less, as determined by surface plasmon resonance, or may inhibit the target with an IC 50 of about 1 ⁇ 10 ⁇ 8 M or less.
  • binding protein may dissociate from the target with a k off rate constant of about 1 ⁇ 10 ⁇ 4 s ⁇ 1 or less, as determined by surface plasmon resonance, or may inhibit its activity with an IC 50 of about 1 ⁇ 10 ⁇ 9 M or less.
  • the engineered binding protein comprises a heavy chain constant region, such as an IgG1, IgG2, IgG3, IgG4, IgA, IgE, IgM or IgD constant region.
  • the heavy chain constant region is an IgG1 heavy chain constant region or an IgG4 heavy chain constant region.
  • the binding protein can comprise a light chain constant region, either a kappa light chain constant region or a lambda light chain constant region.
  • the binding protein comprises a kappa light chain constant region.
  • the binding protein portion can be, for example, a Fab fragment or a single chain Fv fragment.
  • the engineered binding protein comprises an engineered effector function known in the art (see, e.g., Winter, et al. U.S. Pat. Nos. 5,648,260; 5,624,821).
  • the Fc portion of a binding protein mediates several important effector functions e.g. cytokine induction, ADCC, phagocytosis, complement dependent cytotoxicity (CDC) and half-life/clearance rate of binding protein and antigen-binding protein complexes. In some cases these effector functions are desirable for therapeutic binding protein but in other cases might be unnecessary or even deleterious, depending on the therapeutic objectives.
  • Neonatal Fc receptors are the critical components determining the circulating half-life of binding proteins.
  • at least one amino acid residue is replaced in the constant region of the binding protein, for example the Fc region of the binding protein, such that effector functions of the binding protein are altered.
  • the engineered binding protein is derivatized or linked to another functional molecule (e.g., another peptide or protein).
  • a labeled binding protein of the invention can be derived by functionally linking a binding protein or binding protein portion of the invention (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another binding protein (e.g., a bispecific binding protein or a diabody), a detectable agent, a cytotoxic agent, a pharmaceutical agent, and/or a protein or peptide that can mediate associate of the binding protein with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • Useful detectable agents with which a binding protein or binding protein portion of the invention may be derivatized include fluorescent compounds.
  • Exemplary fluorescent detectable agents include fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-1-napthalenesulfonyl chloride, phycoerythrin and the like.
  • a binding protein may also be derivatized with detectable enzymes, such as alkaline phosphatase, horseradish peroxidase, glucose oxidase and the like. When a binding protein is derivatized with a detectable enzyme, it is detected by adding additional reagents that the enzyme uses to produce a detectable reaction product.
  • a binding protein may also be derivatized with biotin, and detected through indirect measurement of avidin or streptavidin binding.
  • the engineered binding protein is further modified to generate glycosylation site mutants in which the O- or N-linked glycosylation site of the binding protein has been mutated.
  • glycosylation site mutants in which the O- or N-linked glycosylation site of the binding protein has been mutated.
  • One skilled in the art can generate such mutants using standard well-known technologies.
  • Glycosylation site mutants that retain the biological activity, but have increased or decreased binding activity, are another object of the present invention.
  • an engineered binding protein of the invention can be further modified with an altered type of glycosylation, such as a hypofucosylated binding protein having reduced amounts of fucosyl residues or a binding protein having increased bisecting GlcNAc structures.
  • an altered glycosylation patterns have been demonstrated to increase the ADCC ability of binding proteins.
  • carbohydrate modifications can be accomplished by, for example, expressing the binding protein in a host cell with altered glycosylation machinery. Cells with altered glycosylation machinery have been described in the art and can be used as host cells in which to express recombinant binding proteins of the invention to thereby produce a binding protein with altered glycosylation. See, for example, Shields, R. L. et al. (2002) J.
  • Binding proteins of the present invention may be produced by any of a number of techniques known in the art. For example, expression from host cells, wherein expression vector(s) encoding the heavy and light chains is (are) transfected into a host cell by standard techniques.
  • the various forms of the term “transfection” are intended to encompass a wide variety of techniques commonly used for the introduction of exogenous DNA into a prokaryotic or eukaryotic host cell, e.g., electroporation, calcium-phosphate precipitation, DEAE-dextran transfection and the like.
  • Preferred mammalian host cells for expressing the recombinant binding proteins of the invention include Chinese Hamster Ovary (CHO cells) (including dhfr-CHO cells, described in Urlaub and Chasin, (1980) Proc. Natl. Acad. Sci. USA 77:4216-4220, used with a DHFR selectable marker, e.g., as described in R. J. Kaufman and P. A. Sharp (1982) Mol. Biol. 159:601621), NSO myeloma cells, COS cells and SP2 cells.
  • Chinese Hamster Ovary CHO cells
  • dhfr-CHO cells described in Urlaub and Chasin, (1980) Proc. Natl. Acad. Sci. USA 77:4216-4220
  • a DHFR selectable marker e.g., as described in R. J. Kaufman and P. A. Sharp (1982) Mol. Biol. 159:601621
  • NSO myeloma cells COS cells
  • bifunctional binding proteins may be produced in which one heavy and one light chain are a binding protein of the invention and the other heavy and light chain are specific for an antigen other than the antigens of interest by crosslinking a binding protein of the invention to a second binding protein by standard chemical crosslinking methods.
  • Glycoengineering of the binding proteins of the invention can be achieved by any methods known in the art. Suitable methods include: (1) glycosylation of purified binding proteins can be modified enzymatically in vitro, (2) the cell culture and production conditions can be modified to bias a defined glycosylation profile of recombinant proteins expressed in the cultured cells, (3) the protein can be engineered to add or eliminate sites for the attachment of glycans or (4) a cell line can be genetically engineered for production of biotherapeutics with a modified glycosylation profile. Exemplary methods of making glycoengineered Fc domain containing binding proteins can be found in the Examples herein.
  • glycoengineering of recombinant binding proteins is achieved by expression of Fc domain-containing binding proteins in cells capable of N-linked glycosylation under specific culture conditions. For example, growing CHO cells expressing recombinant antibodies in chemically defined culture media supplemented with metal ions such as manganese or ferric nitrate increases the G1F and G2F glycoforms of the expressed recombinant antibodies by at least 25-30% (see published U.S. Patent Application No. 2012/0276631, the contents of which are incorporated herein in their entirety and Example 1).
  • the Fc containing binding proteins are hypergalactosylated and/or hypomannosylated by expression in a host cell with a knock down or knock out of its beta galactosidase gene, for example, using beta galactosidase gene-specific RNAi, homologous recombination or Zn finger nuclease inactivation of the beta galactosidase gene (see Examples).
  • the Fc containing binding proteins are hypergalactosylated and/or hypomannosylated by expression in a host cell that overexpresses a galactosyl transferase.
  • mammalian cell lines are genetically engineered to modify the glycosylation profile of expressed recombinant binding proteins.
  • cells can be genetically engineered to overexpress human ⁇ 1, 4-galactosyltransferase (E.C. 2.4.1.38; Weikert et al., Nature Biotechnology 17, 1116-1121 (1999)) or knock-out/knock down of (3-galactosidase proteins.
  • the host cell is genetically engineered with one or more sialyltransferase enzymes, e.g., an a2,6 sialyltransferase (e.g., ST6Gal-1).
  • Any natural or engineered cell e.g., prokaryotic or eukaryotic
  • mammalian cells are employed to effect glycosylation.
  • the N-glycans that are produced in mammalian cells are commonly referred to as complex N-glycans (see e.g., Drickamer K, Taylor M E (2006). Introduction to Glycobiology, 2nd ed., which is incorporated herein by reference in its entirety).
  • the glycoengineered binding polypeptides may be recovered from the culture supernatant of a glycoengineered host cell and subjected to one or more purification steps, such as, for example, ion-exchange or affinity chromatography, to further increase the G/M ratio of the binding composition.
  • purification steps such as, for example, ion-exchange or affinity chromatography
  • Suitable methods of purification will be apparent to a person of ordinary skill in the art.
  • a person of ordinary skill in the art will appreciate that different combinations of purification methods, disclosed above, can lead to production of the polypeptide compositions with extremely high levels of galactosylation and extremely low levels of mannosylation.
  • the hypergalactosylated and/or hypomannosylated binding protein compositions obtained from glycoengineered host cells can be further glycoengineered using in vitro techniques.
  • the G/M ratio of said composition can be further increased by subjecting the composition to treatment with galactosyltransferases in vitro.
  • Galactosyltransferases are commercially available (Sigma Chemical Co, St. Louis, Mo.; Boehringer Mannheim, Indianapolis, Ind. and Genzyme, Cambridge Mass.).
  • compositions of the present invention can be further purified or modified so that they have an increased amount of sialic acid compared to reference antibody composition.
  • the addition of charged sialic acid residue can help facilitate separation of the sialylated glycoforms by ion exchange chromatography (see e.g., FIG. 7C ).
  • the sialylation levels of the composition can be increased for instance by subjecting the composition to treatment with sialyltransferases (e.g., an alpha 2,6 sialyltransferase).
  • hypergalactosylated and/or hypomannosylated binding protein compositions produced in CHO cells can be sialylated in vitro by subjecting the purified or partially purified binding protein composition to a sialyltransferase and the appropriate saccharide based substrate.
  • a sialyltransferase and the appropriate saccharide based substrate can be employed as described, for example, in the U.S. Pat. No. 7,473,680, which is incorporated herein by reference.
  • Sialyltransferase enzymes are known in the art and are commercially available.
  • sialyltransferase enzyme e.g., an a2,6 sialyltransferase (e.g., ST6Gal-1).
  • ST6Gal sialyltransferases are known in the art and are commercially available (see, e.g., Takashima, Biosci. Biotechnol. Biochem. 72:1 155-1 167 (2008); Weinstein et al., J. Biol. Chem. 262:17735-17743 (1987)).
  • ST6Gal-1 catalyzes the transfer of sialic acid from a sialic acid donor (e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid) to a terminal galactose residue of glycans through an a2,6 linkage.
  • a sialic acid donor e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid
  • a purified or partially purified binding protein composition may contacted with an ST6Gal sialyltransferase (e.g., a recombinantly expressed and purified ST6Gal sialyltransferase) in the presence of a sialic acid donor, e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid, manganese, and/or other divalent metal ions.
  • an ST6Gal sialyltransferase e.g., a recombinantly expressed and purified ST6Gal sialyltransferase
  • a sialic acid donor e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid, manganese, and/or other divalent metal ions.
  • the composition can be sialylated in vivo by expressing the binding protein in a CHO cell that has been glycoengineered to express a sialyltransferase.
  • sialyltransferase enzymes useful in the claimed methods are ST3Gal III, which is also referred to as alpha-(2,3)sialyltransferase (EC 2.4.99.6), and alpha-(2,6)sialyltransferase (EC 2.4.99.1).
  • the alpha-2,3-sialyltransferase may be the human alpha-2,3-sialyltransferase, known as SIAT4C or STZ (GenBank accession number L23767), and described, for example, in the U.S. Patent Publication No. 20050181359.
  • the binding protein composition can be passed through a column having a lectin which is known to bind sialic acid in order to enrich for sialylated glycoforms.
  • lectins display different affinities for alpha 2,6 versus alpha 2,3 linkages between galactose and sialic acid.
  • the lectin is isolated from Sambuccus nigra.
  • SNA Sambuccus nigra agglutinin
  • MAA Maakia amurensis
  • cell culture conditions can be manipulated to change the sialylation content. For example, to increase the sialic acid content, production rate is decreased and osmolality is generally maintained within a lower margin suitable for the particular host cell being cultured. Osmolality in the range from about 250 mOsm to about 450 mOsm is appropriate for increased sialic acid content.
  • This and other suitable cell culture conditions are described in, e.g., U.S. Pat. No. 6,656,466.
  • a process for manufacturing a glycoengineered binding composition of the invention by performing additional purification.
  • a process for manufacturing a composition of the invention comprising the following steps: i) recombinantly expressing the glycoengineered of interest in a host cell (e.g., a glycoengineered CHO cell of the invention) and; ii) purifying the binding protein of interest by subjecting a liquid containing said binding composition to one or more chromatographic steps.
  • the respective manufacturing process leads to the production homogenous glycoprotein compositions which are in particular suitable for use in pharmaceutical formulations.
  • compositions can be subjected to further chromatographic purification including, for example, ion exchange chromatography such anion exchange chromatography or cation exchange chromatography.
  • Additional chromatography steps may include any of the following: a) reverse phase chromatography (RPC); b) size exclusion chromatography (SEC); and c) hydrophobic interaction chromatography (HIC); (d) affinity chromatography such as dye affinity chromatography, immune affinity chromatography, lectin affinity chromatography or perborate affinity chromatography, (e) filtration such as diafiltration, ultrafiltration or nanofiltration, and/or (f) at least one virus inactivation step.
  • RPC reverse phase chromatography
  • SEC size exclusion chromatography
  • HIC hydrophobic interaction chromatography
  • affinity chromatography such as dye affinity chromatography, immune affinity chromatography, lectin affinity chromatography or perborate affinity chromatography
  • filtration such as diafiltration, ultrafiltration or nanofiltration, and/or (f) at least
  • the process of the present invention includes an anion exchange chromatography (AEX) as a chromatography step.
  • AEX chromatography is performed subsequent to SEC chromatography and prior to HIC chromatography. Additional steps may be performed in addition to and also between the steps.
  • the purification methods may provide glycoengineered binding protein compositions in high purity, which may then be formulated as a pharmaceutical composition.
  • the purity may be above 90% hypergalactosylated binding protein, preferably >95% w/w, more preferably >99% w/w, even more preferably >99.5% w/w, based on total protein.
  • the level of mannosylated species e.g., M3-M9 is less than 10%, preferably ⁇ 5% w/w, more preferably ⁇ 1% w/w, even more preferably ⁇ 0.5% w/w, based on total protein.
  • the glycoprotein composition comprises only trace amounts of oligomannose glycoforms.
  • the binding protein compositions which form the starting material for the purification process may be provided in or obtained by recombinant techniques such as, e.g., in cell culture harvests of glycoengineered host cells of the invention.
  • the starting material as obtained from a cell harvest is clarified first (e.g. by filtration) and then optionally concentrated (e.g. by using ultrafiltration) and/or buffer exchanged (e.g. through a diafiltration step) prior to being captured by the first chromatographic step.
  • steps of chromatography typically commercially available resins are used, preferably polymer-based resins or agarose-based resins. It is also possible to use membrane chromatography in which the resin is replaced by a functionalized membrane such as SARTOBIND® membranes (Sartorius) or CHROMASORB® (Millipore).
  • the glycoengineered binding compositions of the invention are subjected to an anion exchange (AEX) chromatography step.
  • the anion exchange chromatography is usually performed by equilibrating and loading the column, followed by a wash and subsequent elution.
  • the anion exchange chromatography is carried out, e.g., with a quaternary ammonium resin, such as CAPTOQ® (obtainable from GE Healthcare), or a resin having similar characteristics such as TOYOPEARL QEA® (obtainable from Tosoh), or FRACTOGEL EMD®, FRACTOGEL TMAE® or FRACTOGEL HICAP® (obtainable from Merck KGaA, Darmstadt Germany).
  • a quaternary ammonium resin such as CAPTOQ® (obtainable from GE Healthcare)
  • TOYOPEARL QEA® obtainable from Tosoh
  • FRACTOGEL EMD® FRACTOGEL TMAE®
  • FRACTOGEL HICAP® obtained
  • anion exchange resins include, but are not limited to, quaternary amine resins or “Q-resins” (e.g., Q-Sepharose®, QAE Sephadex®); diethylaminoethane (DEAE) resins (e.g., DEAE-Trisacryl®, DEAE Sepharose®, benzoylated naphthoylated DEAE, diethylaminoethyl Sephacel®); Amberjet® resins; Amberlyst® resins; Amberlite® resins (e.g., Amberlite® IRA-67, Amberlite® strongly basic, Amberlite® weakly basic), cholestyramine resin, ProPac®resins (e.g., ProPac® SAX-10, ProPac® WAX-10, ProPac® WCX-10); TSK-GEL® resins (e.g., TSKgel DEAE-NPR; TSKgel DEAE
  • Typical mobile phases for anionic exchange chromatography include relatively polar solutions, such as water and polar organic solvents (e.g., acetonitrile and organic alcohols such as methanol, ethanol, and isopropanol).
  • the mobile phase comprises about 0%, 1%, 2%, 4%, 6%, 8%, 10%, 12%, 14%, 16%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 100% acetonitrile.
  • the mobile phase comprises between about 1% to about 100%, about 5% to about 95%, about 10% to about 90%, about 20% to about 80%, about 30% to about 70%, or about 40% to about 60% acetonitrile at any given time during the course of the separation.
  • the mobile phase is buffered. In certain embodiments, the mobile phase is not buffered. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 14. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 10. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 8. In certain embodiments, the mobile phase is buffered to a pH of about 7. Exemplary buffers for anion exchange chromatography are included in Table 1.
  • the anion exchange chromatography resin may be equilibrated, loaded and washed by using a buffer having a mildly alkaline pH, e.g. at or about 7.2 to at or about 9.0.
  • Suitable buffers include, for example borate buffer, triethanolamine/iminodiacetic acid, Tris (2-Amino-2-hydroxymethyl-propane-1,3-diol), sodium phosphate, ammonium acetate, tricine (N-(Tri(hydroxymethyl)methyl)glycine), bicine (2-(bis(2-hydroxyethyl)amino)ethanoic acid), TES, HEPES, TAPS(N-Tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid).
  • Elution from the ion-exchange resin is achieved by increasing the conductivity of the mobile phase through the addition of salt, preferably NaCl.
  • Suitable buffers include, for example borate buffer, triethanolamine/iminodiacetic acid Tris, ammonium acetate, tricine, bicine, TES, HEPES, TAPS. Preferred is ammonium acetate.
  • the anion exchange chromatography can be utilized to selectively elute different charged glycoforms mainly originating from different sialylation levels.
  • differently charged glycoforms such as differently sialylated glycoforms
  • elution can be performed in a stepwise fashion, first using one elution buffer and then using the other elution buffer, optionally also using one or more intermediate elution steps with different mixtures of the elution buffers.
  • elution can be performed using a gradient, starting with a first mixing ratio of the elution buffers (e.g. 100% of the first elution buffer) and gradually changing to a second mixing ratio of the elution buffers (e.g. 100% of the second elution buffer).
  • the elution buffer used first (buffer A) in general can be a) a mildly acidic buffer which is salt-free, or b) a neutral or mildly basic buffer with low salt content such as NaCl (preferably between 20 and 200 mM). Buffer A can be used to elute glycoforms of low charge, e.g., low degree of sialylation.
  • buffer A has a pH e.g. at or about 3.0 to at or about 6.5, or at or about 4.0 to at or about 6.0, most preferably at or about 5.
  • buffer A has a pH e.g. at or about 7.0 to 9.0, preferably 8.5.
  • the elution buffer used second in general is a salt-containing mildly alkaline buffer of a higher salt content than buffer A which can be used to elute glycoprotein of high charge, e.g. high degree of sialylation.
  • Buffer B has a pH e.g. at or about 7.0 to at or about 9.0, or at or about 8.0 to at or about 9.0, most preferably at or about 8.5.
  • the salt is preferably NaCl.
  • the salt content in buffer B is preferably from 200 mM to 1M.
  • buffer A is 10 mM sodium phosphate
  • pH 7.5 and buffer B is 10 mM sodium phosphate/500 mM sodium chloride, pH 5.5.
  • the different glycoforms loaded onto the anion exchange chromatography column will elute in different fractions depending on their charge.
  • the glycoprotein to be purified may be present in the fractions of the flow-through, i.e. it binds to the anion exchange chromatography column only weakly or not at all, it may be eluted with the first elution buffer, at a specific mixing ratio of the first and second elution buffer, or with the second elution buffer.
  • the glycoprotein fractions which are used for the further purification steps and thus, the glycoforms which are to be purified mainly depend on the desired applications of the glycoprotein.
  • the other glycoforms which are not of interest can be removed using the anion exchange chromatography step.
  • Chromatofocusing is a chromatography technique that separates glycoforms according to differences in their isoelectric point (pI).
  • a charged stationary phase can be used and the proteins loaded onto the chromatofocusing column can be eluted using a pH gradient.
  • the stationary phase may be positively charged and the pH gradient may develop from a first pH to a second, lower pH, for example from about pH 9 to about pH 6 or from about pH 7 to about pH 4. Due to the specific conditions of the chromatofocusing, glycoforms elute in order of their isoelectric points and preferably proteins of a specific pI are focused into narrow bands.
  • glycoforms at a pH higher than their pI are negatively charged and attach to the positively charged stationary phase, thereby being slowed down.
  • the pH in the elution gradient reaches the pI of the glycoform, it is overall neutral in charge and thus migrates with the flow of the mobile phase.
  • the glycoform is repulsed by the stationary phase due to its positive charge, thus accelerating it.
  • glycoforms at the rear of a zone will migrate more rapidly than those at the front. In this setting, the glycoform with the highest pI elutes first and the glycoform with the lowest pI will elute last.
  • Suitable stationary phases are, for example, media substituted with charged, buffering amines such as MONO P (obtainable from GE Healthcare) or other anion exchange chromatography material.
  • buffering amines such as MONO P (obtainable from GE Healthcare) or other anion exchange chromatography material.
  • suitable buffing systems such as POLYBUFFER 74® or POLYBUFFER 76® (obtainable from GE Healthcare) can be used.
  • Equilibration, loading and washing of the column can be done using any condition where the glycoprotein of interest and/or any impurities bind to the column material.
  • conditions as described above for the anion exchange chromatography can be used.
  • a buffer having a pH equal to or higher than the starting pH of the elution gradient is used for equilibration, loading and/or washing.
  • an increasing pH gradient preferably a buffer having a pH equal to or lower than the starting pH of the elution gradient is used for equilibration, loading and/or washing.
  • Reverse phase chromatography refers to a chromatography step wherein a non-polar stationary phase and preferably a polar mobile phase are used.
  • reverse phase chromatography normally polar compounds are eluted first while non-polar compounds are retained.
  • the reverse phase chromatography is usually performed by equilibrating and loading the column, followed by a wash and subsequent elution, each with a buffer preferably containing an organic solvent such as acetonitrile or isopropanol.
  • the organic solvent such as isopropanol can be used for virus inactivation subsequent to elution.
  • the organic solvent is a water miscible organic solvent such as acetonitrile or an alcohol (such as methanol, ethanol, etc./).
  • Reversed phase column material is made of a resin to which a hydrophobic material may be attached.
  • Typical column materials are silica and polystyrene; hydrophobic ligands may optionally be attached.
  • the resin is substituted with a hydrophobic ligand, typically selected from (but not limited to) aliphates, such as C.sub.2, C.sub.4, C.sub.6, C.sub.8, C.sub.10, C.sub.12, C.sub.14, C.sub.16, or C.sub.18 or derivatives of these, e.g.
  • Suitable polystyrene based resins include, without limitation, resins supplied by Rohm Haas (e.g. Amberlite XAD® or Amberchrom CG®), Polymer Labs (e.g. PLRP-S®), GE Healthcare (e.g. Source RPC®), Applied Biosystems (e.g. Poros R®).
  • a particularly preferred resin is Source 30 RPC® (GE Healthcare).
  • the purification process can include a virus inactivation step.
  • Virus inactivation may be achieved by incubating the protein loaded onto, bound to or eluted from the column in the presence of an organic solvent, preferably isopropanol or ethanol.
  • the incubation time and incubation temperature preferably are chosen so as to affect a desired degree of virus inactivation and in particular depend on the concentration and nature of the organic solvent used. Furthermore, these parameters should also be adjusted depending on the stability of the binding protein composition to be purified.
  • the protein is incubated for at least 15 min, preferably for at least 30 min, at least 45 min, at least 1 h, at least 2 h, at least 3 h or at least 6 h.
  • the incubation can be performed at low temperature such as at or below 4° C. or at or below 10° C., or it can be performed at about room temperature.
  • the incubation can be performed directly after the sample has been loaded onto the column, during or after the washing step, after applying the elution buffer but prior to elution of the glycoprotein, or after elution of the binding protein.
  • virus inactivation is preferably done at an isopropanol concentration of at least 15% (v/v), preferably at about 18% (v/v).
  • the binding protein is preferably incubated for about 2 h, preferably at room temperature.
  • the virus inactivation is performed after elution of the glycoprotein from the reverse phase chromatography column, preferably in the elution buffer used.
  • further components may be added to the glycoprotein solution after elution from the column, in particular for enhancing the virus inactivation and/or the binding protein stability.
  • the purification process may include a step of size exclusion chromatography, e.g. for further purifying and/or re-buffering of the binding protein composition.
  • Size exclusion chromatography comprises the step of equilibrating and loading the eluate of the previous chromatography step to a gel filtration matrix equilibrated with a buffer having a composition which is desired for storage or further processing of the glycoprotein at a pH of typically between 6.5 and 9.
  • the gel is typically selected from the groups of polymeric gels including, but not limited to dextra-based gels such as SEPHADEX® (e.g. SEPHADEX G-25®) or polyacrylamide gels such as SEPHACRYL® (e.g.
  • SEPHACRYL-5400® agarose-based gels such as SUPEROSE® or SEPHAROSE® (e.g. SEPHAROSE CL-4B®), and composite gels prepared from two kinds of gels such as SUPERDEX 200® combining DEXTRAN® (SEPHADEX®) and crosslinked Agarose (SUPEROSE®) gels.
  • SUPEROSE® e.g. SEPHAROSE CL-4B®
  • composite gels prepared from two kinds of gels such as SUPERDEX 200® combining DEXTRAN® (SEPHADEX®) and crosslinked Agarose (SUPEROSE®) gels.
  • Buffers may be selected from the group consisting sodium phosphate, ammonium acetate, MES (2-(N-morpholino)ethanesulfonic acid), Bis-Tris (2-bis(2-hydroxyethyl)amino-2-(hydroxymethyl)-1,3-propanediol), ADA (N-(2-Acetamido) iminodiacetic acid), PIPES (piperazine-N,N′-bis(2-ethanesulfonic acid), ACES (N-(2-Acetamido)-2-aminoethanesulfonic acid), BES (N,N-Bis(2-hydroxyethyl)-2-aminoethane-sulfonic acid), MOPS (3-(N-morpholino) propanesulfonic acid), TES (N-Tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid), HEPES (N-2-Hydroxyethyl-piperazine-N′-2-ethan
  • Said buffer may additionally comprise an inorganic salt, e.g., a halide of an alkaline metal, e.g., potassium chloride or sodium chloride and/or an antioxidant, such as L-methionine, t-butyl-4-methoxyphenol, 2,6-bis(1,1-dimethylethyl)-4-methyl phenol; potassium or sodium bimetabisulfite, sodium bisulfite.
  • the size exclusion chromatography may further comprise the step of eluting the binding protein from said gel filtration matrix by isocratic elution, i.e. the elution buffer has about the same, preferably the same composition as the buffer used for equilibration and/or loading.
  • the flow through may be recorded by UV absorption at 280 nm and the fraction containing the glycoprotein is collected.
  • HIC is a separation method that takes advantage of the hydrophobic properties of the proteins.
  • the adsorption is promoted by the hydrophobic interactions between non-polar regions on the protein and immobilized hydrophobic ligands on a solid support. Adsorption is achieved at high salt concentrations in the aqueous mobile phase and elution is facilitated by decreasing the salt concentration.
  • the hydrophobic interaction chromatography material is a matrix substituted with hydrophobic ligands such as ethyl-, butyl-, phenyl- or hexyl-groups.
  • Preferred material is a matrix substituted with a butyl or a phenyl ligand.
  • HIC resins are known in the art and include resins such as BUTYL SEPHAROSE® (GE Healthcare), PHENYL SEPHAROSE® (low and high substitution), OCTYL SEPHAROSE® and ALKYL SEPHAROSE® (all of GE Healthcare; other sources of HIC resins include Biosepra, France; E. Merck, Germany; BioRad USA).
  • Alternative resins that may be used are as follows: TOYOPEARL BUTYL 650M® (obtainable from Tosoh Biosep Inc.), PHENYL SEPHAROSE 6 FAST FLOW® (low sub); PHENYL SEPHAROSE 6 FAST FLOW® (high sub); BUTYL SEPAROSE 4 FAST FLOW®; OCTYL SEPHAROSE 4 FAST FLOW®; PHENYL SEPHAROSE HIGH PERFORMANCE®; SOURCE 15ETHC); SOURCE 15ISOCI; SOURCE 15PHE® all from GE Biosciences (800) 526-3593. Still further resins are: HYDROCELL® C3 or C4; HYDROCELL PHENYL® from BioChrom Labs Inc.
  • Equilibration, loading, wash and elution buffers may be selected from the group consisting of sodium phosphate, MES, Bis-Tris, ADA, PIPES, ACES, BES, MOPS, TES, HEPES. Binding on the HIC resin is in general achieved by using an equilibration and loading buffer with a high conductivity, obtained e.g. through the addition of salt such as NaCl, (NH4)2SO4 or Na2SO4, preferably ammonium sulfate. Exemplary salt concentrations are 1 to 2M.
  • the wash generally uses the loading buffer.
