# Patent

## Title
Heterodimer protein composition

## Abstract

According to the present invention, a heterodimer protein composition that is composed of a first polypeptide comprising an immunoglobulin heavy chain constant region and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin light chain constant region (CL) and Fc region, and also has a deletion or substitution of Cys residues involved in disulfide bonds between CL and CH1, a purification method of the protein composition thereof, a preparation method of the protein composition thereof, a DNA and a vector encoding the protein composition thereof are provided.

## Background
BACKGROUND OF THE INVENTION
1. Field of the Invention
The present invention relates to a heterodimer protein composition that is efficiently and stably separated and purified.
2. Brief Description of the Background Art
Monoclonal antibodies are biological polymers having high binding affinity and specificity for antigens, and applied as molecular targeted therapeutics for the treatment of cancer, immune disorders or the like. The known action mechanisms of immunoglobulin G (hereinafter, abbreviated to IgG) which is widely used as a therapeutic monoclonal antibody include neutralization of antigens, receptor agonist or antagonist action, induction of apoptosis, phagocytosis, induction of complement or effector cell-dependent cytotoxicity, delivery of chemotherapeutic agents, toxins, and radioactive isotopes, or the like.
IgG antibodies are tetrameric molecules composed of two antibody heavy chains (hereinafter, abbreviated to H chain) and two antibody light chains (hereinafter, abbreviated to L chain), consisting of a variable region as an antigen-binding site and a constant region having a constant amino acid sequence (FIG. 1).
Each structure of an antibody is known to be involved in the various roles. The antigen-binding site is formed by a heavy chain variable region (hereinafter, abbreviated to VH) and a light chain variable region (hereinafter, abbreviated to VL), and various antigen specificities and binding affinities are caused by variability in primary sequence and higher-order structure.
Each constant region of IgG H chain (hereinafter, abbreviated to CH) is composed of CH1, hinge, CH2, and CH3 domains, and among them, hinge, CH2, and CH3 constitute the Fc region (hereinafter, also simply referred to as Fc). Fc binds to the Fcγ receptor (hereinafter, abbreviated to FcγR) present on leukocytes to be involved in release of inflammatory mediators, phagocytosis, and antibody-dependent cellular cytotoxicity (hereinafter, abbreviated to ADCC), and also binds to complement components to be involved in complement-dependent cytotoxicity (hereinafter, abbreviated to CDC).
Further, Fc of IgG antibody binds to the neonatal Fc receptor (hereinafter, abbreviated to FcRn) in the endosome under low pH conditions, and avoids lysosomal degradation to be involved in extension of the blood half-life. The primary sequence of Fc region varies depending on its subclasses (IgG1, IgG2, IgG3, IgG4), and its binding activity for FcγR, FcRn and complement components also differs, for this reason, they cause differences in biological properties (Non-Patent Document 1).
IgG antibody molecule has two fragments called as Fab, which is composed of VH, CH1, VL, and L chain constant region (hereinafter, abbreviated to CL), and these two Fabs form the bivalent binding with antigen molecules. This bivalent binding activity increases avidity for antigens, as well as induces intracellular signaling by cross-linking antigens when the antibodies bind to antigen molecules such as receptors present on the surface of cell membrane.
In order to avoid the bivalent antigen-binding activity of IgG antibody, antibody engineering consideration has been made, such as preparation of monovalent antibodies having a single antigen-binding site or antibody variants having an Fc variant containing substitution of amino acid residues for removing the FcγR binding activity. Meanwhile, Fab fragment including an antigen-binding site shows a monovalent binding activity for antigens, but shows a short blood half-life and is not useful as a therapeutic agent because there is no Fc (Non-Patent Document 2).
Meanwhile, bispecific antibodies are allowed to have the action mechanisms that cannot be achieved by the conventional IgG monoclonal antibodies, because of their bispecificity. For example, bispecific T cell engager [BiTE (registered trade name)] binds with both CD3 and a cancer antigen to recruit T cells and to efficiently damage cancer cells (Non-Patent Document 3). In addition, bispecific antibodies have a possibility of inhibiting activated intracellular signaling by crosslinking the inhibitory Feγ receptor FcγRIIb with the receptor (Non-Patent Documents 4 and 5).
The first technology of producing bispecific antibodies is a production method using a fusion cell of two hybridomas, called quadroma. Theoretically, tetramers composed of two different H chains and two different L chains are produced as a mixture of up to 10 assemblies, of which only one is the desired antibody having bispecific activity. It is difficult to separate the desired bispecific antibodies from by-products that are similar in physicochemical properties (Non-Patent Document 6).
The known methods for reducing the kind of by-products of the bispecific antibody are a method of introducing a substitution of amino acid residues stabilizing a “heterologous assembly” of the different H chains into CH3 domain (Non-Patent Documents 7, 8, and 9, and Patent Document 4), and a method of stabilizing heterologous assembly of H chains by using chimeric CH3 domains of IgG1 antibody and IgA antibody (Patent Document 1).
In this regard, a method of removing the undesirable by-products generated by “homologous assembly” of homologous H chains during expression of the bispecific antibodies in a purification step has been reported, and a purification method using a difference in binding affinity of IgG antibody subclasses for Protein A has also been known.
