# Patent

## Title
Glycoprotein

## Abstract

The invention relates to a composition comprising a glycoprotein comprising the Fc domain of an antibody, or a fragment thereof, comprising an Asn (asparagine) residue and an oligosaccharide structure attached thereto, wherein said oligosaccharide structure has a structure according to formula I; and wherein at least 20% of the oligosaccharide structures attached to glycoprotein in the composition consist of oligosaccharide structures according to formula (I).

## Background
This application is a National Stage Application of PCT/FI2012/051239, filed 13 Dec. 2012, which claims benefit of Ser. No. 20116264, filed 13 Dec. 2011 in Finland, Ser. No. 61/569,900, filed 13 Dec. 2011 in the United States and Ser. No. 61/569,906, filed 13 Dec. 2011 in the United States and which applications are incorporated herein by reference. To the extent appropriate, a claim of priority is made to each of the above disclosed applications.
FIELD OF THE INVENTION
The invention relates to a glycoprotein, a composition, a host cell and a method of producing the glycoprotein or composition.
BACKGROUND OF THE INVENTION
Glycoproteins mediate many essential functions in humans and other mammals, including signalling, cell-to-cell communication and molecular recognition and association. Antibodies or immunoglobulins are glycoproteins that play a central role in the humoral immune response and that are used increasingly as therapeutics. Antigen-specific recognition by antibodies results in the formation of immune complexes that may activate multiple effector mechanisms.
There are five major classes of immunoglobulins (Igs): IgA, IgD, IgE, IgG and IgM. Several of these may further be divided into subclasses (isotypes), e.g. IgG1, IgG2, IgG3 and IgG4. Papain digestion of antibodies produces two identical antigen binding fragments called Fab fragments and a residual Fc fragment. In human IgG molecules, the Fc region is generated by papain cleavage N-terminal to Cys 226. The Fc region is central to the effector function of the antibodies and interaction with various molecules, such as Fcγ receptors (FcγRI, FcγRIIa, FcγRIIb, FcγRIIc, FcγRIIIa and FcγRIIIb), rheumatoid factor (RF), Protein G and A, complement factors (C3b, C1q) and lectin receptors (MBL, MR, DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin)). The interaction of antibodies and antibody-antigen complexes with cells of the immune system mediates a variety of responses, including antibody-dependent cell-mediated cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC). In order to be useful in therapy, an antibody, or a fragment thereof, should therefore have suitable effector functions.
The Fc domain sequence of IgG comprises a single site for N-linked glycosylation within its CH2 domain at an asparagine residue 297 (Asn297) numbered according to the EU index (Kabat et al., Sequences of proteins of immunological interest, 5th ed., US Department of Health and Human Services, NIH Publication No. 91-3242). Typically the oligosaccharide structures attached to the Fc domain comprise biantennary chains with varying galactosylation.
It is known that the oligosaccharide structure attached to the Fc domain influences the binding of IgG to Fc receptors and other molecules that interact with the antibody molecule, such as C1q (Raju 2008, Curr Opin Immunol 20, 471-478). Thus variations in the oligosaccharide structure (i.e. different glycoforms) of the Fc domain influence ADCC and CDC activity. Subsequently, modification of said oligosaccharide structure may affect the therapeutic activity of an antibody or a fragment thereof. The ability to produce glycoproteins and compositions comprising thereof that are enriched for particular oligosaccharide structures is highly desirable.
Purpose of the Invention
The purpose of the present invention is to disclose novel glycoproteins comprising an Fc domain and oligosaccharide structures attached thereto that have increased cytotoxic potential due to increased affinity to Fc receptors. Another purpose of the present invention is to disclose said glycoproteins that have improved potency to activate leukocytes.
SUMMARY
The composition according to the present invention is characterized by what is presented in claim 1.



BRIEF DESCRIPTION OF THE DRAWINGS
The accompanying drawings, which are included to provide a further understanding of the invention and constitute a part of this specification, illustrate embodiments of the invention and together with the description help to explain the principles of the invention. In the drawings:
FIG. 1 shows TNF-α production assay with human peripheral blood mononuclear cells (PBMC) from five donors (PBMC1-5) incubated with humanized IgG1 antibody glycoform coated surfaces in 96-well plates; the TNF-α levels have been normalized for each donor relative to the non-fucosylated glycoform: index=100 for the non-fucosylated glycoform;
FIG. 2 demonstrates C1q binding results (relative affinity on the y-axis) of humanized IgG1 antibody glycoforms; and
FIG. 3 shows FcγRIIa binding results (relative affinity on the y-axis) of humanized IgG1 antibody glycoforms.



DETAILED DESCRIPTION OF THE INVENTION
The present inventors have surprisingly found that a certain subset of oligosaccharide structures present in glycoproteins comprising an Fc domain or a fragment thereof mediate greatly improved cytotoxicity as compared to oligosaccharide structures typically present in said glycoproteins. This effect is due to e.g. improved ADCC and CDC activity and binding to molecules such as FcγRIIIa, FcγRIIa and C1q.
The present invention relates to a glycoprotein comprising the Fc domain of an antibody, or a fragment thereof, comprising an Asn (asparagine) residue and an oligosaccharide structure attached thereto, wherein said oligosaccharide structure has a structure according to formula I:




wherein

(β-N-Asn)=β-N linkage to Asn.

The glycoprotein of the invention comprises the Fc domain of an IgG molecule, or a fragment thereof, which comprises a site for N-linked glycosylation at an Asn residue.
In this context, the term “non-fucosylated monoantennary glycoform” should be understood as meaning a glycoprotein comprising the Fc domain of an antibody, or a fragment thereof, comprising an Asn (asparagine) residue and an oligosaccharide structure attached thereto, wherein said oligosaccharide structure has a structure according to formula I.
In this context, the term “Fc domain” should be understood as meaning a C-terminal region of an antibody or an immunoglobulin heavy chain (“antibody” and “immunoglobulin” are used herein interchangeably). Although the boundaries of the Fc domain of an immunoglobulin heavy chain might vary, the human IgG heavy chain Fc domain is usually defined to stretch from an amino acid residue at position Cys226 to the carboxyl-terminus thereof. The Fc domain generally comprises two constant domains, CH2 and CH3. The “CH2 domain” of a human IgG Fc domain usually extends from about amino acid 231 to about amino acid 340. The “CH3 domain” of a human IgG Fc domain usually extends from about amino acid 341 to about amino acid residue 447 of a human IgG (i.e. comprises the residues C-terminal to a CH2 domain). The term “Fc domain” is also intended to include naturally occurring allelic variants of the “Fc domain” as well as variants having alterations which produce substitutions, additions, or deletions but which do not decrease substantially the ability of the Fc domain to bind effector molecules such as Fc receptors or mediate antibody dependent cellular cytotoxicity. For example, one or more amino acids can be deleted from the N-terminus or C-terminus of the Fc domain of an immunoglobulin without substantial loss of biological function. Such variants, or fragments, of an Fc domain can be selected according to general rules known in the art (See, e.g., Bowie, J. U. et al., Science 247:1306-10 (1990).
In one embodiment of the invention, the Asn residue corresponds to asparagine at position 297 (Asn297) of human IgG wherein the numbering corresponds to the EU index according to Kabat. In this context, the term “according to Kabat” should be understood as meaning the numbering as described in Kabat et al., Sequences of proteins of immunological interest, 5th ed., US Department of Health and Human Services, NIH Publication No. 91-3242. A person skilled in the art can easily identify the amino acid residue corresponding to Asn297 by performing a sequence alignment. The amino acid residue corresponding to Asn297 will align with Asn297. While Asn297 is the N-glycosylation site typically found in murine and human IgG molecules, this site is not the only site that can be envisioned, nor does this site necessarily have to be maintained. Using known methods for mutagenesis, a skilled person can alter a DNA molecule encoding an Fc_domain of the present invention so that the N-glycosylation site at Asn297 is deleted, and can further alter the DNA molecule so that one or more N-glycosylation sites are created at other positions within the Fc_domain. It is preferred that N-glycosylation sites are created within the CH2 region of the antibody molecule.
In one embodiment of the present invention, the Fc domain comprises two heavy chain sequences each comprising at least one Asn residue. In one embodiment of the present invention, one or two of the Fc domain Asn residues are N-glycosylated with oligosaccharide structure according to the invention. In a preferred embodiment of the present invention, two Fc domain Asn residues are N-glycosylated with oligosaccharide structures according to the invention.
In one embodiment of the present invention, the glycoprotein is capable of interacting with at least one molecule selected from the group consisting of FcγRI, FcγRIIa, FcγRIIb, FcγRIIc, FcγRIIIa, FcγRIIIb, rheumatoid factor, Protein G, protein A, C3b, C1q, MBL, MR, and DC-SIGN.
In one embodiment of the present invention, the glycoprotein exhibits increased interaction with at least one molecule selected from the group consisting of FcγRI, FcγRIIa, FcγRIIc, FcγRIIIa, FcγRIIIb, C1q and C3b. In this context, the term “increased interaction” should be understood as meaning increased interaction as compared with a glycoprotein comprising a normal oligosaccharide structure attached thereto. In one embodiment a glycoprotein of the invention exhibits increased interaction with at least one effector molecule, as compared to the glycoprotein comprising normal oligosaccharide structure, where interaction is determined e.g. as disclosed in the Examples herein. In this context, the term “effector molecule” should be understood as meaning a molecule selected from the group consisting of FcγRI, FcγRIIa, FcγRIIc, FcγRIIIa, FcγRIIIb, C1q and C3b, as compared to the glycoprotein comprising normal oligosaccharide structure. In some embodiments, the interaction of the glycoprotein with an effector molecule is increased by about 1.20 fold to about 100 fold, or about 1.5 fold to about 50 fold, or about 2 fold to about 25 fold. In other embodiments, the interaction of the glycoprotein with an effector molecule is increased by at least about 1.10 fold, or at least about 1.20 fold, or at least about 1.30 fold, or at least about 1.4 fold, or at least about 1.5 fold, or at least about 1.6 fold, or at least about 1.70 fold, or at least about 1.8 fold, or at least about 1.9 fold, or at least about 2.0 fold, or at least about 2.5 fold, or at least about 3 fold, or at least about 3.5 fold, or at least about 4.0 fold, or at least about 4.5 fold, or at least about 5.0 fold, or at least about 5.5 fold, or at least about 6 fold, or at least about 7 fold, or at least about 8 fold, or at least about 10 fold, as compared to the glycoprotein comprising normal oligosaccharide structure, where effector molecule interaction is determined as disclosed in the Examples herein. In one embodiment, the effector molecule that the glycoprotein has increased interaction with is FcγRIIIa. In another embodiment, the effector molecule that glycoprotein has increased interaction with is FcγRI (as compared to glycoprotein comprising normal oligosaccharide structure). In still another embodiment, the effector molecule that the glycoprotein has increased interaction with is FcγRIIa. In still another embodiment, the effector molecule that the glycoprotein has increased interaction with is FcγRIIc. In still another embodiment, the effector molecule that the glycoprotein has increased interaction with is FcγRIIIb. In still another embodiment, the effector molecule that the glycoprotein has increased interaction with is C1q. In still another embodiment, the effector molecule that the glycoprotein has increased interaction with is C3b.
In this context, the term “normal oligosaccharide structure” should be understood as meaning an N-glycan structure commonly found attached to an Fc domain comprising the structure shown in the following formula:




wherein

(β-N-Asn)=β-N linkage to Asn; and the notation 0-1 in e.g. (Galβ4)0-1 should be understood as meaning either absent (0) or present (1); in other words, the notation (Galβ4)0 means that the Gal residue is not present, and the notation (Galβ4)1 means that one Gal residue is present. In this context, the term “normal glycoform” should be understood as meaning a glycoprotein comprising a normal oligosaccharide structure. Said normal oligosaccharide structure is present in the majority of antibodies and other glycoproteins comprising an Fc domain produced in mammalian cells.