  • Elution in the step of hydrophobic interaction chromatography is preferably carried out by reducing the conductivity of the mobile phase (reducing salt concentration). The reduction can be achieved in a linear way or step-wise.
  • a step of ultrafiltration Prior to the first chromatography step, it may be desirable to carry out a step of ultrafiltration, in order to concentrate the crude binding protein. Furthermore, additionally a step of diafiltration may be performed prior to the first chromatography step in order to perform a buffer exchange.
  • the ultrafiltration step and the diafiltration step may be performed simultaneously or sequentially.
  • the ultrafiltration and/or diafiltration is preferably carried out using a membrane having a cut-off of at or about 3-30 kD, most preferably at or about 10 kD. It is preferred to perform during ultrafiltration and/or diafiltration a buffer exchange to a pre-formulation buffer, e.g.
  • sodium phosphate sodium citrate, MES, Bis-Tris, ADA, PIPES, ACES, BES, MOPS, TES, HEPES, preferably sodium phosphate, preferably sodium-phosphate containing stabilizers e.g. sucrose and antioxidants like L-methionine.
  • the pH preferably is in the range of 6.5 to 7.5, more preferably about 7.0 to 7.1.
  • the binding protein composition resulting from the purification process as described above and containing purified glycoprotein may be frozen for storage as is, or after purification, the eluate may be subjected to lyophilisation (“freeze-drying”) to remove solvent.
  • compositions comprising one or more population of binding proteins, either alone or in combination with prophylactic agents, therapeutic agents, and/or pharmaceutically acceptable carriers are provided.
  • the pharmaceutical compositions provided herein are for use in, but not limited to, diagnosing, detecting, or monitoring a disorder, in preventing, treating, managing, or ameliorating a disorder or one or more symptoms thereof, and/or in research.
  • the formulation of pharmaceutical compositions, either alone or in combination with prophylactic agents, therapeutic agents, and/or pharmaceutically acceptable carriers, is known to one skilled in the art (US Patent Publication No. 20090311253 A1).
  • the pharmaceutical composition is formulated together, or co-administered with, at least one additional agent.
  • the additional agent may be selected from the group consisting of: therapeutic agent, imaging agent, cytotoxic agent, angiogenesis inhibitors; kinase inhibitors; co-stimulation molecule blockers; adhesion molecule blockers; anti-cytokine antibody or functional fragment thereof; detectable label or reporter; a TNF antagonist; an anti-rheumatic; a muscle relaxant, a narcotic, a non-steroid anti-inflammatory drug (NSAID), an analgesic, an anesthetic, a sedative, a local anesthetic, a neuromuscular blocker, an antimicrobial, an antipsoriatic, a corticosteriod, an anabolic steroid, an erythropoietin, an immunoglobulin, an immunosuppressive, a growth hormone, a hormone replacement drug, a radiopharmaceutical, an antidepressant
  • the binding protein compositions of the invention are formulated together with, or co-administered with, an immunosuppressive or anergy-inducing agent.
  • an immunosuppressive or anergy-inducing agent include Rapamycin (also known as Sirolimus) or analogs thereof, e.g., CCI-779, or FK-506 (also known as Tacrolimus) or analogs thereof.
  • Rapamycin also known as Sirolimus
  • FK-506 also known as Tacrolimus
  • the agents may be formulated in a nanoparticle (e.g., a polymeric nanoparticle), optionally together with the binding protein composition.
  • Biocompatible materials useful for making the nanoparticles include, but are not limited to, bio-degradable polymeric materials including, but not limited to, hydrogel, collagen, alginate, poly(glycolide) (PGA), poly(L-lactide) (PLA), poly(lactide-co-glycolide) (PLGA), polyethylene glycol (PEG), polyesters, polyanhydrides, polyorthoesters, polyamides; non-polymeric biodegradable ceramic materials including, but not limited to, calcium phosphate, hydroxyapatite, tricalcium phosphate; or a combination thereof.
  • bio-degradable polymeric materials including, but not limited to, hydrogel, collagen, alginate, poly(glycolide) (PGA), poly(L-lactide) (PLA), poly(lactide-co-glycolide) (PLGA), polyethylene glycol (PEG), polyesters, polyanhydrides, polyorthoesters, polyamides; non-polymeric biodegradable ceramic
  • the nanoparticles are fabricated from poly(lactic-co-glycolic acid) (PLGA), which is FDA approved for delivery of therapeutics.
  • PLGA poly(lactic-co-glycolic acid)
  • the nanoparticles have a diameter ranging from 10-1000 nm, or any values therebetween, such as 50-900 nm, 100-800 nm, 200-500 nm, 300-400 nm, etc.
  • the nanoparticles have a diameter from 300 nm to 500 nm, or any values therebetween, such as 300-450 nm, 300-400 nm, 330-480 nm, 350-450 nm, 350-400 nm, etc.
  • immunosupressant-containing nanoparticles are described in WO2012149255 and WO2012149259, the contents of each of which are hereby incorporated by reference in their entirety.
  • Methods of making and administering immunosupressant-containing nanoparticle compositions are known in the art (see e.g., Das et al, J Biomed Mater Res A. 2008 Mar. 15;84(4):885-98, and Haddadi et al., J Biomed Mater Res A. 2008 Jun. 15;85(4):983-92, the contents of each of which are hereby incorporated by reference in their entirety).
  • Methods of administering a prophylactic or therapeutic agent provided herein include, but are not limited to, parenteral administration (e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous), epidural administration, intratumoral administration, mucosal administration (e.g., intranasal and oral routes) and pulmonary administration (e.g., aerosolized compounds administered with an inhaler or nebulizer).
  • parenteral administration e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous
  • epidural administration e.g., epidural administration
  • mucosal administration e.g., intranasal and oral routes
  • pulmonary administration e.g., aerosolized compounds administered with an inhaler or nebulizer
  • Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage.
  • dosage unit form refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • An exemplary, non-limiting range for a therapeutically or prophylactically effective amount of a binding protein provided herein is 0.1-20 mg/kg, for example, 1-10 mg/kg. It is to be noted that dosage values may vary with the type and severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens may be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition.
  • TNF-associated disorder in a subject by administering to the individual in need of such treatment a therapeutically effective amount of a composition comprising a glycoengineered population of TNF binding proteins disclosed herein.
  • Such methods can be used to treat any TNF-associated disorder including, without limitation:
  • Tumor necrosis factor has an established role in the pathophysiology of sepsis, with biological effects that include hypotension, myocardial suppression, vascular leakage syndrome, organ necrosis, stimulation of the release of toxic secondary mediators and activation of the clotting cascade (see e.g., Moeller, A., et al. (1990) Cytokine 2:162-169; U.S. Pat. No. 5,231,024 to Moeller et al.; European Patent Publication No. 260 610 B1 by Moeller, A.; Tracey, K. J. and Cerami, A. (1994) Annu. Rev. Med. 45:491-503; Russell, D and Thompson, R. C. (1993) Curr. Opin. Biotech. 4:714-721). Accordingly, a TNF binding proteins of the invention can be used to treat sepsis in any of its clinical settings, including septic shock, endotoxic shock, gram negative sepsis and toxic shock syndrome.
  • a combination of the invention can be coadministered with one or more additional therapeutic agents that may further alleviate sepsis, such as an interleukin-1 inhibitor (such as those described in PCT Publication Nos. WO 92/16221 and WO 92/17583), the cytokine interleukin-6 (see e.g., PCT Publication No. WO 93/11793) or an antagonist of platelet activating factor (see e.g., European Patent Application Publication No. EP 374 510).
  • additional therapeutic agents such as an interleukin-1 inhibitor (such as those described in PCT Publication Nos. WO 92/16221 and WO 92/17583), the cytokine interleukin-6 (see e.g., PCT Publication No. WO 93/11793) or an antagonist of platelet activating factor (see e.g., European Patent Application Publication No. EP 374 510).
  • additional therapeutic agents such as an interleukin-1 inhibitor (such as those described in
  • a TNF binding proteins of the invention is administered to a human subject within a subgroup of sepsis patients having a serum or plasma concentration of IL-6 above 500 pg/ml (e.g., above 1000 pg/ml) at the time of treatment (see PCT Publication No. WO 95/20978 by Daum, L., et al.).
  • Tumor necrosis factor has been implicated in playing a role in the pathophysiology of a variety of autoimmune diseases.
  • TNF-alpha has been implicated in activating tissue inflammation and causing joint destruction in rheumatoid arthritis (see e.g., Moeller, A., et al. (1990) Cytokine 2:162-169; U.S. Pat. No. 5,231,024 to Moeller et al.; European Patent Publication No. 260 610 B1 by Moeller, A.; Tracey and Cerami, supra; Arend, W. P. and Dayer, J M. (1995) Arth. Rheum. 38:151-160; Fava, R. A., et al. (1993) Clin.
  • TNF-alpha also has been implicated in promoting the death of islet cells and in mediating insulin resistance in diabetes (see e.g., Tracey and Cerami, supra; PCT Publication No. WO 94/08609). TNF-alpha also has been implicated in mediating cytotoxicity to oligodendrocytes and induction of inflammatory plaques in multiple sclerosis (see e.g., Tracey and Cerami, supra). Chimeric and humanized murine anti-hTNF-alpha antibodies have undergone clinical testing for treatment of rheumatoid arthritis (see e.g., Elliott, M. J., et al.
  • compositions of the invention can be used to treat autoimmune diseases, in particular those associated with inflammation, including rheumatoid arthritis, rheumatoid spondylitis, osteoarthritis and gouty arthritis, allergy, multiple sclerosis, autoimmune diabetes, autoimmune uveitis and nephrotic syndrome.
  • the combination is administered systemically, although for certain disorders, local administration of the anti-TNF and/or JAK inhibitor at a site of inflammation may be beneficial (e.g., local administration in the joints in rheumatoid arthritis or topical application to diabetic ulcers, alone or in combination with a cyclohexane-ylidene derivative as described in PCT Publication No. WO 93/19751).
  • Compositions of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of autoimmune diseases, as discussed further herein.
  • Tumor necrosis factor has been implicated in mediating biological effects observed in a variety of infectious diseases.
  • TNF-alpha has been implicated in mediating brain inflammation and capillary thrombosis and infarction in malaria.
  • TNF-alpha also has been implicated in mediating brain inflammation, inducing breakdown of the blood-brain bather, triggering septic shock syndrome and activating venous infarction in meningitis.
  • TNF-alpha also has been implicated in inducing cachexia, stimulating viral proliferation and mediating central nervous system injury in acquired immune deficiency syndrome (AIDS).
  • the compositions of the invention can be used in the treatment of infectious diseases, including bacterial meningitis (see e.g., European Patent Application Publication No.
  • compositions of the invention also can be used to alleviate symptoms associated with infectious diseases, including fever and myalgias due to infection (such as influenza) and cachexia secondary to infection (e.g., secondary to AIDS or ARC).
  • Tumor necrosis factor has been implicated as a key mediator of allograft rejection and graft versus host disease (GVHD) and in mediating an adverse reaction that has been observed when the rat antibody OKT3, directed against the T cell receptor CD3 complex, is used to inhibit rejection of renal transplants (see e.g., Eason, J. D., et al. (1995) Transplantation 59:300-305; Suthanthiran, M. and Strom, T. B. (1994) New Engl. J. Med. 331:365-375). Accordingly, compositions of the invention, can be used to inhibit transplant rejection, including rejections of allografts and xenografts and to inhibit GVHD.
  • GVHD graft versus host disease
  • a TNF binding protein is used in combination with OKT3 to inhibit OKT3-induced reactions.
  • a TNF binding protein is used in combination with one or more antibodies directed at other targets involved in regulating immune responses, such as the cell surface molecules CD25 (interleukin-2 receptor-.alpha.), CD11a (LFA-1), CD54 (ICAM-1), CD4, CD45, CD28/CTLA4, CD80 (B7-1) and/or CD86 (B7-2).
  • a TNF binding protein of the invention is used in combination with one or more general immunosuppressive agents, such as cyclosporin A or FK506.
  • Tumor necrosis factor has been implicated in inducing cachexia, stimulating tumor growth, enhancing metastatic potential and mediating cytotoxicity in malignancies. Accordingly, a TNF binding protein of the invention can be used in the treatment of malignancies, to inhibit tumor growth or metastasis and/or to alleviate cachexia secondary to malignancy.
  • the compositions may be administered systemically or locally to the tumor site.
  • Tumor necrosis factor has been implicated in the pathophysiology of adult respiratory distress syndrome (ARDS), including stimulating leukocyte-endothelial activation, directing cytotoxicity to pneumocytes and inducing vascular leakage syndrome.
  • ARDS adult respiratory distress syndrome
  • a TNF binding protein of the invention can be used to treat various pulmonary disorders, including adult respiratory distress syndrome (see e.g., PCT Publication No. WO 91/04054), shock lung, chronic pulmonary inflammatory disease, pulmonary sarcoidosis, pulmonary fibrosis and silicosis.
  • the compositions may be administered systemically or locally to the lung surface, for example as an aerosol.
  • a composition of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of pulmonary disorders, as discussed further in herein.
  • Tumor necrosis factor has been implicated in the pathophysiology of inflammatory bowel disorders (see e.g., Tracy, K. J., et al. (1986) Science 234:470-474; Sun, X M., et al. (1988) J. Clin. Invest. 81:1328-1331; MacDonald, T. T., et al. (1990) Clin. Exp. Immunol. 81:301-305).
  • Chimeric murine anti-hTNF-alpha antibodies have undergone clinical testing for treatment of Crohn's disease (van Dullemen, H. M., et al. (1995) Gastroenterology 109:129-135).
  • compositions of the invention also can be used to treat intestinal disorders, such as idiopathic inflammatory bowel disease, which includes two syndromes, Crohn's disease and ulcerative colitis.
  • a composition of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of intestinal disorders, as discussed further in herein.
  • compositions of the invention also can be used to treat various cardiac disorders, including ischemia of the heart (see e.g., European Patent Application Publication No. EP 453 898) and heart insufficiency (weakness of the heart muscle) (see e.g., PCT Publication No. WO 94/20139).
  • ischemia of the heart see e.g., European Patent Application Publication No. EP 453 898
  • heart insufficiency weakness of the heart muscle
  • compositions of the invention also can be used to treat various other disorders in which TNF-alpha activity is detrimental.
  • diseases and disorders in which TNF-alpha activity has been implicated in the pathophysiology, and thus which can be treated using a TNF binding protein of the invention include inflammatory bone disorders and bone resorption disease (see e.g., Bertolini, D. R., et al. (1986) Nature 319:516-518; Konig, A., et al. (1988) J. Bone Miner. Res. 3:621-627; Lerner, U. H. and Ohlin, A. (1993) J. Bone Miner. Res. 8:147-155; and Shankar, G. and Stern, P. H.
  • a mouse galactosyltransferase ⁇ 1, 4 (Genbank accession number: D00314) was amplified by PCR and cloned downstream of CMV promoter of the pcDNATM 3.3 TOPO® Mammalian Expression Vector (Invitrogen Life Sciences, Catalog Number: K8300-01) as shown in FIG. 2A .
  • the nucleic acid and corresponding amino acid sequence of mouse galactosyltransferase ⁇ 1, 4 is shown in FIG. 2B .
  • a knock out in one of the alleles of the beta galactosidase gene ( Cricetulus griseus Glb1 (Gene ID: 100767446); mRNA sequence: NCBI Reference Sequence: XM_007630176.1; genomic sequence NW_003613697.1 from 2278553 to 2336708) of the adalimumab-producing DHFR-deficient CHO cell line was generated using zinc finger nuclease following procedures that are well known in the art (Santiago et al., Proc. Natl. Acad. Sci. USA. 2008; 105(15):5809-14; Remy et al., Transgenic Res.
  • IL17xTNF DVD-Ig-producing CHO cells are electroporated with the mouse galactosyltransferase ⁇ 1, 4 expression vector and G418 (Geneticin®, Life Technologies Catalog Number 10131035) is added to the cell media 48 hours after the transfection at a final concentration of 500 ⁇ g/ml for 2-3 weeks. Media is changed once every other day. Stable neomycin resistant transformants are isolated and cultured for 1-3 passages prior to cryopreservation.
  • High Gal/Low Man CHO cells can be either overexpressing galactosyltransferase ⁇ 1, 4, as described in Example 1, or have a knockout of an allele of the endogenous beta galactosidase gene as described in Example 2.
  • the High Gal/Low Man adalimumab-producing CHO cell line was adapted to chemically defined media for 7 (2 to 3 day each) passages in a combination of 250 mL and 500 mL Corning vented non-baffled shake flasks before freezing.
  • High Gal/Low Man adalimumab produced by the ZFN-B 1 CHO cell (as described in Example 2) is referred to herein as ZFN-B 1.
  • High Gal/Low Man adalimumab produced by the GALTR-11 and Ga188-D2E7 CHO cell clones that overexpress ⁇ -1, 4 galactosyltransferase (as described in Example 1) are referred to herein as GALTR-11 and Gal88-D2E7, respectively.
  • a High Gal/Low Man anti-TNF ⁇ IL17 DVD-Ig (ABT-122) produced by the cell line of Example 3 is referred to herein as Ga179-DVD-Ig.
  • GALTR-11 for in-vitro sialylation, the buffer was changed to 35 mM tris acetate, pH 7.4 through dialysis and the concentration adjusted to approximately 5 mg/mL.
  • In vitro sialylation was accomplished by incubating GALTR-11 with activated sialic acid, or more specifically, activated CMP-N-acetyl neuraminic acid (CMP-NANA) and a specific enzyme, ⁇ -2,6 sialyltransferase that attaches the sialic acid (NANA) on to the penultimate galactose residue in an ⁇ -2,6 linkage.
  • CMP-NANA activated CMP-N-acetyl neuraminic acid
  • ⁇ -2,6 sialyltransferase that attaches the sialic acid (NANA) on to the penultimate galactose residue in an ⁇ -2,6 linkage.
  • the CMP-NANA was added in a 1:2 CMP-NANA:GALTR-11 ratio and the enzyme was added in a 1:10 enzyme:GALTR-11 ratio, or 4 mg of enzyme to approximately 40 mg of antibody.
  • the volume of the reaction mix was brought up to 15 mL and incubated overnight at 37° C. with gentle shaking.
  • the level of incorporated sialic acid was quantified by weak ion exchange chromatography using a Shimadzu HPLC equipped with an analytical ProPac® WCX-10 column (4 ⁇ 250 mm). Sample was loaded at 94% mobile phase A(10 mM sodium phosphate, pH 7.5) and 6% buffer B (10 mM sodium phosphate, 500 mM sodium chloride, pH 5.5) and then eluted by the gradient and conditions shown in Table 1 to obtain the glycoengineered adalimumab composition referred to herein as SA-D2E7.
  • FIG. 7C Chromatograms of the SA-D2E7 composition are shown in FIG. 7C .
  • Sialylated GALTR-11 was be separated from the rest of the antibodies containing other glycoforms (i.e., high mannose, GOF, etc.) since sialic acids impart a negative charge to antibodies due to the loss of a proton by the carboxylic group at physiological pH.
  • the other glycoforms are neutral and eluted from the column in the same peak while sialylated GALTR-11 eluted earlier.
  • Sialylated GALTR-11 will elute from an anion exchange column at different retention times depending on the level of sialic acids it contains.
  • the weak ion exchange chromatography method used to collect SA-D2E7 was a modification of the analytical method described above.
  • a GE AKTA Avant system was used with a preparative ProPac® WCX-10 column (22 ⁇ 250 mm) at a flow rate of 25 mL/min The initial gradient was also stretched out longer, to increase the separation between the early eluting peaks.
  • the glycan profiles of the ZFN-B1, GALTR-11, Ga188-D2E7, SA-D2E7 and Ga179-DVD were determined.
  • the PGC SPE column is sequentially washed with 1 mL methanol and 2 ⁇ 1 mL of a 0.1% (v/v) aqueous trifluoroacetic acid (TFA).
  • TFA trifluoroacetic acid
  • the oligosaccharides are dissolved in 200 ⁇ L of a 0.1% (v/v) aqueous TFA, applied to the column and washed with 2 ⁇ 1 mL of a 0.1% (v/v) aqueous TFA.
  • the elution of the glycans is performed by applying 2 ⁇ 400 uL of a 25% (v/v) aqueous acetonitrile containing 0.1% (v/v) TFA and the eluate is vacuum-dried.
  • the separation of the N-glycans is performed as follows: from 80% to 70% (v/v) B in 15 mM; from 70% to 55% (v/v) B in 150 mM; from 55% to 10% (v/v) B in 5 mM; 10% (v/v) B during 10 mM; from 10% to 80% (v/v) in 1 mM; 80% (v/v) B during 45 minutes (reequilibration).
  • the detection of the fluorescent derivatives is performed by fluorescence detection (FD) with an excitation wavelength of 330 nm and an emission wavelength of 420 nm.
  • PBMC Peripheral blood mononuclear cells
  • Monocytes were cultured in RPMI1640 medium (Cellgro) supplemented 2 mM L-glutamine, 100 ng/ml of recombinant human GM-CSF (Abbvie) and 5 ng/ml of human IL-4 (Peprotech), 100 ⁇ g/ml penicillin, and streptomycin, and 10% fetal bovine serum at a density of 1 ⁇ 10 6 cells/ml at 37° C. with 5% CO2 for 5 days.
  • LPS stimulated PBCs monocyte or DCs were blocked with human IgG and stained with pH Rodo red labeled D2E7 on ice, then incubated at 37° C.
  • an isotype matched control antibody (AB446) was used. All the antibodies were conjugated with A488 using antibody labeling kit (Invitrogen) according to manufacturer's protocol.
  • Monocytes and T cells were gated based on the expression of CD14 (Biolegend) and CD3 (eBioscience) respectively. Samples were analyzed on a Becton Dickinson Fortessa® flow cytometer, and analysis was performed using Flowjo® software (TreeStar Inc., Ashland, Oreg., USA).
  • monocytes were stimulated with LPS for 4, 7, 9 or 24 hours in the presence of Alexa 488 conjugated AB436 antibodies.
  • Cells were permeabilized and nucleus was stained with DAPI. The images were acquired using confocal microscope (Zeiss).
  • the monocyte derived DCs were stimulated with LPS for 4 hours in the presence of anti-TNF adalimumab or matched isotype control antibodies.
  • the anti-TNFalpha specific adalimumab antibodies and control antibodies were conjugated with pH sensitive dye pH Roco Red (Invitrogen) according to manufacturer's protocol.
  • the cells were analyzed by fluorescent microscope and FACS. Where indicated, the surface of the cells was stained with A488-conjugated anti-HLA-A,B.C (W6/32, Biolegend) antibodies and the nucleus was stained with Nuce® blue (Invitrogen).
  • pH sensitive dye pH Roco Red Invitrogen
  • the surface TNFalpha was stained with pH Rodo Red conjugated anti-TNFalpha antibody (AB441).
  • the stained cells were cultured in RPMI medium for the indicated time and the internalization was assessed as an increase in fluorescence using BD Fortessa flow cytometer (see FIGS. 3A-3C ).
  • the results indicate that that the glycoengineered Adalimumab preparations of the invention exhibit pronounced decrease immunogenicity as a result of their reduced internalization and antigenic presentation by dendritic cells.
  • Non-hypergalactosylated adalimumab (D2E7) and hypergalactosylated adalimumab (ZFN-B1) monoclonal antibodies were administered to CD-1 or BALB/C mice by slow intravenous bolus dose injection at a 5mg/kg dose. Blood samples were collected from each mouse at 1, 24 and 96 hours and 7, 10, 14 and 21 days post dose. Blood samples were collected from each rat at 0.25, 4, and 24 hours and 2, 3, 7, 10, 14, 21 and 28 days post dose. All samples were stored at ⁇ 80° C. until analysis.
  • Serum samples were analyzed using an anti-TNF capture assay depicted in FIG. 4 in which a biotinylated humanTNFoc was used for capture and a labeled anti-human Sulfo-Tag for detection.
  • the assay was carried out in 1% final serum concentration.
  • the lower limit of quantitation (LLOQ) was 0.004 ⁇ g/mL.
  • the low control was 0.1 ⁇ g/mL.
  • Standard curve fitting and data evaluation was performed using XLfit4 software with a four-parameter logistic fit. Plates passed when at least 2 ⁇ 3 of the QC's were within 30% of the expected values.
  • Pharmacokinetic parameters for each animal were calculated using WinNonlin® software Version 5.0.1 (Pharsight Corporation, Mountain View, Calif.) by non-compartmental analysis using linear trapezoidal fit (NCA Models # 201 for IV dosing). For calculations in WinNonlin, the time of dosing was defined as Day 0 Time 0 hr.
  • FIG. 5A The serum concentrations as a function of time are shown in FIG. 5A (ZFN-B1) and FIG. 5B (D2E7).
  • the pharmacokinetic parameters for High Gal ZFN-B1 administered mice # 3 and 5 are depicted in FIG. 5C .
  • the result show that 4 of 5 animals administered anti-TNF hypergalactosylated ZFN-B1 monoclonal antibody had measurable antibody levels out to 21 days ( FIG. 5A ).
  • the High Gal ZFN-B1 administered mouse #3 displayed a long half-life and low CL (24.5 days and 0.14 mL/h/kg).
  • all the animals administered the anti-TNF D2E7 monoclonal antibody displayed probable anti-drug antibodies (ADA).
  • ADA probable anti-drug antibodies

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Abstract

Provided are glycoengineered populations of Fc domain-containing binding proteins with a reduced anti-drug immune response (ADA). Also provided are methods of treating disease using such compositions, and methods and host for making such compositions.

Description

    RELATED APPLICATIONS
  • This application claims priority to U.S. Provisional Application No. 61/904,487, filed Nov. 15, 2013 and U.S. Provisional Application No. 62/051,669, filed Sep. 17, 2014, the contents of which are hereby incorporated by reference herein in their entireties.
    • FIELD OF THE INVENTION
  • The present invention relates to compositions of recombinant Fc binding proteins, e.g., recombinant antibodies, which exhibit improved properties (e.g., a reduced anti-drug immune response) as a result of their optimized glycosylation profile.
    • BACKGROUND
  • The use of therapeutic binding proteins has revolutionized the treatment of many diseases, including cancer, inflammatory bowel disease (IBD), ankylosing spondylitis, multiple sclerosis, psoriasis and rheumatoid arthritis (RA). Despite their success in improving the quality of life of patients, long-term treatment with therapeutic binding proteins is often associated with the emergence of anti-drug antibodies (ADA) against the therapeutic agent. The development of ADA results in progressively lower serum drug levels and a diminished treatment efficacy.
  • For example, a 2011 study of rheumatoid arthritis patients treated with adalimumab revealed the development of anti-drug antibodies resulted in significantly lower remission rates. Two-thirds of the anti-adalimumab antibody-positive patients developed antibodies to the drug within the first 28 weeks of treatment. The presence of anti-adalimumab antibodies was further shown to substantially reduce serum adalimumab concentrations. Similar results have been reported for infliximab, adalimumab, and natalizumab (see Bartelds et al., JAMA. 2011; 305(14):1460-1468). Such ADA immune responses, therefore, decrease the overall efficacy and utility of therapeutic binding proteins.
  • Accordingly, there is a need in the art for recombinant protein therapeutics compositions that exhibit a reduced ADA response relative to current therapeutic binding proteins.
    • SUMMARY OF THE INVENTION
  • The present disclosure provides novel binding protein compositions exhibiting a surprisingly reduced anti-drug antibody (ADA) immune response as a result of their optimized glycoprofile. These compositions generally comprise a population of Fc domain-containing binding proteins that are hypergalactosylated (e.g., enriched for binding proteins with highly galactosylated glycoforms) and/or hypomannosylated (e.g., deficient in binding proteins with highly mannosylated glycoforms) on the Fc glycosylation site of the binding proteins. Thus, the compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1. Also provided are methods of treating a disorder using these compositions, and methods and host cells for making such compositions.
  • The binding protein compositions disclosed herein are particularly advantageous in that they exhibit a longer serum half-life than non-hypergalactosylated and/or non-hypomannosylated Fc domain-containing binding protein compositions and, therefore, require less frequent dosing to be efficacious.
  • Accordingly, in one aspect, the instant disclosure provides a hypergalactosylated population of Fc domain-containing binding proteins, wherein the total percent amount of G1 and G2 glycoforms in the population is more than 50% (e.g., more than 80%, more than 90%, more than 95% or more than 99%). In certain embodiments, the total percent amount of G1 and G2 glycoforms in the population is more than 80%. In certain embodiments, the G1 and G2 glycoforms in the population are fucosylated. In certain embodiments, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%). In certain embodiments, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population is more than 80%. In certain embodiments, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population are fucosylated.
  • In other aspects, the binding protein compositions of the invention are also hypomannosylated. For example, the binding protein composition of the inventions may exhibit less than 10% of highly mannosylated glycoforms (oligomannose species, e.g., M3-M9 glycoforms) in population of Fc-domain-containing binding proteins. In certain embodiments, less than 5% (e.g., less than 1% or less than 0.1%) of the Fc domain-containing binding proteins in the population are highly mannosylated.