Lindhofer et al. have disclosed a purification method of bispecific antibodies consisting of rat IgG2b and mouse IgG2a, based on the properties of rat IgG2b binds to Protein A and mouse IgG2a doesn't bind to Protein A. That is, it is known that a heterodimer of rat IgG2b and mouse IgG2a and a homodimer of mouse IgG2a bind to Protein A, and heterodimeric bispecific antibody can be isolated by pH control during elution (Non-Patent Document 10).
Further, Samuel et al. have proposed a method of specifically purifying human IgG type bispecific antibody by using a difference in the affinity for Protein A. It has been also disclosed that of the two different H chains constituting the bispecific antibody, the CH3 domain of one H chain is subjected to modification of amino acid residues of Arg at position 435 and Phe at position 436 of the EU index, thereby reducing the binding affinity for Protein A, and as a result, heterodimeric IgG type bispecific antibody can be separated and purified from three molecules having different Protein A affinities by pH control during elution (Patent Document 2).
A heterodimeric monovalent antibody consisting of a human IgG1 antibody H chain and a fusion protein of a human κ light chain and an Fc molecule of human IgG1 has been reported as one of the antibody molecules prepared by application of a heterodimeric structure (Patent Document 3).
However, it has been known that when this molecule is expressed, homodimers of H chain-H chain are not secreted, but heterodimers of H chain-fusion protein, homodimers of fusion protein, and multimers are secreted into the culture supernatant, and conjugation of a tag sequence to H chain is required in order to obtain the specific heterodimeric monovalent antibody from the secreted proteins, and this tag should be used for purification. For the use of this monovalent antibody molecule as a drug, side effects caused by possible multimers having unexpected biological activities and a cumbersome and expensive affinity purification using a tag sequence are challenging problems.
CITATION LIST
Patent Documents


    [Patent Document 1] WO 2007/110205
    [Patent Document 2] WO 2010/151792
    [Patent Document 3] WO 2007/048037
    [Patent Document 4] WO 2009/089004


Non-Patent Documents


    [Non-Patent Document 1] Cater et al, Nature Review, 2006; 6: 343.
    [Non-Patent Document 2] Labrjin A F et al, Current Opinion in Immunology, 2008; 20:1
    [Non-Patent Document 3] Wolf et al, Drug Discovery Today, 2005; 10: 1237
    [Non-Patent Document 4] Kufer et al, TRENDS in Biotech., 2004; 22: 238
    [Non-Patent Document 5] Jackman et al., J. Biol. Chem., 2010; 285: 20850
    [Non-Patent Document 6] Cater et al. J. Immunol. Methods, 2001; 248: 7
    [Non-Patent Document 7] Ridway et al. Protein Eng., 1996; 9: 617
    [Non-Patent Document 8] Merchant et al., Nature Biotech., 1998; 16: 677
    [Non-Patent Document 9] Gunasekaran et al., J. Biol. Chem., 2010; 285: 19637
    [Non-Patent Document 10] Lindhofer H et al., J. Immunol., 1995; 155: 219


SUMMARY OF THE INVENTION
With respect to the previously known heterodimer proteins, their production efficiency was low and unstable, and specific production, separation and purification of heterodimer protein molecules were difficult. Accordingly, there is a need for a heterodimer protein composition that can be efficiently and stably produced, a purification method and a preparation method of the protein composition.
The heterodimer protein of the present invention is composed of a first polypeptide comprising an immunoglobulin heavy chain constant region (CH) and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin light chain constant region (CL) and Fc region, and it can be efficiently and stably produced by inhibiting the amounts of multimers, halfmers and multimer/halfmer produced during production of the heterodimer proteins, resulting from deletion or substitution of Cys residues involved in disulfide bonds between L chain-H chain molecules in the IgG antibody.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a diagram of IgG antibody.
FIG. 2A is a diagram showing the structure of the heterodimer protein of the present invention.
FIG. 2B is a diagram showing the structures of typical monovalent to tetravalent antibodies that can prepared based on the heterodimer scaffold protein (HSP) structure of the present invention.
FIG. 3A shows the amino acid sequence (IgG1-CH) of the H chain constant region of IgG1 type monovalent antibody. The amino acid residues underlined represent amino acid residue substitution-introduced region (Table 1), and the numbers represent those defined by the EU index.
FIG. 3B shows the amino acid sequence (IgG4-CH) of the H chain constant region of IgG4 type monovalent antibody. The amino acid residues underlined represent amino acid residue substitution-introduced region (Table 1), and the numbers represent those defined by the EU index.
FIG. 4A shows the amino acid sequence (IgG1-L) of CL-Fc of IgG1 type monovalent antibody. The amino acid residues underlined represent amino acid residue substitution-introduced region (Table 2), and the numbers represent those defined by the EU index.
FIG. 4B shows the amino acid sequence (IgG4-L) of CL-Fc of IgG4 type monovalent antibody. The amino acid residues underlined represent amino acid residue substitution-introduced region (Table 2), and the numbers represent those defined by the EU index.
FIG. 5 shows the structures of various monovalent antibodies.
FIG. 6 shows the amino acid sequence of the second polypeptide of bispecific antibody.