In this context, the term “hybrid-type oligosaccharide structure” should be understood as meaning an N-glycan structure comprising the structure shown in the formula below:




wherein Y=3 or 6; (β-N-Asn)=β-N linkage to Asn; and the notation 0-1 in e.g. (Galβ4)0-1 should be understood as meaning either absent or present; when Neu5Ac is present also Gal is present; and at least one of the optional Manα6 and Manα3 groups is present; in other words, the notation (Galβ4)0 means that the Gal residue is not present, and the notation (Galβ4)1 means that one Gal residue is present. In this context, the term “hybrid-type glycoform” should be understood as meaning a glycoprotein comprising a hybrid-type oligosaccharide structure.

In this context, the term “monoantennary oligosaccharide structure” should be understood as meaning an N-glycan structure comprising a structure shown in the formula below:




wherein Y=3 or 6; (β-N-Asn)=β-N linkage to Asn; and the notation 0-1 in e.g. (Galβ4)0-1 should be understood as meaning either absent or present; when Neu5Ac is present also Gal is present; in other words, the notation (Galβ4)0 means that the Gal residue is not present, and the notation (Galβ4)1 means that one Gal residue is present. In this context, the term “monoantennary glycoform” should be understood as meaning a glycoprotein comprising a monoantennary oligosaccharide structure.