  • In certain embodiments, the binding protein compositions of the invention have a G/M ratio of greater than 1:1 (e.g., at least 2:1, 5:1, 10:1, 80:1 or at least 99:1). In certain embodiments, the population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1). In certain embodiments, the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1). In certain embodiments, the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • In certain embodiments, the Fc domain-containing binding proteins in the population comprise an antigen-binding portion of an antibody. In certain embodiments, the antibody is selected from the group consisting of alemtuzumab, bevacizumab, cetuximab, edrecolomab, gemtuzumab ozogamicin, ibritumomab tiuxetan, ofatumumab, panitumumab, rituximab, tositumomab, trastuzumab, arcitumomab, capromab pendetide, nofetumomab, satumomab, basiliximab, daclizumab, muromonab-cd3, infliximab, natalizumab, adalimumab, certolizumab, golimumab, infliximab, tocilizumab, omalizumab, abciximab, bevacizumab, ranibzumab, natalizumab, efalizumab, ustekinumab, palivizumab, ruplizumab, denosumab, eculizumab, alefacept, abatacept, etanercept, romiplostim, rilonacept, aflibercept, belatacept, or rilonacept. In certain embodiments, the Fc domain-containing binding proteins in the population comprise a non-antibody antigen-binding portion. In certain embodiments, the hypergalactosylated population is a hypergalactosylated population of dual variable domain immunoglobulins (DVD-Ig).
  • In certain aspects, the invention provides compositions wherein the binding proteins in the population bind to tumor necrosis factor alpha (TNFoc). In certain embodiments, the binding protein is selected from the group consisting of etanercept, infliximab, adalimumab, or golimumab. In certain exemplary embodiments, the binding protein is the anti-TNF antibody adalimumab or a variant thereof. In certain embodiments, the anti-TNF antibody is an Fc variant of adalimumab (D2E7) comprising the heavy and light chain variable region sequences of adalimumab and a variant Fc region with an amino acid substitution that confers enhanced serum half-life. In certain exemplary embodiments, the variant Fc region is a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence (wherein amino acid numbering is according to the EU numbering convention as in Kabat). In other embodiments, the anti-TNF antibody is a variant of adalimumab which exhibits pH-sensitive binding to the TNF antigen. In one exemplary embodiment, the pH-sensitive variant of adalimumab is a D2E7SS22 comprising the heavy chain of SEQ ID NO: 1 and the light chain of SEQ ID NO: 2. In another exemplary embodiment, the pH-sensitive variant comprises the heavy and light chain variable regions of D2E7SS2 and a variant Fc region (e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence).
  • In certain embodiments, the binding compositions of the invention are produced in a cultured mammalian host cell line (e.g., a CHO cell line). In certain embodiments, the host cell line has been glycoengineered to produce the hypergalactosylated and/or hypomannosylated binding proteins of the invention. In certain exemplary embodiments, the binding proteins of the invention are obtained from a glycoengineered CHO cell. In one exemplary embodiment, the glycoengineered CHO cell contains a heterologous galactosyltransferase gene (e.g., mouse galactosyltransferase Beta 1,4). In another exemplary embodiment, the glycoengineered CHO cell contains a knockdown of one of the alleles of the Beta galactosidase gene. Exemplary glycoengineered host cells include the GALtr11 CHO cell line and the ZFN-B1 CHO cell line described in Examples 1 and 2 herein, respectively.
  • In a second aspect, the instant disclosure provides a method of reducing a subject's anti-drug antibody (ADA) response to a population of Fc domain-containing binding proteins, the method comprising glycoengineering (e.g., hypergalactosylating and/or hypomannosylating) a population of Fc domain-containing binding proteins by increasing the G/M ratio of the population of Fc domain-containing binding proteins, such that the glycoengineered population of Fc domain-containing binding proteins has a greater serum half-life than the non-glycoengineered population of Fc domain-containing binding proteins. In certain embodiments, said glycoengineering comprises expressing the Fc domain-containing binding proteins in a glycoengineered host cell (e.g., a CHO cell that has been glycoengineered to express hypergalactosylated and/or hypomannosylated binding proteins), and isolating the hypergalactosylated and/or hypomannosylated binding proteins from the host cell.
  • In certain embodiments of the second aspect, the population is glycoengineered such that the total percent amount of G1 and G2 glycoforms in the hypergalactosylated population is more than 80%. In certain embodiments of the second aspect, the G1 and G2 glycoforms in the hypergalactosylated population are fucosylated. In certain embodiments of the second aspect, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population is more than 50% (e.g., more than 80%, or more than 99%). In certain embodiments of the second aspect, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population is more than 80%. In certain embodiments of the second aspect, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are fucosylated.
  • In certain embodiments of the second aspect, the methods of the invention comprise glycoengineering a population of Fc domain-containing binding proteins such that the population exhibits less than 10% of highly mannosylated glycoforms (oligomannose species, e.g., M3-M9 glycoforms). In certain embodiments of the second aspect, less than 5% of the Fc domain-containing binding proteins in the population comprise M3-M9 glycoforms. In certain embodiments of the second aspect, less than 1% of the Fc domain-containing binding proteins in the population comprise M3-M9 glycoforms. In certain embodiments of the second aspect, less than 0.1% of the Fc domain-containing binding proteins in the population comprise M3-M9 glycoforms.
  • In certain embodiments of the second aspect, the methods of the invention comprise glycoengineering a population of Fc domain-containing binding proteins such that population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1). In certain embodiments of the second aspect, the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1). In certain embodiments of the second aspect, the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1).
  • In certain embodiments of the second aspect, the Fc domain-containing binding proteins in the population comprise an antigen-binding portion of an antibody. In certain embodiments of the second aspect, the Fc domain-containing binding proteins in the population comprise a non-antibody antigen-binding portion. In certain embodiments of the second aspect, the Fc domain-containing binding proteins in the hypergalactosylated population comprise a dual variable domain immunoglobulin (DVD-Ig).
  • In certain embodiments of the second aspect, the binding proteins of the invention are selected from the group consisting of alemtuzumab, bevacizumab, cetuximab, edrecolomab, gemtuzumab ozogamicin, ibritumomab tiuxetan, ofatumumab, panitumumab, rituximab, tositumomab, trastuzumab, arcitumomab, capromab pendetide, nofetumomab, satumomab, basiliximab, daclizumab, muromonab-cd3, infliximab, natalizumab, adalimumab, certolizumab, golimumab, infliximab, tocilizumab, omalizumab, abciximab, bevacizumab, ranibzumab, natalizumab, efalizumab, ustekinumab, palivizumab, ruplizumab, denosumab, eculizumab, alefacept, abatacept, etanercept, romiplostim, rilonacept, aflibercept, belatacept, or rilonacept.
  • In certain embodiments of the second aspect, the binding proteins of the invention comprise an antigen-binding portion that binds to tumor necrosis factor alpha (TNFα). In certain embodiments, the binding portion is selected from the group consisting etanercept, infliximab, adalimumab, or golimumab. In certain exemplary embodiments, the binding protein is adalimumab. In other exemplary embodiments, the binding protein is an Fc variant of adalimumab. In other embodiments, the binding protein is D2E7SS22 or an Fc variant thereof.
  • In certain embodiments, the compositions of the invention do not exhibit an increased level of antibody-dependent cellular cytotoxicity (ADCC) activity and/or an increased level of complement-dependent cellular cytotoxicity (CDC) activity as compared to a composition that is not glycoengineered according to the methods of the invention (e.g., a composition that is not hypergalactosylated and/or hypomannosylated).
  • In a third aspect, the instant disclosure provides a glycoengineered host cell (e.g., a CHO cell) that produces a glycoengineered population of Fc domain-containing binding proteins having an enhanced G/M ratio of greater than 10:1 (e.g., greater than 50:1, 90:1 or 99:1). In certain embodiments, the glycoengineered population of Fc domain-containing binding proteins has one or more of the following properties: the total percent amount of G1 and G2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%); the total percent amount of G1, G2, G1S1, G2S1 or G2S2 glycoforms in the population is more than 50% (e.g., more than 80%, or more than 99%); less than 10% (e.g., less than 1%, or less than 0.1%) of the Fc domain-containing binding proteins in the population comprise highly mannosylated (e.g., M3-M9) glycoforms; a G1/2:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1): a GS:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1); or a Gtotal:M ratio of at least 10:1 (e.g., at least 50:1, at least 80:1, or at least 99:1). In certain embodiments of the third aspect, the G1, G2, G1S1, G2S1 or G2S2 glycoforms in the hypergalactosylated population are fucosylated.
  • In a fourth aspect, the instant disclosure provides a method of treating a disorder in a subject in need thereof, comprising administering to the subject an effective amount of the hypergalactosylated population of Fc domain-containing binding proteins described herein. In certain embodiments of the fourth aspect, the disorder is a TNFc associated disorder.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • The skilled artisan will understand that the drawings, described below, are for illustration purposes only. The figures are not intended to limit the scope of the teachings in any way.
  • FIG. 1A is a schematic of the processing and maturation of an N-glycan. The mature Dol-P-P-glycan is transferred to Asn-X-Ser/Thr sequons during protein synthesis as proteins are being translocated into the ER. Following transfer of the 14-sugar Glc3Man9GlcNAc2 glycan to protein, glucosidases in the ER remove the three glucose residues, and ER mannosidase removes a mannose residue. These reactions are intimately associated with the folding of the glycoprotein assisted by the lectins calnexin and calreticulin, and they determine whether the glycoprotein continues to the Golgi or is degraded. Another lectin, termed EDEM (ER degradation-enhancing α-mannosidase I-like protein), binds to mannose residues on misfolded glycoproteins and escorts them via retrotranslocation into the cytoplasm for degradation. For most glycoproteins, additional mannose residues are removed in the cis compartment of the Golgi until Man5GlcNAc2Asn is generated. The action of GlcNAcT-1 on Man5GlcNAc2Asn in the medial-Golgi initiates the first branch of an N-glycan. The action of α-mannosidase II generates the substrate for GlcNAcT-II. The resulting biantennary N-glycan is extended by the addition of fucose, galactose, and sialic acid to generate a complex N-glycan with two branches (reviewed in Annual Review of Biochemistry, from R. Kornfeld and S. Kornfeld. 1985. Annu. Rev. Biochem. 54: 631-634).
  • FIG. 1B is a schematic of an exemplary N-Glycan structure of an Fc region of an antibody.
  • FIG. 1C is a schematic depicting exemplary non-galactosylated glycans imparting immunogenic properties to biologics.
  • FIG. 1D is a schematic depicting exemplary galactosylated glycans imparting non-immunogenic properties to biologics.
  • FIG. 2A shows the cloning of mouse beta1-4 galactosyltransferase into the mammalian expression vector, pCDN3.3.
  • FIG. 2B shows the DNA sequence (SEQ ID NO: 1) and corresponding amino acid sequence (SEQ ID NO: 2) of the mouse beta1-4 galactosyltransferase.
  • FIG. 2C shows the percentage of individual glycoforms of anti-human TNFα expressed in standard and High-Gal CHO cell lines. D2E7 is adalimumab (Humira®) expressed in a standard CHO production cell line, ZFN-B1 is adalimumab expressed in a CHO cell line with a knockout in one of the alleles of the beta galactosidase gene; Galtr-11 and Gal88-D2E7 are glycoengineered adalimumab preparations obtained from CHO cell lines overexpressing β-1, 4 galactosyltransferase; SA-D2E7 is a glycoengineered adalimumab preparation obtained from a CHO cell line with a knockout in one of the alleles of the beta galactosidase gene and overexpressing β-1, 4 galactosyltransferase (ZFN B1 Gal-T-11) and further subjected to in vitro sialyltransferase treatment and ion-exchange purification; and Gal79 DVD-Ig is a glycoengineered IL17xTNF DVD-Ig (ABT-122) obtained from a CHO cell line overexpressing β-1, 4 galactosyltransferase.
  • FIG. 2D shows a mass spectrometry (MALDI-TOF) analysis of the glycoengineered Galtr-11 adalimumab preparation in FIG. 2C. Prominent peaks indicate the presence of the G1F (50,800 Da) and G2F (50,962 Da) glycoforms.
  • FIG. 2E shows a mass spectrometry (MALDI-TOF) analysis of the glycoengineered SA-D2E7 adalimumab preparation of FIG. 2C before (bottom panel) and after (top panel) treatment with sialyltransferase. Prominent peaks indicate the presence of GIF (50,800 Da), G2F (50,962 Da), G2S1F (A1F; 51,253 Da), and G2S2F (51,544 Da) glycoforms.
  • FIG. 3A shows the pinocytosis by human dendritic cells of non-glycoengineered adalimumab (D2E7/Humira®) and glycoengineered adalimumab (ZFN-B1) produced in a CHO cell line with a knockout of one of the alleles of the beta galactosidase gene.
  • FIG. 3B shows the internalization of transmembrane TNFα induced in dendritic cells by non-glycoengineered adalimumab (D2E7/Humira®) and glycoengineered adalimumab (ZFN-B1) produced in a CHO cell line with a knockout of one of the alleles of the beta galactosidase gene.
  • FIG. 3C shows the pinocytosis by human dendritic cells of non-glycoengineered adalimumab (D2E7/Humira®) and glycoengineered adalimumab (Ga188-D2E7 and SA-D2E7).
  • FIG. 4 is a schematic of the anti-TNFα capture assay employed for Drug Metabolism and Pharmacokinetics (DMPK) Bioanalysis of the glycoengineered compositions of the invention.
  • FIG. 5A shows the pharmacokinetic (PK) profile of a glycoengineered (hypergalactosylated and hypomannosylated) preparation of anti-TNFα mAb (ZFN-B-1; lot 2168407) Serum Concentrations after 5 mg/kg IV Dosing in CD-1 Mice (W14-0201).
  • FIG. 5B shows the pharmacokinetic (PK) profile of a non-glycoengineered preparation of anti-TNFα mAb D2E7 (HUMIRA®; lot 2158962) Serum Concentrations after 5 mg/kg IV dosing in CD-1 Mice (W14-0203).
  • FIG. 5C shows the pharmacokinetic (PK) parameters of the glycoengineered anti-TNFα High Galactose mAb ZFN-B-1 (lot 2168407) after 5 mg/kg IV Dosing in CD-1 Mice.
  • FIG. 6 is a schematic depicting exemplary naturally-occurring N-glycan glycoforms. Mammalian cells have a more diverse range of modifications than any of the other organisms. Certain motifs extending the N-glycan arms (lactosamine chains, terminal GalNAc, terminal sialylation, fucosylation) are also found in mammalian O-glycans.
  • FIG. 7A depicts an exemplary 2-AB HPLC quantitative analysis of glycoengineered binding compositions of the invention. Cell line 236 is a galactosyl transferase transfected CHO cell line producing Adalimumab (D2E7). ZFN-B 1 is a CHO cell line producing Adalimumab and containing a knockdown of the Beta galactosidase gene. ABT-122 is an IL17xTNF DVD-Ig.
  • FIG. 7B depicts an exemplary 2-AB HPLC quantitative analysis of the Galtr-11 (pink trace, second from top) and SA-D2E7 (blue trace, second from bottom) glycoengineered binding compositions of the invention as compared to a non-glycoengineered form of adalimumab (Humira®; top trace). The bottom trace corresponds to sialylated glycan standards.
  • FIG. 7C depicts an exemplary ion exchange chromatogram (WCX-10 HPLC) of the Galtr-11 (blue trace, second from top) and SA-D2E7 (bottom green trace) glycoengineered binding compositions of the invention, as compared to a non-glycoengineered form of adalimumab (Humira®; top red trace). The addition of sialic acid imparts a charge to the glycan resulting in earlier elution from the ion-exchange column
    •  DETAILED DESCRIPTION OF THE INVENTION
  • The present disclosure provides novel glycoengineered binding protein compositions exhibiting a surprisingly reduced anti-drug antibody (ADA) immune response as a result of their optimized glycoprofile. These compositions generally comprise a population of Fc domain-containing binding proteins that are hypergalactosylated (e.g., enriched for binding proteins with highly galactosylated glycoforms) and/or hypomannosylated (e.g., deficient in binding proteins with highly mannosylated glycoforms) on the Fc glycosylation site of the binding proteins. Thus, the compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1. Also provided are methods of treating a disorder using these compositions, and methods and host cells for making such compositions.
  • The glycoengineered binding protein compositions disclosed herein are particularly advantageous in that they exhibit a longer serum half-life than non-glycoengineered Fc domain-containing binding protein compositions and, therefore, require less frequent dosing to be efficacious.
    • I. DEFINITIONS
  • Unless otherwise defined herein, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. The meaning and scope of the terms should be clear, however, in the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Generally, nomenclature used in connection with, and techniques of, cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein are those well-known and commonly used in the art.
  • In order that the present invention may be more readily understood, certain terms are first defined.
  • As used herein the term “Fc domain-containing binding protein” refers to a protein that specifically binds to an antigen, wherein the protein comprises an Fc domain, or an Fc-receptor binding fragment thereof, comprising an N-glycan. In certain embodiments, the N-glycan is an N-linked biantennary glycans present in the CH2 domain of an immunoglobulin constant (Fc) region (e.g., at EU position 297). “N-glycans” are attached at an amide nitrogen of an asparagine or an arginine residue in a protein via an N-acetylglucosamine residue. These “N-linked glycosylation sites” occur in the peptide primary structure containing, for example, the amino acid sequence asparagine-X-serine/threonine, where X is any amino acid residue except proline and aspartic acid. Such N-Glycans are fully described in, for example, Drickamer K, Taylor M E (2006). Introduction to Glycobiology, 2nd ed., which is incorporated herein by reference in its entirety.
  • In one embodiment, “N glycan” refers to the Asn-297 N-linked biantennary glycans present in the CH2 domain of an immunoglobulin constant (Fc) region. These oligosaccharides may contain terminal mannose, N-acetyl-glucosamine, Galactose or Sialic acid (see FIGS. 1C and 1D).
  • As used herein, the term “glycoengineering” refers to any art-recognized method for altering the glycoform profile of a binding protein composition. Such methods include expressing a binding protein composition in a genetically engineered host cell (e.g., a CHO cell) that has been genetically engineered to express a heterologous glycosyltransferase or glycosidase. In other embodiments, the glycoengineering methods comprise culturing a host cell under conditions that bias for particular glycoform profiles.
  • As used herein the term “hypergalactosylated population” refers to a population of Fc domain-containing binding proteins in which the galactose content of the N glycan is increased as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence. A hypergalactosylated population can be expressed as having an increased number of G1 and G2 glycoforms as compared to the reference population of Fc domain-containing binding proteins.
  • As used herein, the term “hypomannosylated population” refers to a population of Fc domain-containing binding proteins in which the mannose content of the N glycan is decreased as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence. A hypomannosylated population can be expressed as having a decreased number of oligomannose glycoforms (e.g., M3-M9 glycoforms) as compared to the reference population of Fc domain-containing binding proteins. In some embodiments, the mannose content is determined by measuring the content of one or more of oligomannose glycoforms selected from the group consisting of Man3, Man4, Man5, Man6, Man7, Man 8 and Man 9. In other embodiments, the oligomannose content is determined by measuring at least Man 5, Man 6, and Man 7. In certain embodiments, the oligomannose content is determined by measuring all M3-M9 glycoforms.
  • As used herein the terms “G0 glycoform,” “G1 glycoform,” and “G2 glycoform” refer to N-Glycan glycoforms that have zero, one or two terminal galactose residues respectively, as depicted in FIGS. 1C and 1D herein. These terms include G0, G1, and G2 glycoforms that are fucosylated (shown as G0F, G1F and G2F respectively in FIGS. 1C and 1D) or comprise a bisecting N-acetylglucosamine residue.
  • In certain embodiments, the G1 and G2 glycoforms further comprise sialic acid residues linked to one or both of the terminal galactose residues to form G1S1, G2S1 and G2S2 glycoforms. As used herein the terms “G1S1 glycoform,” “G2S1 glycoform,” and “G252 glycoform” refer to N-Glycan glycoforms that have a sialic acid residue linked to the sole terminal galactose residue in a G1 glycoform, one of the terminal galactose residue in a G2 glycoform, or both of the terminal galactose residue in a G2 glycoform, respectively (see FIG. 1D herein). These terms include G1S1, G2S1 and G2S2 glycoforms that are fucosylated or comprise a bisecting N-acetylglucosamine residue. In certain embodiments, the sialic residues of G1S1, G2S1 and G2S2 glycoforms are linked by alpha-2,6-sialic acid linkages to the terminal galactose residue of each glycoform in order to enhance the anti-inflammatory activity of the binding molecule (see e.g., Anthony et al., PNAS 105: 19571-19578, 2008).
  • As used herein the terms “G1F glycoform,” “G2F glycoform,” “G1S1F glycoform,” “G2S1F glycoform,” and “G2S2F glycoform” refer to “G1 glycoform,” and “G2 glycoform” “G1S1 glycoform,” “G2S1 glycoform,” and “G252 glycoform” that are fucosylated.
  • As used herein, the term“M3-M9 glycoforms” refers to the mannosylated glycoforms depicted in FIG. 1C.
  • As used herein, the term “G/M ratio” or “Gtotal:M ratio” refers to the ratio of the total percent amount of all galactose containing glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of oligomannose (e.g., M3-M9) glycoforms.
  • As used herein, the term“G1/2:M ratio” refers to the ratio of the total percent amount of G1 and G2 glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of M3-M8 glycoforms.
  • As used herein, the term “GS:M ratio” refers to the ratio of the total percent amount G1S1, G2S1 and G2S2 glycoforms in a population of Fc-domain containing binding proteins relative to the total percent amount of M3-M9 glycoforms.
  • As used herein the term “reference binding composition” or “reference antibody” refers to a binding composition having the substantially the same amino acid sequence as (e.g., having about 90-100% identical amino acid sequence) of a glycoengineered antibody composition of the invention disclosed herein, e.g., a binding composition to which it is compared. In some embodiments, the reference composition is a FDA approved therapeutic Fc-domain containing binding protein (e.g., antibody) or a biosimilar thereof. In other embodiments, the reference binding composition comprises a non-hypergalactosylated population of Fc-domain containing binding proteins.
  • As used herein the term “non-hypergalactosylated population” refers a population of Fc domain-containing binding proteins in which the amount of G1 and/or G2 glycoforms are not enriched relative to the G0 glycoforms, as compared to a reference population of Fc domain-containing binding proteins having the same amino acid sequence.
  • As used herein, the term “more than” means more than or equal to, and the term “less than” means less than or equal to.
  • As used herein, the term “infliximab” refers to the anti-TNF antibody marketed as REMICADE™, having Chemical Abstracts Service (CAS) designation 170277-31-3.
  • As used herein, the term “golimumab” refers to the anti-TNF antibody marketed as SIMPONI™, having Chemical Abstracts Service (CAS) designation 476181-74-5.
  • As used herein, the term “adalimumab” refers to the anti-TNF antibody marketed as HUMIRA™, having Chemical Abstracts Service (CAS) designation 331731-18-1.
  • As used herein, the term “infliximab” refers to the anti-TNF immunoadhesin marketed as ENBREL™, having Chemical Abstracts Service (CAS) designation 1094-08-2.
  • The term “human TNF-alpha”, as used herein, is intended to refer to a human cytokine that exists as a 17 kD secreted form and a 26 kD membrane associated form, the biologically active form of which is composed of a trimer of noncovalently bound 17 kD molecules. The structure of human TNF-alpha is described further in, for example, Pennica, D., et al. (1984) Nature 312:724-729; Davis, J. M., et al. (1987) Biochemistry 26:1322-1326; and Jones, E. Y., et al. (1989) Nature 338:225-228. The term human TNF-alpha is intended to include recombinant human TNF-alpha, which can be prepared by standard recombinant expression methods or purchased commercially (R & D Systems, Catalog No. 210-TA, Minneapolis, Minn.)
  • The term “antibody”, as used herein, broadly refers to any immunoglobulin (Ig) molecule comprised of four polypeptide chains, two heavy (H) chains and two light (L) chains, or any functional fragment, mutant, variant, or derivation thereof, which retains the essential epitope binding features of an Ig molecule. Such mutant, variant, or derivative antibody formats are known in the art. Non-limiting embodiments of which are discussed below.
  • In a full-length antibody, each heavy chain is comprised of a heavy chain variable region (abbreviated herein as HCVR or VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CH1, CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as LCVR or VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, 1-R3, CDR3, FR4 Immunoglobulin molecules can be of any type (e.g., IgG, IgE, IgM, IgD, IgA and IgY), class (e.g., IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2) or subclass.
  • The term “Fc domain” is used to define the C-terminal region of an immunoglobulin heavy chain, which may be generated by papain digestion of an intact antibody. The Fc domain may be a native sequence Fc domain or a variant Fc domain. The Fc domain of an immunoglobulin generally comprises two constant domains, a CH2 domain and a CH3 domain, and optionally comprises a CH4 domain Replacements of amino acid residues in the Fc portion to alter antibody effector function are known in the art (Winter, et al. U.S. Pat. Nos. 5,648,260; 5,624,821). The Fc domain of an antibody mediates several important effector functions e.g. cytokine induction, ADCC, phagocytosis, complement dependent cytotoxicity (CDC) and half-life/clearance rate of antibody and antigen-antibody complexes. In certain embodiments, at least one amino acid residue is altered (e.g., deleted, inserted, or replaced) in the Fc domain of an Fc domain-containing binding protein such that effector functions of the binding protein are altered.
  • The term “antigen-binding portion” of an antibody (or simply “antibody portion”), as used herein, refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen. It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Such antibody embodiments may also be bispecific, dual specific, or multi-specific formats; specifically binding to two or more different antigens. Examples of binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) an Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CH1 domains; (ii) an F(ab′).sub.2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CH1 domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341:544-546, Winter et al., PCT publication WO 90/05144 A1 herein incorporated by reference), which comprises a single variable domain; and (vi) an isolated complementarity determining region (CDR). Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883). Such single chain antibodies are also intended to be encompassed within the term “antigen-binding portion” of an antibody. Other forms of single chain antibodies, such as diabodies are also encompassed. Diabodies are bivalent, bispecific antibodies in which VH and VL domains are expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger, P., et al. (1993) Proc. Natl. Acad. Sci. USA 90:6444-6448; Poljak, R. J., et al. (1994) Structure 2:1121-1123). Such antibody binding portions are known in the art (Kontermann and Dubel eds., Antibody Engineering (2001) Springer-Verlag. New York. 790 pp. (ISBN 3-540-41354-5). In addition single chain antibodies also include “linear antibodies” comprising a pair of tandem Fv segments (VH-CH1-VH-CH1) which, together with complementary light chain polypeptides, form a pair of antigen binding regions (Zapata et al. Protein Eng. 8(10):1057-1062 (1995); and U.S. Pat. No. 5,641,870).
  • As used herein, the terms “VH domain” and “VL domain” refer to single antibody variable heavy and light domains, respectively, comprising FR (Framework Regions) 1, 2, 3 and 4 and CDR (Complementary Determinant Regions) 1, 2 and 3 (see Kabat et al. (1991) Sequences of Proteins of Immunological Interest. (NIH Publication No. 91-3242, Bethesda).
  • As used herein, the term “CDR” or “complementarity determining region” means the noncontiguous antigen combining sites found within the variable region of both heavy and light chain polypeptides. These particular regions have been described by Kabat et al., J. Biol. Chem. 252, 6609-6616 (1977) and Kabat et al., Sequences of protein of immunological interest. (1991), and by Chothia et al., J. Mol. Biol. 196:901-917 (1987) and by MacCallum et al., J. Mol. Biol. 262:732-745 (1996) where the definitions include overlapping or subsets of amino acid residues when compared against each other. The amino acid residues which encompass the CDRs as defined by each of the above cited references are set forth for comparison. Preferably, the term “CDR” is a CDR as defined by Kabat, based on sequence comparisons.
  • As used herein the term “framework (FR) amino acid residues” refers to those amino acids in the framework region of an immunoglobulin chain. The term “framework region” or “PR region” as used herein, includes the amino acid residues that are part of the variable region, but are not part of the CDRs (e.g., using the Kabat definition of CDRs).
  • As used herein, the term “specifically binds to” refers to the ability of a binding protein to bind to an antigen with an Kd of at least about 1×10−6 M, 1×10−7 M, 1×10−8 M, 1×10−9 M, 1×10−10 M, 1×10−11 M, 1×10−12 M, or more, and/or bind to an antigen with an affinity that is at least two-fold greater than its affinity for a nonspecific antigen. It shall be understood, however, that the binding protein are capable of specifically binding to two or more antigens which are related in sequence. For example, the binding polypeptides of the invention can specifically bind to both human and a non-human (e.g., mouse or non-human primate) orthologs of an antigen.
  • The term “polypeptide” as used herein, refers to any polymeric chain of amino acids. The terms “peptide” and “protein” are used interchangeably with the term polypeptide and also refer to a polymeric chain of amino acids. The term “polypeptide” encompasses native or artificial proteins, protein fragments and polypeptide analogs of a protein sequence. A polypeptide may be monomeric or polymeric.
  • “Pharmacokinetics” refers to the process by which a drug is absorbed, distributed, metabolized, and excreted by an organism. The pharmacokinetic (PK) profile of Fc containing binding proteins can be easily determined in rodents using methods known to one skilled in the art (U.S. Published Patent Application No. 2009/0311253).