FIG. 7 shows the structure of bispecific antibody.
FIGS. 8A (a) and (b) show the results of SDS-PAGE analysis of anti-HER2 IgG4 type monovalent antibodies, 4D5/mvG4-1 DF and 4D5/mvG4-2 DF under non-reducing conditions. In the SDS-PAGE analysis, elution fractions 1 to 3 eluted at each pH in Protein A purification were used. Arrows in the figure represent multimer bands.
FIG. 8B shows the results of SDS-PAGE analysis of anti-HER2 IgG4 type monovalent antibodies, 4D5/mvG4-3 DF and 4D5/mvG4-4 DF under non-reducing conditions. In the SDS-PAGE analysis, purified proteins collectively eluted at pH 3.0 in Protein A purification were used. Arrows in the figure represent halfmer bands.
FIG. 9 shows the results of cation exchange chromatography of anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-2 DF. Peaks (1) to (10) in the figure represent fractionated fractions.
FIG. 10 shows the results of Western blot analysis of anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-2 DF sample (FIG. 9) fractionated by cation exchange chromatography. Anti-kappa chain antibody was used for L chain detection, anti-His tag antibody was used for H chain detection, and anti-human IgG antibody was used for IgG detection. Peaks (2), (4), (5), (6), (7) and (10) were below the detection limits.
FIG. 11 shows the results of SDS-PAGE, L chain-specific western blot, and H chain-specific western blot of fraction X which is one of the fractions eluted at pH 3.5 and fraction Y eluted at pH 5.0 in Protein A purification of anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-2 DF, and 4D5/mvG4-3 DF purified by use of Protein A or Protein G. As shown in Table 5, the fractions X and Y of 4D5/mvG4-2 DF are an elution fraction having HL form as a main component and an elution fraction having LL form as a main component, respectively. Protein G-purified product and Protein A-purified product of 4D5/mvG4-3 DF were obtained by performing Protein G or Protein A purification of the cell culture supernatant obtained at the same time and then by eluting them collectively.
FIG. 12 shows the amount of HL heterodimer of IgG4 type monovalent antibody by sandwich ELISA. The experiment was performed at N=3. The vertical axis represents the binding activity of HL heterodimer, and the horizontal axis represents the HL heterodimer concentration (μg/mL).
FIG. 13A shows the amount of IgG4 type monovalent antibody HL heterodimer in each protein A purification fraction by sandwich ELISA. The experiment was performed at N=3. The vertical axis represents the binding activity of HL heterodimer, and the horizontal axis represents the HL heterodimer concentration (μg/mL).
FIG. 13B shows the amount of IgG4 type monovalent antibody HL heterodimer in each protein A purification fraction by sandwich ELISA. The experiment was performed at N=3. The vertical axis represents the binding activity of HL heterodimer, and the horizontal axis represents the HL heterodimer concentration (μg/mL).
FIG. 14A shows the results of flow cytometry for evaluating competitive binding inhibition of various monovalent antibodies in the binding assay of anti-HER2 humanized antibody Herceptin, in which the binding activity for HER2 positive human breast cancer cell line SK-BR-3 is shown. Relative fluorescence intensity in the figure was calculated by (average fluorescence intensity of sample)/(average fluorescence intensity of hIgG1_Alx). The experiment was performed at N=2. In all figures, the vertical axis represents relative fluorescence intensity (RFI), and the horizontal axis represents the concentrations (nM) of IgG1 antibody and monovalent antibody competitively reacted.
FIG. 14B shows the results of flow cytometry for evaluating competitive binding inhibition of various monovalent antibodies in the binding assay of anti-CD20 humanized antibody GA101, in which the binding activity for CD20 positive human lymphoma cell line Raji is shown. Relative fluorescence intensity in the figure was calculated by (average fluorescence intensity of sample)/(average fluorescence intensity of hIgG1_Alx). The experiment was performed at N=2. In all figures, the vertical axis represents relative fluorescence intensity (RFI), and the horizontal axis represents the concentrations (nM) of IgG1 antibody and monovalent antibody competitively reacted.
FIGS. 15A (a) and (b) show antibody dependent cellular cytotoxicity (ADCC) activity for human breast cancer cell line SK-BR-3 and BT-20 by the IgG1 type anti-HER2 monovalent antibodies, in which fraction (FIG. 13) showing the highest content of HL heterodimer was used as 4D5/mvG1-1 DF. In the experiment, PBMC obtained from another donor was used. The experiment was performed at N=3. The vertical axis represents the ADCC activity, and the horizontal axis represents the antibody concentration (nM).
FIGS. 15B (a) and (b) show ADCC activity for human breast cancer cell line BT-20 by the IgG1 type and IgG4 type anti-HER2 monovalent antibodies. In the experiment, PBMC obtained from another donor was used. The experiment was performed at N=3. The vertical axis represents the ADCC activity, and the horizontal axis represents the antibody concentration (nM).
FIGS. 16(a) to (c) show ADCC activity of anti-CD20 IgG1 type monovalent antibody for Burkitt lymphoma cell lines Raji and ST-486 and chronic B cell leukemia cell line MEC-1. The vertical axis represents the ADCC activity (%), and the horizontal axis represents the antibody concentration (nM).