In one embodiment of the present invention, the glycoprotein exhibits improved interaction with C1q. In this context, the term “improved interaction” should be understood as meaning improved interaction as compared with a glycoprotein comprising normal oligosaccharide structure. This embodiment exhibits increased CDC.
In one embodiment of the present invention, the glycoprotein exhibits increased ADCC. In this context, the term “increased ADCC” should be understood as meaning increased ADCC as compared with a glycoprotein comprising normal oligosaccharide structure. This embodiment has increased cytotoxic activity. ADCC may be measured e.g. using the TNF-α production assay described in Example 3 or the ADCC assay described in Example 8. In certain embodiments, a glycoprotein of the invention has increased ADCC or CDC activity, as compared to the glycoprotein comprising normal oligosaccharide structure. In some embodiments, ADCC or CDC activity is increased by about 1.20 fold to about 100 fold, or about 1.5 fold to about 50 fold, or about 2 fold to about 25 fold, as compared to the glycoprotein comprising normal oligosaccharide structure. In other embodiments, the ADCC or CDC activity of a glycoprotein is increased by at least about 1.10 fold, 1.10 fold, or at least about 1.20 fold, or at least about 1.30 fold, or at least about 1.4 fold, or at least about 1.5 fold, or at least about 1.6 fold, or at least about 1.70 fold, or at least about 1.8 fold, or at least about 1.9 fold, or at least about 2.0 fold, or at least about 2.5 fold, or at least about 3 fold, or at least about 3.5 fold, or at least about 4.0 fold, or at least about 4.5 fold, or at least about 5.0 fold, or at least about 5.5 fold, or at least about 6 fold, or at least about 7 fold, or at least about 8 fold, or at least about 10 fold, or at least about 25 fold, as compared to the glycoprotein comprising normal oligosaccharide structure.
In this context, the term “oligosaccharide structure” should be understood as meaning glycan structure or portions thereof, which comprises sugar residues. Such sugar residues may comprise e.g. mannose, N-acetylglucosamine, glucose, galactose, sialic acid or fucose linked to each other through glycosidic bonds in a particular configuration.
In one embodiment of the present invention, the term “oligosaccharide structure” should be understood as meaning an N-glycan.
A person skilled in the art will appreciate that glycoproteins are typically produced in vivo and in vitro as a plurality of variants comprising a mixture of specific oligosaccharide structures attached thereto. In other words, glycoproteins are typically present as different glycoforms.
In this context, the term “glycoform” should be understood as meaning a glycoprotein of the invention comprising specific oligosaccharide structures sharing a common structural feature.
As known in the art (see e.g. “Essentials of Glycobiology”, 2nd edition, Ed. Varki, Cummings, Esko, Freeze, Stanley, Bertozzi, Hart & Etzler; Cold Spring Harbor Laboratory Press, 2009) and used herein, the term “glycan” should be understood to refer to homo- or heteropolymers of sugar residues, which may be linear or branched. “N-glycan”, a term also well known in the art, refers to a glycan conjugated by a β-N-linkage (nitrogen linkage through a β-glycosidic bond) to an asparagine (Asn) residue of a protein. Carbohydrate nomenclature in this context is essentially according to recommendations by the IUPAC-IUB Commission on Biochemical Nomenclature (e.g. Carbohydrate Res. 1998, 312, 167; Carbohydrate Res. 1997, 297, 1; Eur. J. Biochem. 1998, 257, 293).
In this context, the abbreviation “Man” should be understood as meaning D-mannose; “GlcNAc” refers to N-acetyl-D-glucosamine (2-acetamido-2-deoxy-D-glucose); “Fuc” refers to L-fucose; “Gal” refers to D-galactose; terms “Neu5Ac”, “NeuNAc” and “sialic acid” refer to N-acetylneuraminic acid; all monosaccharide residues are in pyranose form; all monosaccharides are D-sugars except for L-fucose; “Hex” refers to a hexose sugar; “HexNAc” refers to an N-acetylhexosamine sugar; and “dHex” refers to a deoxyhexose sugar. In one embodiment of the present invention, “sialic acid” may also refer to other sialic acids in addition to N-acetylneuraminic acid, such as N-glycolylneuraminic acid (Neu5Gc).
The notation of the oligosaccharide structure and the glycosidic bonds between the sugar residues comprised therein follows that commonly used in the art, e.g. “Manα2Man” should be understood as meaning two mannose residues linked by a covalent linkage between the first carbon atom of the first mannose residue to the second carbon atom of the second mannose residue linked by an oxygen atom in the alpha configuration. Furthermore, in this context, the notation of the oligosaccharide structure “Neu5AcαYGalβ” wherein Y=3 or 6 should be understood as meaning a structure comprising a N-acetylneuraminic acid residue linked to a galactose residue by a covalent linkage between the second carbon atom of the N-acetylneuraminic acid residue to either the third or the sixth carbon atom of the galactose residue linked by an oxygen atom in the alpha configuration.
In this context, the notation “Galβ4GlcNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc” should be understood as referring to an oligosaccharide structure according to formula I. In other words, brackets in the context of this type of notation indicate branches in the oligosaccharide structure.
In one embodiment of the present invention, the glycoprotein comprises an Fc domain which is a human Fc domain, or a fragment thereof.
In one embodiment of the present invention, the glycoprotein is a fusion protein comprising an Fc domain, or a fragment thereof. Said fusion protein may, in addition to the Fc domain, or a fragment thereof, comprise e.g. a receptor moiety having a different biological function. Fusion protein should also be understood as meaning antibody like molecules which combine the “binding domain” of a heterologous “adhesin” protein (e.g. a receptor, ligand or enzyme) with an Fc domain. Structurally, these immunoadhesins comprise a fusion of the adhesin amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site (antigen combining site) of an antibody (i.e. is “heterologous”) and an Fc domain sequence. Examples of immunoadhesins include but are not limited to etanercept (available e.g. under the trade mark ENBREL®), which is a soluble TNF receptor 2 protein fused to the Fc region of human IgG1, carcionembryonic antigen-immunoglobulin Fc fusion protein (CEA-Fc) and factor IX-Fc fusion protein.
In one embodiment of the invention, the glycoprotein is a human antibody. In this context, the term “human antibody”, as it is commonly used in the art, is to be understood as meaning antibodies having variable regions in which both the framework and complementary determining regions (CDRs) are derived from sequences of human origin.
In one embodiment of the invention, the glycoprotein is a humanized antibody. In this context, the term “humanized antibody”, as it is commonly used in the art, is to be understood as meaning antibodies wherein residues from a CDR of an antibody of human origin are replaced by residues from a CDR of a nonhuman species (such as mouse, rat or rabbit) having the desired specificity, affinity and capacity.
In one embodiment of the invention, the glycoprotein is a chimeric antibody comprising a human Fc domain. In this context, the term “chimeric antibody”, as it is commonly used in the art, is to be understood as meaning antibodies wherein residues in an antibody of human origin are replaced by residues from an antibody of a nonhuman species (such as mouse, rat or rabbit) having the desired specificity, affinity and capacity.
In this context, the terms “antibody” and “immunoglobulin”, as commonly used in the art, should be understood as being used interchangeably.
In one embodiment of the invention, the glycoprotein is an IgG (immunoglobulin G) antibody.
In one embodiment of the invention, the glycoprotein is an IgG1, IgG2, IgG3 or IgG4 antibody.
In one embodiment of the present invention, the glycoprotein is a monoclonal antibody.
In one embodiment of the present invention, the glycoprotein is an antibody directed against human vascular endothelial growth factor (VEGF), epidermal growth factor receptor 1 (EGFR), tumor necrosis factor alpha (TNF-α), CD20, epidermal growth factor receptor 2 (HER2/neu), CD52, CD33, CD11a, glycoprotein IIb/IIIa, CD25, IgE, IL-2 receptor, or respiratory syncytial virus (RSV). However, these antibody targets are provided as examples only, to which the invention is not limited; a skilled person will appreciate that the glycoprotein of the invention is not limited to any particular antibody or form thereof.
In one embodiment of the present invention, the glycoprotein is the antibody bevacizumab (available e.g. under the trademark AVASTIN®), tositumomab (BEXXAR®), etanercept (ENBREL®), trastuzumab (HERCEPTIN®), adalimumab (HUMIRA®), alemtuzumab (CAMPATH®), gemtuzumab ozogamicin (MYLOTARG®), efalizumumab (RAPTIVE®), rituximab (RITUXAN®), infliximab (REMICADE®), abciximab (REOPRO®), baasiliximab (SIMULECT®), palivizumab (SYNAGIS®), omalizumab (XOLAIR®), daclizumab (ZENAPAX®), cetuximab (ERBITUX®), panitumumab (VECTIBIX®) or ibritumomab tiuxetan (ZEVALIN®). However, these antibodies are provided as examples only, to which the invention is not limited; a skilled person will appreciate that the glycoprotein of the invention is not limited to any particular antibody or form thereof.
Monoclonal antibodies to the target of interest may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique originally described by Kohler and Milstein, 1975, Nature 256:495-497, the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A. 80:2026-2030) and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci. U.S.A. 81:6851-6855; Neuberger et al., 1984, Nature 312:604-608; Takeda et al., 1985, Nature 314:452-454) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies having a desired specificity.
In one embodiment of the present invention, the glycoprotein further comprises a conjugated molecule selected from a group consisting of a detection-enabling molecule and a therapy-enabling molecule. Examples of detection-enabling molecules are molecules conveying affinity such as biotin or a His tag comprising at least five histidine (His) residues; molecules that have enzymatic activity such as horseradish peroxidase (HRP) or alkaline phosphatase (AP); various fluorescent molecules such as FITC, TRITC, and the Alexa and Cy dyes; gold; radioactive atoms or molecules comprising such; chemiluminescent or chromogenic molecules and the like, which molecules provide a signal for visualization or quantitation. A therapy-enabling molecule may be a molecule used for e.g. increasing valence, size, stability and/or prolonged circulation of antibodies and other therapeutic proteins, e.g. a polyethylene glycol (PEG) or poly(vinylpyrrolidone) (PVP) moiety, a radioactive atom or molecule comprising said atom to be used for radiotherapy, or e.g.a toxin or a prodrug activating enzyme.