  • The term “recombinant host cell” (or simply “host cell”), as used herein, is intended to refer to a cell into which exogenous DNA has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell, but, to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. Preferably host cells include prokaryotic and eukaryotic cells selected from any of the Kingdoms of life. Preferred eukaryotic cells include protist, fungal, plant and animal cells. Most preferably host cells include but are not limited to the prokaryotic cell line E. Coli; mammalian cell lines CHO, HEK 293 and COS; the insect cell line Sf9; and the fungal cell Saccharomyces cerevisiae. In certain embodiments, the host cell is an engineered CHO cell, e.g., a CHO cell transformed with a heterologous galactosyltransferase and/or a heterologous sialyltransferase.
    • II. Glycoengineered Binding Protein Compositions
  • In certain aspects, the invention provides a composition comprising a population of Fc-domain containing binding proteins that are hypergalactosylated and/or hypomannosylated. In certain embodiments, the population of Fc domain-containing binding proteins employed in the compositions and methods disclosed herein has an increased amount of G1 and/or G2 glycoforms relative to the G0 glycoforms, as compared to a reference population comprising a reference Fc domain-containing binding protein with the same amino acid sequence. In certain embodiments, all of the Fc-domain binding polypeptides in the population may be directed to the same antigen or epitope. In other embodiments, all of the Fc-domain binding polypeptides in the population are encoded by the same nucleic acid sequence.
  • In certain embodiments, the population of Fc domain-containing binding proteins comprises less than 70%, less than 69%, less than 68%, less than 67%, less than 66%, less than 65%, less than 64%, less than 63%, less than 62%, less than 61%, less than 60%, less than 59%, less than 58%, less than 57%, less than 56%, less than 55%, less than 54%, less than 53%, less than 52%, less than 51%, less than 50%, less than 49%, less than 48%, less than 47%, less than 46%, less than 45%, less than 44%, less than 43%, less than 42%, less than 41%, less than 40%, less than 39%, less than 38%, less than 37%, less than 36%, less than 35%, less than 34%, less than 33%, less than 32%, less than 31%, less than 30%, less than 29%, less than 28%, less than 27%, less than 26%, less than 25%, less than 24%, less than 23%, less than 22%, less than 21%, less than 20%, less than 19%, less than 18%, less than 17%, less than 16%, less than 15%, less than 14%, less than 13%, less than 12%, less than 11%, less than 10%, less than 9%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2%, or less than 1% of the G0 glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises 70%, 69%, 68%, 67%, 66%, 65%, 64%, 63%, 62%, 61%, 60%, 59%, 58%, 57%, 56%, 55%, 54%, 53%, 52%, 51%, 50%, 49%, 48%, 47%, 46%, 45%, 44%, 43%, 42%, 41%, 40%, 39%, 38%, 37%, 36%, 35%, 34%, 33%, 32%, 31%, 30%, 29%, 28%, 27%, 26%, 25%, 24%, 23%, 22%, 21%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or 1% of the G0 glycoform.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the G1 glycoforms. In certain embodiments, the G1 glycoforms in the hypergalactosylated population are G1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G1 glycoform. In certain embodiments, the G1 glycoforms in the hypergalactosylated population are G1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60%, more than 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the G2 glycoforms. In certain embodiments, the G2 glycoforms in the hypergalactosylated population are G2F glycoforms.
  • In certain embodiments, the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30,31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2 glycoform. In certain embodiments, the G2 glycoforms in the hypergalactosylated population are G2F glycoforms.
  • In certain embodiments, the total percent amount of G1 and G2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and 99%, between 52% and 99%, between 53% and 99%, between 54% and 99%, between 55% and 99%, between 56% and 99%, between 57% and 99%, between 58% and 99%, between 59% and 99%, between 60% and 99%, between 61% and 99%, between 62% and 99%, between 63% and 99%, between 64% and 99%, between 65% and 99%, between 66% and 99%, between 67% and 99%, between 68% and 99%, between 69% and 99%, between 70% and 99%, between 71% and 99%, between 72% and 99%, between 73% and 99%, between 74% and 99%, between 75% and 99%, between 76% and 99%, between 77% and 99%, between 78% and 99%, between 79% and 99%, between 80% and 99%, between 81% and 99%, between 82% and 99%, between 83% and 99%, between 84% and 99%, between 85% and 99%, between 86% and 99%, between 87% and 99%, between 88% and 99%, between 89% and 99%, between 90% and 99%, between 91% and 99%, between 92% and 99%, between 93% and 99%, between 94% and 99%, between 95% and 99%, between 96% and 99%, between 97% and 99%, or between 98% and 99%. In certain embodiments, the G1 and G2 glycoforms in the population are G1F and G2F glycoforms.
  • In certain embodiments, the total percent amount of G1 and G2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%, between 20% and 63%, between 20% and 62%, between 20% and 61%, between 20% and 60%, between 20% and 59%, between 20% and 58%, between 20% and 57%, between 20% and 56%, between 20% and 55%, between 20% and 54%, between 20% and 53%, between 20% and 52%, between 20% and 51%, between 20% and 50%, between 20% and 49%, between 20% and 48%, between 20% and 47%, between 20% and 46%, between 20% and 45%, between 20% and 44%, between 20% and 43%, between 20% and 42%, between 20% and 41%, between 20% and 40%, between 20% and 39%, between 20% and 38%, between 20% and 37%, between 20% and 36%, between 20% and 35%, between 20% and 34%, between 20% and 33%, between 20% and 32%, between 20% and 31%, between 20% and 30%, between 20% and 29%, between 20% and 28%, between 20% and 27%, between 20% and 26%, between 20% and 25%, between 20% and 24%, between 20% and 23%, between 20% and 22%, or between 20% and 21%. In certain embodiments, the G1 and G2 glycoforms in the population are G1F and G2F glycoforms.
  • In certain embodiments, the population of Fc domain-containing binding proteins employed in the compositions and methods disclosed herein has an increased amount of G1S1, G2S1 and G2S2 glycoforms relative to the G0 glycoforms, as compared to a reference population comprising a reference Fc domain-containing binding protein with the same amino acid sequence.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the G1S1 glycoforms. In certain embodiments, the G1S1 glycoforms in the population are G1S1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G1S1 glycoform. In certain embodiments, the G1S1 glycoforms in the population are G1S1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the G2S1 glycoforms. In certain embodiments, the G2S1 glycoforms in the hypergalactosylated population are G2S1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2S1 glycoform. In certain embodiments, the G2S1 glycoforms in the population are G2S1F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the G2S2 glycoforms. In certain embodiments, the G2S2 glycoforms in the population are G2S2F glycoforms.
  • In one embodiment, the population of Fc domain-containing binding proteins comprises 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30, 31%, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40, 41%, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% of the G2S2 glycoform. In certain embodiments, the G2S2 glycoforms in the population are G2S2F glycoforms.
  • In certain embodiments, the total percent amount of G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and 99%, between 52% and 99%, between 53% and 99%, between 54% and 99%, between 55% and 99%, between 56% and 99%, between 57% and 99%, between 58% and 99%, between 59% and 99%, between 60% and 99%, between 61% and 99%, between 62% and 99%, between 63% and 99%, between 64% and 99%, between 65% and 99%, between 66% and 99%, between 67% and 99%, between 68% and 99%, between 69% and 99%, between 70% and 99%, between 71% and 99%, between 72% and 99%, between 73% and 99%, between 74% and 99%, between 75% and 99%, between 76% and 99%, between 77% and 99%, between 78% and 99%, between 79% and 99%, between 80% and 99%, between 81% and 99%, between 82% and 99%, between 83% and 99%, between 84% and 99%, between 85% and 99%, between 86% and 99%, between 87% and 99%, between 88% and 99%, between 89% and 99%, between 90% and 99%, between 91% and 99%, between 92% and 99%, between 93% and 99%, between 94% and 99%, between 95% and 99%, between 96% and 99%, between 97% and 99%, or between 98% and 99%. In certain embodiments, the G1S1, G2S1 and G2S2 glycoforms in the population are G1S1F, G2S1F and G2S2F glycoforms.
  • In certain embodiments, the total percent amount of G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%, between 20% and 63%, between 20% and 62%, between 20% and 61%, between 20% and 60%, between 20% and 59%, between 20% and 58%, between 20% and 57%, between 20% and 56%, between 20% and 55%, between 20% and 54%, between 20% and 53%, between 20% and 52%, between 20% and 51%, between 20% and 50%, between 20% and 49%, between 20% and 48%, between 20% and 47%, between 20% and 46%, between 20% and 45%, between 20% and 44%, between 20% and 43%, between 20% and 42%, between 20% and 41%, between 20% and 40%, between 20% and 39%, between 20% and 38%, between 20% and 37%, between 20% and 36%, between 20% and 35%, between 20% and 34%, between 20% and 33%, between 20% and 32%, between 20% and 31%, between 20% and 30%, between 20% and 29%, between 20% and 28%, between 20% and 27%, between 20% and 26%, between 20% and 25%, between 20% and 24%, between 20% and 23%, between 20% and 22%, or between 20% and 21% of the G1S1, G1S2 and G2S2 glycoforms. In certain embodiments, the G1S1, G2S1 and G2S2 glycoforms in the population are G1S1F, G2S1F and G2S2F glycoforms.
  • In certain embodiments, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 21% and 99%, between 22% and 99%, between 23% and 99%, between 24% and 99%, between 25% and 99%, between 26% and 99%, between 27% and 99%, between 28% and 99%, between 29% and 99%, between 30% and 99%, between 31% and 99%, between 32% and 99%, between 33% and 99%, between 34% and 99%, between 35% and 99%, between 36% and 99%, between 37% and 99%, between 38% and 99%, between 39% and 99%, between 40, 41% and 99%, between 42% and 99%, between 43% and 99%, between 44% and 99%, between 45% and 99%, between 46% and 99%, between 47% and 99%, between 48% and 99%, between 49% and 99%, between 50% and 99%, between 51% and 99%, between 52% and 99%, between 53% and 99%, between 54% and 99%, between 55% and 99%, between 56% and 99%, between 57% and 99%, between 58% and 99%, between 59% and 99%, between 60% and 99%, between 61% and 99%, between 62% and 99%, between 63% and 99%, between 64% and 99%, between 65% and 99%, between 66% and 99%, between 67% and 99%, between 68% and 99%, between 69% and 99%, between 70% and 99%, between 71% and 99%, between 72% and 99%, between 73% and 99%, between 74% and 99%, between 75% and 99%, between 76% and 99%, between 77% and 99%, between 78% and 99%, between 79% and 99%, between 80% and 99%, between 81% and 99%, between 82% and 99%, between 83% and 99%, between 84% and 99%, between 85% and 99%, between 86% and 99%, between 87% and 99%, between 88% and 99%, between 89% and 99%, between 90% and 99%, between 91% and 99%, between 92% and 99%, between 93% and 99%, between 94% and 99%, between 95% and 99%, between 96% and 99%, between 97% and 99%, or between 98% and 99%. In certain embodiments, the Gl, G2, G1S1, G2S1 and G2S2 glycoforms in the population are G1F, G2F, G1S1F, G2S1F and G2S2F glycoforms.
  • In certain embodiments, the total percent amount of G1, G2, G1S1, G2S1 and G2S2 glycoforms in the population of Fc domain-containing binding proteins is between 20% and 99%, between 20% and 98%, between 20% and 97%, between 20% and 96%, between 20% and 95%, between 20% and 94%, between 20% and 93%, between 20% and 92%, between 20% and 91%, between 20% and 90%, between 20% and 89%, between 20% and 88%, between 20% and 87%, between 20% and 86%, between 20% and 85%, between 20% and 84%, between 20% and 83%, between 20% and 82%, between 20% and 81%, between 20% and 80%, between 20% and 79%, between 20% and 78%, between 20% and 77%, between 20% and 76%, between 20% and 75%, between 20% and 74%, between 20% and 73%, between 20% and 72%, between 20% and 71%, between 20% and 70%, between 20% and 69%, between 20% and 68%, between 20% and 67%, between 20% and 66%, between 20% and 65%, between 20% and 64%, between 20% and 63%, between 20% and 62%, between 20% and 61%, between 20% and 60%, between 20% and 59%, between 20% and 58%, between 20% and 57%, between 20% and 56%, between 20% and 55%, between 20% and 54%, between 20% and 53%, between 20% and 52%, between 20% and 51%, between 20% and 50%, between 20% and 49%, between 20% and 48%, between 20% and 47%, between 20% and 46%, between 20% and 45%, between 20% and 44%, between 20% and 43%, between 20% and 42%, between 20% and 41%, between 20% and 40%, between 20% and 39%, between 20% and 38%, between 20% and 37%, between 20% and 36%, between 20% and 35%, between 20% and 34%, between 20% and 33%, between 20% and 32%, between 20% and 31%, between 20% and 30%, between 20% and 29%, between 20% and 28%, between 20% and 27%, between 20% and 26%, between 20% and 25%, between 20% and 24%, between 20% and 23%, between 20% and 22%, or between 20% and 21% of the G1S1, G1S2 and G2S2 glycoforms. In certain embodiments, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are G1F, G2F, G1S1F, G2S1F and G2S2F glycoforms.
  • In one embodiment, the sialylated glycoforms (e.g., G1S1, G2S1 and G2S2 glycoforms) in the population of Fc domain-containing binding proteins have increased levels of terminal alpha 2,6-sialic acid linkages on their Fc glycans. In certain embodiments, more than 20%, more than 21%, more than 22%, more than 23%, more than 24%, more than 25%, more than 26%, more than 27%, more than 28%, more than 29%, more than 30%, more than 31%, more than 32%, more than 33%, more than 34%, more than 35%, more than 36%, more than 37%, more than 38%, more than 39%, more than 40%, more than 41%, more than 42%, more than 43%, more than 44%, more than 45%, more than 46%, more than 47%, more than 48%, more than 49%, more than 50%, more than 51%, more than 52%, more than 53%, more than 54%, more than 55%, more than 56%, more than 57%, more than 58%, more than 59%, more than 60, 61%, more than 62%, more than 63%, more than 64%, more than 65%, more than 66%, more than 67%, more than 68%, more than 69%, more than 70%, more than 71%, more than 72%, more than 73%, more than 74%, more than 75%, more than 76%, more than 77%, more than 78%, more than 79%, more than 80%, more than 81%, more than 82%, more than 83%, more than 84%, more than 85%, more than 86%, more than 87%, more than 88%, more than 89%, more than 90%, more than 91%, more than 92%, more than 93%, more than 94%, more than 95%, more than 96%, more than 97%, more than 98%, or more than 99% of the sialylated glycoforms contain alpha 2,6-linkages.
  • In certain embodiments, the G1, G2, G1S1, G2S1 and G2S2 glycoforms in the hypergalactosylated population are G1F, G2F, G1S1F, G2S1F and G2S2F glycoforms.
  • In certain embodiments, the compositions of the invention are obtained from host cells (e.g., CHO cells or other mammalian host cells) capable of expressing a population of hyperglycosylated and/or hypomannosylated Fc domain-containing binding proteins when grown in culture. In certain embodiments, the composition is obtained from host cells that are genetically engineered for the production of a hyperglycosylated and/or hypomannosylated binding proteins. For example, the host cell (e.g., a CHO cell) may be genetically engineered to overexpress a heterologous galactosyltransferase such as human (3 1, 4-galactosyltransferase (E.C. 2.4.1.38; Weikert et al., Nature Biotechnology 17, 1116-1121 (1999)) or a mammalian homolog thereof (e.g., mouse galactosyltransferase β 1, 4 (Genbank accession number: D00314). Additionally or alternatively, the host cell is a CHO cell having a knock out at least one of the alleles of the beta galactosidase gene (Cricetulus griseus Glb1 (Gene ID: 100767446); mRNA sequence: NCBI Reference Sequence: XM_007630176.1; genomic sequence NW_003613697.1 from 2278553 to 2336708). In other embodiments, the binding protein composition is obtained from a host cell that is cultured under conditions such that hypergalactosylated and/or hypomannosylated binding proteins are produced. In some embodiments, the binding protein is expressed in a host cell with one or more sialyltransferase enzymes, e.g., an a 2,6 sialyltransferase (e.g., ST6Gal-1).
  • Exemplary binding protein compositions of the invention may be obtained from cultured mammalian (e.g., CHO) host cells have a “high Gal/low Man” glycoform profile which provides for unexpectedly improved properties (e.g., reduced ADA activity and/or prolonged half-life). Notably, this glycoform profile differs from the highly mannosylated glycoprofile of binding proteins produced in the milk of transgenic animals (see, e.g., US 2014/0296490). Accordingly, in certain embodiments, the glycoengineered binding protein compositions disclosed herein are not obtained from the milk of transgenic animals e.g., transgenic goats. Antibody compositions with high oligomannose content are thought to promote the ADA response and/or reduce serum half-life. By contrast, binding protein compositions of the invention exhibit a low degree of terminally mannosylated glycoforms (e.g., M3-M9 glycoforms). For example, in certain embodiments, binding protein compositions of the invention comprise a population of Fc domain-containing binding proteins comprising less than 10%, less than 9%, less than 8%, less than 7%, less than 6%, less than 5%, less than 4%, less than 3%, less than 2% or less than 1% of oligomannose (e.g., M3-M9) glycoforms.
  • Thus, the compositions of the invention may be characterized as having glycan structures with a G/M ratio (galactose content/mannose content) of greater than 1:1, e.g., greater than 10:1, 50:1 or 99:1. In certain embodiments, the population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1 (e.g., about 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1).
  • In certain embodiments, the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1 (e.g., about 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1).
  • In certain embodiments, the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1 (e.g., about 10:1, 11:1, 12:1, 13:1, 14:1, 15:1, 16:1, 17:1, 18:1, 19:1, 20:1, 21:1, 22:1, 23:1, 24:1, 25:1, 26:1, 27:1, 28:1, 29:1, 30:1, 31:1, 32:1, 33:1, 34:1, 35:1, 36:1, 37:1, 38:1, 39:1, 40:1, 41:1, 42:1, 43:1, 44:1, 45:1, 46:1, 47:1, 48:1, 49:1, 50:1, 51:1, 52:1, 53:1, 54:1, 55:1, 56:1, 57:1, 58:1, 59:1, 60:1, 61:1, 62:1, 63:1, 64:1, 65:1, 66:1, 67:1, 68:1, 69:1, 70:1, 71:1, 72:1, 73:1, 74:1, 75:1, 76:1, 77:1, 78:1, 79:1, 80:1, 81:1, 82:1, 83:1, 84:1, 85:1, 80:1, 87:1, 88:1, 89:1, 90:1, 91:1, 92:1, 93:1, 94:1, 95:1, 96:1, 97:1, 98:1, 99:1, 100:1, 200:1, 300:1, 400:1, 500:1, 600:1, 700:1, 800:1, 900:1, or 1000:1).
  • Glycoengineered binding compositions of the invention may exhibit improvement in at least one biological activity as compared to a reference binding composition. Biological activity of the preparation can be analyzed by any known method. In some embodiments, a binding activity of the binding composition is improved (e.g., binding to a ligand or receptor). In some embodiments, a therapeutic activity of the glycoengineered binding composition is improved (e.g., an activity in decreasing severity or symptom of a disease or condition, or in delaying appearance of a symptom of a disease or condition). In some embodiments, a pharmacologic activity of the glycoengineered binding composition is improved (e.g., bioavailability, pharmacokinetics, pharmacodynamics). Methods of analyzing bioavailability, pharmacokinetics, and pharmacodynamics of glycoprotein therapeutics are well known in the art.
  • Glycoengineered binding protein compositions of the invention may exhibit reduced ADA activity and/or enhanced half-life without also exhibiting enhanced complement dependent cytotoxicity (CDC) activity and/or enhanced antibody-dependent cellular cytotoxicity (ADCC) activity. In certain embodiments, the glycoengineered binding protein composition of the invention exhibit reduced ADCC and/or CDC activity relative to a reference binding protein composition comprising the same polypeptide sequence but is not glycoengineered (e.g., hypergalactosylated and/or hypomannosylated) according to the methods of the invention. In one embodiment, the reference binding protein composition is not hypergalactosylated and hypomannosylated. In another embodiment, the reference composition is transgenically produced in mammary gland epithelial cells.
  • In certain embodiments, the ADCC and/or CDC activity of the glycoengineered composition of the invention is at least 1.1 time lower, at least 1.2 times lower, at least 1.3 times lower, at least 1.4 times lower, at least 1.5 times lower, at least 1.6 times lower, at least 1.7 times lower, at least 1.8 times lower, at least 10 times lower, at least 20 times lower, at least 50 times lower or up to 100 times lower when compared to the reference composition. Methods for determining the level of CDC are known in the art and are often based on determining the amount of cell lysis. Methods for determining the level of ADCC are also known in the art and may be based on evaluating binding to CD16. Commercial kits for determining CDC and/or ADCC activity can be purchased for instance from Genscript (Piscataway, N.J.) and Promega (Madison, Wis.).
  • In certain embodiments, the glycoengineered binding protein compositions of the invention do not induce B-cell depletion. In other embodiments, the glycoengineered binding protein compositions of the invention are not produced in mammary gland epithelial cells.
  • In other embodiments, the hypergalactosylated compositions of the invention exhibit reduced ADA activity and/or enhanced half-life relative to the reference antibody composition. In certain embodiments, the ADA activity of the glycoengineered composition of the invention is at least 1.1 times lower, at least 1.2 times lower, at least 1.3 times lower, at least 1.4 times lower, at least 1.5 times lower, at least 1.6 times lower, at least 1.7 times lower, at least 1.8 times lower, at least 10 times lower, at least 20 times lower, at least 50 times lower or up to 100 times lower when compared to the reference composition. In other embodiments, the serum half-life of the glycoengineered composition of the invention is at least 6 hours, 12 hours, 1 day, 2 days , 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 2 weeks, 3 weeks, or 4 weeks longer than the reference composition.
  • In certain embodiments, the glycoengineered binding protein compositions of the invention exhibit decreased internalization by dendritic cells in a dendritic cell internalization (DCI) assay, as compared to a reference binding protein composition. In an exemplary DCI assay, the glycoengineered binding protein compositions may be fluorescently labelled with a pH-sensitive fluorophore (e.g., pHrodo Red) and combined with dendritic cells and an immunostimulant (e.g., LPS). Internalization of the fluorescently labelled antibodies may be quantified by measuring (e.g., via FACS cell sorting) the fluorescence which occurs upon uptake and exposure of the fluorophore-labelled antibody to the acidic pH in the endosomal compartments of the dendritic cell. Exemplary DCI assays are described in Example 6 herein. Accordingly, in certain embodiments, the glycoengineered binding protein compositions of the invention exhibit at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or at least 100% reduction in fluorescent intensity as compared to a reference antibody composition comprising the same binding polypeptide sequence. In certain embodiments, the glycoengineered binding protein composition is a hypergalactosylated and/or hypomannosylated preparation of adalimumab and the reference binding protein composition is a commercially available or non-glycoengineered preparation of adalimumab (e.g.., Humira®). In another embodiment, the reference binding protein composition is a binding protein composition (e.g., an adalimumab composition) obtained from the milk of a transgenic animal.
    • Quantification of Glycoforms
  • The glycosylation pattern of the compositions of the invention can be determined by many methods known in the art. For example, methods of analyzing carbohydrates on proteins have been described in U.S. Patent Applications US 2006/0057638 and US 2006/0127950 and : Guile G R, et al. Anal Biochem. 1996 Sep. 5; 240(2):210-26; Packer et al., Glycoconj J. 1998 August; 15(8):737-47; Barb, Biochemistry 48:9705-9707 (2009); Anumula, J. Immunol. Methods 382:167-176 (2012); Gilar et al., Analytical Biochem. 417:80-88 (2011).
  • In some instances, glycan structure and composition as described herein are analyzed, for example, by one or more enzymatic methods, chromatographic methods, mass spectrometry (MS) methods, electrophoretic methods, nuclear magnetic resonance (NMR) methods, and combinations thereof. Exemplary enzymatic methods include contacting a composition with one or more enzymes under conditions and for a time sufficient to release one or more glycan(s) (e.g., one or more exposed glycan(s)). In some instances, the one or more enzymes include(s) PNGase F. Exemplary chromatographic methods include, but are not limited to, Strong Anion Exchange chromatography using Pulsed Amperometric Detection (SAX-PAD), Weak Anion Exchange chromatography, liquid chromatography (LC), high performance liquid chromatography (HPLC), ultra performance liquid chromatography (UPLC), thin layer chromatography (TLC), amide column chromatography, and combinations thereof. Exemplary mass spectrometry (MS) methods include, but are not limited to, tandem MS, LC-MS, LC-MS/MS, matrix assisted laser desorption ionisation mass spectrometry (MALDI-MS), Fourier transform mass spectrometry (FTMS), ion mobility separation with mass spectrometry (IMS-MS), electron transfer dissociation (ETD-MS), and combinations thereof. Exemplary electrophoretic methods include, but are not limited to, capillary electrophoresis (CE), CE-MS, gel electrophoresis, agarose gel electrophoresis, acrylamide gel electrophoresis, SDS-polyacrylamide gel electrophoresis (SDS-PAGE) followed by Western blotting using antibodies that recognize specific glycan structures, and combinations thereof. Exemplary nuclear magnetic resonance (NMR) methods include, but are not limited to, one-dimensional NMR (1 D-NMR), two-dimensional NMR (2D-NMR), correlation spectroscopy magnetic-angle spinning NMR (COSY-NMR), total correlated spectroscopy NMR (TOCSY-NMR), heteronuclear single-quantum coherence NMR (HSQC-NMR), heteronuclear multiple quantum coherence (HMQC-NMR), rotational nuclear overhauser effect spectroscopy NMR (ROESY-NMR), nuclear overhauser effect spectroscopy (NOESY-NMR), and combinations thereof. Additional techniques for the detection, analysis, and/or isolation of particular glycans are described in WO2008/128216; WO2008/128220; WO2008/128218; WO2008/130926; WO2008/128225; WO2008/130924; WO2008/128221 ; WO2008/128228; WO2008/128227; WO2008/128230; WO2008/128219; WO2008/128222; WO2010/071817; WO2010/071824; WO2010/085251 ; WO2011/069056; and WO2011/127322, each of which is incorporated herein by reference in its entirety). For example, in some instances, glycans are characterized using one or more of chromatographic methods, electrophoretic methods, nuclear magnetic resonance methods, and combinations thereof.
  • In exemplary embodiments, the compositions of the invention are analyzed using the art-recognized 2-AB labelling methodology (see U.S. Pat. No. 5,747,347 and Bigge et al., Anal. Biochem., 230: 229-238 (1995) which are incorporated by reference herein in their entireties). 2-AB labelling kits are commercially available (see, e.g., GlycoProfile™ 2-AB Labeling from Sigma Aldrich, St. Louis, Mo.). 2-AB labeling technology employs the fluorophores 2-AB (2-aminobenzamide) or 2-AA (anthranilic acid or 2-aminbenzoic acid) to label the free reducing sugars of a glycoform. Glycans with a free reducing sugar exist in equilibrium between the cyclic (closed ring) and acyclic (open ring) structure. A stable Schiff's base is formed when the carbonyl atom of an acyclic reducing sugar is linked to the amine moiety of the fluorophore in a nucleophilic matter. Following formation of the Schiff's base, the resulting imine group is reduced using sodium cyanoborohydride, resulting in a stable labeled glycan. The 2-AB reagent has an excitation range of 200-450 nm, with an excitation peak at 330 nm, and an emission range of 300-750 nm, with an emission peak at 420 nm.
  • Prior to labeling, N-glycan samples may be prepared by enzymatic (e.g., PNGase F) or chemical deglycosylation (e.g., hydrazinolysis) of an antibody composition in order to release the N-glycans from the antibodies, and removing any contaminating protein, peptides, salts, detergents, and any additional contaminating substances. Once the N-glycan samples have been labeled, a variety of methods exist to analyze them, including, for example, HPLC, separation by ion exchange chromatography (e.g., high-performance anion exchange), normal phase HPLC, and size exclusion chromatography. Labeled glycans can also be detected using SDS-PAGE and mass spectrometry (e.g., electrospray ionization (ESI) or matrix assisted laser absorption ionization (MALDI-TOF).
  • The percent content of each labeled glycoform can be quantified using art-recognized methods. For example, the glycoforms can be quantified based on the N-glycan peaks of a chromatogram, such as a NP HPLC spectrum. Exemplary chromatograms of binding protein composition of the invention are depicted in FIG. 7. Thus, the glycoform profile in a population of Fc-containing binding proteins can be determined by releasing the N-glycans from the binding proteins, resolving the N-glycans on a chromatogram, identifying the N-glycan that corresponds to a specific peak, determining the peak intensity and applying the data to a quantitative formula.
  • For example, the galactosylation state of a particular binding protein composition can be quantified according to the following formula:
  • ∑ f = 1 n ( number of Gal ) * ( % relative Area ) ∑ f = 1 n ( number of A ) * ( % relative Area ) * 100
  • wherein:
  • n represents the number of analyzed N-glycan peaks of the chromatogram,
  • “number of Gal” represents the number of Galactose motifs on the antennae of the glycan corresponding to the peak;
  • “number of A” corresponds to the number of antennae of the glycan form corresponding to the peak; and “% relative Area” corresponds to % of the Area under the corresponding peak.