FIG. 17 shows the results of SDS-PAGE analysis of anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-4F, anti-CD74 IgG4 type monovalent antibody hLL1/mvG4-4F, HER2-CD74 bispecific antibody hLL1-4D5/mvG4-4F and CD74-CD20 bispecific antibody hLL1-2F2/mvG4-4F under non-reducing and reducing conditions.
FIGS. 18(a) and (b) show the binding activity of HER2-CD74 bispecific antibody hLL1-4D5/mvG4-4F for recombinant HER2 protein and recombinant CD74 protein by ELISA. The vertical axis represents the antigen-binding activity (OD415-490) and the horizontal axis represents the bispecific antibody concentration (nM). Anti-HER2 humanized antibody Herceptin and anti-CD74 antibody hLL1 antibody were used as a positive control IgG1 antibody for each antigen.
FIG. 19 shows complement-dependent cytotoxicity (CDC activity) of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and anti-CD20 IgG1 antibody GA101/IgG1 for Burkitt lymphoma cell line ST-486. The vertical axis represents the CDC activity (%) and the horizontal axis represents the mol concentration (nM) of each monovalent antibody and IgG1 antibody.
FIG. 20(a) shows the binding amounts of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and anti-CD20 IgG1 antibody GA101/IgG1 to Burkitt lymphoma cell line Raji. FIG. 20(b) shows the binding amount of complement factor C1q. In both figures, the vertical axis represents relative fluorescence intensity (RFI) value, and the horizontal axis represents the mol concentration (nM) of each monovalent antibody and IgG1 antibody.
FIG. 21(a) shows the binding amounts of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and anti-CD20 IgG1 antibody GA101/IgG1 to Burkitt lymphoma cell line ST-486. FIG. 21(b) shows the binding amount of complement factor C1q. In both figures, the vertical axis represents relative fluorescence intensity (RFI) value, and the horizontal axis represents the mol concentration (nM) of each monovalent antibody and IgG1 antibody.
FIG. 22A shows the amino acid sequence of H chain constant region domain of the heterodimer protein including the CDC enhanced-constant region. The amino acid numbers are represented according to the EU index defined by Kabat et al., and ● represents the CDC enhanced-amino acid substitution sites of the IgG1 type and ★ represents the amino acid substitution sites for the heterodimer protein.
FIG. 22B shows the amino acid sequence of CL-Fc chain of the heterodimer protein including the CDC enhanced-constant region. The amino acid numbers are represented according to the EU index defined by Kabat et al., and ● represents the CDC enhanced-amino acid substitution sites of the IgG1 type and ★ represents the amino acid substitution sites for the heterodimer protein.
FIG. 23 shows the results of SDS-PAGE using the purified proteins of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and anti-CD20 CDC enhanced-monovalent antibody GA101/mvCom. DTT− represents a non-reduced state and DTT+ represents a reduced state.
FIGS. 24(a) and (b) show CDC activity of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and CDC enhanced anti-CD20 high monovalent antibody GA101/mvCom for Burkitt lymphoma cell line Raji or chronic B cell leukemia cell MEC-1. The vertical axis represents the CDC activity (%), and the horizontal axis represents the mol concentration (nM) of each monovalent antibody and IgG1 antibody.
FIGS. 25(a) and (b) show ADCC activity of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 and CDC enhanced anti-CD20 monovalent antibody GA101/mvCom for Burkitt lymphoma cell line Raji or chronic B cell leukemia cell MEC-1. The vertical axis represents the ADCC activity (%), and the horizontal axis represents the mol concentration (nM) of each monovalent antibody and IgG1 antibody.



DETAILED DESCRIPTION OF THE INVENTION
The present invention relates to the following (1) to (25).
(1) A heterodimer protein that is composed of a first polypeptide comprising an immunoglobulin CH and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin CL and Fc region, and also has a deletion or substitution of Cys residues involved in disulfide bonds between L chain-H chain molecules in the IgG antibody.
(2) A heterodimer protein that is composed of a first polypeptide comprising an immunoglobulin CH and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin CL and Fc region, in which the second polypeptide is a polypeptide having a reduced binding activity for a CH binder.
(3) The heterodimer protein described in (1) or (2), in which the second polypeptide is a polypeptide having a substitution of the amino acid residue at position 214 of the EU index of Kabat et al. (hereinafter, referred to as EU index) with Ser.
(4) The heterodimer protein described in any one of (1) to (3), in which the first polypeptide is a polypeptide including CH1 domain, hinge domain, CH2 domain and CH3 domain, and the second polypeptide is a polypeptide including CL domain, hinge domain, CH2 domain and CH3 domain.
(5) The heterodimer protein described in any one of (2) to (4), in which the CH binder is any one selected from anti-CH1 domain antibody, anti-hinge antibody, anti-CH2 domain antibody, anti-CH3 domain antibody, Fc receptor protein, Protein A and Protein G.
(6) The heterodimer protein described in any one of (1) to (5), in which the immunoglobulin subclass is any one selected from IgG1, IgG2 and IgG4.