The present invention also relates to a composition comprising the glycoprotein of the present invention.
In one embodiment of the invention, the composition further comprises a glycoprotein having a different oligosaccharide structure. In other words, the composition further comprises one or more glycoforms.
In one embodiment of the invention, at least 20% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 33% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 50% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 66.7% (2⁄3) of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 90% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 95% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the invention, at least 99% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.
In one embodiment of the present invention, the feature “at least 20% of the oligosaccharide structures attached to glycoprotein in the composition consist of oligosaccharide structures according to formula I” or any other feature indicating the percentage or the proportion of specific oligosaccharide structures should be understood as referring to a feature indicating that the indicated proportion, e.g. at least 20%, of all oligosaccharide structures attached to any glycoprotein in the composition, said any glycoprotein comprising a glycoprotein of the invention and optionally one or more other glycoproteins, consist of the specific oligosaccharide structures, e.g. those according to formula I. The percentage or proportion of oligosaccharide structures or portions thereof attached to glycoprotein or glycoproteins in the composition may be measured e.g. by releasing all oligosaccharide structures attached to any glycoprotein in the composition and determining the percentage or proportion of the specific oligosaccharide structures therein, as described e.g. in the Examples.
In one embodiment of the present invention, the feature “at least 20% of the oligosaccharide structures attached to glycoprotein in the composition consist of oligosaccharide structures according to formula I” or any other feature indicating the percentage or the proportion of specific oligosaccharide structures should be understood as referring to a feature indicating that the indicated proportion, e.g. at least 20%, of the Fc domain oligosaccharide structures attached to the Fc domains in the composition, said Fc domains comprised in a glycoprotein of the invention and optionally in one or more other glycoproteins, consist of the specific oligosaccharide structures, e.g. those according to formula I. The percentage or proportion of oligosaccharide structures or portions thereof attached to Fc domain or Fc domains in the composition may be measured e.g. by isolating the Fc domains or antibodies in the composition, releasing all oligosaccharide structures attached to the Fc domains and determining the percentage or proportion of the specific oligosaccharide structures therein, as described e.g. in the Examples.
In one embodiment of the invention, no more than 50% of the oligosaccharide structures attached to glycoprotein in the composition comprise α1,6-linked fucose (Fuc) residue.
Said Fuc residue, as shown in the hybrid-type and monoantennary glycan formulas above, is attached to the GlcNAc residue present in the core Manβ4GlcNAcβ4GlcNAc structure that is linked by a β-N linkage to Asn. In other words, no more than said proportion of the oligosaccharide structures attached to glycoprotein in the composition are core fucosylated.
In this context, the term “core fucosylated” should be understood as meaning an oligosaccharide structure wherein a α1,6-linked fucose (Fuc) residue, as shown in the hybrid-type and monoantennary glycan formulas above, is attached to the core GlcNAc residue present in the core Manβ4GlcNAcβ4GlcNAc structure that is linked by a β-N linkage to Asn.
In one embodiment of the invention, no more than 25% of the oligosaccharide structures attached to glycoprotein in the composition comprise the Fuc residue.
In one embodiment of the invention, no more than 10% of the oligosaccharide structures attached to glycoprotein in the composition comprise the Fuc residue.
In one embodiment of the invention, no more than 5% of the oligosaccharide structures attached to glycoprotein in the composition comprise the Fuc residue.
In one embodiment of the invention, no more than 1% of the oligosaccharide structures attached to glycoprotein in the composition comprise the Fuc residue.
In one embodiment of the invention, about 0% of the oligosaccharide structures attached to glycoprotein in the composition comprise α1,6-linked fucose (Fuc) residue.
In one embodiment of the present invention, the composition is a pharmaceutical composition.
In this context, the term “pharmaceutical composition” should be understood as a composition for administration to a patient, preferably a human patient.
In one embodiment of the present invention, the pharmaceutical composition comprises a composition for e.g. oral, parenteral, transdermal, intraluminal, intraarterial, intrathecal and/or intranasal administration or for direct injection into tissue. Administration of the pharmaceutical composition may be effected in different ways, e.g. by intravenous, intraperitoneal, subcutaneous, intramuscular, topical or intradermal administration. The pharmaceutical composition of the present invention may further comprise a pharmaceutically acceptable carrier. Examples of suitable pharmaceutically acceptable carriers are well known in the art and include e.g. phosphate buffered saline solutions, water, oil/water emulsions, wetting agents, and liposomes. Compositions comprising such carriers may be formulated by methods well known in the art. Dosages and dosage regimens, as known in the art, may vary depending on a number of factors and may be determined depending on e.g. the patient's age, size, the nature of the glycoprotein, and the administration route. The pharmaceutical composition may further comprise other components such as vehicles, additives, preservatives, other pharmaceutical compositions administrated concurrently, and the like.
The present invention further relates to the composition or glycoprotein according to the invention for use in therapy.
In one embodiment of the present invention, the glycoprotein is administered in a therapeutically effective amount to a human or animal.
The present invention further relates to the glycoprotein according to the invention for use in the treatment of cancer, autoimmune disease, inflammatory disorder, infection or any other disease where cytotoxic activity towards cells or tissues is desired.
In one embodiment of the present invention, the term “cytotoxic activity” should be understood as meaning improved ADCC. In this context, the term “improved ADCC” should be understood as meaning improved ADCC as compared with a glycoprotein comprising normal oligosaccharide structure.
In one embodiment of the present invention, the term “cytotoxic activity” should be understood as meaning improved CDC. In this context, the term “improved CDC” should be understood as meaning improved CDC as compared with a glycoprotein comprising normal oligosaccharide structure.
The present invention further relates to a host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention, wherein said host cell has reduced activity of mannosidase II and core fucosylation compared to the parent cell.
The present invention further relates to a host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention, wherein said host cell has reduced activity of GnTII β1,2-N-acetylglucosaminyltransferase and core fucosylation compared to the parent cell. In this context, the term “host cell” should be understood as meaning any cell suitable for producing the glycoprotein of the invention.
In this context, the term “protein moiety” should be understood as meaning the glycoprotein without the oligosaccharide structure attached.
In one embodiment of the present invention, the host cell produces the glycoprotein of the invention under the culturing conditions.
In one embodiment of the present invention, the host cell is a mammalian cell. Mammalian cells are particularly suitable hosts for production of glycoproteins, due to their capability to glycosylate proteins in the most compatible form for human application (Cumming et al., Glycobiology 1: 115-30 (1991); Jenkins et al., Nature Biotechnol. 14:975-81 (1996)).
In one embodiment of the present invention, the mammalian cell is a CHO cell, cell line CHO-K1 (ATCC CCL-61), cell line DUXB11 (ATCC CRL-9096) and cell line Pro-5 (ATCC CRL-1781) registered at ATCC, commercially available cell line CHO-S (Cat #11619 of Life Technologies)), a BHK cell (including the commercially available cell line ATCC accession no. CCL 10), a NS0 cell, NS0 cell line (RCB 0213) registered at RIKEN Cell Bank, The Institute of Physical and Chemical Research, subcell lines obtained by naturalizing these cell lines to media in which they can grow, and the like), a SP2/0 cell, a SP2/0-Ag14 cell, SP2/0-Ag14 cell (ATCC CRL-1581) registered at ATCC, sub-cell lines obtained by naturalizing these cell lines to media in which they can grow (ATCC CRL-1581.1), and the like), a YB2/0 cell, a PER cell, a PER.C6 cell, sub-cell lines obtained by naturalizing these cell lines to media in which they can grow, and the like, a rat myeloma cell line YB2/3HL.P2.G11.16Ag.20 cell (including cell lines established from Y3/Ag1.2.3 cell (ATCC CRL-1631), YB2/3HL.P2.G11.16Ag.20 cell, YB2/3HL.P2.G11.16Ag.20 cell (ATCC CRL-1662) registered at ATCC, sub-lines obtained by naturalizing these cell lines to media in which they can grow, and the like), a hybridoma cell, a human leukemic Namalwa cell, an embryonic stem cell, or a fertilized egg cell.
In one embodiment of the present invention, the activity of mannosidase II in the host cell is decreased by addition of a mannosidase II inhibitor. Mannosidase II (EC 3.2.1.114) refers to a mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase enzyme which hydrolyses the terminal (1->3)- and (1->6)-linked alpha-D-mannose residues in the mannosyl-oligosaccharide GlcNAcMan5GlcNAc2. In one embodiment of the invention, the mannosidase II enzyme is a mammalian enzyme. Examples of mannosidase II enzymes include human mannosidase II A1 (MAN2A1; Gene ID: 4124; Accession No. NM_002372, protein: NP_002363.2 (SEQ ID NO: 1)), human mannosidase II A2 (MAN2A2; Gene ID: 4122; Accession No. NM_006122, protein NP_006113 (SEQ ID NO: 2)), mouse MAN2A1 (Accession No. NM_008549, protein NP_032575.2 (SEQ ID NO: 3)), mouse MAN2A2 (Accession No. NM_172903, protein NP_766491.2 (SEQ ID NO: 4)), rat MAN2A1 (Accession No. NM_012979, protein NP_037111.2 (SEQ ID NO: 5)), and rat MAN2A2 (Accession No. NM_001107527, protein NP_001100997.1 (SEQ ID NO: 6)).