  • Similarly, the mannosylation state of a particular binding protein composition can be determined according to the same formula, but where the “number of Gal” is substituted for “number of Man”. “Number of Man” represents that number of Mannose motifs on the antennae of the glycan corresponding to the peak.
    • III. Binding Proteins
  • In one aspect, the invention provides a population of Fc domain-containing binding proteins (e.g., TNF binding proteins) with a reduced anti-drug immune response.
  • Any Fc domain-containing binding protein known in the art that comprises an N-Glycan structure is suitable for use in the compositions disclosed herein. In certain embodiments, the binding proteins are therapeutic antibodies or immunoadhesin molecules. In certain embodiments, the binding proteins are FDA approved therapeutic binding proteins. In certain embodiments, the binding proteins are antibodies (e.g., monoclonal antibodies). For example, the binding protein may be selected from the group consisting of alemtuzumab, bevacizumab, cetuximab, edrecolomab, gemtuzumab ozogamicin, ibritumomab tiuxetan, ofatumumab, panitumumab, rituximab, tositumomab, trastuzumab, arcitumomab, capromab pendetide, nofetumomab, satumomab, basiliximab, daclizumab, muromonab-cd3, infliximab, natalizumab, adalimumab, certolizumab, golimumab, infliximab, tocilizumab, omalizumab, abciximab, bevacizumab, ranibzumab, natalizumab, efalizumab, ustekinumab, palivizumab, ruplizumab, denosumab, eculizumab, alefacept, abatacept, etanercept, romiplostim, rilonacept, aflibercept, belatacept, and rilonacept.
  • In certain embodiments, the Fc domain-containing binding proteins bind to human TNF. Exemplary binding proteins which bind to human TNF include etanercept, infliximab, adalimumab, and golimumab.
  • In certain exemplary embodiments, the binding protein is the anti-TNF antibody adalimumab or a variant thereof. In certain embodiments, the anti-TNF antibody is an Fc variant of adalimumab (D2E7) comprising the heavy and light chain variable region sequences of adalimumab (see, e.g., U.S. Pat. No. 6,090,382) and a variant Fc region with an amino acid substitution that confers enhanced serum half-life. In certain exemplary embodiments, the variant Fc region is a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence (wherein amino acid numbering is according to the EU numbering convention as in Kabat). In other embodiments, the anti-TNF antibody is a variant of adalimumab which exhibits pH-sensitive binding to the TNF antigen. PH-sensitive variants may exhibit reduced binding of the TNF-antigen at an acidic pH, thereby promoting release from the endosomal compartment and prolonging serum half-life. For example, pH-sensitive variants comprise histidine mutations within the CDRs of heavy or light chain variable regions of adalimumab. Exemplary pH-sensitive variants of Adalimumab include D2E7SS22.
  • The heavy chain of D2E7SS22 is provided in SEQ ID NO: 1 (variant Histidine bolded and underlined; C-terminal lysine in parentheses may be present or absent):
  • EVQLVESGGGLVQPGRSLRLSCAASGFTFD H YAMHWVRQAPGKGLEWVSA
    ITWNSGHIDYADSVEGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAKVS
    YLSTASSLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLV
    KDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQ
    TYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPK
    PKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQY
    NSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREP
    QVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPP
    VLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPG
    (K)
  • The light chain of D2E7SS22 is provided in SEQ ID NO:2 (variant Histidine bolded and underlined):
  • DIQMTQSPSSLSASVGDRVTITCRAS H SIRNYLSWYQQKPGKAPKLLIYA
    ASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDVATYYCQRYNRAPYTFGQ
    GTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKV
    DNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQG
    LSSPVTKSFNRGEC
  • In another exemplary embodiment, the pH-sensitive variant comprises the heavy and light chain variable regions of D2E7SS22 and a variant Fc region (e.g., a human IgG1 Fc region comprising the mutations T250Q and M428L relative to a wild-type human IgG1 sequence).
  • In certain embodiments, the binding proteins comprise an antigen binding fragment of an antibody. In exemplary embodiments, the binding protein comprises a single chain variable region sequence (ScFv). Single chain variable region sequences comprise a single polypeptide having one or more antigen binding sites, e.g., a VL domain linked by a flexible linker to a VH domain. ScFv molecules can be constructed in a VH-linker-VL orientation or VL-linker-VH orientation. The flexible hinge that links the VL and VH domains that make up the antigen binding site preferably comprises from about 10 to about 50 amino acid residues. Connecting peptides are known in the art. Binding proteins of the invention may comprise at least one scFv and/or at least one constant region.
  • In certain embodiments, the binding proteins are multivalent (e.g., tetravalent) antibodies which are produced by fusing a DNA sequence encoding an antibody with a ScFv molecule (e.g., an altered ScFv molecule). For example, in one embodiment, these sequences are combined such that the ScFv molecule (e.g., an altered ScFv molecule) is linked at its N-terminus or C-terminus to an Fc fragment of an antibody via a flexible linker (e.g., a gly/ser linker). In another embodiment a tetravalent antibody of the current disclosure can be made by fusing an ScFv molecule to a connecting peptide, which is fused to a CH1 domain.
  • In certain embodiments, the binding proteins comprise an altered minibody. Altered minibodies of the current disclosure are dimeric molecules made up of two polypeptide chains each comprising an ScFv molecule (e.g., an altered ScFv molecule comprising an altered VH domain described supra) which is fused to a CII3 domain or portion thereof via a connecting peptide. Minibodies can be made by constructing an ScFv component and connecting peptide-CH3 component using methods described in the art (see, e.g., U.S. Pat. No. 5,837,821 or WO 94/09817A1). In another embodiment, a tetravalent minibody can be constructed. Tetravalent minibodies can be constructed in the same manner as minibodies, except that two ScFv molecules are linked using a flexible linker. The linked scFv-scFv construct is then joined to a CH3 domain.
  • In certain embodiments, the binding proteins comprise a diabody. Diabodies are dimeric, tetravalent molecules each having a polypeptide similar to scFv molecules, but usually having a short (less than 10 and preferably 1-5) amino acid residue linkers connecting both variable domains, such that the VL and VH domains on the same polypeptide chain cannot interact. Instead, the VL and VH domain of one polypeptide chain interact with the VH and VL domain (respectively) on a second polypeptide chain (see, for example, WO 02/02781). Diabodies of the current disclosure comprise an scFv molecule fused to a CH3 domain.
  • In certain embodiments, the binding proteins comprise multispecific or multivalent antibodies comprising one or more variable domain in series on the same polypeptide chain, e.g., tandem variable domain (TVD) polypeptides. Exemplary TVD polypeptides include the “double head” or “Dual-Fv” configuration described in U.S. Pat. No. 5,989,830. In the Dual-Fv configuration, the variable domains of two different antibodies are expressed in a tandem orientation on two separate chains (one heavy chain and one light chain), wherein one polypeptide chain has two times a VH in series separated by a peptide linker (VH1-linker-VH2) and the other polypeptide chain consists of complementary VL domains connected in series by a peptide linker (VL1-linker-VL2). In the cross-over double head configuration, the variable domains of two different antibodies are expressed in a tandem orientation on two separate polypeptide chains (one heavy chain and one light chain), wherein one polypeptide chain has two VH in series separated by a peptide linker (VH1-linker-VH2) and the other polypeptide chain consists of complementary VL domains connected in series by a peptide linker in the opposite orientation (VL2-linker-VL1). Additional antibody variants based on the “Dual-Fv” format include the Dual-Variable-Domain IgG (DVD-IgG) bispecific antibody (see U.S. Pat. No. 7,612,181 and the TBTI format (see US 2010/0226923 A1). The addition of constant domains to respective chains of the Dual-Fv (CH1-Fc to the heavy chain and kappa or lambda constant domain to the light chain) leads to functional bispecific antibodies without any need for additional modifications (i.e., obvious addition of constant domains to enhance stability).
  • In certain embodiments, the binding proteins comprise a cross-over dual variable domain IgG (CODV-IgG) bispecific antibody based on a “double head” configuration (see US20120251541 A1, which is incorporated by reference herein in its entirety). CODV-IgG antibody variants generally have one polypeptide chain with VL domains connected in series to a CL domain (VL1-L1-VL2-L2-CL) and a second polypeptide chain with complementary VH domains connected in series in the opposite orientation to a CH1 domain (VH2-L3-VH1-L4-CH1), where the polypeptide chains form a cross-over light chain-heavy chain pair. In certain embodiment, the second polypeptide may be further connected to an Fc domain (VH2-L3-VH1-L4-CH1-Fc).
  • In certain embodiments, the binding proteins comprise an immunoadhesin molecule comprising a non-antibody binding region (e.g., a receptor, ligand, or cell-adhesion molecule) fused to an antibody constant region (see e.g., Ashkenazi et al., Methods, 1995 8(2), 104-115, which is incorporated by reference herein in its entirety).
  • In certain embodiments, the binding proteins comprise an immunoglobulin-like domain. Suitable immunoglobulin-like domains include, without limitation, fibronectin domains (see, for example, Koide et al. (2007), Methods Mol. Biol. 352: 95-109, which is incorporated by reference herein in its entirety), DARPin (see, for example, Stumpp et al. (2008) Drug Discov. Today 13 (15-16): 695-701, which is incorporated by reference herein in its entirety), Z domains of protein A (see, Nygren et al. (2008) FEBS J. 275 (11): 2668-76, which is incorporated by reference herein in its entirety), lipocalins (see, for example, Skerra et al. (2008) FEBS J. 275 (11): 2677-83, which is incorporated by reference herein in its entirety), Affilins (see, for example, Ebersbach et al. (2007) J. Mol. Biol. 372 (1): 172-85, which is incorporated by reference herein in its entirety), Affitins (see, for example, Krehenbrink et al. (2008). J. Mol. Biol. 383 (5): 1058-68 , which is incorporated by reference herein in its entirety), Avimers (see, for example, Silverman et al. (2005) Nat. Biotechnol. 23 (12): 1556-61 , which is incorporated by reference herein in its entirety), Fynomers, (see, for example, Grabulovski et al. (2007) J Biol Chem 282 (5): 3196-3204 , which is incorporated by reference herein in its entirety), and Kunitz domain peptides (see, for example, Nixon et al. (2006) Curr Opin Drug Discov Devel 9 (2): 261-8, which is incorporated by reference herein in its entirety).
  • In certain embodiments, the Fc domain-containing binding proteins of the invention are capable of binding one or more targets selected from the group consisting of ABCF1; ACVR1; ACVR1B; ACVR2; ACVR2B; ACVRL1; ADORA2A; Aggrecan; AGR2; AICDA; AIF1; AIG1; AKAP1; AKAP2; AMH; AMHR2; ANGPT1; ANGPT2; ANGPTL3; ANGPTL4; ANPEP; APC; APOC1; AR; AZGP1 (zinc-a-glycoprotein); B7.1; B7.2; BAD; BAFF; BAG1; BAI1; BCL2; BCL6; BDNF; BLNK; BLR1 (MDR15); BlyS; BMP1; BMP2; BMP3B (GDF10); BMP4; BMP6; BMP8; BMPRIA; BMPR1B; BMPR2; BPAG1 (plectin); BRCA1; C19orf10 (IL27w); C3; C4A; C5; C5R1; CANT1; CASP1; CASP4; CAV1; CCBP2 (D6/JAB61); CCL1 (1-309); CCL11 (eotaxin); CCL13 (MCP-4); CCL15 (MIP-1d); CCL16 (HCC-4); CCL17 (TARC); CCL18 (PARC); CCL19 (MIP-3b); CCL2 (MCP-1); MCAF; CCL20 (MIP-3a); CCL21 (MIP-2); SLC; exodus-2; CCL22 (MDC/STC-1); CCL23 (MPIF-1); CCL24 (MPIF-2/eotaxin-2); CCL25 (TECK); CCL26 (eotaxin-3); CCL27 (CTACK/ILC); CCL28; CCL3 (MIP-1a); CCL4 (MIP-1b); CCLS (RANTES); CCL7 (MCP-3); CCL8 (mcp-2); CCNA1; CCNA2; CCND1; CCNE1; CCNE2; CCR1 (CKR1/HM 145); CCR2 (mcp-1RB/RA); CCR3 (CKR3/CMKBR3); CCR4; CCRS (CMKBRS/ChemR13); CCR6 (CMKBR6/CKR-L3/STRL22/DRY6); CCR7 (CKR7/EB11); CCR8 (CMKBR8/TER1/CKR-L1); CCR9 (GPR-9-6); CCRL1 (VSHK1); CCRL2 (L-CCR); CD164; CD19; CD1C; CD20; CD200; CD-22; CD24; CD28; CD3; CD37; CD38; CD3E; CD3G; CD3Z; CD4; CD40; CD40L; CD44; CD45RB; CD52; CD69; CD72; CD74; CD79A; CD79B; CD8; CD80; CD81; CD83; CD86; CDH1 (E-cadherin); CDH10; CDH12; CDH13; CDH18; CDH19; CDH20; CDH5; CDH7; CDH8; CDH9; CDK2; CDK3; CDK4; CDKS; CDK6; CDK7; CDK9; CDKN1A (p21Wap1/Cip1); CDKN1B (p27Kip1); CDKN1C; CDKN2A (p161NK4a); CDKN2B; CDKN2C; CDKN3; CEBPB; CER1; CHGA; CHGB; Chitinase; CHST10; CKLFSF2; CKLFSF3; CKLFSF4; CKLFSF5; CKLFSF6; CKLFSF7; CKLFSF8; CLDN3; CLDN7 (claudin-7); CLN3; CLU (clusterin); CMKLR1; CMKOR1 (RDC1); CNR1; COL18A1; COL1A1; COL4A3; COL6A1; CR2; CRP; CSF1 (M-CSF); CSF2 (GM-CSF); CSF3 (GCSF); CTLA4; CTNNB1 (b-catenin); CTSB (cathepsin B); CX3CL1 (SCYD1); CX3CR1 (V28); CXCL1 (GRO1); CXCL10 (IP-10); CXCL11 (1-TAC/IP-9); CXCL12 (SDF1); CXCL13; CXCL14; CXCL16; CXCL2 (GRO2); CXCL3 (GRO3); CXCLS (ENA-78/LIX); CXCL6 (GCP-2); CXCL9 (MIG); CXCR3 (GPR9/CKR-L2); CXCR4; CXCR6 (TYMSTR/STRL33/Bonzo); CYBS; CYC1; CYSLTR1; DAB2IP; DES; DKFZp451J0118; DNCL1; DPP4; E2F1; ECGF1; EDG1; EFNA1; EFNA3; EFNB2; EGF; EGFR; ELAC2; ENG; ENO1; ENO2; ENO3; EPHB4; EPO; ERBB2 (Her-2); EREG; ERK8; ESR1; ESR2; F3 (TF); FADD; FasL; FASN; FCER1A; FCER2; FCGR3A; FGF; FGF1 (aFGF); FGF10; FGF11; FGF12; FGF12B; FGF13; FGF14; FGF16; FGF17; FGF18; FGF19; FGF2 (bFGF); FGF20; FGF21; FGF22; FGF23; FGF3 (int-2); FGF4 (HST); FGFS; FGF6 (HST-2); FGF7 (KGF); FGF8; FGF9; FGFR3; FIGF (VEGFD); FIL1 (EPSILON); FIL1 (ZETA); FLJ12584; FLJ25530; FLRT1 (fibronectin); FLT1; FOS; FOSL1 (FRA-1); FY (DARC); GABRP (GABAa); GAGEB1 ; GAGEC1 ; GALNAC4S-6ST; GATA3; GDF5 ; GFI1; GGT1 ; GM-CSF; GNAS1; GNRH1; GPR2 (CCR10); GPR31; GPR44; GPR81 (FKSG80); GRCC10 (C10); GRP; GSN (Gelsolin); GSTP1; HAVCR2; HDAC4; HDACS; HDAC7A; HDAC9; HGF; HIF1A; HIP1; histamine and histamine receptors; HLA-A; HLA-DRA; HM74; HMOX1; HUMCYT2A; ICEBERG; ICOSL; ID2; IFN-a; IFNA1; IFNA2; IFNA4; IFNA5; IFNA6; IFNA7; IFNB1; IFNgamma; IFNW1; IGBP1; IGF1; IGF1R; IGF2; IGFBP2; IGFBP3; IGFBP6; IL-1; IL10; IL10RA; IL10RB; IL11; IL11RA; IL-12; IL12A; IL12B; IL12RB1; IL12RB2; IL13; IL13RA1; IL13RA2; IL14; IL15; IL15RA; IL16; IL17; IL17B; IL17C; IL17R; IL18; IL18BP; IL18R1; IL18RAP; IL19; ILIA; IL1B; IL1F10; IL1F5; IL1F6; IL1F7; IL1F8; IL1F9; IL1HY1; IL1R1; IL1R2; IL1RAP; IL1RAPL1; IL1RAPL2; IL1RL1; IL1RL2IL1RN; IL2; IL20; IL20RA; IL21R; IL22; IL22R; IL22RA2; IL23; IL24; IL25; IL26; IL27; IL28A; IL28B; IL29; IL2RA; IL2RB; IL2RG; IL3; IL30; IL3RA; IL4; IL4R; ILS; IL5RA; IL6; IL6R; IL6ST (glycoprotein 130); IL7; IL7R; IL8; IL8RA; IL8RB; IL8RB; IL9; IL9R; ILK; INHA; INHBA; INSL3; INSL4; IRAK1; IRAK2; ITGAl; ITGA2; ITGA3; ITGA6 (a6 integrin); ITGAV; ITGB3; ITGB4 (b 4 integrin); JAG1; JAK1; JAK3; JUN; K6HF; KAI1; KDR; KITLG; KLFS (GC Box BP); KLF6; KLK10; KLK12; KLK13; KLK14; KLK15; KLK3; KLK4; KLK5; KLK6; KLK9; KRT1; KRT19 (Keratin 19); KRT2A; KRTHB6 (hair-specific type II keratin); LAMAS; LEP (leptin); Lingo-p75; Lingo-Troy; LPS; LTA (TNF-b); LTB; LTB4R (GPR16); LTB4R2; LTBR; MACMARCKS; MAG or Omgp; MAP2K7 (c-Jun); MDK; MIB1; midkine; MIF; MIP-2; MKI67 (Ki-67); MMP2; MMP9; MS4A1; MSMB; MT3 (metallothionectin-III); MTSS1; MUC1 (mucin); MYC; MYD88; NCK2; neurocan; NFKB1; NFKB2; NGFB (NGF); NGFR; NgR-Lingo; NgR-Nogo66 (Nogo); NgR-p75; NgR-Troy; NME1 (NM23A); NOXS; NPPB; NROB1; NROB2; NR1D1; NR1D2; NR1H2; NR1H3; NR1H4; NR1I2; NR1I3; NR2C1; NR2C2; NR2E1; NR2E3; NR2F1; NR2F2; NR2F6; NR3C1; NR3C2; NR4A1; NR4A2; NR4A3; NR5A1; NR5A2; NR6A1; NRP1; NRP2; NTSE; NTN4; ODZ1; OPRD1; P2Rx7; PAP; PART1; PATE; PAWR; PCA3; PCNA; PDGFA; PDGFB; PECAM1; PF4 (CXCL4); PGF; PGR; phosphacan; PIAS2; PIK3CG; PLAU (uPA); PLG; PLXDC1; PPBP (CXCL7); PPID; PR1; PRKCQ; PRKD1; PRL; PROC; PROK2; PSAP; PSCA; PTAFR; PTEN; PTGS2 (COX-2); PTN; RAC2 (p21Rac2); RARB; RGS1; RGS13; RGS3; RNF110 (ZNF144); ROBO2; S100A2; SCGB1D2 (lipophilin B); SCGB2A1 (mammaglobin 2); SCGB2A2 (mammaglobin 1); SCYE1 (endothelial Monocyte-activating cytokine); SDF2; SERPINAl; SERPINA3; SERPINB5 (maspin); SERPINE1 (PAI-1); SERPINF1; SHBG; SLA2; SLC2A2; SLC33A 1; SLC43A1; SLIT2; SPP1; SPRR1B (Spr1); ST6GAL1; STAB1; STAT6; STEAP; STEAP2; TB4R2; TBX21; TCP10; TDGF1; TEK; TGFA; TGFB1; TGFB11; TGFB2; TGFB3; TGFB1; TGFBR1; TGFBR2; TGFBR3; TH1L; THBS1 (thrombospondin-1); THB S2; THBS4; THPO; TIE (Tie-1); TIMP3; tissue factor; TLR10; TLR2; TLR3; TLR4; TLRS; TLR6; TLR7; TLR8; TLR9; TNF; TNF-α; TNFAIP2 (B94); TNFAIP3; TNFRSF1A; TNFRSF1A; TNFRSF1B; TNFRSF21; TNFRSFS; TNFRSF6 (Fas); TNFRSF7; TNFRSF8; TNFRSF9; TNFSF10 (TRAIL); TNFSF11 (TRANCE); TNFSF12 (APO3L); TNFSF13 (April); TNFSF13B; TNFSF14 (HVEM-L); TNFSF15 (VEGI); TNFSF18; TNFSF4 (OX40 ligand); TNFSF5 (CD40 ligand); TNFSF6 (FasL); TNFSF7 (CD27 ligand); TNFSF8 (CD30 ligand); TNFSF9 (4-IBB ligand); TOLLIP; Toll-like receptors; TOP2A (topoisomerase Iia); TP53; TPM1; TPM2; TRADD; TRAF1; TRAF2; TRAF3; TRAF4; TRAF5; TRAF6; TREM1; TREM2; TRPC6; TSLP; TWEAK; VEGF; VEGFB; VEGFC; versican; VHL C5; VLA-4; XCL1 (lymphotactin); XCL2 (SCM-1b); XCR1 (GPRS/CCXCR1); YY1; and ZFPM2.
    • IV. Engineered Binding Proteins
  • In certain preferred embodiments, the binding proteins produced using the methods and compositions disclosed herein exhibit improved properties (e.g., affinity or stability) with respect to a corresponding parental reference binding protein. For example, the engineered binding protein may dissociate from its target antigen with a koff rate constant of about 0.1 s−1 or less, as determined by surface plasmon resonance, or inhibit the activity of the target antigen with an IC50 of about 1×10−6M or less. Alternatively, the binding protein may dissociate from the target antigen with a koff rate constant of about 1×10−25−1 or less, as determined by surface plasmon resonance, or may inhibit activity of the target antigen with an IC50 of about 1×10−7M or less. Alternatively, the binding protein may dissociate from the target with a koff rate constant of about 1×10−3s−1 or less, as determined by surface plasmon resonance, or may inhibit the target with an IC50 of about 1×10−8M or less. Alternatively, binding protein may dissociate from the target with a koff rate constant of about 1×10−4s−1 or less, as determined by surface plasmon resonance, or may inhibit its activity with an IC50 of about 1×10−9M or less. Alternatively, binding protein may dissociate from the target with a koff rate constant of about 1×10−5s−1 or less, as determined by surface plasmon resonance, or inhibit its activity with an IC50 of about 1×10− 10M or less. Alternatively, binding protein may dissociate from the target with a koff rate constant of about 1×10−5s−1 or less, as determined by surface plasmon resonance, or may inhibit its activity with an IC50 of about 1×10−11M or less.
  • In certain embodiments, the engineered binding protein comprises a heavy chain constant region, such as an IgG1, IgG2, IgG3, IgG4, IgA, IgE, IgM or IgD constant region. Preferably, the heavy chain constant region is an IgG1 heavy chain constant region or an IgG4 heavy chain constant region. Furthermore, the binding protein can comprise a light chain constant region, either a kappa light chain constant region or a lambda light chain constant region. The binding protein comprises a kappa light chain constant region. Alternatively, the binding protein portion can be, for example, a Fab fragment or a single chain Fv fragment.
  • In certain embodiments, the engineered binding protein comprises an engineered effector function known in the art (see, e.g., Winter, et al. U.S. Pat. Nos. 5,648,260; 5,624,821). The Fc portion of a binding protein mediates several important effector functions e.g. cytokine induction, ADCC, phagocytosis, complement dependent cytotoxicity (CDC) and half-life/clearance rate of binding protein and antigen-binding protein complexes. In some cases these effector functions are desirable for therapeutic binding protein but in other cases might be unnecessary or even deleterious, depending on the therapeutic objectives. Certain human IgG isotypes, particularly IgG1 and IgG3, mediate ADCC and CDC via binding to FcγRs and complement C1q, respectively. Neonatal Fc receptors (FcRn) are the critical components determining the circulating half-life of binding proteins. In still another embodiment at least one amino acid residue is replaced in the constant region of the binding protein, for example the Fc region of the binding protein, such that effector functions of the binding protein are altered.
  • In certain embodiments, the engineered binding protein is derivatized or linked to another functional molecule (e.g., another peptide or protein). For example, a labeled binding protein of the invention can be derived by functionally linking a binding protein or binding protein portion of the invention (by chemical coupling, genetic fusion, noncovalent association or otherwise) to one or more other molecular entities, such as another binding protein (e.g., a bispecific binding protein or a diabody), a detectable agent, a cytotoxic agent, a pharmaceutical agent, and/or a protein or peptide that can mediate associate of the binding protein with another molecule (such as a streptavidin core region or a polyhistidine tag).
  • Useful detectable agents with which a binding protein or binding protein portion of the invention may be derivatized include fluorescent compounds. Exemplary fluorescent detectable agents include fluorescein, fluorescein isothiocyanate, rhodamine, 5-dimethylamine-1-napthalenesulfonyl chloride, phycoerythrin and the like. A binding protein may also be derivatized with detectable enzymes, such as alkaline phosphatase, horseradish peroxidase, glucose oxidase and the like. When a binding protein is derivatized with a detectable enzyme, it is detected by adding additional reagents that the enzyme uses to produce a detectable reaction product. For example, when the detectable agent horseradish peroxidase is present, the addition of hydrogen peroxide and diaminobenzidine leads to a colored reaction product, which is detectable. A binding protein may also be derivatized with biotin, and detected through indirect measurement of avidin or streptavidin binding.
  • In other embodiment, the engineered binding protein is further modified to generate glycosylation site mutants in which the O- or N-linked glycosylation site of the binding protein has been mutated. One skilled in the art can generate such mutants using standard well-known technologies. Glycosylation site mutants that retain the biological activity, but have increased or decreased binding activity, are another object of the present invention.
  • Additionally or alternatively, an engineered binding protein of the invention can be further modified with an altered type of glycosylation, such as a hypofucosylated binding protein having reduced amounts of fucosyl residues or a binding protein having increased bisecting GlcNAc structures. Such altered glycosylation patterns have been demonstrated to increase the ADCC ability of binding proteins. Such carbohydrate modifications can be accomplished by, for example, expressing the binding protein in a host cell with altered glycosylation machinery. Cells with altered glycosylation machinery have been described in the art and can be used as host cells in which to express recombinant binding proteins of the invention to thereby produce a binding protein with altered glycosylation. See, for example, Shields, R. L. et al. (2002) J. Biol. Chem. 277:26733-26740; Umana et al. (1999) Nat. Biotech. 17:176-1, as well as, European Patent No: EP 1,176,195; PCT Publications WO 03/035835; WO 99/54342 80, each of which is incorporated herein by reference in its entirety. Using techniques known in the art a practitioner may generate binding proteins exhibiting human protein glycosylation. For example, yeast strains have been genetically modified to express non-naturally occurring glycosylation enzymes such that glycosylated proteins (glycoproteins) produced in these yeast strains exhibit protein glycosylation identical to that of animal cells, especially human cells (U.S. patent Publication Nos. 20040018590 and 20020137134 and PCT publication WO2005100584 A2).
    • V. Production of Glycoengineered Binding Proteins
  • Binding proteins of the present invention may be produced by any of a number of techniques known in the art. For example, expression from host cells, wherein expression vector(s) encoding the heavy and light chains is (are) transfected into a host cell by standard techniques. The various forms of the term “transfection” are intended to encompass a wide variety of techniques commonly used for the introduction of exogenous DNA into a prokaryotic or eukaryotic host cell, e.g., electroporation, calcium-phosphate precipitation, DEAE-dextran transfection and the like. Although it is possible to express the binding proteins of the invention in either prokaryotic or eukaryotic host cells, expression of binding proteins in eukaryotic cells is preferable, and most preferable in mammalian host cells, because such eukaryotic cells (and in particular mammalian cells) are more likely than prokaryotic cells to assemble and secrete a properly folded and immunologically active binding protein.
  • Preferred mammalian host cells for expressing the recombinant binding proteins of the invention include Chinese Hamster Ovary (CHO cells) (including dhfr-CHO cells, described in Urlaub and Chasin, (1980) Proc. Natl. Acad. Sci. USA 77:4216-4220, used with a DHFR selectable marker, e.g., as described in R. J. Kaufman and P. A. Sharp (1982) Mol. Biol. 159:601621), NSO myeloma cells, COS cells and SP2 cells. When recombinant expression vectors encoding binding protein genes are introduced into mammalian host cells, the binding proteins are produced by culturing the host cells for a period of time sufficient to allow for expression of the binding protein in the host cells or, more preferably, secretion of the binding protein into the culture medium in which the host cells are grown. Binding proteins can be recovered from the culture medium using standard protein purification methods. Additional methods of culturing antibody-producing mammalian cells are also taught, for example, in U.S. Pat. 8,663,945 which is incorporated herein in its entirety.