(7) The heterodimer protein described in any one of (1) to (6), in which the second polypeptide is a polypeptide having a substitution of the amino acid residue at position 435 of the EU index with Arg.
(8) The heterodimer protein described in any one of (1) to (7), in which the immunoglobulin subclass is IgG4.
(9) The heterodimer protein described in (8), in which the first polypeptide is a polypeptide having a substitution of the amino acid residue at position 131 of the EU index with Ser.
(10) The heterodimer protein described in (9), in which the first polypeptide and the second polypeptide are polypeptides having a substitution of the amino acid residue at position 228 of the EU index with Pro.
(11) The heterodimer protein described in (10), in which the first polypeptide and the second polypeptide are polypeptides having a substitution of the amino acid residue at position 409 of the EU index with Lys.
(12) The heterodimer protein described in (11), in which the first polypeptide and the second polypeptide are polypeptides having a substitution of the amino acid residue at position 235 of the EU index with Glu.
(13) The heterodimer protein described in any one of (1) to (7), in which the immunoglobulin subclass is IgG1.
(14) The heterodimer protein described in (13), in which the first polypeptide is a polypeptide having a substitution of the amino acid residue at position 220 of the EU index with Ser.
(15) The heterodimer protein described in (14), in which the second polypeptide is a polypeptide including a hinge domain having a deletion of the amino acid residues at positions 216 to 220 of the EU index or a polypeptide having a substitution of the amino acid residue at position 220 of the EU index with Ser.
(16) The heterodimer protein described in (15), in which the sugar chain with no fucose bound to N-acetylglucosamine at the reducing end of the sugar chain among the total N-glycoside linked sugar chains binding to the Fc region included in the heterodimer protein is 20% or more.
(17) The heterodimer protein described in (15) or (16), in which the first polypeptide and/or the second polypeptide are(is) a polypeptide including at least one amino acid residue substitution selected from P247I, F243L, R292P, Y300L, Y300F, P396L, T393A, H433P, S239D, S298A, A330L, I332E, E333A, K334A, L235E, P238A, N297A, K322A, P331S, K326A, S267E, H268F, S324T, K274Q, N276K, Y296F, K326W, K326Y, E333A, E333S, A339T, A339D, D356E, L358M, N384S, K392N, T394F, T394Y, V397M and V422I.
(18) The heterodimer protein described in any one of (1) to (17), in which the first polypeptide and/or the second polypeptide are(is) a polypeptide having at least one binding protein bound to the N-terminus and/or the C-terminus of CH and CL-Fc.
(19) The heterodimer protein described in (18), in which the binding protein is any one selected from an antibody variable region, a single chain Fv(scFv), a single variable domain (VHH), a ligand protein, and a receptor protein.
(20) The heterodimer protein described in any one of (1) to (19), selected from (i) a heterodimer protein, in which the first polypeptide is a polypeptide having an immunoglobulin VH bound to the N-terminus of CH and the second polypeptide is a polypeptide having an immunoglobulin VL bound to the N-terminus of CL-Fc, and (ii) a heterodimer protein, in which the first polypeptide is a polypeptide having VL bound to the N-terminus of CH and the second polypeptide is a polypeptide having VH bound to the N-terminus of CL-Fc.
(21) The heterodimer protein described in any one of (1) to (20), selected from (i) a heterodimer protein, in which the first polypeptide is a polypeptide having VH bound to the C-terminus of CH and the second polypeptide is a polypeptide having VL bound to the C-terminus of C-Fc, and (ii) a heterodimer protein, in which the first polypeptide is a polypeptide having VL bound to the C-terminus of CH and the second polypeptide is a polypeptide having VH bound to the C-terminus of CL-Fc.
(22) The heterodimer protein described in any one of (1) to (21), which is any one selected from a monovalent antibody, a divalent antibody, a trivalent antibody, and a tetravalent antibody.
(23) DNA encoding the heterodimer protein described in any one of (1) to (22).
(24) A cell expressing the heterodimer protein, which includes a protein expression vector containing the DNA described in (23).
(25) A method for preparing a heterodimer protein, including the processes of culturing the cell expressing the heterodimer protein described in (24) and purifying the heterodimer protein from the culture supernatant.
The present invention relates to a heterodimer protein that is composed of a first polypeptide comprising an immunoglobulin heavy chain constant region (CH) and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin light chain constant region (CL) and Fc region, and also has a deletion or substitution of Cys residues involved in disulfide bonds between L chain-H chain molecules in the IgG antibody, a purification method of the protein, a preparation method of the protein, a DNA and a vector encoding the protein.
1. Structure of Heterodimer Protein
The heterodimer protein of the present invention may be a heterodimer protein that is composed of a first polypeptide comprising an immunoglobulin CH and a second polypeptide comprising CL-Fc prepared by fusion of an immunoglobulin CL and antibody Fc region, and also has a deletion or substitution of Cys residues involved in disulfide bonds between L chain-H chain molecules in the typical IgG antibody.
Hereinafter, unless otherwise particularly mentioned, the amino acid numbering is based on the EU index numbering as in Kabat et al. [Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services (1991)] (hereinafter, referred to as only EU index). In addition, the amino acid residue before substitution was described before a number, and the amino acid residue after substitution was described after the number.