In one embodiment of the present invention, the mannosidase II inhibitor is swainsonine.
In one embodiment of the present invention, the activity of mannosidase II, GnTII or core fucosylation in the host cell is decreased by RNA interference (RNAi). RNAi refers to the introduction of homologous double stranded RNA to specifically target the transcription product of a gene, resulting in a null or hypomorphic phenotype. RNA interference requires an initiation step and an effector step. In the first step, input double-stranded (ds) RNA is processed into nucleotide ‘guide sequences’. These may be single- or double-stranded. The guide RNAs are incorporated into a nuclease complex, called the RNA-induced silencing complex (RISC), which acts in the second effector step to destroy mRNAs that are recognized by the guide RNAs through base-pairing interactions. RNAI molecules are thus double stranded RNAs (dsRNAs) that are very potent in silencing the expression of the target gene. The invention provides dsRNAs complementary to the mannosidase II gene, GnTII gene and/or genes encoding enzymes involved in core fucosylation.
The ability of dsRNA to suppress the expression of a mannosidase II gene, GnTII gene and/or genes encoding enzymes involved in core fucosylation corresponding to its own sequence is also called post-transcriptional gene silencing or PTGS. The only RNA molecules normally found in the cytoplasm of a cell are molecules of single-stranded mRNA. If the cell finds molecules of double-stranded RNA, dsRNA, it uses an enzyme to cut them into fragments containing in general 21-base pairs (about 2 turns of a double helix). The two strands of each fragment then separate enough to expose the antisense strand so that it can bind to the complementary sense sequence on a molecule of mRNA. This triggers cutting the mRNA in that region thus destroying its ability to be translated into a polypeptide. Introducing dsRNA corresponding to a particular gene will knock out the cell's endogenous expression of that gene. A possible disadvantage of simply introducing dsRNA fragments into a cell is that gene expression is only temporarily reduced. However, a more permanent solution is provided by introducing into the cells a DNA vector that can continuously synthesize a dsRNA corresponding to the gene to be suppressed.
RNAi molecules are prepared by methods well known to the person skilled in the art. In general, an isolated nucleic acid sequence comprising a nucleotide sequence which is substantially homologous to the sequence of at least one of the mannosidase II gene, GnTII gene and/or genes encoding enzymes involved in core fucosylation and which is capable of forming one or more transcripts able to form a partially of fully double stranded (ds) RNA with (part of) the transcription product of said mannosidase II gene, GnTII gene and/or genes encoding enzymes involved in core fucosylation will function as an RNAi molecule. The double stranded region may be in the order of between 10-250, preferably 10-100, more preferably 20-50 nucleotides in length.
RNA interference (RNAi) is a method for regulating gene expression. For example, double-stranded RNA complementary to mannosidase II gene, GnTII gene and/or genes encoding enzymes involved in core fucosylation can decrease the amount of the enzyme expressed in an antibody expressing cell line, resulting in an increased level of glycoprotein of the invention. Unlike in gene knockouts, where the level of expression of the targeted gene is reduced to zero, by using different fragments of the particular gene, the amount of inhibition can vary, and a particular fragment may be employed to produce an optimal amount of the desired glycoprotein or composition thereof. An optimal level can be determined by methods well known in the art, including in vivo and in vitro assays for Fc receptor binding, effector function including ADCC, efficacy, and toxicity. The use of the RNAi knockdown approach, rather than a complete knockout, allows the fine tuning of the amount of glycan structures according to the invention to an optimal level, which may be of great benefit, if the production of glycoproteins bearing less than 100% of oligosaccharides according to Formula I is desirable.
In one embodiment of the present invention, the activity of mannosidase II, GnTII or core fucosylation in the host cell is decreased by gene disruption (knockout). A person skilled in the art can identify all necessary mannosidase II, GnTII and/or fucosylation genes in the host cell based on e.g. sequence similarity to the human genes described in the Examples. For example, all necessary genes encoding mannosidase II isoforms in a human cell are MAN2A1 (mannosidase II) and MAN2A2 (mannosidase IIx).
In one embodiment of the present invention, the host cell has reduced activity of GnTII compared to the parent cell. “Activity of GnTII” should be understood as meaning correlation between a level of GnTII enzyme activity to transfer a GlcNAc residue to the oligosaccharide structure according to Formula I attached to the glycoprotein of the invention and % portion of the GlcNAc's transferred to the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention. A host cell has “reduced or decreased activity of GnTII” when said cell produces lower % portion of the GlcNAc's transferred to the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention compared to parent cell without manipulations to decrease GnTII activity when cultured in similar or identical conditions. “GnTII” refers to mannosyl (alpha-1,6-)-glycoproteinbeta-1,2-N-acetylglucosaminyltransferase. The protein is a Golgi enzyme catalyzing an essential step in the conversion of oligomannose to complex N-glycans. The term preferably refers to the mammalian enzyme. Examples of GnTII enzymes include human GnTII (Gene ID: 4247; Accession Nos. NM_001015883, NM_002408, NP_001015883 and NP_002399 (SEQ ID NO: 7)), rat GnTII (GeneID: 94273 Accession Nos. NM_053604 and NP_446056 (SEQ ID NO: 8)), mouse (Accession No. NM_146035; protein Accession No. NP_666147 (SEQ ID NO: 9)), and Chinese hamster (Accession No. XM_003513994; protein Accession No. XP_003514042 (SEQ ID NO: 10); from CHO-K1 cells). The term “GNTII” refers to a gene or polynucleotide encoding a GnTII enzyme, including the coding region, non-coding region preceding (leader) and following coding regions, introns, and exons of a GNTII sequence. In particular, the GNTII gene includes the promoter.
In one embodiment of the present invention, the host cell has reduced activity of a fucosyltransferase.
In one embodiment of the present invention, the host cell has reduced activity of an enzyme involved in biosynthesis or intracellular transport of GDP-fucose.
In this context, the term “core fucosylation” should be understood as meaning any enzymatic activity capable of biosynthesis of GDP-fucose or of adding a Fuc residue to the core GlcNAc residue present in the core Manβ4GlcNAcβ4GlcNAc N-glycan structure that is linked by a β-N linkage to Asn, or proteins needed for intracellular transport or GDP-fucose.
In this context “reduced activity of core fucosylation” or “the activity of core fucosylation is decreased” means herein any method which results reduction or lack of core fucosylation of glycoproteins of the invention, preferably in a host cell. A host cell has “reduced activity of core fucosylation” or “the activity of core fucosylation is decreased” when said cell produces lower % portion of the fucose residues in the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention compared to parent cell without manipulations to decrease or reduce activity of core fucosylation when cultured in similar or identical conditions. In one embodiment of the present invention, reduction of core fucosylation is achieved by using Lec13 CHO host cell which is a lectin-resistant Chinese Hamster Ovary (CHO) mutant cell line displaying a defective fucose metabolism and therefore has a diminished ability to add fucose to complex carbohydrates. That cell line is described in Ripka and Stanley, Somatic Cell & Molec. Gen. 12(1):51-62 (1986); and Ripka et al. Arch. Biochem. Biophys. 249(2):533-545 (1986) and is available from the Albert Einstein College of Medicine of Yeshiva University, Bronx, N.Y. Lec13 cells are believed to lack the transcript for GDP-D-mannose-4,6-dehydratase, a key enzyme for fucose metabolism. Ohyama et al. J. Biol. Chem. 273(23):14582-14587 (1988). GDP-D-mannose-4,6-dehydratase generates GDP-mannose-4-keto-6-D-deoxymannose from GDP-mannose, which is then converted by the FX protein to GDP-L-fucose. Expression of fucosylated oligosaccharides is dependent on the GDP-L-fucose donor substrates and fucosyltransferase(s). In one embodiment of the present invention, Lec13 cells are manipulated to have reduced activity of GnTII. In one embodiment that can be combined with preceding embodiments Lec13 cells are manipulated to express optimized or increased levels of β4-galactosyltransferase activity, preferably by activating endogenous β4-galactosyltransferase or transfecting, for example, human β4-galactosyltransferase into said Lec13 cells.
Reduced activity of core fucosylation in a host cell is also achieved by reducing the activity of an enzyme relating to the synthesis of an intracellular sugar nucleotide, GDP-fucose. The enzymes include GMD (GDP-mannose 4,6-dehydratase); (b) Fx (GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase); (c) GFPP (GDP-beta-L-fucose pyrophosphorylase). Reduction of core fucosylation can also be achieved by reducing the activity of α-1,6-fucosyltransferase or FUT8. As the method for obtaining such cells, any technique can be used, so long as it can reduce or delete the activity of core fucosylation. Examples of the technique for reducing or deleting the enzyme activity include, a gene disruption technique targeting a gene encoding the enzyme, a technique for introducing a dominant negative mutant of a gene encoding the enzyme, a technique for introducing mutation into the enzyme, and a technique for inhibiting transcription and/or translation of a gene encoding the enzyme. Methods to reduce activity of core fucosylation in CHO cells are described in, inter alia, US patents U.S. Pat. No. 7,393,683 and U.S. Pat. No. 6,946,292 by Kyowa Hakko Kirin Co. Ltd.
In this context, the term “parent cell” should be understood as meaning a host cell before decreasing or deleting activity of the mannosidase II or GnTII, and core fucosylation in said cell.
The present invention further relates to a method for producing the glycoprotein according to the invention comprising the steps of