  • Host cells can also be used to produce functional binding protein fragments, such as Fab fragments or scFv molecules. It will be understood that variations on the above procedure are within the scope of the present invention. For example, it may be desirable to transfect a host cell with DNA encoding functional fragments of either the light chain and/or the heavy chain of a binding protein of this invention. Recombinant DNA technology may also be used to remove some, or all, of the DNA encoding either or both of the light and heavy chains that is not necessary for binding to the antigens of interest. The molecules expressed from such truncated DNA molecules are also encompassed by the binding proteins of the invention. In addition, bifunctional binding proteins may be produced in which one heavy and one light chain are a binding protein of the invention and the other heavy and light chain are specific for an antigen other than the antigens of interest by crosslinking a binding protein of the invention to a second binding protein by standard chemical crosslinking methods.
  • In a preferred system for recombinant expression of a binding protein, or antigen-binding portion thereof, of the invention, a recombinant expression vector encoding both the binding protein heavy chain and the binding protein light chain is introduced into DHFR-CHO cells by calcium phosphate-mediated transfection. Within the recombinant expression vector, the binding protein heavy and light chain genes are each operatively linked to CMV enhancer/AdMLP promoter regulatory elements to drive high levels of transcription of the genes. The recombinant expression vector also carries a DHFR gene, which allows for selection of CHO cells that have been transfected with the vector using methotrexate selection/amplification. The selected transformant host cells are cultured to allow for expression of the binding protein heavy and light chains and intact binding protein is recovered from the culture medium. Standard molecular biology techniques are used to prepare the recombinant expression vector, transfect the host cells, select for transformants, culture the host cells and recover the binding protein from the culture medium. Still further the invention provides a method of synthesizing a recombinant binding protein of the invention by culturing a host cell of the invention in a suitable culture medium until a recombinant binding protein of the invention is synthesized. The method can further comprise isolating the recombinant binding protein from the culture medium.
  • Glycoengineering of the binding proteins of the invention can be achieved by any methods known in the art. Suitable methods include: (1) glycosylation of purified binding proteins can be modified enzymatically in vitro, (2) the cell culture and production conditions can be modified to bias a defined glycosylation profile of recombinant proteins expressed in the cultured cells, (3) the protein can be engineered to add or eliminate sites for the attachment of glycans or (4) a cell line can be genetically engineered for production of biotherapeutics with a modified glycosylation profile. Exemplary methods of making glycoengineered Fc domain containing binding proteins can be found in the Examples herein.
  • In certain embodiments, glycoengineering of recombinant binding proteins is achieved by expression of Fc domain-containing binding proteins in cells capable of N-linked glycosylation under specific culture conditions. For example, growing CHO cells expressing recombinant antibodies in chemically defined culture media supplemented with metal ions such as manganese or ferric nitrate increases the G1F and G2F glycoforms of the expressed recombinant antibodies by at least 25-30% (see published U.S. Patent Application No. 2012/0276631, the contents of which are incorporated herein in their entirety and Example 1). In one embodiment, the Fc containing binding proteins are hypergalactosylated and/or hypomannosylated by expression in a host cell with a knock down or knock out of its beta galactosidase gene, for example, using beta galactosidase gene-specific RNAi, homologous recombination or Zn finger nuclease inactivation of the beta galactosidase gene (see Examples). In another embodiment, the Fc containing binding proteins are hypergalactosylated and/or hypomannosylated by expression in a host cell that overexpresses a galactosyl transferase. In other embodiments, the glycosylation of purified recombinant binding proteins is modified through enzymatic means, in vitro. For example, one or more glycosyltransferases may be employed to add specific saccharide residues to N-Glycans, and one or more glycosidases may be employed to remove unwanted saccharides from the N-linked glycan. Such enzymatic means are well known in the art (see. e.g., WO/2007/005786, which is incorporated herein by reference in its entirety). For example, purified recombinant antibodies can be hypergalactosylated in vitro in the presence of galactosyltransferase (see Warnock D. et al. (2005) In vitro galactosylation of human IgG at 1 kg scale using recombinant galactosyltransferase. Biotechnol. Bioeng. 92, 831-842). In Vitro Galactosylation and Sialylation of Glycoproteins with Terminal N-Acetylglucosamine and Galactose Residues has also been reported (Raju et al. Biochemistry, 2001, 40 (30), pp 8868-8876).
  • In other embodiments, mammalian cell lines are genetically engineered to modify the glycosylation profile of expressed recombinant binding proteins. For example, cells can be genetically engineered to overexpress human β 1, 4-galactosyltransferase (E.C. 2.4.1.38; Weikert et al., Nature Biotechnology 17, 1116-1121 (1999)) or knock-out/knock down of (3-galactosidase proteins. In other embodiments, the host cell is genetically engineered with one or more sialyltransferase enzymes, e.g., an a2,6 sialyltransferase (e.g., ST6Gal-1). Any natural or engineered cell (e.g., prokaryotic or eukaryotic) can be employed. In general, mammalian cells are employed to effect glycosylation. The N-glycans that are produced in mammalian cells are commonly referred to as complex N-glycans (see e.g., Drickamer K, Taylor M E (2006). Introduction to Glycobiology, 2nd ed., which is incorporated herein by reference in its entirety).
  • The glycoengineered binding polypeptides may be recovered from the culture supernatant of a glycoengineered host cell and subjected to one or more purification steps, such as, for example, ion-exchange or affinity chromatography, to further increase the G/M ratio of the binding composition. Suitable methods of purification will be apparent to a person of ordinary skill in the art. A person of ordinary skill in the art will appreciate that different combinations of purification methods, disclosed above, can lead to production of the polypeptide compositions with extremely high levels of galactosylation and extremely low levels of mannosylation. For example, the hypergalactosylated and/or hypomannosylated binding protein compositions obtained from glycoengineered host cells can be further glycoengineered using in vitro techniques. For example, the G/M ratio of said composition can be further increased by subjecting the composition to treatment with galactosyltransferases in vitro. Galactosyltransferases are commercially available (Sigma Chemical Co, St. Louis, Mo.; Boehringer Mannheim, Indianapolis, Ind. and Genzyme, Cambridge Mass.).
  • Additionally or alternatively, compositions of the present invention can be further purified or modified so that they have an increased amount of sialic acid compared to reference antibody composition. The addition of charged sialic acid residue can help facilitate separation of the sialylated glycoforms by ion exchange chromatography (see e.g., FIG. 7C). For example, the sialylation levels of the composition can be increased for instance by subjecting the composition to treatment with sialyltransferases (e.g., an alpha 2,6 sialyltransferase). For example, hypergalactosylated and/or hypomannosylated binding protein compositions produced in CHO cells can be sialylated in vitro by subjecting the purified or partially purified binding protein composition to a sialyltransferase and the appropriate saccharide based substrate. Further, one may employ an enzymatic reaction with a sialyltransferase and a donor of sialic acid as described, for example, in the U.S. Pat. No. 7,473,680, which is incorporated herein by reference. Sialyltransferase enzymes are known in the art and are commercially available. Methods and compositions described herein include the use of a sialyltransferase enzyme, e.g., an a2,6 sialyltransferase (e.g., ST6Gal-1). A number of ST6Gal sialyltransferases are known in the art and are commercially available (see, e.g., Takashima, Biosci. Biotechnol. Biochem. 72:1 155-1 167 (2008); Weinstein et al., J. Biol. Chem. 262:17735-17743 (1987)). ST6Gal-1 catalyzes the transfer of sialic acid from a sialic acid donor (e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid) to a terminal galactose residue of glycans through an a2,6 linkage. Accordingly, a purified or partially purified binding protein composition may contacted with an ST6Gal sialyltransferase (e.g., a recombinantly expressed and purified ST6Gal sialyltransferase) in the presence of a sialic acid donor, e.g., cytidine 5′-monophospho-N-acetyl neuraminic acid, manganese, and/or other divalent metal ions.
  • Additionally or alternatively, the composition can be sialylated in vivo by expressing the binding protein in a CHO cell that has been glycoengineered to express a sialyltransferase. Suitable non-limiting examples of sialyltransferase enzymes useful in the claimed methods are ST3Gal III, which is also referred to as alpha-(2,3)sialyltransferase (EC 2.4.99.6), and alpha-(2,6)sialyltransferase (EC 2.4.99.1). The alpha-2,3-sialyltransferase may be the human alpha-2,3-sialyltransferase, known as SIAT4C or STZ (GenBank accession number L23767), and described, for example, in the U.S. Patent Publication No. 20050181359. In yet other embodiments, the binding protein composition can be passed through a column having a lectin which is known to bind sialic acid in order to enrich for sialylated glycoforms. A person of the ordinary skill in the art will appreciate that different lectins display different affinities for alpha 2,6 versus alpha 2,3 linkages between galactose and sialic acid. Thus, selecting a specific lectin will allow enrichment of antibodies with the desired type of linkage between the sialic acid and the galactose. In one embodiment, the lectin is isolated from Sambuccus nigra. A person of the ordinary skill in the art will appreciate that the Sambuccus nigra agglutinin (SNA) is specific for sialic acids linked to galactose or N-acetylgalactosamine by alpha (2-6) linkages. Shibuya et al, J. Biol. Chem., 262: 1596-1601 (1987). In contrast, the Maakia amurensis (“MAA”) lectin binds to sialic acid linked to galactose by a(2-3) linkages. Wang et al, J Biol. Chem., 263: 4576-4585 (1988). Thus, a fraction of the polypeptides containing at least one IgG Fc region having a desired linkage between the galactose and the sialic acid will be retained in the column while a fraction lacking such linkage will pass through. The sialylated fraction of the polypeptides containing at least one IgG Fc region can be eluted by another wash with a different stringency conditions. Thus, it is possible to obtain a preparation of the polypeptide of the present invention wherein the content of sialic acid is increased compared to the normal content.
  • In addition, a person of average skill in the art will appreciate that cell culture conditions can be manipulated to change the sialylation content. For example, to increase the sialic acid content, production rate is decreased and osmolality is generally maintained within a lower margin suitable for the particular host cell being cultured. Osmolality in the range from about 250 mOsm to about 450 mOsm is appropriate for increased sialic acid content. This and other suitable cell culture conditions are described in, e.g., U.S. Pat. No. 6,656,466. Patel et al., Biochem J, 285, 839-845 (1992) have reported that the content of sialic acid in antibody linked sugar side chains differs significantly if antibodies were produced as ascites or in serum-free or serum containing culture media. Moreover, Kunkel et al., Biotechnol. Prog., 16, 462-470 (2000) have shown that the use of different bioreactors for cell growth and the amount of dissolved oxygen in the medium influenced the amount of galactose and sialic acid in antibody linked sugar moieties.
    • VII. Purification of Glycoengineered Binding Proteins
  • Also provided is a process for manufacturing a glycoengineered binding composition of the invention by performing additional purification. In an embodiment, a process for manufacturing a composition of the invention is provided, comprising the following steps: i) recombinantly expressing the glycoengineered of interest in a host cell (e.g., a glycoengineered CHO cell of the invention) and; ii) purifying the binding protein of interest by subjecting a liquid containing said binding composition to one or more chromatographic steps. The respective manufacturing process leads to the production homogenous glycoprotein compositions which are in particular suitable for use in pharmaceutical formulations.
  • Accordingly, the compositions can be subjected to further chromatographic purification including, for example, ion exchange chromatography such anion exchange chromatography or cation exchange chromatography. Additional chromatography steps may include any of the following: a) reverse phase chromatography (RPC); b) size exclusion chromatography (SEC); and c) hydrophobic interaction chromatography (HIC); (d) affinity chromatography such as dye affinity chromatography, immune affinity chromatography, lectin affinity chromatography or perborate affinity chromatography, (e) filtration such as diafiltration, ultrafiltration or nanofiltration, and/or (f) at least one virus inactivation step. In an exemplary embodiment the process of the present invention includes an anion exchange chromatography (AEX) as a chromatography step. In another embodiment, AEX chromatography is performed subsequent to SEC chromatography and prior to HIC chromatography. Additional steps may be performed in addition to and also between the steps.
  • The purification methods may provide glycoengineered binding protein compositions in high purity, which may then be formulated as a pharmaceutical composition. For example, the purity may be above 90% hypergalactosylated binding protein, preferably >95% w/w, more preferably >99% w/w, even more preferably >99.5% w/w, based on total protein. In exemplary embodiments, the level of mannosylated species (e.g., M3-M9) is less than 10%, preferably <5% w/w, more preferably <1% w/w, even more preferably <0.5% w/w, based on total protein. In certain embodiments, the glycoprotein composition comprises only trace amounts of oligomannose glycoforms.
  • The binding protein compositions which form the starting material for the purification process may be provided in or obtained by recombinant techniques such as, e.g., in cell culture harvests of glycoengineered host cells of the invention. Typically, the starting material as obtained from a cell harvest, is clarified first (e.g. by filtration) and then optionally concentrated (e.g. by using ultrafiltration) and/or buffer exchanged (e.g. through a diafiltration step) prior to being captured by the first chromatographic step. In the steps of chromatography typically commercially available resins are used, preferably polymer-based resins or agarose-based resins. It is also possible to use membrane chromatography in which the resin is replaced by a functionalized membrane such as SARTOBIND® membranes (Sartorius) or CHROMASORB® (Millipore).
    • Anion Exchange (AEX) Chromatography
  • In certain embodiments, the glycoengineered binding compositions of the invention are subjected to an anion exchange (AEX) chromatography step. The anion exchange chromatography is usually performed by equilibrating and loading the column, followed by a wash and subsequent elution. The anion exchange chromatography is carried out, e.g., with a quaternary ammonium resin, such as CAPTOQ® (obtainable from GE Healthcare), or a resin having similar characteristics such as TOYOPEARL QEA® (obtainable from Tosoh), or FRACTOGEL EMD®, FRACTOGEL TMAE® or FRACTOGEL HICAP® (obtainable from Merck KGaA, Darmstadt Germany). Other exemplary anion exchange resins (i.e., the stationary phase) include, but are not limited to, quaternary amine resins or “Q-resins” (e.g., Q-Sepharose®, QAE Sephadex®); diethylaminoethane (DEAE) resins (e.g., DEAE-Trisacryl®, DEAE Sepharose®, benzoylated naphthoylated DEAE, diethylaminoethyl Sephacel®); Amberjet® resins; Amberlyst® resins; Amberlite® resins (e.g., Amberlite® IRA-67, Amberlite® strongly basic, Amberlite® weakly basic), cholestyramine resin, ProPac®resins (e.g., ProPac® SAX-10, ProPac® WAX-10, ProPac® WCX-10); TSK-GEL® resins (e.g., TSKgel DEAE-NPR; TSKgel DEAE-5PW); and Acclaim® resins. In certain embodiments, the anion exchange resin is a Q resin. In certain embodiments, the anion exchange resin is a DEAE resin. In certain embodiments, the DEAE resin is a TSK-GEL® DEAE resin.
  • Typical mobile phases for anionic exchange chromatography include relatively polar solutions, such as water and polar organic solvents (e.g., acetonitrile and organic alcohols such as methanol, ethanol, and isopropanol). Thus, in certain embodiments, the mobile phase comprises about 0%, 1%, 2%, 4%, 6%, 8%, 10%, 12%, 14%, 16%, 18%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or about 100% acetonitrile. In certain embodiments, the mobile phase comprises between about 1% to about 100%, about 5% to about 95%, about 10% to about 90%, about 20% to about 80%, about 30% to about 70%, or about 40% to about 60% acetonitrile at any given time during the course of the separation.
  • In certain embodiments, the mobile phase is buffered. In certain embodiments, the mobile phase is not buffered. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 14. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 10. In certain embodiments, the mobile phase is buffered to a pH between about 7 to about 8. In certain embodiments, the mobile phase is buffered to a pH of about 7. Exemplary buffers for anion exchange chromatography are included in Table 1.
  • The anion exchange chromatography resin may be equilibrated, loaded and washed by using a buffer having a mildly alkaline pH, e.g. at or about 7.2 to at or about 9.0. Suitable buffers include, for example borate buffer, triethanolamine/iminodiacetic acid, Tris (2-Amino-2-hydroxymethyl-propane-1,3-diol), sodium phosphate, ammonium acetate, tricine (N-(Tri(hydroxymethyl)methyl)glycine), bicine (2-(bis(2-hydroxyethyl)amino)ethanoic acid), TES, HEPES, TAPS(N-Tris(hydroxymethyl)methyl-3-aminopropanesulfonic acid). Elution from the ion-exchange resin is achieved by increasing the conductivity of the mobile phase through the addition of salt, preferably NaCl. Suitable buffers include, for example borate buffer, triethanolamine/iminodiacetic acid Tris, ammonium acetate, tricine, bicine, TES, HEPES, TAPS. Preferred is ammonium acetate.
  • In certain exemplary embodiments, the anion exchange chromatography can be utilized to selectively elute different charged glycoforms mainly originating from different sialylation levels. For the selective elution of differently charged glycoforms, such as differently sialylated glycoforms, one may use two or more, preferably two elution buffers A and B which differ in pH and/or salt content, each of them being based on e g ammonium acetate, borate buffer, triethanolamine/iminodiacetic acid, Tris, sodium phosphate, ammonium acetate, tricine, bicine, TES, HEPES or TAPS, preferred is ammonium acetate. Using different elution buffers, elution can be performed in a stepwise fashion, first using one elution buffer and then using the other elution buffer, optionally also using one or more intermediate elution steps with different mixtures of the elution buffers. Alternatively or additionally, elution can be performed using a gradient, starting with a first mixing ratio of the elution buffers (e.g. 100% of the first elution buffer) and gradually changing to a second mixing ratio of the elution buffers (e.g. 100% of the second elution buffer). The elution buffer used first (buffer A) in general can be a) a mildly acidic buffer which is salt-free, or b) a neutral or mildly basic buffer with low salt content such as NaCl (preferably between 20 and 200 mM). Buffer A can be used to elute glycoforms of low charge, e.g., low degree of sialylation. In variant a) buffer A has a pH e.g. at or about 3.0 to at or about 6.5, or at or about 4.0 to at or about 6.0, most preferably at or about 5. In variant b) buffer A has a pH e.g. at or about 7.0 to 9.0, preferably 8.5. The elution buffer used second (buffer B) in general is a salt-containing mildly alkaline buffer of a higher salt content than buffer A which can be used to elute glycoprotein of high charge, e.g. high degree of sialylation. Buffer B has a pH e.g. at or about 7.0 to at or about 9.0, or at or about 8.0 to at or about 9.0, most preferably at or about 8.5. The salt is preferably NaCl. The salt content in buffer B is preferably from 200 mM to 1M. In certain exemplary embodiments, buffer A is 10 mM sodium phosphate, pH 7.5 and buffer B is 10 mM sodium phosphate/500 mM sodium chloride, pH 5.5.
  • Using different elution buffers and a gradient or stepwise elution, the different glycoforms loaded onto the anion exchange chromatography column will elute in different fractions depending on their charge. For example, the glycoprotein to be purified may be present in the fractions of the flow-through, i.e. it binds to the anion exchange chromatography column only weakly or not at all, it may be eluted with the first elution buffer, at a specific mixing ratio of the first and second elution buffer, or with the second elution buffer. The glycoprotein fractions which are used for the further purification steps and thus, the glycoforms which are to be purified, mainly depend on the desired applications of the glycoprotein. The other glycoforms which are not of interest can be removed using the anion exchange chromatography step.
  • As an alternative or additionally to standard anion exchange chromatography, chromatofocusing can be performed. Chromatofocusing is a chromatography technique that separates glycoforms according to differences in their isoelectric point (pI). In particular, a charged stationary phase can be used and the proteins loaded onto the chromatofocusing column can be eluted using a pH gradient. For example, the stationary phase may be positively charged and the pH gradient may develop from a first pH to a second, lower pH, for example from about pH 9 to about pH 6 or from about pH 7 to about pH 4. Due to the specific conditions of the chromatofocusing, glycoforms elute in order of their isoelectric points and preferably proteins of a specific pI are focused into narrow bands. Thus, as glycoforms at a pH higher than their pI are negatively charged and attach to the positively charged stationary phase, thereby being slowed down. When the pH in the elution gradient reaches the pI of the glycoform, it is overall neutral in charge and thus migrates with the flow of the mobile phase. At a pH lower than the pI of the protein, the glycoform is repulsed by the stationary phase due to its positive charge, thus accelerating it. Thereby glycoforms at the rear of a zone will migrate more rapidly than those at the front. In this setting, the glycoform with the highest pI elutes first and the glycoform with the lowest pI will elute last.
  • Suitable stationary phases are, for example, media substituted with charged, buffering amines such as MONO P (obtainable from GE Healthcare) or other anion exchange chromatography material. For forming the pH gradient for elution, suitable buffing systems such as POLYBUFFER 74® or POLYBUFFER 76® (obtainable from GE Healthcare) can be used. Equilibration, loading and washing of the column can be done using any condition where the glycoprotein of interest and/or any impurities bind to the column material. For example, conditions as described above for the anion exchange chromatography can be used. When using a decreasing pH gradient, preferably a buffer having a pH equal to or higher than the starting pH of the elution gradient is used for equilibration, loading and/or washing. When using an increasing pH gradient, preferably a buffer having a pH equal to or lower than the starting pH of the elution gradient is used for equilibration, loading and/or washing.
    • Reverse Phase Chromatography
  • Reverse phase chromatography refers to a chromatography step wherein a non-polar stationary phase and preferably a polar mobile phase are used. In reverse phase chromatography, normally polar compounds are eluted first while non-polar compounds are retained. The reverse phase chromatography is usually performed by equilibrating and loading the column, followed by a wash and subsequent elution, each with a buffer preferably containing an organic solvent such as acetonitrile or isopropanol. The organic solvent such as isopropanol can be used for virus inactivation subsequent to elution. Preferably the organic solvent is a water miscible organic solvent such as acetonitrile or an alcohol (such as methanol, ethanol, etc./). Reversed phase column material is made of a resin to which a hydrophobic material may be attached. Typical column materials are silica and polystyrene; hydrophobic ligands may optionally be attached. In case of substituted resins, the resin is substituted with a hydrophobic ligand, typically selected from (but not limited to) aliphates, such as C.sub.2, C.sub.4, C.sub.6, C.sub.8, C.sub.10, C.sub.12, C.sub.14, C.sub.16, or C.sub.18 or derivatives of these, e.g. cyanopropyl (CN-propyl), or branched aliphates, or benzene-based aromates, such as phenyl, or other polar or non-polar ligands. The ligand may be a mixture of two or more of these ligands. Suitable polystyrene based resins include, without limitation, resins supplied by Rohm Haas (e.g. Amberlite XAD® or Amberchrom CG®), Polymer Labs (e.g. PLRP-S®), GE Healthcare (e.g. Source RPC®), Applied Biosystems (e.g. Poros R®). A particularly preferred resin is Source 30 RPC® (GE Healthcare).
    • Viral Inactivation
  • In certain embodiments, the purification process can include a virus inactivation step. Virus inactivation may be achieved by incubating the protein loaded onto, bound to or eluted from the column in the presence of an organic solvent, preferably isopropanol or ethanol. The incubation time and incubation temperature preferably are chosen so as to affect a desired degree of virus inactivation and in particular depend on the concentration and nature of the organic solvent used. Furthermore, these parameters should also be adjusted depending on the stability of the binding protein composition to be purified. For example, the protein is incubated for at least 15 min, preferably for at least 30 min, at least 45 min, at least 1 h, at least 2 h, at least 3 h or at least 6 h. The incubation can be performed at low temperature such as at or below 4° C. or at or below 10° C., or it can be performed at about room temperature. The incubation can be performed directly after the sample has been loaded onto the column, during or after the washing step, after applying the elution buffer but prior to elution of the glycoprotein, or after elution of the binding protein. If isopropanol is used as the organic solvent, virus inactivation is preferably done at an isopropanol concentration of at least 15% (v/v), preferably at about 18% (v/v). In this case, the binding protein is preferably incubated for about 2 h, preferably at room temperature. Preferably, the virus inactivation is performed after elution of the glycoprotein from the reverse phase chromatography column, preferably in the elution buffer used. However, optionally further components may be added to the glycoprotein solution after elution from the column, in particular for enhancing the virus inactivation and/or the binding protein stability.
    • Size Exclusion Chromatography
  • The purification process may include a step of size exclusion chromatography, e.g. for further purifying and/or re-buffering of the binding protein composition. Size exclusion chromatography comprises the step of equilibrating and loading the eluate of the previous chromatography step to a gel filtration matrix equilibrated with a buffer having a composition which is desired for storage or further processing of the glycoprotein at a pH of typically between 6.5 and 9. For performing size exclusion chromatography, the gel is typically selected from the groups of polymeric gels including, but not limited to dextra-based gels such as SEPHADEX® (e.g. SEPHADEX G-25®) or polyacrylamide gels such as SEPHACRYL® (e.g. SEPHACRYL-5400®), agarose-based gels such as SUPEROSE® or SEPHAROSE® (e.g. SEPHAROSE CL-4B®), and composite gels prepared from two kinds of gels such as SUPERDEX 200® combining DEXTRAN® (SEPHADEX®) and crosslinked Agarose (SUPEROSE®) gels. Buffers may be selected from the group consisting sodium phosphate, ammonium acetate, MES (2-(N-morpholino)ethanesulfonic acid), Bis-Tris (2-bis(2-hydroxyethyl)amino-2-(hydroxymethyl)-1,3-propanediol), ADA (N-(2-Acetamido) iminodiacetic acid), PIPES (piperazine-N,N′-bis(2-ethanesulfonic acid), ACES (N-(2-Acetamido)-2-aminoethanesulfonic acid), BES (N,N-Bis(2-hydroxyethyl)-2-aminoethane-sulfonic acid), MOPS (3-(N-morpholino) propanesulfonic acid), TES (N-Tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid), HEPES (N-2-Hydroxyethyl-piperazine-N′-2-ethanesulfonic acid), sodium phosphate or ammonium acetate. Said buffer may additionally comprise an inorganic salt, e.g., a halide of an alkaline metal, e.g., potassium chloride or sodium chloride and/or an antioxidant, such as L-methionine, t-butyl-4-methoxyphenol, 2,6-bis(1,1-dimethylethyl)-4-methyl phenol; potassium or sodium bimetabisulfite, sodium bisulfite. The size exclusion chromatography may further comprise the step of eluting the binding protein from said gel filtration matrix by isocratic elution, i.e. the elution buffer has about the same, preferably the same composition as the buffer used for equilibration and/or loading. The flow through may be recorded by UV absorption at 280 nm and the fraction containing the glycoprotein is collected.
    • Hydrophobic Interaction Chromatography (HIC)
  • HIC is a separation method that takes advantage of the hydrophobic properties of the proteins. The adsorption is promoted by the hydrophobic interactions between non-polar regions on the protein and immobilized hydrophobic ligands on a solid support. Adsorption is achieved at high salt concentrations in the aqueous mobile phase and elution is facilitated by decreasing the salt concentration. The hydrophobic interaction chromatography material is a matrix substituted with hydrophobic ligands such as ethyl-, butyl-, phenyl- or hexyl-groups. Preferred material is a matrix substituted with a butyl or a phenyl ligand. Hydrophobic Interaction Chromatography (HIC) resins are known in the art and include resins such as BUTYL SEPHAROSE® (GE Healthcare), PHENYL SEPHAROSE® (low and high substitution), OCTYL SEPHAROSE® and ALKYL SEPHAROSE® (all of GE Healthcare; other sources of HIC resins include Biosepra, France; E. Merck, Germany; BioRad USA). Alternative resins that may be used are as follows: TOYOPEARL BUTYL 650M® (obtainable from Tosoh Biosep Inc.), PHENYL SEPHAROSE 6 FAST FLOW® (low sub); PHENYL SEPHAROSE 6 FAST FLOW® (high sub); BUTYL SEPAROSE 4 FAST FLOW®; OCTYL SEPHAROSE 4 FAST FLOW®; PHENYL SEPHAROSE HIGH PERFORMANCE®; SOURCE 15ETHC); SOURCE 15ISOCI; SOURCE 15PHE® all from GE Biosciences (800) 526-3593. Still further resins are: HYDROCELL® C3 or C4; HYDROCELL PHENYL® from BioChrom Labs Inc. (812) 234-2558. Equilibration, loading, wash and elution buffers may be selected from the group consisting of sodium phosphate, MES, Bis-Tris, ADA, PIPES, ACES, BES, MOPS, TES, HEPES. Binding on the HIC resin is in general achieved by using an equilibration and loading buffer with a high conductivity, obtained e.g. through the addition of salt such as NaCl, (NH4)2SO4 or Na2SO4, preferably ammonium sulfate. Exemplary salt concentrations are 1 to 2M. The wash generally uses the loading buffer. Elution in the step of hydrophobic interaction chromatography is preferably carried out by reducing the conductivity of the mobile phase (reducing salt concentration). The reduction can be achieved in a linear way or step-wise.