In the present invention, the Cys residues involved in disulfide bonds between CL and CH typically refer to Cys residues that are needed to form intermolecular disulfide bonds between H chain and L chain of an antibody.
Therefore, the heterodimer protein of the present invention has a deletion or substitution of Cys residues that are included in CH of the first polypeptide and/or CL-Fc of the second polypeptide and also involved in disulfide bonds between L chain-H chain molecules in IgG antibody. Formation of unnecessary multimers can be reduced by the deletion or substitution of the Cys residues.
Examples of the Cys residues in L chain that are involved in disulfide bonds between CL and CH1 can include the Cys residue at position 214 of the EU index of human κ and λ chains.
Further, examples of the Cys residues in H chain that are involved in disulfide bonds between CL and CH1 can include the Cys residue at position 220 of human IgG1 and the Cys residue at position 131 of IgG4 antibody.
Further, deletion or substitution of amino acid residues is also possible. Therefore, substitution or deletion of the Cys residues of CH1 domain or hinge domain is also possible, together with substitution or deletion of the Cys residues included in CL.
In the heterodimer protein of the present invention, therefore, CH of the first polypeptide and CL-Fc of the second polypeptide are connected by disulfide bonds only in the hinge domain.
Further, the heterodimer protein of the present invention is a protein that is composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc prepared by fusion of CL and Fc, in which the second polypeptide is a polypeptide having a reduced binding activity for a CH binder.
In the present invention, the second polypeptide having a reduced or no binding activity for the CH binder and/or the Fc-binding protein refers to the second polypeptide having a reduced or no binding activity for the CH binder and/or the Fc binder by addition, deletion and/or substitution of amino acid sequence of CL-Fc of the second polypeptide.
The CH binder may be any one as long as it specifically binds to the antibody H chain constant region, such as proteins, chemicals, resins or the like, and examples thereof can include Fc-binding protein, antibody H chain constant region (CH)-binding antibody or the like.
Specific example of the Fc-binding protein can include Staphylococcus Aureus-derived Protein A, hemolytic Streptococcus-derived Protein G, Fc receptor, subclasses (FcγRI, IIA, IIB, IIIA, IIIB) thereof, binding fragments of the above proteins or the like.
The CH-binding antibody can be any antibody as long as it binds to at least one selected from CH1 domain, hinge domain, CH2 domain and CH3 domain, and it can be a monoclonal antibody or a polyclonal antibody.
CH1 domain is not included in the second polypeptide constituting the heterodimer of the present invention and CH1 domain is included in the first polypeptide. Therefore, the heterodimer protein of the present invention can be purified by using anti-CH1 antibody as the CH binder.
In the present invention, the second polypeptide having a reduced or no binding activity for the CH binder means that the binding activity is substantially reduced or depleted by a reduction in the affinity for the CH binder. The second polypeptide having a reduced or defective binding activity is a second polypeptide, of which binding activity for the CH binder is reduced or depleted by addition, deletion or substitution of amino acid residues in the second polypeptide having the binding activity for the CH binder, compared to the original second polypeptide having no addition, deletion or substitution of amino acid residues. The binding activity for the CH binder can be examined by using a measurement system such as binding ELISA, surface plasmon resonance method (SPR) or the like, described below.
Therefore, in the heterodimer protein of the present invention, the first polypeptide comprising CH specifically binds to the above described CH binder and the second polypeptide comprising g CL-Fc has a reduced or no binding activity for the CH binder, and thus only the heterodimer protein composed of the first polypeptide and the second polypeptide binds to the CH binder, and can be specifically separated and purified.
Herein, when the heterodimer protein of the present invention is expressed in cells, homodimers of the first polypeptide comprising CH are not secreted out of the cells. Monomers and homodimers of the second polypeptide comprising CL-Fc are secreted out of the cells, but since all of them have a reduced or no binding activity for the CH binder, by purification based on the specific binding activity for the CH binder, the heterodimer protein composed of the first polypeptide and the second polypeptide can be specifically separated and purified.
As the method for specifically expressing, separating, and purifying the heterodimer protein of the present invention without use of a CH binder, a fusion protein prepared by fusion of a proper tag with the N- or C-terminus of the first polypeptide of the present invention can be used.
Specific examples of the tag can include a histidine tag (hereinafter, abbreviated to His tag), a myc tag, a FLAG tag, a hemagglutinin (HA) tag, a glutathione-S transferase (GST) tag or the like. The above described method can be applied in combinations with separation and purification of the heterodimer protein of the present invention.
In the present invention, the second polypeptide having a reduced or no binding activity for the CH binder is prepared by performing addition, deletion and substitution of amino acid sequences of CL-Fc included in the second polypeptide.
Example of the CL-Fc having a reduced or no binding activity for Protein A can include CL-Fc having a deletion or substitution of at least one amino acid residue selected from positions 253, 310, 433, 435, and 436 of the EU index, preferably, CL-Fc having a substitution of the amino acid residue at position 435 of the EU index, and CL-Fc having a substitution of the amino acid residues at positions 435 and 436 of the EU index, and more preferably, CL-Fc having a substitution of His at position 435 with Arg and a substitution of Tyr at position 436 with Phe, and CL-Fc having a substitution of His at position 435 with Arg.