    a) culturing the host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention in the presence of mannosidase II inhibitor and GDP-fucose synthesis inhibitor; and
    b) contacting the product of step a) with an α-mannosidase; and, optionally
    c) contacting the product of step b) with a sialidase and/or UDP-Gal and a β1,4-galactosyltransferase.


In one embodiment of the present invention, the α-mannosidase is Jack bean α-mannosidase.
In one embodiment of the present invention, the host cell is cultured in the presence of swainsonine in a concentration of at least 60 μM.
In one embodiment of the present invention, the host cell is cultured in the presence of swainsonine in a concentration of at least 100 μM.
In one embodiment of the present invention, the host cell is cultured in the presence of GDP-fucose synthesis inhibitor as described in Example 1.
In one embodiment of the present invention, the host cell has optimized activity of β1,4-galactosyltransferase compared to the parent cell.
In one embodiment of the present invention, the host cell is manipulated to express optimized levels of a β4-galactosyltransferase activity to generate glycoprotein composition of the invention. In one embodiment, the host cell is selected for the optimized level of a β4-galactosyltransferase activity to generate glycoprotein composition of the invention. In one embodiment, the host cell is manipulated to increase the activity of a β4-galactosyltransferase to generate glycoprotein composition of the invention.
Specifically, such host cell may be manipulated to comprise a recombinant nucleic acid molecule encoding a β4-galactosyltransferase activity operatively linked to a constitutive or regulated promoter system. In one embodiment, the host cell is transformed or transfected with a nucleic acid molecule comprising a gene encoding a β4-galactosyltransferase activity. In one embodiment, the host cell is manipulated such that an endogenous β4-galactosyltransferase has been activated by insertion of a regulated promoter element into the host cell chromosome. In one embodiment, the host cell has been manipulated such that an endogenous β4-galactosyltransferase activity has been activated by insertion of a constitutive promoter element, a transposon, or a retroviral element into the host cell chromosome.
Alternatively, a host cell may be employed that naturally produce, are induced to produce, and/or are selected to produce β4-galactosyltransferase, of increased levels of β4-galactosyltransferase activity. In one embodiment, the host cell has been selected in such way that an endogenous β4-galactosyltransferase is activated. For example, the host cell may be selected to carry a mutation triggering expression of an endogenous β4-galactosyltransferase activity.
In one embodiment, the activity of a β4-galactosyltransferase in the host cell is increased compared to the parent cell to generate glycoprotein composition of the invention. In this context, the term “parent cell” should be understood as meaning a host cell before increasing activity of a β4-galactosyltransferase in said cell.
“Activity of β4-galactosyltransferase” or “levels of β4-galactosyltransferase activity” should be understood as meaning correlation between a level of β4-galactosyltransferase enzyme activity to transfer a Gal residue in the oligosaccharide structure according to Formula I attached to the glycoprotein of the invention and % portion of the galactose residues in the oligosaccharide structures according to formula I attached to glycoproteins in the composition of the invention. A host cell has “increased activity of β4-galactosyltransferase” when said cell produces higher % portion of the galactose residues in the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention compared to parent cell without manipulations to increase β4-galactosyltransferase activity when cultured in similar or identical conditions. A host cell has “optimized activity of β4-galactosyltransferase” when said cell produces higher or lower % portion of the galactose residues in the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention compared to parent cell without manipulations to optimize β4-galactosyltransferase activity when cultured in similar or identical conditions. Optimal levels of β4-galactosyltransferase activity in a host cell depend on % portion of the galactose residues in the oligosaccharide structures according to Formula I attached to glycoproteins in the composition of the invention. Typically, host cell is manipulated to have increased levels of β4-galactosyltransferase activity compared to parent cell when cultured in similar or identical conditions.
β4-galactosyltransferase refers to β-1,4-galactosyl transferase I. In one embodiment, β4-galactosyltransferase is a mammalian enzyme. Examples of β4-galactosyltransferase include but are not limited to human β4-galactosyltransferase I (GENBANK (NIH genetic sequence database) Accession No. P15291; SEQ ID NO: 11), rat β4-galactosyltransferase (GENBANK Accession No. NP.sub.445739; SEQ ID NO: 12), mouse β4-galactosyltransferase (GENBANK Accession No. P15535; SEQ ID NO: 13), and Chinese hamster β4-galactosyltransferase I (GENBANK Accession No. NP.sub. 001233620; SEQ ID NO: 14). Other β4-galactosyltransferases include human B4GALT2(GENBANK Accession No. 060909), human B4GALT3 (GENBANK Accession No. 060512), human B4GALT4 GENBANK Accession No. 060513), and human B4GALT5 GENBANK Accession No. 043286) and their homologues in mouse, rat, and Chinese hamster.
The present invention further relates to a host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention, wherein said host cell has reduced activity of GnTII, reduced activity of core fucosylation, and optimized, or increased, levels of β4-galactosyltransferase activity compared to the parent cell.
In one embodiment, host cell has reduced activity of GnTII, reduced activity of core fucosylation, and the activity of a β4-galactosyltransferase is optimized or increased.
In one embodiment, the host cell is manipulated to express optimized levels of a β4-galactosyltransferase activity, has reduced activity of GnTII and reduced activity of core fucosylation to generate the glycoprotein composition of the invention. In one embodiment that may be combined with the preceding embodiments the host cell is essentially devoid of the activity of GnTII. In one embodiment that may be combined with the preceding embodiments the host cell lacks core fucosylation.
In one embodiment, heterogeneity of glycoprotein composition of the present invention is decreased by expressing optimized levels of a β4-galactosyltransferase in the host cell. In one embodiment, heterogeneity of glycoprotein composition of the present invention is decreased by decreasing the activity of one or more sialyltransferase in the host cell compared to the parent cell. In one embodiment, a sialyltransferase is an α2,6-sialyltransferase. α2,6-sialyltransferases include but are not limited to a rat α2,6-sialyltransferases (GENBANK accession No. P13721, SEQ ID NO: 15 and GENBANK accession No. Q701R3, SEQ ID NO: 16), human α2,6-sialyltransferase I (GENBANK accession No. P15907; SEQ ID NO: 17) or human α2,6-sialyltransferase II (GENBANK accession No. Q96JF0; SEQ ID NO: 18), mouse α2,6-sialyltransferases (GENBANK accession No. NP.sub.666045; SEQ ID NO: 19 and GENBANK accession No. Q76K27; SEQ ID NO: 20) and Chinese hamster α2,6-sialyltransferases (GENBANK accession No. NP.sub.001233744; SEQ ID NO: 21 and GENBANK accession No. XP.sub.003499570; SEQ ID NO: 22) or their isoforms.
In one embodiment, the α2,3-sialyltransferase is a mammalian enzyme. In one embodiment of the present invention, the a2,3-sialyltransferase is a human ST3GAL2, ST3GAL4 and ST3GAL6 enzyme (GENBANK accession No. Q16842, SEQ ID NO: 23; GENBANK accession No. Q11206, SEQ ID NO: 24; and GENBANK accession No. Q9Y274, SEQ ID NO: 25) or their isoforms. In one embodiment of the present invention, the α2,3-sialyltransferase is a rat α2,3-sialyltransferase (GENBANK accession Nos. Q11205, P61131, and P61943), mouse α2,3-sialyltransferase (GENBANK accession Nos. Q11204, Q91Y74, and Q8VIB3) or Chinese hamster α2,3-sialyltransferase (GENBANK accession Nos. NP.sub.001233628, and XP.sub. 003509939) or their isoforms.
For example, in the case of CHO cells it is known that CHO derived recombinant glycoproteins have exclusively α2,3-linked sialic acids, since the CHO genome does not include a gene which codes for a functional α2,6-sialyltransferase. If a glycoprotein composition of the present invention is desired to be produced in CHO cell, the activity of GnTII is decreased, the activity of core fucosylation is decreased, and the activity of β4-galactosyltransferase is optimized or increased in said CHO cell. In one embodiment, the activity of an α-2,3-sialyltransferase in the CHO cell is decreased. In one embodiment that may be combined with the preceding embodiments the CHO cell is essentially devoid of the activity of a GnTII. In one embodiment that may be combined with the preceding embodiments the CHO cell is essentially devoid of the activity of an α2,3-sialyltransferase. In one embodiment that may be combined with the preceding embodiments the CHO cell lacks core fucosylation. In cells other than CHO cells, activities of α2,3-sialyltransferase and α2,6-sialyltransferase may be decreased. Methods to decrease activity of α2,3-sialyltransferase and α2,6-sialyltransferase include but are not limited to RNAi and knock-out techniques as described for GnTII and core fucosylation above.
“Activity of α2,3/6-sialyltransferase” or “level of α2,3/6-sialyltransferase activity” should be understood as meaning correlation between a level of α2,3/6-sialyltransferase enzyme activity to transfer a Neu5Ac residue in the oligosaccharide structure attached to the glycoprotein of the invention and % portion of the Neu5Ac residues in the oligosaccharide structures attached to glycoproteins in the composition of the invention. A host cell has “reduced or decreased activity of α2,3/6-sialyltransferase” or “decreased or reduced level α2,3/6-sialyltransferase of activity” when said cell produces lower % portion of the Neu5Ac residues in the oligosaccharide structures attached to glycoproteins in the composition of the invention compared to parent cell without manipulations to decreased α2,3/6-sialyltransferase activity when cultured in similar or identical conditions.
In one embodiment of the present invention, the host cell further has increased activity of a sialidase compared to the parent cell.
In one embodiment of the present invention, activity of a sialidase, especially a cytosolic sialidase activity is increased in the host cell compared to the parent cell. In one embodiment of the present invention, a host cell expressing β4-galactosyltransferase is selected so that activity of a sialidase is increased, the activity of a sialidase produced by the host cell being such that sialic acid residues in the carbohydrate side-chains of glycoprotein produced by the host cell are cleaved, or are cleaved to an extent which affects the function of the glycoprotein.
In one embodiment of the present invention, the host cell further has reduced activity of α2,3-sialyltransferase and/or reduced activity of α2,6-sialyltransferase compared to the parent cell.
Methods which are well known to those skilled in the art can be used to construct a polynucleotide encoding the protein moiety of a glycoprotein according to the invention, the coding sequence of a β4-galactosyltransferase, appropriate transcriptional/translational control signals, possible reporter genes as well as GnTII, enzymes involved in core fucosylation and α2,3/6-sialyltransferase knock-out or RNAi constructs. These methods include in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination.
Methods which are well known to those skilled in the art can be used to express a polynucleotide encoding the protein moiety of a glycoprotein according to the invention, nucleic acids encoding a β4-galactosyltransferase, and above deletion and RNAi constructs in a host cell. Nucleic acids may be expressed under the control constitutive promoters or using regulated expression systems such as a tetracycline-regulated expression system, a lac-switch expression system, and a metallothionein metal-inducible expression system. The optimal expression levels will be different for each protein of interest, and will be determined using routine experimentation. Expression levels are determined by methods generally known in the art, including Western blot analysis using a glycosyl transferase or a glycosyl hydrolase specific antibody, protein tag specific antibodies, Northern blot analysis using a glycosyl transferase or a glycosyl hydrolase specific nucleic acid probe, or measurement of enzymatic activity. Alternatively, a lectin may be employed which binds to glycans that are substrates or products of the glycosyl transferases or glycosyl hydrolases, for example, agglutinins from Erythrina cristagalli (ECA) and Ricinus communis (RCA) binding to Galβ1-4GlcNAc, Sambucus nigra (SNA) binding to α2,6-linked sialic acid, Maackia amurensis (MAA) binding to α2,3-linked sialic acid, Galanthus nivalis (GNA) and Hippeastrum hybrid (HHA) binding to α-mannose, Lens culinaris (LCA) binding to N-glycan core α1,6-linked fucose, and the like.
For the methods of this invention, stable expression is generally preferred to transient expression and also is more amenable to large scale production. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with the respective coding nucleic acids controlled by appropriate expression control elements and a selectable marker. Following the introduction of foreign DNA, a number of selection systems may be used, which are well known to those skilled in the art.
The host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention or producing the glycoprotein composition of the present invention may be identified, for example, by detection by immunoassay, by its biological activity, or by mass spectrometric means described below.
The glycoprotein or the glycoprotein composition produced by the host cell of the invention can be assessed immunologically, for example by Western blots, immunoassays such as radioimmuno-precipitation, enzyme-linked immunoassays and the like. In one embodiment, glycoprotein composition is assayed in in vitro or in vivo tests, for example, as described in Examples.
The present invention provides host cells for the producing composition comprising a glycoprotein comprising the Fc domain of an antibody, or a fragment thereof, comprising an Asn residue and an oligosaccharide structure attached thereto, and that the oligosaccharide structure has a structure according to Formula I. Generally, the host cell has been transformed to express nucleic acids encoding the protein moiety of the glycoprotein for which the production of glycoforms according to Formula I are desired, along with at least one nucleic acid encoding a RNAi, knock-out, or any other construct meant for decreasing the activity of mannosidase II, GnTII, core fucosylation, and/or α2,3/6-sialyltransferase, or nucleic acids encoding a β4-galactosyltransferase or sialidase to increase the activity of β4-galactosyltransferase and/or a sialidase. Typically, the transfected cells are selected to identify and isolate clones that express the any of the above nucleic acids as well as nucleic acids encoding the protein moiety of the glycoprotein. Transfected cells may be assayed with methods described above and Examples to identify and select host cells having optimized levels of β4-galactosyltransferase activity as well as decreased activity of mannosidase II, GnTII, α2,3/6-sialyltransferase and/or core fucosylation. Host cells transfected with nucleic acids encoding the protein moiety of the glycoprotein and cultured under conditions suitable for expression of the protein moiety of the glycoprotein may be assayed with methods described above and Examples to identify and select host cells having optimized levels of β4-galactosyltransferase activity and decreased activity of GnTII and core fucosylation. In one embodiment, the host cell has been selected for expression of endogenous β4-galactosyltransferase or non-expression of mannosidase II, GnTII, α2,3/6-sialyltransferase and/or core fucosylation activity.
For example, host cells may be selected carrying mutations which trigger expression of otherwise silent β4-galactosyltransferase activity. For example, host cells may be selected carrying mutations which inactivate expression of otherwise active mannosidase II, GnTII, α2,3/6-sialyltransferase or core fucosylation activity.
In one embodiment of the present invention, a method for the producing composition of the invention comprises the steps of a) transforming a host cell with vectors or constructs comprising nucleic acid molecules encoding a protein moiety of the glycoprotein of the invention, b) transforming the host cell with vectors or constructs comprising nucleic acid molecules reducing the activity of mannosidase II, GnTII, α2,3/6-sialyltransferase and/or core fucosylation, or culturing said cells in the presence of mannosidase II and GDP-fucose synthesis inhibitor, c) transforming the host cell with vectors or constructs comprising nucleic acid molecules encoding optimized levels of β4-galactosyltransferase activity, d) culturing the host cell under conditions that allow synthesis of said protein moiety of the glycoprotein and gene products of steps b) and c); and e) recovering said glycoprotein composition from said culture.
The method according to the invention may further comprise the step of recovering the glycoprotein from cell culture or from a reaction mixture. The glycoprotein composition may be recovered as crude, partially purified or highly purified fractions using any of the well-known techniques for obtaining glycoprotein from cell cultures. This step may be performed by e.g. precipitation, purification by using techniques such as lectin chromatography or contacting the glycoprotein with immobilized Fc receptor, carbohydrate-binding protein or protein G or A, or any other method that produces a preparation suitable for further use.
The methods of producing the glycoprotein according to the invention usually produce a mixture of glycoforms, i.e. a mixture of glycoprotein comprising the oligosaccharide structure according to the invention together with other glycoforms comprising related (sharing a common structural feature) oligosaccharide structures.
Therefore the present invention further relates to a method for producing the composition according to the invention comprising the steps of

    a) culturing the host cell comprising a polynucleotide encoding the protein moiety of a glycoprotein according to the invention in the presence of mannosidase II inhibitor and GDP-fucose synthesis inhibitor; and
    b) contacting the product of step a) with an α-mannosidase.