    • Other Purification Steps
  • Prior to the first chromatography step, it may be desirable to carry out a step of ultrafiltration, in order to concentrate the crude binding protein. Furthermore, additionally a step of diafiltration may be performed prior to the first chromatography step in order to perform a buffer exchange. The ultrafiltration step and the diafiltration step may be performed simultaneously or sequentially. The ultrafiltration and/or diafiltration is preferably carried out using a membrane having a cut-off of at or about 3-30 kD, most preferably at or about 10 kD. It is preferred to perform during ultrafiltration and/or diafiltration a buffer exchange to a pre-formulation buffer, e.g. selected from the group consisting of sodium phosphate, sodium citrate, MES, Bis-Tris, ADA, PIPES, ACES, BES, MOPS, TES, HEPES, preferably sodium phosphate, preferably sodium-phosphate containing stabilizers e.g. sucrose and antioxidants like L-methionine. The pH preferably is in the range of 6.5 to 7.5, more preferably about 7.0 to 7.1.
  • Further optional steps which can be performed in the purification process according to the invention include one or more sterile filtration steps. These steps can be used to remove biological contaminations such as eukaryotic and/or prokaryotic cells, in particular bacteria, and/or viruses. Preferably, these steps are performed at or near the end of the purification process to prevent a further contamination after the sterile filtration step. For removal of bacteria or other cells, the filter used for sterile filtration preferably has a pore size of 0.22 μm or less, preferably 0.1 μm or less. For removal of viruses or virus-like particles, a nanofiltration step may also be performed.
    • Storage/Lyophilisation
  • The binding protein composition resulting from the purification process as described above and containing purified glycoprotein may be frozen for storage as is, or after purification, the eluate may be subjected to lyophilisation (“freeze-drying”) to remove solvent.
    • VIII. Pharmaceutical Compositions
  • In one aspect, pharmaceutical compositions comprising one or more population of binding proteins, either alone or in combination with prophylactic agents, therapeutic agents, and/or pharmaceutically acceptable carriers are provided. The pharmaceutical compositions provided herein are for use in, but not limited to, diagnosing, detecting, or monitoring a disorder, in preventing, treating, managing, or ameliorating a disorder or one or more symptoms thereof, and/or in research. The formulation of pharmaceutical compositions, either alone or in combination with prophylactic agents, therapeutic agents, and/or pharmaceutically acceptable carriers, is known to one skilled in the art (US Patent Publication No. 20090311253 A1).
  • In another aspect, the pharmaceutical composition is formulated together, or co-administered with, at least one additional agent. For example, the additional agent may be selected from the group consisting of: therapeutic agent, imaging agent, cytotoxic agent, angiogenesis inhibitors; kinase inhibitors; co-stimulation molecule blockers; adhesion molecule blockers; anti-cytokine antibody or functional fragment thereof; detectable label or reporter; a TNF antagonist; an anti-rheumatic; a muscle relaxant, a narcotic, a non-steroid anti-inflammatory drug (NSAID), an analgesic, an anesthetic, a sedative, a local anesthetic, a neuromuscular blocker, an antimicrobial, an antipsoriatic, a corticosteriod, an anabolic steroid, an erythropoietin, an immunoglobulin, an immunosuppressive, a growth hormone, a hormone replacement drug, a radiopharmaceutical, an antidepressant, an antipsychotic, a stimulant, an asthma medication, a beta agonist, an inhaled steroid, an oral steroid, an epinephrine or analog, a cytokine, and a cytokine antagonist.
  • In certain exemplary embodiments, the binding protein compositions of the invention are formulated together with, or co-administered with, an immunosuppressive or anergy-inducing agent. Exemplary such agents include Rapamycin (also known as Sirolimus) or analogs thereof, e.g., CCI-779, or FK-506 (also known as Tacrolimus) or analogs thereof. The agents may be formulated in a nanoparticle (e.g., a polymeric nanoparticle), optionally together with the binding protein composition. Biocompatible materials useful for making the nanoparticles include, but are not limited to, bio-degradable polymeric materials including, but not limited to, hydrogel, collagen, alginate, poly(glycolide) (PGA), poly(L-lactide) (PLA), poly(lactide-co-glycolide) (PLGA), polyethylene glycol (PEG), polyesters, polyanhydrides, polyorthoesters, polyamides; non-polymeric biodegradable ceramic materials including, but not limited to, calcium phosphate, hydroxyapatite, tricalcium phosphate; or a combination thereof. In a preferred embodiment, the nanoparticles are fabricated from poly(lactic-co-glycolic acid) (PLGA), which is FDA approved for delivery of therapeutics. In certain embodiments, the nanoparticles have a diameter ranging from 10-1000 nm, or any values therebetween, such as 50-900 nm, 100-800 nm, 200-500 nm, 300-400 nm, etc. In preferred embodiments, the nanoparticles have a diameter from 300 nm to 500 nm, or any values therebetween, such as 300-450 nm, 300-400 nm, 330-480 nm, 350-450 nm, 350-400 nm, etc. Exemplary immunosupressant-containing nanoparticles are described in WO2012149255 and WO2012149259, the contents of each of which are hereby incorporated by reference in their entirety. Methods of making and administering immunosupressant-containing nanoparticle compositions are known in the art (see e.g., Das et al, J Biomed Mater Res A. 2008 Mar. 15;84(4):885-98, and Haddadi et al., J Biomed Mater Res A. 2008 Jun. 15;85(4):983-92, the contents of each of which are hereby incorporated by reference in their entirety).
  • Methods of administering a prophylactic or therapeutic agent provided herein include, but are not limited to, parenteral administration (e.g., intradermal, intramuscular, intraperitoneal, intravenous and subcutaneous), epidural administration, intratumoral administration, mucosal administration (e.g., intranasal and oral routes) and pulmonary administration (e.g., aerosolized compounds administered with an inhaler or nebulizer). The formulation of pharmaceutical compositions for specific routes of administration, and the materials and techniques necessary for the various methods of administration are available and known to one skilled in the art (US Patent Publication No. 20090311253 A1).
  • Dosage regimens may be adjusted to provide the optimum desired response (e.g., a therapeutic or prophylactic response). For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation. It is especially advantageous to formulate parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. The term “dosage unit form” refers to physically discrete units suited as unitary dosages for the mammalian subjects to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms provided herein are dictated by and directly dependent on (a) the unique characteristics of the active compound and the particular therapeutic or prophylactic effect to be achieved, and (b) the limitations inherent in the art of compounding such an active compound for the treatment of sensitivity in individuals.
  • An exemplary, non-limiting range for a therapeutically or prophylactically effective amount of a binding protein provided herein is 0.1-20 mg/kg, for example, 1-10 mg/kg. It is to be noted that dosage values may vary with the type and severity of the condition to be alleviated. It is to be further understood that for any particular subject, specific dosage regimens may be adjusted over time according to the individual need and the professional judgment of the person administering or supervising the administration of the compositions, and that dosage ranges set forth herein are exemplary only and are not intended to limit the scope or practice of the claimed composition.
    • IX. Methods of Treatment Using Tnf Binding Molecules
  • In one aspect, provided herein are methods of treating a TNF-associated disorder in a subject by administering to the individual in need of such treatment a therapeutically effective amount of a composition comprising a glycoengineered population of TNF binding proteins disclosed herein. Such methods can be used to treat any TNF-associated disorder including, without limitation:
  • 1) Sepsis
  • Tumor necrosis factor has an established role in the pathophysiology of sepsis, with biological effects that include hypotension, myocardial suppression, vascular leakage syndrome, organ necrosis, stimulation of the release of toxic secondary mediators and activation of the clotting cascade (see e.g., Moeller, A., et al. (1990) Cytokine 2:162-169; U.S. Pat. No. 5,231,024 to Moeller et al.; European Patent Publication No. 260 610 B1 by Moeller, A.; Tracey, K. J. and Cerami, A. (1994) Annu. Rev. Med. 45:491-503; Russell, D and Thompson, R. C. (1993) Curr. Opin. Biotech. 4:714-721). Accordingly, a TNF binding proteins of the invention can be used to treat sepsis in any of its clinical settings, including septic shock, endotoxic shock, gram negative sepsis and toxic shock syndrome.
  • Furthermore, to treat sepsis, a combination of the invention can be coadministered with one or more additional therapeutic agents that may further alleviate sepsis, such as an interleukin-1 inhibitor (such as those described in PCT Publication Nos. WO 92/16221 and WO 92/17583), the cytokine interleukin-6 (see e.g., PCT Publication No. WO 93/11793) or an antagonist of platelet activating factor (see e.g., European Patent Application Publication No. EP 374 510). Other combination therapies for the treatment of sepsis are discussed further in herein.
  • Additionally, in certain embodiments, a TNF binding proteins of the invention is administered to a human subject within a subgroup of sepsis patients having a serum or plasma concentration of IL-6 above 500 pg/ml (e.g., above 1000 pg/ml) at the time of treatment (see PCT Publication No. WO 95/20978 by Daum, L., et al.).
  • 2) Autoimmune Diseases
  • Tumor necrosis factor has been implicated in playing a role in the pathophysiology of a variety of autoimmune diseases. For example, TNF-alpha has been implicated in activating tissue inflammation and causing joint destruction in rheumatoid arthritis (see e.g., Moeller, A., et al. (1990) Cytokine 2:162-169; U.S. Pat. No. 5,231,024 to Moeller et al.; European Patent Publication No. 260 610 B1 by Moeller, A.; Tracey and Cerami, supra; Arend, W. P. and Dayer, J M. (1995) Arth. Rheum. 38:151-160; Fava, R. A., et al. (1993) Clin. Exp. Immunol. 94:261266). TNF-alpha also has been implicated in promoting the death of islet cells and in mediating insulin resistance in diabetes (see e.g., Tracey and Cerami, supra; PCT Publication No. WO 94/08609). TNF-alpha also has been implicated in mediating cytotoxicity to oligodendrocytes and induction of inflammatory plaques in multiple sclerosis (see e.g., Tracey and Cerami, supra). Chimeric and humanized murine anti-hTNF-alpha antibodies have undergone clinical testing for treatment of rheumatoid arthritis (see e.g., Elliott, M. J., et al. (1994) Lancet 344:1125-1127; Elliot, M. J., et al. (1994) Lancet 344:1105-1110; Rankin, E. C., et al. (1995) Br. J. Rheumatol. 34:334-342).
  • Compositions of the invention can be used to treat autoimmune diseases, in particular those associated with inflammation, including rheumatoid arthritis, rheumatoid spondylitis, osteoarthritis and gouty arthritis, allergy, multiple sclerosis, autoimmune diabetes, autoimmune uveitis and nephrotic syndrome. Typically, the combination is administered systemically, although for certain disorders, local administration of the anti-TNF and/or JAK inhibitor at a site of inflammation may be beneficial (e.g., local administration in the joints in rheumatoid arthritis or topical application to diabetic ulcers, alone or in combination with a cyclohexane-ylidene derivative as described in PCT Publication No. WO 93/19751). Compositions of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of autoimmune diseases, as discussed further herein.
  • 3) Infectious Diseases
  • Tumor necrosis factor has been implicated in mediating biological effects observed in a variety of infectious diseases. For example, TNF-alpha has been implicated in mediating brain inflammation and capillary thrombosis and infarction in malaria. TNF-alpha also has been implicated in mediating brain inflammation, inducing breakdown of the blood-brain bather, triggering septic shock syndrome and activating venous infarction in meningitis. TNF-alpha also has been implicated in inducing cachexia, stimulating viral proliferation and mediating central nervous system injury in acquired immune deficiency syndrome (AIDS). Accordingly, the compositions of the invention, can be used in the treatment of infectious diseases, including bacterial meningitis (see e.g., European Patent Application Publication No. EP 585 705), cerebral malaria, AIDS and AIDS-related complex (ARC) (see e.g., European Patent Application Publication No. EP 230 574), as well as cytomegalovirus infection secondary to transplantation (see e.g., Fietze, E., et al. (1994) Transplantation 58:675-680). Compositions of the invention, also can be used to alleviate symptoms associated with infectious diseases, including fever and myalgias due to infection (such as influenza) and cachexia secondary to infection (e.g., secondary to AIDS or ARC).
  • 4) Transplantation
  • Tumor necrosis factor has been implicated as a key mediator of allograft rejection and graft versus host disease (GVHD) and in mediating an adverse reaction that has been observed when the rat antibody OKT3, directed against the T cell receptor CD3 complex, is used to inhibit rejection of renal transplants (see e.g., Eason, J. D., et al. (1995) Transplantation 59:300-305; Suthanthiran, M. and Strom, T. B. (1994) New Engl. J. Med. 331:365-375). Accordingly, compositions of the invention, can be used to inhibit transplant rejection, including rejections of allografts and xenografts and to inhibit GVHD. Although the combination may be used alone, it can be used in combination with one or more other agents that inhibit the immune response against the allograft or inhibit GVHD. For example, in one embodiment, a TNF binding protein is used in combination with OKT3 to inhibit OKT3-induced reactions. In another embodiment, a TNF binding protein is used in combination with one or more antibodies directed at other targets involved in regulating immune responses, such as the cell surface molecules CD25 (interleukin-2 receptor-.alpha.), CD11a (LFA-1), CD54 (ICAM-1), CD4, CD45, CD28/CTLA4, CD80 (B7-1) and/or CD86 (B7-2). In yet another embodiment, a TNF binding protein of the invention is used in combination with one or more general immunosuppressive agents, such as cyclosporin A or FK506.
  • 5) Malignancy
  • Tumor necrosis factor has been implicated in inducing cachexia, stimulating tumor growth, enhancing metastatic potential and mediating cytotoxicity in malignancies. Accordingly, a TNF binding protein of the invention can be used in the treatment of malignancies, to inhibit tumor growth or metastasis and/or to alleviate cachexia secondary to malignancy. The compositions may be administered systemically or locally to the tumor site.
  • 6) Pulmonary Disorders
  • Tumor necrosis factor has been implicated in the pathophysiology of adult respiratory distress syndrome (ARDS), including stimulating leukocyte-endothelial activation, directing cytotoxicity to pneumocytes and inducing vascular leakage syndrome. Accordingly, a TNF binding protein of the invention, can be used to treat various pulmonary disorders, including adult respiratory distress syndrome (see e.g., PCT Publication No. WO 91/04054), shock lung, chronic pulmonary inflammatory disease, pulmonary sarcoidosis, pulmonary fibrosis and silicosis. The compositions may be administered systemically or locally to the lung surface, for example as an aerosol. A composition of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of pulmonary disorders, as discussed further in herein.
  • 7) Intestinal Disorders
  • Tumor necrosis factor has been implicated in the pathophysiology of inflammatory bowel disorders (see e.g., Tracy, K. J., et al. (1986) Science 234:470-474; Sun, X M., et al. (1988) J. Clin. Invest. 81:1328-1331; MacDonald, T. T., et al. (1990) Clin. Exp. Immunol. 81:301-305). Chimeric murine anti-hTNF-alpha antibodies have undergone clinical testing for treatment of Crohn's disease (van Dullemen, H. M., et al. (1995) Gastroenterology 109:129-135). The compositions of the invention, also can be used to treat intestinal disorders, such as idiopathic inflammatory bowel disease, which includes two syndromes, Crohn's disease and ulcerative colitis. A composition of the invention also can be administered with one or more additional therapeutic agents useful in the treatment of intestinal disorders, as discussed further in herein.
  • 8) Cardiac Disorders
  • The compositions of the invention, also can be used to treat various cardiac disorders, including ischemia of the heart (see e.g., European Patent Application Publication No. EP 453 898) and heart insufficiency (weakness of the heart muscle) (see e.g., PCT Publication No. WO 94/20139).
  • 9) Other Disorders
  • The compositions of the invention, also can be used to treat various other disorders in which TNF-alpha activity is detrimental. Examples of other diseases and disorders in which TNF-alpha activity has been implicated in the pathophysiology, and thus which can be treated using a TNF binding protein of the invention, include inflammatory bone disorders and bone resorption disease (see e.g., Bertolini, D. R., et al. (1986) Nature 319:516-518; Konig, A., et al. (1988) J. Bone Miner. Res. 3:621-627; Lerner, U. H. and Ohlin, A. (1993) J. Bone Miner. Res. 8:147-155; and Shankar, G. and Stern, P. H. (1993) Bone 14:871-876); hepatitis, including alcoholic hepatitis (see e.g., McClain, C. J. and Cohen, D. A. (1989) Hepatology 9:349-351; Felver, M. E., et al. (1990) Alcohol. Clin. Exp. Res. 14:255-259; and Hansen, J., et al. (1994) Hepatology 20:461-474), viral hepatitis (Sheron, N., et al. (1991) J. Hepatol. 12:241-245; and Hussain, M. J., et al. (1994) J. Clin. Pathol. 47:1112-1115), and fulminant hepatitis; coagulation disturbances (see e.g., van der Poll, T., et al. (1990) N. Engl. J. Med. 322:1622-1627; and van der Poll, T., et al. (1991) Frog. Clin. Biol. Res. 367:55-60); burns (see e.g., Giroir, B. P., et al. (1994) Am. J. Physiol. 267:H118-124; and Liu, X. S., et al. (1994) Burns 20:40-44); reperfusion injury (see e.g., Scales, W. E., et al. (1994) Am. J. Physiol. 267:G1122-1127; Serrick, C., et al. (1994) Transplantation 58:1158-1162; and Yao, Y. M., et al. (1995) Resuscitation 29:157-168); keloid formation (see e.g., McCauley, R. L., et al. (1992) J. Clin. Immunol. 12:300-308), scar tissue formation; pyrexia; periodontal disease; obesity; and radiation toxicity.
  • In certain embodiments, an compositions of the invention is used for the treatment of a TNF-associated disorder selected from the group consisting of osteoarthritis, rheumatoid arthritis, juvenile chronic arthritis, septic arthritis, Lyme arthritis, psoriatic arthritis, reactive arthritis, spondyloarthropathy, systemic lupus erythematosus, Crohn's disease, ulcerative colitis, inflammatory bowel disease, insulin dependent diabetes mellitus, thyroiditis, asthma, allergic diseases, psoriasis, dermatitis, scleroderma, graft versus host disease, organ transplant rejection, acute or chronic immune disease associated with organ transplantation, sarcoidosis, atherosclerosis, disseminated intravascular coagulation, Kawasaki's disease, Grave's disease, nephrotic syndrome, chronic fatigue syndrome, Wegener's granulomatosis, Henoch-Schoenlein purpurea, microscopic vasculitis of the kidneys, chronic active hepatitis, uveitis, septic shock, toxic shock syndrome, sepsis syndrome, cachexia, infectious diseases, parasitic diseases, acute transverse myelitis, Huntington's chorea, Parkinson's disease, Alzheimer's disease, stroke, primary biliary cirrhosis, hemolytic anemia, malignancies, heart failure, myocardial infarction, Addison's disease, sporadic polyglandular deficiency type I, polyglandular deficiency type II (Schmidt's syndrome), adult (acute) respiratory distress syndrome, alopecia, alopecia greata, seronegative arthropathy, arthropathy, Reiter's disease, psoriatic arthropathy, ulcerative colitic arthropathy, enteropathic synovitis, Chlamydia-associated arthropathy, Yersinia-associated arthropathy, Salmonella-associated arthropathy, spondyloarthropathy, atheromatous disease/arteriosclerosis, atopic allergy, autoimmune bullous disease, pemphigus vulgaris, pemphigus foliaceus, pemphigoid, linear IgA disease, autoimmune haemolytic anaemia, Coombs positive haemolytic anaemia, acquired pernicious anaemia, juvenile pernicious anaemia, myalgic encephalitis/Royal Free disease, chronic mucocutaneous candidiasis, giant cell arteritis, primary sclerosing hepatitis, cryptogenic autoimmune hepatitis, acquired immunodeficiency syndrome, acquired immunodeficiency related diseases, hepatitis B, hepatitis C, common varied immunodeficiency (common variable hypogammaglobulinaemia), dilated cardiomyopathy, female infertility, ovarian failure, premature ovarian failure, fibrotic lung disease, cryptogenic fibrosing alveolitis, post-inflammatory interstitial lung disease, interstitial pneumonitis, connective tissue disease associated interstitial lung disease, mixed connective tissue disease associated lung disease, systemic sclerosis associated interstitial lung disease, rheumatoid arthritis associated interstitial lung disease, systemic lupus erythematosus associated lung disease, dermatomyositis/polymyositis associated lung disease, Sjogren's disease associated lung disease, ankylosing spondylitis associated lung disease, vasculitic diffuse lung disease, haemosiderosis associated lung disease, drug-induced interstitial lung disease, fibrosis, radiation fibrosis, bronchiolitis obliterans, chronic eosinophilic pneumonia, lymphocytic infiltrative lung disease, postinfectious interstitial lung disease, gouty arthritis, autoimmune hepatitis, type-1 autoimmune hepatitis (classical autoimmune or lupoid hepatitis), type-2 autoimmune hepatitis (anti-LKM antibody hepatitis), autoimmune mediated hypoglycemia, type B insulin resistance with acanthosis nigricans, hypoparathyroidism, acute immune disease associated with organ transplantation, chronic immune disease associated with organ transplantation, osteoarthrosis, primary sclerosing cholangitis, psoriasis type 1, psoriasis type 2, idiopathic leucopaenia, autoimmune neutropaenia, renal disease NOS, glomerulonephritides, microscopic vasculitis of the kidneys, Lyme disease, discoid lupus erythematosus, male infertility idiopathic or NOS, sperm autoimmunity, multiple sclerosis (all subtypes), sympathetic ophthalmia, pulmonary hypertension secondary to connective tissue disease, Goodpasture's syndrome, pulmonary manifestation of polyarteritis nodosa, acute rheumatic fever, rheumatoid spondylitis, Still's disease, systemic sclerosis, Sjorgren's syndrome, Takayasu's disease/arteritis, autoimmune thrombocytopaenia, idiopathic thrombocytopaenia, autoimmune thyroid disease, hyperthyroidism, goitrous autoimmune hypothyroidism (Hashimoto's disease), atrophic autoimmune hypothyroidism, primary myxoedema, phacogenic uveitis, primary vasculitis, vitiligo, acute liver disease, chronic liver diseases, alcoholic cirrhosis, alcohol-induced liver injury, cholestasis, idiosyncratic liver disease, drug-induced hepatitis, non-alcoholic steatohepatitis, allergy, group B streptococci (GBS) infection, mental disorders (e.g., depression and schizophrenia), Th2 Type and Th1 Type mediated diseases, acute and chronic pain (different forms of pain), cancers such as lung, breast, stomach, bladder, colon, pancreas, ovarian, prostate and rectal cancer and hematopoietic malignancies (leukemia and lymphoma), abetalipoproteinemia, acrocyanosis, acute and chronic parasitic or infectious processes, acute leukemia, acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), acute or chronic bacterial infection, acute pancreatitis, acute renal failure, adenocarcinomas, atrial ectopic beats, AIDS dementia complex, alcohol-induced hepatitis, allergic conjunctivitis, allergic contact dermatitis, allergic rhinitis, allograft rejection, alpha-1-antitrypsin deficiency, amyotrophic lateral sclerosis, anemia, angina pectoris, anterior horn cell degeneration, antiphospholipid syndrome, anti-receptor hypersensitivity reactions, aortic and peripheral aneurysms, aortic dissection, arterial hypertension, arteriosclerosis, arteriovenous fistula, ataxia, atrial fibrillation (sustained or paroxysmal), atrial flutter, atrioventricular block, B cell lymphoma, bone graft rejection, bone marrow transplant (BMT) rejection, bundle branch block, Burkitt's lymphoma, burns, cardiac arrhythmias, cardiac stun syndrome, cardiac tumors, cardiomyopathy, cardiopulmonary bypass inflammation response, cartilage transplant rejection, cerebellar cortical degenerations, cerebellar disorders, chaotic or multifocal atrial tachycardia, chemotherapy associated disorders, chronic myelocytic leukemia (CML), chronic alcoholism, chronic inflammatory pathologies, chronic lymphocytic leukemia (CLL), chronic obstructive pulmonary disease (COPD), chronic salicylate intoxication, colorectal carcinoma, congestive heart failure, conjunctivitis, contact dermatitis, cor pulmonale, coronary artery disease, Creutzfeldt-Jakob disease, culture negative sepsis, cystic fibrosis, cytokine therapy associated disorders, dementia pugilistica, demyelinating diseases, dengue hemorrhagic fever, dermatitis, dermatologic conditions, diabetes, diabetic arteriosclerotic disease, diffuse Lewy body disease, dilated congestive cardiomyopathy, disorders of the basal ganglia, Down's syndrome in middle age, drug-induced movement disorders induced by drugs which block CNS dopamine receptors, drug sensitivity, eczema, encephalomyelitis, endocarditis, endocrinopathy, epiglottitis, Epstein-Barr virus infection, erythromelalgia, extrapyramidal and cerebellar disorders, familial hemophagocytic lymphohistiocytosis, fetal thymus implant rejection, Friedreich's ataxia, functional peripheral arterial disorders, fungal sepsis, gas gangrene, gastric ulcer, glomerular nephritis, graft rejection of any organ or tissue, gram negative sepsis, gram positive sepsis, granulomas due to intracellular organisms, hairy cell leukemia, Hallervorden-Spatz disease, Hashimoto's thyroiditis, hay fever, heart transplant rejection, hemochromatosis, hemodialysis, hemolytic uremic syndrome/thrombolytic thrombocytopenic purpura, hemorrhage, hepatitis A, His bundle arrhythmias, HIV infection/HIV neuropathy, Hodgkin's disease, hyperkinetic movement disorders, hypersensitivity reactions, hypersensitivity pneumonitis, hypertension, hypokinetic movement disorders, hypothalamic-pituitary-adrenal axis evaluation, idiopathic Addison's disease, idiopathic pulmonary fibrosis, antibody mediated cytotoxicity, asthenia, infantile spinal muscular atrophy, inflammation of the aorta, influenza A, ionizing radiation exposure, iridocyclitis/uveitis/optic neuritis, ischemia-reperfusion injury, ischemic stroke, juvenile rheumatoid arthritis, juvenile spinal muscular atrophy, Kaposi's sarcoma, kidney transplant rejection, legionella, leishmaniasis, leprosy, lesions of the corticospinal system, lipedema, liver transplant rejection, lymphedema, malaria, malignant lymphoma, malignant histiocytosis, malignant melanoma, meningitis, meningococcemia, metabolic migraine headache, idiopathic migraine headache, mitochondrial multisystem disorder, mixed connective tissue disease, monoclonal gammopathy, multiple myeloma, multiple systems degenerations (Menzel, Dejerine-Thomas, Shy-Drager, and Machado-Joseph), myasthenia gravis, mycobacterium avium intracellulare, mycobacterium tuberculosis, myelodysplastic syndrome, myocardial infarction, myocardial ischemic disorders, nasopharyngeal carcinoma, neonatal chronic lung disease, nephritis, nephrosis, neurodegenerative diseases, neurogenic muscular atrophies, neutropenic fever, non-Hodgkin's lymphoma, occlusion of the abdominal aorta and its branches, occlusive arterial disorders, orchitis/epididymitis, orchitis/vasectomy reversal procedures, organomegaly, osteoporosis, pancreas transplant rejection, pancreatic carcinoma, paraneoplastic syndrome/hypercalcemia of malignancy, parathyroid transplant rejection, pelvic inflammatory disease, perennial rhinitis, pericardial disease, peripheral atherosclerotic disease, peripheral vascular disorders, peritonitis, pernicious anemia, pneumocystis carinii pneumonia, pneumonia, POEMS syndrome (polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes syndrome), post perfusion syndrome, post pump syndrome, post-MI cardiotomy syndrome, preeclampsia, progressive supranucleo palsy, primary pulmonary hypertension, radiation therapy, Raynaud's phenomenon, Raynaud's disease, Refsum's disease, regular narrow QRS tachycardia, renovascular hypertension, reperfusion injury, restrictive cardiomyopathy, sarcomas, senile chorea, senile dementia of Lewy body type, seronegative arthropathies, shock, sickle cell anemia, skin allograft rejection, skin changes syndrome, small bowel transplant rejection, solid tumors, specific arrhythmias, spinal ataxia, spinocerebellar degenerations, streptococcal myositis, structural lesions of the cerebellum, subacute sclerosing panencephalitis, syncope, syphilis of the cardiovascular system, systemic anaphylaxis, systemic inflammatory response syndrome, systemic onset juvenile rheumatoid arthritis, telangiectasia, thromboangiitis obliterans, thrombocytopenia, toxicity, transplants, trauma/hemorrhage, type III hypersensitivity reactions, type IV hypersensitivity, unstable angina, uremia, urosepsis, urticaria, valvular heart diseases, varicose veins, vasculitis, venous diseases, venous thrombosis, ventricular fibrillation, viral and fungal infections, viral encephalitis/aseptic meningitis, viral-associated hemophagocytic syndrome, Wernicke-Korsakoff syndrome, Wilson's disease, xenograft rejection of any organ or tissue, acute coronary syndromes, acute idiopathic polyneuritis, acute inflammatory demyelinating polyradiculoneuropathy, acute ischemia, adult Still's disease, alopecia greata, anaphylaxis, anti-phospholipid antibody syndrome, aplastic anemia, arteriosclerosis, atopic eczema, atopic dermatitis, autoimmune dermatitis, autoimmune disorder associated with streptococcus infection, autoimmune enteropathy, autoimmune hearing loss, autoimmune lymphoproliferative syndrome (ALPS), autoimmune myocarditis, autoimmune premature ovarian failure, blepharitis, bronchiectasis, bullous pemphigoid, cardiovascular disease, catastrophic antiphospholipid syndrome, celiac disease, cervical spondylosis, chronic ischemia, cicatricial pemphigoid, clinically isolated syndrome (CIS) with risk for multiple sclerosis, childhood onset psychiatric disorder, chronic obstructive pulmonary disease (COPD), dacryocystitis, dermatomyositis, diabetic retinopathy, disk herniation, disk prolapse, drug induced immune hemolytic anemia, endocarditis, endometriosis, endophthalmitis, episcleritis, erythema multiforme, erythema multiforme major, gestational pemphigoid, Guillain-Barre syndrome (GBS), hay fever, Hughes syndrome, idiopathic Parkinson's disease, idiopathic interstitial pneumonia, IgE-mediated allergy, immune hemolytic anemia, inclusion body myositis, infectious ocular inflammatory disease, inflammatory demyelinating disease, inflammatory heart disease, inflammatory kidney disease, IPF/UIP, iritis, keratitis, keratojunctivitis sicca, Kussmaul disease or Kussmaul-Meier disease, Landry's paralysis, Langerhan's cell histiocytosis, livedo reticularis, macular degeneration, microscopic polyangiitis, Morbus Bechterev, motor neuron disorders, mucous membrane pemphigoid, multiple organ failure, myasthenia gravis, myelodysplastic syndrome, myocarditis, nerve root disorders, neuropathy, non-A non-B hepatitis, optic neuritis, osteolysis, ovarian cancer, pauciarticular JRA, peripheral artery occlusive disease (PAOD), peripheral vascular disease (PVD), peripheral artery disease (PAD), phlebitis, polyarteritis nodosa (or periarteritis nodosa), polychondritis, polymyalgia rheumatica, poliosis, polyarticular JRA, polyendocrine deficiency syndrome, polymyositis, polymyalgia rheumatica (PMR), post-pump syndrome, primary Parkinsonism, prostate and rectal cancer and hematopoietic malignancies (leukemia and lymphoma), prostatitis, pure red cell aplasia, primary adrenal insufficiency, recurrent neuromyelitis optica, restenosis, rheumatic heart disease, SAPHO (synovitis, acne, pustulosis, hyperostosis, and osteitis), secondary amyloidosis, shock lung, scleritis, sciatica, secondary adrenal insufficiency, silicone associated connective tissue disease, Sneddon-Wilkinson dermatosis, spondylitis ankylosans, Stevens-Johnson syndrome (SJS), systemic inflammatory response syndrome, temporal arteritis, toxoplasmic retinitis, toxic epidermal necrolysis, transverse myelitis, TRAPS (tumor-necrosis factor receptor type 1 (TNFR)-associated periodic syndrome), type 1 allergic reaction, type II diabetes, urticaria, usual interstitial pneumonia (UIP), vasculitis, vernal conjunctivitis, viral retinitis, Vogt-Koyanagi-Harada syndrome (VKH syndrome), and wet macular degeneration. In a particular embodiment, the TNF-associated disease or disorder is rheumatoid arthritis.