With respect to other CH-binding proteins, the binding activity for the CH-binding protein can be reduced by performing addition, deletion and substitution of amino acid sequence of CL-Fc of the heterodimer protein of the invention bound to the binding protein. For example, the second polypeptide having a reduced binding activity for each CH-binding protein or antibody can be prepared by performing substitution and/or deletion of at least one amino acid residue included in the epitope that is present on CL-Fc of the heterodimer protein of the present invention, such as the binding site in the Fc bound by Protein G, an epitope bound by anti-Fc antibody, and an epitope bound by anti-hinge domain antibody.
The antibody can be a polyclonal antibody or a monoclonal antibody. If the epitope is clearly specified by each antibody, amino acid residues included in the epitope of any antibody can be substituted.
Further, the heterodimer protein of the present invention is a protein that is composed of a first polypeptide comprising CH and a second polypeptide comprising CL-Fc prepared by fusion of CL and Fc, in which the second polypeptide is a polypeptide having a reduced binding activity for the CH binder, and also has a deletion or substitution of Cys residues involved in disulfide bonds between L chain-H chain molecules in the IgG antibody.
The heterodimer protein of the present invention is a protein composed of a first polypeptide comprising CH and a second polypeptide comprising CL-Fc prepared by fusion of CL and Fc, in which the second polypeptide is a polypeptide having a reduced binding activity for the CH binder and CH and CL-Fc are connected by disulfide bonds only in the hinge domain.
Specifically, the heterodimer protein of the present invention is a protein that is composed of a first polypeptide comprising CH and a second polypeptide comprising CL-Fc, in which the second polypeptide is any one polypeptide selected from the group consisting of (i) a polypeptide having a substitution of the amino acid residue at position 214 with other amino acid residue, (ii) a polypeptide having a substitution of the amino acid residue at position 220 with other amino acid residue, (iii) a polypeptide having a substitution of the amino acid residue at position 214 with Ser, (iv) a polypeptide having a substitution of the amino acid residue at position 220 with Ser, (v) a polypeptide having a substitution of the amino acid residue at position 435 with Arg, (vi) a polypeptide having substitutions of the amino acid residues at positions 214 and 435 with Ser and Arg, (vii) a polypeptide having substitutions of the amino acid residues at positions 220 and 435 with Ser and Arg, and (viii) a polypeptide having substitutions of the amino acid residues at positions 214, 435 and 436 with Ser, Arg and Phe, numbered of the EU index.
Further, the heterodimer protein of the present invention is a protein that is composed of the first polypeptide and the second polypeptide having a binding domain bound to at least one selected from the N-terminus and the C-terminus of CH and CL-Fc, in which the second polypeptide is a polypeptide having a reduced or no binding activity for the CH binder.
In the present invention, the binding domain can be any protein as long as it is a protein having a binding activity for other molecule, and specifically, it can include an antibody fragment, an antibody variable region (hereinafter, abbreviated to V), single chain Fv (scFv), Fab, Fab′, F(ab′)2, diabody, disulfide-stabilized Fv (dsFv) and a peptide comprising CDR, a single variable domain (VHH), a ligand protein, a receptor protein or the like.
CH included in the first polypeptide of the heterodimer protein of the present invention is composed of CH1 domain, hinge domain, CH2 domain and CH3 domain which constitute an antibody constant region. Any isotype is available, but IgG isotype is preferred.
The IgG subclass may be any subclass of IgG1, IgG2 and IgG4. Further, the first polypeptide can include a hinge domain of each immunoglobulin isotype/subclass, or a hinge domain having addition, deletion or substitution of a part of its amino acid sequence. A hinge domain of isotype/subclass identical to Fc and a hinge domain having substitution of the amino acid residue can be preferred. Further, the hinge domain can be extended or shortened to be suitable for the production of the heterodimer protein of the present invention.
In the present invention, the CH comprised in the first polypeptide can be a CH having any amino acid sequence as long as it is suitable for the efficient and stable production of the heterodimer protein, and preferably, a CH including addition, deletion and substitution of amino acid sequence.
Specifically, it can include CH including at least one amino acid residue substitution selected from substitutions of the amino acid residue at position 131 with S, the amino acid residue at position 133 with K, the amino acid residue at position 220 with S, the amino acid residue at position 228 with P, and the amino acid residue at position 409 with K, numbered of the EU index.
The number of the amino acid residue to be substituted is 1 to 15, preferably 1 to 10, more preferably 1 to several, and most preferably 1 to 5 amino acid residues. In the case of IgG1 subclass, CH including a substitution of C220S of the hinge domain can be exemplified.
The amino acid residue at position 220 of the EU index is known to be involved in the disulfide bond with L chain in IgG1, and the substitution or deletion of this amino acid residue can cause a defect in the disulfide bond of CL-hinge domain.
In the case of IgG4 subclass, CH including at least one amino acid residue substitution selected from C131S and R133K of CH1 domain, S228P of hinge domain, and R409K, R409T, R409M and R409L of CH3 domain, preferably CH including amino acid residue substitutions of C131S and R409K, more preferably, CH including amino acid residue substitutions of C131S, R133K and R409K, and CH including amino acid residue substitutions of C131S, R133K, S228P and R409K can be exemplified.