The present invention also relates to a method for producing the glycoprotein according to the invention or the composition according to the invention, comprising the steps of
a) culturing a host cell according to the invention; and, optionally
b) contacting the product of step a) with an α-mannosidase and/or or a sialidase, and/or with UDP-Gal and a β1,4-galactosyltransferase.
The method according to the invention may further comprise the step of recovering the composition from cell culture or from a reaction mixture. This step may be performed by e.g. precipitation, purification by using techniques such as lectin chromatography or any other method that produces a preparation suitable for further use.
The method according to the invention may further comprise the step of adding a pharmaceutical carrier or any other ingredients suitable for a pharmaceutical composition.
In one embodiment of the present invention, the method for producing the glycoprotein according to the invention or the composition according to the invention comprises the steps of

    a) culturing a host cell according to the invention; and
    b) contacting the product of step a) with α-mannosidase.


The glycoprotein or glycoprotein composition of any above step may be contacted in vitro with β4-galactosyltransferase in the presence of UDP-Gal, with a sialidase, and/or with an α-mannosidase.
The present invention further relates to a method of diagnosing or treating cancer, autoimmune disease, inflammatory disorder, infection or any other disease where cytotoxic activity towards cells or tissues is desired, wherein the composition according to the invention or the glycoprotein according to the invention is administered to a human or animal in an effective amount. The effective amount may vary depending on a number of factors and may be determined depending on e.g. the patient's age, size, the nature of the glycoprotein, and the administration route.
In this context, the term “treatment” should be understood as the administration of an effective amount of a therapeutically active compound of the present invention with the purpose of easing, ameliorating, alleviating, inhibiting, slowing down progression, or reduction of disease burden or eradicating (curing) symptoms of the disease or disorder in question. In one embodiment of the present invention, the term “treatment” should also be understood as meaning a prophylactive therapy meaning preventative therapy without meaning an absolute prevention or cure, but reduction of occurrence, or alleviation, inhibition, slowing down progression of the disease, or reduction of disease burden in the future partially in a patient.
The embodiments of the invention described hereinbefore may be used in any combination with each other. Several of the embodiments may be combined together to form a further embodiment of the invention. A product, or a use, or a method to which the invention is related, may comprise at least one of the embodiments of the invention described hereinbefore.
The glycoprotein of the invention has a number of advantages over glycoproteins comprising other oligosaccharide structures typically attached to said glycoproteins, such as normal oligosaccharide structures. The non-fucosylated monoantennary N-glycan structure according to formula I greatly increases the binding of the glycoprotein of the invention to Fcγ receptors, especially FcγRIIIa and FcγRIIa, and subsequently leads to improved ADCC and activation of immune effector cells; it also increases the binding of the glycoprotein of the invention to complement factors, especially C1q, and subsequently leads to improved CDC. Thus the glycoprotein of the invention leads to increased cytotoxic activity. Furthermore, the oligosaccharide structure according to formula I is relatively simple and does not significantly alter the stability of the glycoprotein. The glycoprotein of the invention is also relatively easy to produce in e.g. mammalian cell culture.
EXAMPLES
In the following, the present invention will be described in more detail. Reference will now be made in detail to the embodiments of the present invention, examples of which are illustrated in the accompanying drawings. The description below discloses some embodiments of the invention in such detail that a person skilled in the art is able to utilize the invention based on the disclosure. Not all steps of the embodiments are discussed in detail, as many of the steps will be obvious for the person skilled in the art based on this specification.
Example 1
Production of Humanized IgG1 Antibody Glycoforms in CHO Cells
Humanized anti-IL-8 IgG1 antibody producing cell line DP-12 (ATCC number CRL-12445) was grown in DMEM with 4 mM L-glutamine and adjusted with sodium bicarbonate and 4.5 g/L glucose and 200 nM methotrexate, trace elements A and B from Mediatech, 0.002 mg/ml rhInsulin and 10% fetal bovine serum. For antibody production, cells were grown for 3-4 days and the supernatant collected by centrifugation.
Glycosidase inhibitors were added to the culture medium to produce specific antibody glycoforms: hybrid-type glycoform, 10 μg/ml swainsonine (Cayman Chemical); non-fucosylated glycoform, 7.2 μg/ml AV39 (a GDP-fucose synthesis inhibitor; Glykos Finland Ltd., Helsinki, Finland); and non-fucosylated hybrid-type glycoform, 10 μg/ml swainsonine and 7.2 μg/ml AV39.
Antibody glycoforms were purified from cell culture supernatants by protein G affinity chromatography on a 1-mL HITRAP protein G column (protein G column) (GE Healthcare, Uppsala, Sweden) using single step pH gradient elution from 20 mM sodium phosphate, pH 7.0 to 0.1 M citric acid, pH 2.6. The eluted antibody fractions were neutralized immediately with 1 M Na2HPO4 and concentrated in Millipore AMICON ULTRACEL (cellulose membrane) 30K concentrators. The concentrations of antibody glycoforms were adjusted to 0.5 mgml with phosphate-neutralized 0.1 M citric acid.
Mass Spectrometric Analysis of Antibody Glycoforms
For N-glycan analysis antibody solution containing 10-20 μg antibody was applied to N-glycan release; optionally antibodies were first precipitated with 67% (v/v) ice-cold ethanol and pelleted by centrifugation; cells were collected, washed repeatedly with phosphate buffered saline and pelleted by centrifugation.
N-glycan release, purification for analysis, permethylation and MALDI-TOF mass spectrometric fragmentation analysis were performed essentially as described previously (Satomaa et al., Cancer Research 2009, 69, 5811-5819) with minor modifications. N-linked glycans were detached by enzymatic hydrolysis with N-glycosidase F (Glyko). N-glycans were first purified on HYPERSEP C-18 and then on HYPERSEP HYPERCARB 50 mg 96-well plates (Thermo Scientific). The neutral and acidic N-glycans were eluted together from Hypercarb with 0.05% trifluoroacetic acid in 25% acetonitrile in water. Matrix-assisted laser desorption-ionization time-of-light (MALDI-TOF) mass spectrometry was performed with a Bruker Ultraflex III instrument (Bruker Daltonics, Germany). Neutral and acidic N-glycans were detected in positive ion reflector mode as sodium adduct ions using 2,5-dihydroxybenzoic acid (DHB, Aldrich) as the matrix. Each of the steps in the glycan isolation procedure was validated with standard glycan mixtures and mass spectrometric analysis before and after purification step to ensure uniform glycan purification and quantitative detection of sialic acid residues in the analysis conditions. The method was optimized for glycan analysis in the used mz range. For the quantitative glycan profile analyses, mass spectrometric raw data were cleaned by carefully removing the effect of isotopic pattern overlapping, multiple alkali metal adduct signals, products of elimination of water from the reducing oligosaccharides, and other interfering mass spectrometric signals not arising from the original glycans in the sample. The resulting cleaned profiles were normalized to 100% to allow comparison between samples.
Preparation of Antibody Glycoforms: Normal and Hybrid-Type Glycoforms
CHO cell line DP-12 obtained from ATCC producing humanized IgG1 against IL-8 was cultured in normal conditions and with swainsonine. N-glycans were analyzed by mass spectrometric N-glycan profiling showing that the Fc domain N-glycans of the CHO cell supernatant-derived normal IgG glycoform were biantennary complex-type glycoform N-glycans with the major glycan signals at m/z 1485.6, 1647.6 and 1809.9 corresponding to the [M+Na]+ ions of Hex3HexNAc4dHex1, Hex4HexNAc4dHex1 and Hex5HexNAc4dHex1 oligosaccharides, respectively, while the IgG preparate produced with swainsonine (hybrid-type glycoform) was essentially completely (>99%) of the hybrid-type glycoform with the major (75% of total N-glycan signals) glycan signal at m/z 1768.7 corresponding to the [M+Na]+ ion of Hex6HexNAc3dHex1 oligosaccharide. The structure of the major product was the hybrid-type glycoform N-glycan Galβ4GlcNAcβ2Manα3[Manα3(Manα6)Manα6]Manβ4GlcNAcβ4(Fucα6)GlcNAc based on sensitivity to β1,4-galactosidase (recombinant S. pneumoniae galactosidase, Glyko) digestion and known structure of the mannosidase II inhibition product. Other major Fc-domain N-glycan forms were Neu5Acα3Galβ4GlcNAcβ2Manα3[Manα3(Manα6)Manα6]Manβ4GlcNAcβ4(Fucα6)GlcNAc at m/z 2081.7 for the [M-H+2Na]+ ion (19%) according to mass spectrometric analysis and sensitivity to specific α2,3-sialidase (recombinant S. pneumoniae sialidase, Calbiochem) and GlcNAcβ2Manα3[Manα3(Manα6)Manα6]Manβ4GlcNAcβ4(Fucα6)GlcNAc at m/z 1606.6 (6%). In the hybrid-type glycoform no non-fucosylated N-glycans were detected.
The non-fucosylated antibody glycoform produced in the presence of AV39 was similarly analyzed and the major N-glycan signals were the [M+Na]+ ions of Hex3HexNAc4, Hex4HexNAc4 and Hex5HexNAc4, while fucosylated N-glycans accounted for 10% of total signal intensity. The non-fucosylated hybrid-type glycoform produced in the presence of AV39 and swainsonine was similarly analyzed and the major N-glycan signal was the [M+Na]+ ion of Hex6HexNAc3 and no fucosylated glycans were detected.
Non-Fucosylated Monoantennary Glycoforms
The non-fucosylated hybrid-type glycoform produced in the presence of AV39 was subjected to Jack bean α-mannosidase (Sigma Aldrich) digestion in conditions similar to 50-65 U/ml enzyme for 2 days in mM sodium acetate buffer pH 5.5 at +37° C. and purified by protein G affinity chromatography to yield non-fucosylated monoantennary glycoform. Mass spectrometric analysis of this preparate showed that the major N-glycan structure was Galβ4GlcNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc (>70% of total N-glycan signals) and further major Fc-domain N-glycan forms were Neu5Acα3Galβ4GlcNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc and GlcNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc.
Galactosylated Glycoforms
For galactosylation, antibodies were buffer-exchanged to 50 mM MOPS, pH 7.2, 20 mM MnCl2, using a NAP-5 (small scale purification, desalting and buffer exchange) column. 0.5mU/μl of Calbiochem bovine milk β1,4-galactosyltransferase and 5 mM UDP-Gal was added to 6.25 mgml of antibody. Reactions were incubated overnight at +37° C. N-glycans were analyzed as described above. In typical reaction N-glycan galactosylation degree was increased to over 90% of N-glycans and in continued reactions N-glycan galactosylation degree was increased over 99% to essentially completely galactosylated forms.
All the different antibody glycoforms were checked for structural integrity by protein G affinity chromatography as described above as well as polyacrylamide gel electrophoresis.
Example 2
Lectin Chromatography for Enrichment of Specific Glycoforms and Modifications Thereof
Non-fucosylated glycoforms of anti-HER2 humanozed IgG1 antibody were enriched by lectin affinity chromatography using Lens culinaris agglutinin (LCA, Medicago) essentially as described in Tojo et al. (Bio. Pharm. Bull. 32 (9): 1604-1608, 2009) and Shinkawa et al. (J. Biol. Chem. 278: 3466-3473, 2003). LCA coupled to SEPHAROSE (crosslinked, beaded-form of agarose) (15 ml, 6.6 mg/ml, NHS-activated SEPHAROSE (crosslinked, beaded-form of agarose) 4 Fast Flow, GE Healthcare) was packed in TRICORN 10/200 HPLC column (GE Healthcare) and the column was installed in AKTAPURIFIER (protein purification system) HPLC system (GE Healthcare). 10 mg of antibody in 50 mM Tris-H2SO4, 1 mM MnCl2, 1 mM CaCl2, pH 7.4 (buffer A) was applied to the column equilibrated with buffer A and unbound sample was washed from the column 0.5 ml/min with buffer A. Bound antibody was eluted 1 ml/min with 50 mM Tris-H2SO4, 1 mM MnCl2, 1 mM CaCl2, 0.2 M methyl-alpha-D-mannopyranoside (Sigma) pH 7.4 (buffer B). Eluted peak was pooled and applied again to the column for a second round of chromatography. After two consecutive chromatographic steps the eluted peak (about 100-150 μg) contained less than about 10% fucosylated glycoforms.
Example 3
TNF-α Production Assay
TNF-α production assay was done essentially as described in Roda, J. M. et al. (The Journal of Immunology (2006), 177: 120-129). In short, wells of a 96-well flat-bottom plate were coated with glycoform antibodies 50, 100 or 200 μg/ml in PBS o/n at 4° C. and washed with cold PBS and warm RPMI-1640 medium. Peripheral blood mononuclear cells (PBMC) were isolated from healthy volunteers using VACUTAINER CPT (cell preparation tube) (BD), washed with PBS and RPMI-1640 medium and suspended 106 cells/ml in medium supplemented with 10% fetal calf serum, 100 U/ml penicillin, 100 μg/ml streptomycin and glutamine. PBMC were added to antibody coated wells 2×105 cells/well and the plates were incubated o/n 37° C. in humidified atmosphere and 5% CO2. TNF-α production was analyzed from cell culture supernatants using Human TNF-α Immunoassay kit (R&D Systems).
Results of a typical TNF-α production assay are shown in FIG. 1. The relative potencies of the antibody glycoforms to induce TNF-α production and thus mediate FcγRIIIa-dependent cellular cytotoxicity (Roda et al. 2006) were in the following order: non-fucosylated monoantennary>non-fucosylated>>normal IgG (data not shown)>hybrid-type.
Example 4
Receptor Binding Assays
Printing of arrays. Arrays were printed onto SCHOTT NEXTERION H MPX-16 slides (Schott Technical Glass Solutions GmbH, Jena, Germany). Antibody isoform and control protein samples were diluted to 0.5 mgml with a buffer that had been made by bringing 100 mM sodium citrate buffer pH 2.6 to pH 7 by adding 1 M Na2HPO4. The samples were printed at a volume of about 400 pL per spot using a Scienion SCIFLEXARRAYER S5 non-contact printer (Scienion AG, Berlin, Germany). For each sample concentration, 6 replicates were printed. 6 replicate spots of Cy3-labeled protein served as positive control and 6 replicate spots of printing buffer solution served as negative controls. In the arrays the distance between adjacent spots was approximately 380 μm. Arrays of up to 24 different isoforms and control substances were printed resulting in 144 spotsarray. The printed array slides were incubated in 75% humidity in room temperature overnight, allowed to dry in room temperature and stored until use in −20° C. in a desiccator.
Hybridization with Effector Molecules and Reading of Arrays
Preparation of binding proteins for assays. Recombinant human Fc gamma receptor IIa was from R&D Systems Inc. (USA) and Clq complement was from Quidel (San Diego, Calif., USA). These binding proteins were labeled with NETS-activated Cy3 or Cy5 (GE Healthcare, UK) according to manufacturer's instructions and purified from excess reagent by changing the buffer to phosphate buffered saline (PBS) in NAP-5 (small scale purification, desalting and buffer exchange) columns (GE Healthcare, UK).
Assay Procedure to Evaluate Fc Gamma Receptor IIa and C1q Binding Affinities.
Printed slides were blocked with 25 mM ethanolamine in 100 mM borate buffer, pH 8.5 for at least one hour in room temperature. Slides were rinsed three times with PBS-TWEEN (Polysorbate) (0.05-0.1% TWEEN), once with PBS and once with water. A SCHOTT NEXTERION (Microarray Glass Substrates) MPX superstructure (Schott Technical Glass Solutions GmbH, Jena, Germany) was attached to create wells. Arrays were incubated with various concentrations of labeled binding proteins in 60 μl volume of PBS buffer. Incubations were carried out for 2-2.5 h at room temperature, after which the slides were washed five times in PBS-TWEEN (Polysorbate), once with PBS, rinsed with water and dried using nitrogen gas stream. Arrays were imaged using Tecan's LS Reloaded laser scanner (Tecan Group Ltd., Switzerland) at excitation wavelengths of 532 and 633 nm and detection wavelengths of 575 and 692 nm for Cy3 and Cy5, respectively. The images were quantified using Array Pro software.
Results of a typical C1q-binding assay are shown in FIG. 2. The relative affinities of the antibody glycoforms to C1q were in the following order: monoantennary (comprising mixture of non-fucosylated and core fucosylated N-glycans)>normal IgG.
Results of a typical FcγRIIa-binding assay are shown in FIG. 3. The relative affinities of the antibody glycoforms to FcγRIIa were in the following order: non-fucosylated monoantennary>non-fucosylated>normal IgG.
Example 5
Inhibition of Glycosylation Enzymes with Specific siRNAs in HEK-293 Cells
Glycosylation targeted siRNA probes were obtained from Qiagen. Human embryonal kidney HEK-293 cells were cultured in 384-well plates in standard culture conditions and transfected for 48 h with each siRNA in eight replicate experiments. After the transfection, cells were fixed and permeabilized, labelled with lectins PHA-L and AAL (EY Laboratories Inc., USA) labeled with Cy5 as described above and the amount of label was quantitated by image acquisition and analysis with Olympus scanR system. Fold changes were calculated as labeling intensity relative to control cells.
The utilized siRNA probes are identified by Qiagen SI codes as shown in Table 1:











TABLE 1







Gene
Enzyme
Qiagen SI codes









MGAT2
GnTII
SI04248286, SI04308521,





SI04314219, SI00630987



MAN2A1
mannosidase II
SI00036729, SI00036722,





SI00036743, SI00036736



MAN2A2
mannosidase IIx
SI00084672, SI00084679,





SI00084658, SI00084665



GMDS
GDP-mannose 4,6-
SI00428645, SI00428638,




dehydratase (GMD)
SI00428624, SI03106327



TSTA3
GDP-4-keto-6-
SI00050631, SI04437419,




deoxy-D-mannose-
SI03026198, SI04437426,




3,5-epimerase-4-
SI02665089, SI02665096




reductase (FX)



FUT8
N-glycan core
SI03224669, SI03149118




α1,6-




fucosyltransferase




(FucTVIII)










One of the anti-MGAT siRNAs, SI04314219, inhibited branched complex-type N-glycan biosynthesis as judged by decreased labeling with PHA-L (labeling intensity fold change −0.66). This indicated that this siRNA had decreased the activity of GnTII in these cells, leading to increased amounts of monoantennary N-glycans.
Three of the anti-MAN2A1 siRNAs, SI00036729, SI00036722 and SI00036743, inhibited branched complex-type N-glycan biosynthesis as judged by decreased labeling with PHA-L (labeling intensity fold changes −0.20, −0.58 and −0.81, respectively). This indicated that these siRNAs had decreased the activity of mannosidase II in these cells, leading to increased amounts of hybrid-type N-glycans.
One of the anti-MAN2A2 siRNAs, SI00084679, inhibited branched complex-type N-glycan biosynthesis as judged by decreased labeling with PHA-L (labeling intensity fold change −0.34) and increased fucosylation as judged by increased labeling with AAL (labeling intensity fold change 0.37). This indicated that these siRNAs had decreased the activity of mannosidase IIx in these cells, leading to increased amounts of core-fucosylated hybrid-type N-glycans.
One of the anti-GMDS siRNAs, SI00428645, three of the anti-TSTA3 siRNAs, SI00050631, SI04437419 and SI03026198, as well as both anti-FUT8 siRNAs inhibited fucosylation as judged by decreased labeling with AAL (labeling intensity fold changes −1.13, −0.67, −0.05, −0.16, −0.52 and −0.19, respectively). This indicated that these siRNAs had decreased fucosylation activity in these cells, leading to decreased amounts of core-fucosylated N-glycans.
Example 6
In Vivo Half-Life of Humanized Antibody Glycoforms
The purpose of the study was to measure in vivo serum half-life of CHO-expressed anti-IL-8 humanized IgG1 antibody glycoforms in healthy mice following a single i.v. administered dose of antibody. N-glycans were isolated from the non-fucosylated monoantennary trastuzumab glycoform and analysed by MALDI-TOF mass spectrometry as described above. The major N-glycan signals were at m/z 1136.4 corresponding to the sodium adduct ion of GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4 GlcNAc and at m/z 1298.5 corresponding to the sodium adduct ion of Galβ4GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc; the molar ratios of these glycan components were about 40%:60%, respectively. The test animals were female FVB/N mice. Background serum samples (100 μl blood) were taken from all animals three days before the start of the experiment. Serum samples were obtained in serum isolation tubes by centrifuging the blood samples. 50 μg of antibody was injected i.v. via the tail vein in 110 μl phosphate-buffered saline at start of day 1 of the experiment. 100 μl blood samples were taken from all animals 10 min after dosing of test substances and on days 2, 3, 5, 8 and 15. The test substances contained 0.45 g/l anti-IL-8 antibody glycoforms in sterile-filtered phosphate-buffered saline. 100 μl blood samples were collected and serum was isolated. Human IgG concentrations in sera were analysed by anti-human IgG ELISA kit (RD-Biotech, Besancon, France). The rates of elimination from serum of both normal CHO-expressed anti-IL-8 humanized IgG1 antibody and its non-fucosylated monoantennary glycoform were essentially similar in mice: when 50 μg effective dose was administered at day 1, at day 15 the remaining serum concentration of both antibody forms was 2-3 μg/ml.
Example 7
Treatment of Established Ovarian Cancer Xenograft Tumors with Trastuzumab Glycoform Antibodies in Human Leukocyte Grafted Mice
The purpose of the study was to test tumor treatment efficacy of trastuzumab glycoforms in comparison to non-treated animals. The study was performed with double xenograft mouse model of HER2 positive cancer. Immunodeficient mice were grafted with both human immune effector cells and tumor forming cancer cells. Tumors were allowed to grow to approximately 5 mm diameter before antibody treatment. Antibody treatment was given weekly i.v. for three weeks and tumor sizes were measured. The experiments were approved by the appropriate ethical committee and the blood donor gave an informed consent.
The test substance was non-fucosylated monoantennary trastuzumab glycoform as described in the preceding examples, produced transiently with FREESTYLE MAX (formulation for the transfection of plasmid DNA into eukarvotic cells) Expression System (Life Technologies) according to manufacturer's instructions. The trastuzumab amino acid sequences were according to the IMGT database (www.imgt.org) for the light chain (7637_L) and heavy chain (7367_H) sequences. Optimized nucleotide sequences encoding the heavy and light chain sequences with functional signal peptide sequences were purchased from GENEART (gene synthesis service) (Life Technologies) and cloned separately into pCEP4 expression vectors (Life Technologies). For antibody expression, the FREESTYLE CHO-S cells were transfected 1:1 with light chain and heavy chain vectors and cultured in the presence of 10 μg/ml swainsonine and 7.2 μg/ml AV39 as described in the preceding examples. The antibodies were then purified with protein G chromatography and treated with α-mannosidase as described above to produce the non-fucosylated monoantennary trastuzumab glycoform for the experiment. N-glycans were isolated and analysed by MALDI-TOF mass spectrometry as described above. In the non-fucosylated monoantennary trastuzumab glycoform, the major N-glycan signals were at mz 1136.4 corresponding to the sodium adduct ion of GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc (50% of total glycan signal intensity) and at m/z 1298.5 corresponding to the sodium adduct ion of Galβ4GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcN- Ac β3% of total glycan signal intensity).
The test animals were female CIEA NOG mice (Taconic) that lack functional T, B and NK cells and have dysfunctional macrophages and dendritic cells as well as reduced complement activity. The mice were grafted i.v. on day 0 of the experiment with 5×106 peripheral blood mononuclear cells (PBMC), freshly isolated from one human blood donor by gradient centrifugation with VACUTAINER CPT (cell preparation tube)(BD). On day 3 the mice were further grafted s.c. with 5×106 human ovarian cancer SKOV-3i cells originating from ATCC cell line SKOV-3 (HTB-77). The cell line was derived at University of Turku from SKOV-3 xenograft tumors and it was confirmed to express HER2 on the cell surface by flow cytometry, to be susceptible to ADCC by trastuzumab and to form s.c. xenograft tumors to which i.v. administered trastuzumab localizes in vivo.
The first dosing of antibodies was given on day 13 when the tumors had grown to 4-8 mm diameter. The mice with different sized tumors were equally divided into the study groups so that the groups were as similar as possible: eight animals received no treatment and three animals received trastuzumab glycoform treatment. The test substances were prepared 0.5 g/l in sterile-filtered PBS. Antibody treatment was given once weekly for three weeks: i.v. 0.7 mg/kg on days 13, 20 and 27.
Tumor length (L) and width (W) were recorded in mm at various timepoints with ultrasound imaging and at the end of the experiment by direct measurement, and tumor volume (V) in mm3 was calculated according to the formula V=1⁄2LW2. At the end of the experiment, on day 34, average tumor volumes were 197 mm3 in the treatment group (on average 45% growth in tumor volume between day 13 and day 34) and 232 mm3 in the non-treated group (on average 83% growth in tumor volume between day 13 and day 34), demonstrating that the non-fucosylated monoantennary trastuzumab glycoform was therapeutically effective and inhibited established tumor growth in HER2 positive ovarian cancer xenograft mice.
Example 8
Antibody-Dependent Cellular Cytotoxicity (ADCC) of Trastuzumab Glycoforms
The test substances: normal trastuzumab glycoform, non-fucosylated trastuzumab glycoform and non-fucosylated monoantennary trastuzumab glycoform were produced transiently with FREESTYLE MAX Expression System (Life Technologies) in CHO-S cells as described above. For non-fucosylated trastuzumab glycoform expression, the transfected cells were cultured in the presence of 7.2 μg/ml AV39. For non-fucosylated monoantennary trastuzumab glycoform expression, the transfected cells were cultured in the presence of 10 μg/ml swainsonine and 7.2 μg/ml AV39 and the isolated antibody was further treated with α-mannosidase as described above. The antibodies were purified with protein G chromatography. The humanized IgG1 monoclonal antibody omalizumab (Genentech/Novartis) was used as a negative control. N-glycans were isolated and analysed by MALDI-TOF mass spectrometry as described above. In the non-fucosylated monoantennary trastuzumab glycoform, the major N-glycan signals were at mz 1136.4 corresponding to the sodium adduct ion of GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcNAc and at m/z 1298.5 corresponding to the sodium adduct ion of Galβ4GlNAcβ2Manα3(Manα6)Manβ4GlcNAcβ4GlcN-Ac; the molar ratios of these glycan components were 80%:20%, respectively.
HER2 positive SKOV-3 ovarian cancer cells (ATCC) were cultured according to the manufacturer's recommendations and seeded in RPMI medium supplemented with 5% fetal calf serum (medium) into 96-well plates, 10 000 cells/well. Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor's blood with VACUTAINER CPT (cell preparation tube) (BD) according to the manufacturer's instructions, washed with phosphate-buffered saline (PBS) and suspended into the medium. Antibodies were diluted into the medium as a 10-fold dilution series to achieve final antibody concentrations from 10 pg/ml to 1 μg/ml; antibodies were incubated in cell incubator at +37 C. for 1 hour before adding PBMCs. PBMCs were added to the 96-well plate 500 000 cells/well to achieve effector:target cell ratio of 50:1. Controls lacking all or some of the target cells, PBMCs or antibody were also prepared and each test was made in triplicate. Final volume in each well was 150 μL. The reactions were incubated for further 4 hours at +37 C.
Cytotoxicity was assayed with lactate dehydrogenase assay kit (Cytotoxicity detection kit plus, Roche) with absorbance determination at 492 nm. Cytotoxicity as ADCC % was calculated according to the formula:




  
    ADCC
    ⁢
    %
  
  =
  
    
      
        
          A
          ⁢
          
            
          
          ⁢
          492
          ⁢
          
            
          
          ⁢
          
            nm
            ⁡
            
              (
              assay
              )
            
          
        
        -
        
          A
          ⁢
          
            
          
          ⁢
          492
          ⁢
          
            
          
          ⁢
          
            nm
            ⁡
            
              (
              
                SKOV
                ⁢
                
                  
                
                ⁢
                3
              
              )
            
          
        
        -
        
          A
          ⁢
          
            
          
          ⁢
          492
          ⁢
          
            
          
          ⁢
          
            nm
            ⁡
            
              (
              PBMC
              )
            
          
        
      
      
        
          A
          ⁢
          
            
          
          ⁢
          492
          ⁢
          
            
          
          ⁢
          
            nm
            ⁡
            
              (
              
                lysed
                ⁢
                
                  
                
                ⁢
                cells
              
              )
            
          
        
        -
        
          A
          ⁢
          
            
          
          ⁢
          492
          ⁢
          
            
          
          ⁢
          
            nm
            ⁡
            
              (
              
                SKOV
                ⁢
                
                  
                
                ⁢
                3
              
              )
            
          
        
      
    
    ×
    100
    ⁢
    %
  




wherein “assay” is well with all SKOV-3 cells, antibody and PBMCs; “SKOV3” is well with only SKOV-3 cells; “PBMC” is well with only PBMCs; and “lysed cells” is well with SKOV-3 cells that have been lysed with lysing solution of the cytotoxicity kit.

The result was that non-fucosylated trastuzumab glycoform and non-fucosylated monoantennary trastuzumab glycoform had similar ADCC % and they both had higher ADCC % than normal trastuzumab glycoform; and over 10-fold smaller antibody concentration of either non-fucosylated trastuzumab glycoform or non-fucosylated monoantennary trastuzumab glycoform was needed to achieve same ADCC % than normal trastuzumab glycoform, indicating over 10-fold higher ADCC potency; while omalizumab had minimal ADCC activity.
As is clear for a person skilled in the art, the invention is not limited to the examples and embodiments described above, but the embodiments can freely vary within the scope of the claims.

## Claims

1. A pharmaceutical composition comprising a glycoprotein comprising the Fc domain of an antibody, or a fragment thereof, comprising an Asn residue and an oligosaccharide structure attached thereto and a pharmaceutically acceptable carrier, wherein the oligosaccharide structure consists of the structure according to formula I



wherein (β-N-Asn)=β-N linkage to Asn;
wherein at least 50% of the oligosaccharide structures attached to glycoprotein in the composition consist of oligosaccharide structures according to formula I.

2. The pharmaceutical composition according to claim 1, wherein at least 66.7% at least 90%, at least 95%, or at least 99% of the oligosaccharide structures attached to the glycoprotein in the composition consist of oligosaccharide structures according to formula I.

3. The pharmaceutical composition according to claim 1, wherein the Asn residue corresponds to Asn297 of human IgG wherein the numbering corresponds to the EU index as in Kabat.

4. The pharmaceutical composition according to claim 1, wherein the Fc domain is a human Fc domain.

5. The pharmaceutical composition according to claim 1, wherein the glycoprotein is a fusion protein comprising an Fc domain.

6. The pharmaceutical composition according to claim 1, wherein the glycoprotein is a human antibody, a humanized antibody or a chimeric antibody comprising a human Fc domain.

7. The pharmaceutical composition according to claim 1, wherein the glycoprotein is an IgG antibody.

8. The pharmaceutical composition according to claim 1, wherein the glycoprotein is an IgG1 antibody.

9. The pharmaceutical composition according to claim 1, wherein the glycoprotein is an antibody directed against human vascular endothelial growth factor (VEGF), epidermal growth factor receptor 1 (EGFR), tumor necrosis factor alpha (TNF-α), CD20, epidermal growth factor receptor 2 (HER2/neu), CD52, CD33, CD11a, glycoprotein IIb/IIIa, CD25, IgE, interleukin-2 (IL-2) receptor, or respiratory syncytial virus (RSV).

10. The pharmaceutical composition according to claim 1, wherein the glycoprotein is an antibody that is bevacizumab, tositumomab, etanercept, trastuzumab, adalimumab, alemtuzumab, gemtuzumab ozogamicin, efalizumumab, rituximab, infliximab, abciximab, baasiliximab, palivizumab, omalizumab, daclizumab, cetuximab, panitumumab, or ibritumomab tiuxetan.