  • The disclosure may be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting of the disclosure. Scope of the disclosure is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are therefore intended to be embraced herein.
  • Any patent, patent application, publication, or other disclosure material identified in the specification is hereby incorporated by reference herein in its entirety. Any material, or portion thereof, that is said to be incorporated by reference herein, but which conflicts with existing definitions, statements, or other disclosure material set forth herein is only incorporated to the extent that no conflict arises between that incorporated material and the present disclosure material.
    • EXAMPLES
  • Examples have been set forth below for the purpose of illustration and to describe certain specific embodiments of the invention. However, the scope of the claims is not to be in any way limited by the examples set forth herein. Various changes and modifications to the disclosed embodiments will be apparent to those skilled in the art and such changes and modifications including, without limitation, those relating to the packaging vectors, cell lines and/or methods of the invention may be made without departing from the spirit of the invention and the scope of the appended claims.
    • EXAMPLE 1 Generation of Monoclonal Antibody-Producing CHO Cells Overexpressing β 1, 4 Galactosyl-Transferase
  • A mouse galactosyltransferase β 1, 4 (Genbank accession number: D00314) was amplified by PCR and cloned downstream of CMV promoter of the pcDNA™ 3.3 TOPO® Mammalian Expression Vector (Invitrogen Life Sciences, Catalog Number: K8300-01) as shown in FIG. 2A. The nucleic acid and corresponding amino acid sequence of mouse galactosyltransferase β 1, 4 is shown in FIG. 2B.
  • Adalimumab-producing CHO cells were electroporated with the mouse galactosyltransferase β 1, 4 expression vector. After 48 hours of culture, G418 (Geneticin®, Life Technologies Catalog Number 10131035) was added to the cell media at a final concentration of 500 μg/ml and the cells were cultured an additional 2-3 weeks. Media was changed once every other day. Stable neomycin resistant transformants were isolated and expanded in culture for 1-3 passages prior to cryopreservation. Two exemplary cell lines, designated GALTR-11 and Ga188-D2E7 were analyzed further.
    • Example 2 Generation of Monoclonal Antibody-Producing CHO Cells Having a Beta-Galactosidase Knock Down
  • A knock out in one of the alleles of the beta galactosidase gene (Cricetulus griseus Glb1 (Gene ID: 100767446); mRNA sequence: NCBI Reference Sequence: XM_007630176.1; genomic sequence NW_003613697.1 from 2278553 to 2336708) of the adalimumab-producing DHFR-deficient CHO cell line was generated using zinc finger nuclease following procedures that are well known in the art (Santiago et al., Proc. Natl. Acad. Sci. USA. 2008; 105(15):5809-14; Remy et al., Transgenic Res. 2010;19(3): 363-71; Zhang et al., Advances in Biochemical Engineering/Biotechnology Volume 131, 2013, pp 63-87; U.S. Pat. No. 8,313,925). One exemplary cell line, designated ZFN-B1 was analyzed further.
    • Example 3 Generation of DVD-IG-Producing CHO Cells Overexpressing β 1, 4 Galactosyltransferase
  • IL17xTNF DVD-Ig-producing CHO cells are electroporated with the mouse galactosyltransferase β 1, 4 expression vector and G418 (Geneticin®, Life Technologies Catalog Number 10131035) is added to the cell media 48 hours after the transfection at a final concentration of 500 μg/ml for 2-3 weeks. Media is changed once every other day. Stable neomycin resistant transformants are isolated and cultured for 1-3 passages prior to cryopreservation.
    • Example 4A Culture of CHO Cells Producing a High Gal/Low Man FC Containing Binding Protein
  • This exemplary protocol is described for the production of High Gal/Low Man adalimumab but it is generally applicable to the culture of High Gal/Low Man CHO cells expressing any Fc containing binding protein including, but not limited to, DVD-Ig. High Gal/Low Man CHO cells can be either overexpressing galactosyltransferase β 1, 4, as described in Example 1, or have a knockout of an allele of the endogenous beta galactosidase gene as described in Example 2.
  • Growth and production media for the culture of a High Gal/Low Man adalimumab-producing CHO cell line were prepared using a proprietary Life Technologies GIBCO chemically defined media, GIA-1. Basal production and feed media were supplemented with 50 μM Manganese (II) Chloride (Sigma M1787—100 mL; 1.0 M±0.1 M) and 30 mM D(+)Galactose (Sigma G5388—1 kg) (see published U.S. Patent Application No. 2012/0276631 and U.S. Provisional Application 61/886,855). All media were filtered through Corning 0.5 L or 1 L filter systems 0.22 μm Poly (Ether Sulfone) (PES) and stored at 4° C. until use.
  • The High Gal/Low Man adalimumab-producing CHO cell line was adapted to chemically defined media for 7 (2 to 3 day each) passages in a combination of 250 mL and 500 mL Corning vented non-baffled shake flasks before freezing.
  • Upon thaw, for the batch shake flask study, cells were expanded for 3 to 5 passages (2 to 3 days each) in a combination of 250 mL and 500 mL Corning vented non-baffled shake flasks. Production cultures were initiated in duplicate 500 mL Corning vented non-baffled shake flasks (200 mL working volume) at an initial viable cell density (VCD) of approximately 0.5×106 cells/mL. Cultures were maintained on orbital shakers at 110 revolutions per minute (RPM) in a dry incubator at 35° C. and 5% CO2. The shake flask study was run in an extended batch mode by feeding with a glucose solution (1.25% (v/v) of 40% solution) when the media glucose concentration fell below 3 g/L.
  • For the fed-batch bioreactor study, cells were expanded for 8 passages (2 to 3 days each) in Corning vented non-baffled shake flasks maintained on orbital shakers at 110 RPM and in 20 L cell bags (3 L to 10 L working volume) maintained at 20-25 RPM, 7.5° angle, and 0.25 SLPM airflow in a dry incubator at 35° C. and 5% CO2. Production cultures were initiated in duplicate 3 L bioreactors (1.5 L working volume) at 35° C., 30% dissolved oxygen, 200 RPM, pH ramp from 7.1 to 6.9 over 3 days, and pH setpoint of 6.9 thereafter. A fixed split ratio of cells to media of 1:5 was utilized to initiate the production stage cultures. In the fed-batch mode, a chemically-defined feed from Life Technologies GIBCO, JCL-5 (proprietary formulation), was added as follows: 3% (v/v)— day 3, 5%— day 4, 7%— day 5, 10%— day 6, and 10%—day 7. Additional glucose (1.25% (v/v) of 40% solution) was fed when the media glucose concentration fell below 3 g/L.
  • For all studies with CHO cell lines, samples were collected daily and measured for cell density and viability using a Cedex cell counter. Retention samples for titer analysis via Poros A method were collected by centrifugation at 12,000 RPM for 5 min when the culture viability began declining The cultures were harvested by collecting 125 mL aliquots and centrifuging at 3,000 RPM for 30 min when culture viability was near or below 50%. All supernatants were stored at −80° C. until analysis.
  • High Gal/Low Man adalimumab produced by the ZFN-B 1 CHO cell (as described in Example 2) is referred to herein as ZFN-B 1. High Gal/Low Man adalimumab produced by the GALTR-11 and Ga188-D2E7 CHO cell clones that overexpress β-1, 4 galactosyltransferase (as described in Example 1) are referred to herein as GALTR-11 and Gal88-D2E7, respectively. A High Gal/Low Man anti-TNF×IL17 DVD-Ig (ABT-122) produced by the cell line of Example 3 is referred to herein as Ga179-DVD-Ig.
    • Example 4B Production of Highly Sialylated Glycoforms
  • To prepare approximately 40 mg of GALTR-11 for in-vitro sialylation, the buffer was changed to 35 mM tris acetate, pH 7.4 through dialysis and the concentration adjusted to approximately 5 mg/mL. In vitro sialylation was accomplished by incubating GALTR-11 with activated sialic acid, or more specifically, activated CMP-N-acetyl neuraminic acid (CMP-NANA) and a specific enzyme, α-2,6 sialyltransferase that attaches the sialic acid (NANA) on to the penultimate galactose residue in an α-2,6 linkage. The CMP-NANA was added in a 1:2 CMP-NANA:GALTR-11 ratio and the enzyme was added in a 1:10 enzyme:GALTR-11 ratio, or 4 mg of enzyme to approximately 40 mg of antibody. The volume of the reaction mix was brought up to 15 mL and incubated overnight at 37° C. with gentle shaking.
  • The level of incorporated sialic acid was quantified by weak ion exchange chromatography using a Shimadzu HPLC equipped with an analytical ProPac® WCX-10 column (4×250 mm). Sample was loaded at 94% mobile phase A(10 mM sodium phosphate, pH 7.5) and 6% buffer B (10 mM sodium phosphate, 500 mM sodium chloride, pH 5.5) and then eluted by the gradient and conditions shown in Table 1 to obtain the glycoengineered adalimumab composition referred to herein as SA-D2E7.
  • TABLE 1
    WCX-10 Chromatography Conditions
    Item Description/Operating Conditions
    Mobile phase A 10 mM sodium phosphate, pH 7.5
    Mobile phase B 10 mM sodium phosphate/500 mM sodium
    chloride, pH 5.5
    Binary Gradient
    Time (minute) Mobile Phase B %
    Gradient 0.5 6
    20 16
    22 100
    26 100
    28 6
    34 6
    35 0 (stop)
    Flow rate 1.0 mL/min.
    Detector wavelength 280 nm
    Autosampler temperature Nominal 4° C.
    Column oven temperature ambient
    Sample load Up to 100 μL/100 μg
    Run time 35.0 minutes
  • Chromatograms of the SA-D2E7 composition are shown in FIG. 7C. Sialylated GALTR-11 was be separated from the rest of the antibodies containing other glycoforms (i.e., high mannose, GOF, etc.) since sialic acids impart a negative charge to antibodies due to the loss of a proton by the carboxylic group at physiological pH. The other glycoforms are neutral and eluted from the column in the same peak while sialylated GALTR-11 eluted earlier. Sialylated GALTR-11 will elute from an anion exchange column at different retention times depending on the level of sialic acids it contains. Up to four sialic acids can be added to each D2E7 antibody; two for each Fc biantennary glycan. Only the peaks containing three and four sialic acids were collected to ensure relatively pure fractions of SA-D2E7 (containing near 100% of G2S1F and G2S2F type glycans).
  • The weak ion exchange chromatography method used to collect SA-D2E7 was a modification of the analytical method described above. A GE AKTA Avant system was used with a preparative ProPac® WCX-10 column (22×250 mm) at a flow rate of 25 mL/min The initial gradient was also stretched out longer, to increase the separation between the early eluting peaks.
    • Example 5 Analysis of Glycoengineered ADALIMUMAB
  • The glycan profiles of the ZFN-B1, GALTR-11, Ga188-D2E7, SA-D2E7 and Ga179-DVD were determined.
  • For all studies, the harvest samples were protein A purified using standard methods (Pure 1A® Kit, Sigma Aldrich, St. Louis, Mo.) and prepared for the oligosaccharide assay using the following procedures.
  • As a first step in the process of identifying and quantifying the oligosaccharides, total N-glycans were released from protein A-purified hypergalactosylated adalimumab by enzymatic digestion with N-glycanase. Once the glycans were released, the free reducing end of each glycan was labeled by reductive amination with a fluorescent tag, 2-aminobenzamide (2-AB). The resulting labeled glycans were separated by normal-phase HPLC (NP-HPLC) in acetonitrile: 50 mM ammonium formate, pH 4.4, and detected by a fluorescence detector. Quantitation was based on the relative area percent of detected sugars. The results of the analysis for non-hyperglycosylated adalimumab and the hyperglycosylated Adalimumab ZFN-B1, GALTR-11 and Ga188-D2E7 variants are shown in FIG. 2C.
  • N-deglycosylation of the antibody samples may also be carried out according to the manufacturer's procedure using a Prozyme® N-deglycosylation kit (San Leandro, Calif., USA). Briefly, 300 μg of dried antibody sample are recovered in 135 μL of a 10-mM aqueous Tris-HCl buffer pH 8.0, and 4.5 μL of a 10% (v/v) beta-mercaptoethanol aqueous solution is added to reduce the antibody disulfide bridges. The N-deglycosylation is carried out by the addition of 7.5 mU of peptidyl-N-glycosidase (PNGase F) followed by an overnight incubation at 37 C. At this stage, many N-glycans are released as glycosylamines before slowly hydrolyzing into reducing glycans. The full regeneration of reducing glycans is performed by adding to PNGase F-digested antibody samples glacial acetic acid at a final concentration of 5% (v/v) followed by a one hour incubation at room temperature. The freshly regenerated reducing N-glycan mix is purified by a solid phase extraction (SPE) onto a 50-mg Hypersep Hypercarb® porous graphitized carbon (PGC) column (Thermofischer Scientific, Bremen, Germany) (Packer et al., 1998). The PGC SPE column is sequentially washed with 1 mL methanol and 2×1 mL of a 0.1% (v/v) aqueous trifluoroacetic acid (TFA). The oligosaccharides are dissolved in 200 μL of a 0.1% (v/v) aqueous TFA, applied to the column and washed with 2×1 mL of a 0.1% (v/v) aqueous TFA. The elution of the glycans is performed by applying 2×400 uL of a 25% (v/v) aqueous acetonitrile containing 0.1% (v/v) TFA and the eluate is vacuum-dried.
  • The PGC-purified glycans are reductively aminated with 2-aminobenzamide (2-AB) by recovering dried glycans by 10 μL of a 33% (v/v) acetic acid in DMSO containing 0.35 M 2-AB and 1 M sodium cyanoborohydride and the reaction is kept at 37 C for 16 hours. The 2-AB-labeled N-glycans are purified onto a 50-mg Oasis® polymeric HLB SPE column, used in the hydrophilic interaction chromatography (HILIC) mode (Waters, Milford, Mass., USA). The HILIC SPE column is sequentially wetted with 1 mL of a 20% (v/v) aqueous acetonitrile and equilibrated with 2×1 mL of acetonitrile, the 2-AB derivatives dissolved in acetonitrile are then loaded onto the SPE column. After washing the column with 2×1 mL of acetonitrile, the elution of the 2-AB derivatives is next performed by applying 2×500 μL of a 20% (v/v) aqueous acetonitrile. The 1-mL eluate is vacuum-concentrated to 50 μL.
  • The purified 2-AB derivatives are finally profiled by normal-phase high-performance liquid chromatography (NP-HPLC) using a 150×4.6 mm ID TSK-gel amide-80 HILIC HPLC column (TOSOH Bioscience, King of Prussia, Pa., USA) with 3 μm packing particles (Guile et al., 1996). The mobile phase is composed of a mixture of a 50-mM ammonium formate aqueous solution adjusted at pH 4.4 (A) and acetonitrile (B). The operating flow rate and temperature are respectively 1 mL/min and 30 C. 5 μL of the purified 2-AB derivatives are 40-fold diluted using a 80% (v/v) aqueous acetonitrile, and 50 μL of the freshly shaken organic mixture is injected into the HILIC column, and equilibrated with 80% (v/v) B. Once sample injected, the separation of the N-glycans is performed as follows: from 80% to 70% (v/v) B in 15 mM; from 70% to 55% (v/v) B in 150 mM; from 55% to 10% (v/v) B in 5 mM; 10% (v/v) B during 10 mM; from 10% to 80% (v/v) in 1 mM; 80% (v/v) B during 45 minutes (reequilibration). The detection of the fluorescent derivatives is performed by fluorescence detection (FD) with an excitation wavelength of 330 nm and an emission wavelength of 420 nm.
  • MALDI-TOF mass spectroscopy may also be performed to confirm the identity of the apparent hypergalactosylated species. FIG. 2D shows that the major glycans present in a High Gal/Low Man adalimumab preparation (ZFN-B1) are G1F and G2F. FIG. 2E shows the major glycans present in the High Gal/Low Man adalimumab preparation (SA-D2E7) prior to and following treatment with sialyltransferase.
    • Example 6 TNFα Binding and Internalization of Glycoengineered Adalimumab Isolation of Monocytes, Culture and Stimulation:
  • Peripheral blood mononuclear cells (PBMC) were isolated from leukopack of healthy donors by density gradient centrifugation over Ficoll-Paque (GE Health Sciences). Monocytes were isolated by magnetic sorting using CD14 microbeads (Miltenyi Biotec). The purity of the resulting monocytes, as assessed by flow cytometric analysis, was typically greater than 98%. Monocytes were cultured in RPMI1640 medium (Cellgro) supplemented 2 mM L-glutamine, 100 ng/ml of recombinant human GM-CSF (Abbvie) and 5 ng/ml of human IL-4 (Peprotech), 100 μg/ml penicillin, and streptomycin, and 10% fetal bovine serum at a density of 1×106 cells/ml at 37° C. with 5% CO2 for 5 days.
  • To test the surface TNFalpha expression, PBMCs or monocytes were stimulated with ultra-low (0.025 ng/ml), low (0.25 ng/ml) or high (250 ng/ml) of LPS (from Salmonella typhimurium, Sigma-Aldrich) for one hour.
    • Dendritic Cell Differentiation and Stimulation
  • Dendritic cells were generated by culturing monocytes in RPMI1640 medium supplemented with 100 ng/ml of recombinant human GM-CSF (Abbvie) and 5 ng/ml of human IL-4 (Peprotech) for 4 days. To investigate the TNFalpha production, DCs were stimulated with 1 mg/ml LPS (from Salmonella typhimurium, Sigma-Aldrich) for 1 hour.
    • Staining Cells and Flow Cytometric Analysis
  • LPS stimulated PBCs, monocyte or DCs were blocked with human IgG and stained with pHRodo red labeled D2E7 on ice, then incubated at 37° C. As a negative control an isotype matched control antibody (AB446) was used. All the antibodies were conjugated with A488 using antibody labeling kit (Invitrogen) according to manufacturer's protocol. Monocytes and T cells were gated based on the expression of CD14 (Biolegend) and CD3 (eBioscience) respectively. Samples were analyzed on a Becton Dickinson Fortessa® flow cytometer, and analysis was performed using Flowjo® software (TreeStar Inc., Ashland, Oreg., USA).
    • Internalization Assay
  • To investigate the internalization of surface TNF bound adalimumab antibodies, monocytes were stimulated with LPS for 4, 7, 9 or 24 hours in the presence of Alexa 488 conjugated AB436 antibodies. Cells were permeabilized and nucleus was stained with DAPI. The images were acquired using confocal microscope (Zeiss). To study the internalization of anti-TNF adalimumab antibodies by dendritic cells, the monocyte derived DCs were stimulated with LPS for 4 hours in the presence of anti-TNF adalimumab or matched isotype control antibodies. The anti-TNFalpha specific adalimumab antibodies and control antibodies were conjugated with pH sensitive dye pHRoco Red (Invitrogen) according to manufacturer's protocol. The cells were analyzed by fluorescent microscope and FACS. Where indicated, the surface of the cells was stained with A488-conjugated anti-HLA-A,B.C (W6/32, Biolegend) antibodies and the nucleus was stained with Nuce® blue (Invitrogen). To study the internalization kinetics of anti-TNFalpha adalimumab antibodies by membrane TNF on DCs, cells were either left in un-stimulated or stimulated with LPS for 1 hour or 24 hours. The surface TNFalpha was stained with pHRodo Red conjugated anti-TNFalpha antibody (AB441). The stained cells were cultured in RPMI medium for the indicated time and the internalization was assessed as an increase in fluorescence using BD Fortessa flow cytometer (see FIGS. 3A-3C). The results indicate that that the glycoengineered Adalimumab preparations of the invention exhibit pronounced decrease immunogenicity as a result of their reduced internalization and antigenic presentation by dendritic cells.
    • Example 7 Pharmacokinetic Studies
  • Non-hypergalactosylated adalimumab (D2E7) and hypergalactosylated adalimumab (ZFN-B1) monoclonal antibodies were administered to CD-1 or BALB/C mice by slow intravenous bolus dose injection at a 5mg/kg dose. Blood samples were collected from each mouse at 1, 24 and 96 hours and 7, 10, 14 and 21 days post dose. Blood samples were collected from each rat at 0.25, 4, and 24 hours and 2, 3, 7, 10, 14, 21 and 28 days post dose. All samples were stored at −80° C. until analysis.
  • Serum samples were analyzed using an anti-TNF capture assay depicted in FIG. 4 in which a biotinylated humanTNFoc was used for capture and a labeled anti-human Sulfo-Tag for detection. The assay was carried out in 1% final serum concentration. The lower limit of quantitation (LLOQ) was 0.004 μg/mL. The linear range: 15-0.004 μg/mL. The low control was 0.1 μg/mL.
  • Standard curve fitting and data evaluation was performed using XLfit4 software with a four-parameter logistic fit. Plates passed when at least ⅔ of the QC's were within 30% of the expected values. Pharmacokinetic parameters for each animal were calculated using WinNonlin® software Version 5.0.1 (Pharsight Corporation, Mountain View, Calif.) by non-compartmental analysis using linear trapezoidal fit (NCA Models # 201 for IV dosing). For calculations in WinNonlin, the time of dosing was defined as Day 0 Time 0 hr.
  • The serum concentrations as a function of time are shown in FIG. 5A (ZFN-B1) and FIG. 5B (D2E7). The pharmacokinetic parameters for High Gal ZFN-B1 administered mice # 3 and 5 are depicted in FIG. 5C. The result show that 4 of 5 animals administered anti-TNF hypergalactosylated ZFN-B1 monoclonal antibody had measurable antibody levels out to 21 days (FIG. 5A). The High Gal ZFN-B1 administered mouse #3 displayed a long half-life and low CL (24.5 days and 0.14 mL/h/kg). In contrast, all the animals administered the anti-TNF D2E7 monoclonal antibody displayed probable anti-drug antibodies (ADA). The results suggest that anti-drug antibodies decrease as a function of the galactosylation of the administered recombinant Fc binding protein (see FIG. 6).

Claims (27)

1. A glycoengineered binding protein composition comprising a population of Fc domain-containing binding proteins having an G/M ratio of at least 10:1, wherein the total percent amount of G1 and G2 glycoforms in the population is more than 50%, wherein the total percent amount of M3-M9 glycoforms is less than 10%, wherein Fc domain containing binding proteins of the composition comprise the same polypeptide sequence, and wherein the glycoengineered binding protein composition exhibits a lower ADA response and/or a greater serum half-life than a non-hypergalactosylated population of Fc domain-containing binding proteins.
2. The composition of claim 1, wherein the total percent amount of G1 and G2 glycoforms in the population is more than 80%, or more than 99%.
3. The composition of claim 1, wherein less than 5%, or less than 1%, or less than 0.1% of the Fc domain-containing binding proteins in the population comprise M3-M9 glycoforms.
4. The composition of claim 1, wherein the population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
5. The composition of claim 1, wherein the population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
6. The composition of claim 1, wherein the population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
7. The composition of claim 1, wherein the Fc domain-containing binding proteins in the population comprises an antigen-binding portion of an antibody or wherein the Fc domain-containing binding proteins in the population comprise a non-antibody antigen-binding portion, wherein the antigen-binding portion binds to tumor necrosis factor alpha (TNFα).
8.-10. (canceled)
11. The composition of claim 7, wherein the population of Fc domain-containing binding proteins comprises the polypeptide sequence of adalimumab or a variant thereof, wherein the variant of adalimumab is D2E7SS22 and comprises the heavy chain variable region sequence of SEQ ID NO:1 and the light chain variable region sequence of the light chain of SEQ ID NO:2.
12.-16. (canceled)
17. The composition of claim 1, wherein the composition is obtained from a cultured mammalian host cell line, wherein the host cell line is a CHO cell line containing a heterologous galactosyltransferase gene.
18. (canceled)
19. The composition of claim 17, wherein the host cell line is a CHO cell line containing a knockdown of one or both the alleles of a Beta galactosidase gene.
20. A composition comprising the population of Fc domain-containing binding proteins of claim 1 and a pharmaceutically acceptable carrier or excipient.
21. A method of reducing a subject's anti-drug antibody (ADA) response to a first population of Fc domain-containing binding proteins, the method comprising glycoengineering the first population of Fc domain-containing binding proteins to obtain a binding protein composition comprising a second population of Fc-domain containing binding proteins having a G/M ratio of at least 10:1, a total percent amount of G1 and G2 glycoforms of more than 50%, and a total percent amount of M3-M9 glycoforms of less than 10%, wherein the second population of Fc domain-containing binding proteins has a greater serum half-life than the first population of Fc domain-containing binding proteins, wherein the Fc domain-containing binding proteins bind to tumor necrosis factor alpha (TNFα).
22. The method of claim 21, wherein the total percent amount of G1 and G2 glycoforms in the second population is more than 80%, or more than 99%.
23. The method of claim 21, wherein less than 5%, or less than 1%, or less than 0.1% of the Fc domain-containing binding proteins in the second population comprise M3-M9 glycoforms.
24. The method of claim 21, wherein the second population of Fc domain-containing binding proteins has a G1/2:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
25. The method of claim 21, wherein the second population of Fc domain-containing binding proteins has a GS:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
26. The method of claim 21, wherein the second population of Fc domain-containing binding proteins has a Gtotal:M ratio of at least 10:1, at least 50:1, at least 80:1, or at least 99:1.
27.-28. (canceled)
29. The method of claim 21, wherein the first population of Fc domain-containing binding proteins comprises adalimumab or a variant thereof, wherein the variant of adalimumab is D2E7SS22 and comprises the heavy chain variable region sequence of SEQ ID NO:1 and the light chain variable region sequence of the light chain of SEQ ID NO:2.
30.-33. (canceled)
34. The method of claim 21, wherein said glycoengineering comprises expressing the Fc-domain containing binding proteins in cultured mammalian host cell line that has been glycoengineered to produce hypergalactosylated and/or hypomannosylated binding proteins, wherein the host cell line is a CHO cell line containing a heterologous galactosyltransferase gene, wherein the host cell line is a CHO cell line containing a knockdown of one or both the alleles of a Beta galactosidase gene.
35.-37. (canceled)
38. A method of treating a disorder in a subject in need thereof, comprising administering to the subject an effective amount of the glycoengineered composition of any one of claim 1, wherein the disorder is a TNFα associated disorder.
39. (canceled)
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