The amino acid residue at position 409 of the EU index is known to be involved in the stable interaction between CH3-CH3 domains of antibody Fc region, and thus the effect of improving stability of Fc-Fc interaction and the effects of inhibiting Fab-arm exchange and aggregation under low pH can be obtained by amino acid modifications of R409K, R409T, R409M and R409L.
Further, for the purpose of increasing the formation ability of CH3/CH3 heterodimers included in the heterodimer protein, amino acid residue modifications of K409D/K392D and D399K/E356K (WO 2009/089004) or SEED technology using immunoglobulin subclasses (WO 2007/110205) can be also combined in the heterodimer of the present invention.
The Ser residue at position 228 of the EU index is known to be involved in instability of disulfide bonds between hinge domains, and the amino acid modification of S228P is involved in stabilization of hinge domain.
CL included in the second polypeptide of the heterodimer protein of the present invention can be any one of κ chain and λ chain. Further, Fc included in the second polypeptide is composed of hinge domain, CH2 domain and CH3 domain. Any isotype is available, but IgG isotype is preferred. IgG subclass can be any subclass of IgG1, IgG2 and IgG4.
Further, the second polypeptide can include a hinge domain of each immunoglobulin isotype/subclass, or a hinge domain having addition, deletion or substitution of a part of its amino acid sequence. A hinge domain of isotype/subclass identical to Fc and a hinge domain having the amino acid residue substitution can be preferred. Further, the hinge domain can be extended or shortened to be suitable for the production of the heterodimer protein of the present invention.
In the present invention, the CL-Fc included in the second polypeptide can be CL-Fc having any amino acid sequence as long as it is suitable for the efficient and stable production of the heterodimer protein, and preferably, CL-Fc including addition, deletion and substitution in the amino acid sequence.
Specifically, it can include CL-Fc including at least one amino acid residue substitution selected from substitutions of the amino acid residue at position 214 with S, the amino acid residue at position 220 with S, the amino acid residue at position 228 with P, the amino acid residue at position 409 with K, the amino acid residue at position 435 with R, and the amino acid residue at position 436 with F, numbered of the EU index.
The number of the amino acid residue to be substituted is 1 to 15, preferably to 10, more preferably 1 to several, and most preferably 1 to 5 amino acid residues.
In the case of IgG1 subclass, CL-Fc including at least one amino acid residue substitution selected from C214S, C220S, H435R and Y436F, CL-Fc including an amino acid residue substitution of C220S at position 220 of the EU index, CL-Fc including a deletion of EPKSC at positions 216-220 of the EU index, preferably, CL-Fc including amino acid residue substitutions of C214S and H435R and CL-Fc including amino acid residue substitutions of C214S, C220S and H435R, and more preferably, CL-Fc including amino acid residue substitutions of C214S, H435R and Y436F and CL-Fc including amino acid residue substitutions of C214S, C220S, H435R and Y436F can be exemplified.
In the case of IgG4 subclass, CL-Fc including at least one amino acid residue substitution selected from C214S, S228P, L235E, R409K, H435R and Y436F, preferably, CL-Fc including amino acid residue substitutions of C214S and H435R and CL-Fc including amino acid residue substitutions of C214S, R409K and H435R, more preferably, CL-Fc including amino acid residue substitutions of C214S, R409K, H435R and Y436F, and most preferably, CL-Fc including amino acid residue substitutions of C214S, S228P, L235E, R409K, H435R and Y436F can be exemplified.
In the present invention, the monoclonal antibody is an antibody secreted by antibody-producing cells of a single clone. The monoclonal antibody recognizes only a single epitope (also called antigenic determinant), and the amino acid sequence (primary structure) constituting the monoclonal antibody is same.
Examples of the epitope can include a single amino acid sequence recognized and bound by a monoclonal antibody, a conformation of the amino acid sequence, an amino acid sequence bound with a modification residue such as a sugar chain, an amino group, a carboxyl group, phosphate, sulfate or the like, and a conformation of the amino acid sequence bound with the modification residue. The conformation is a naturally occurring three-dimensional structure of a protein, and it refers to a conformation of proteins that are expressed within cells or on cell membrane.
In the present invention, the antibody molecule is also called immunoglobulin (hereinafter, referred to as Ig) and human antibody is classified into the isotypes of IgA1, IgA2, IgD, IgE, IgG1, IgG2, IgG3, IgG4 and IgM, based on the difference in its molecular structure. IgG1, IgG2, IgG3 and IgG4 having relatively high homology in amino acid sequences are generically called IgG.
The antibody molecule is composed of polypeptides, called a heavy chain (hereinafter, referred to as H chain) and a light chain (hereinafter, referred to as L chain).
Further, the H chain is constituted by regions of an H chain variable region (also referred to as VH) and an H chain constant region (also referred to as CH) from its N-terminus, and the L chain is constituted by regions of an L chain variable region (also referred to as VL) and an L chain constant region (also referred to as CL) from its N-terminus. Regarding CH, α, δ, ε, γ and μ chains are known for each subclasses. Regarding CL, λ and κ are known.
A domain refers to a functional structural unit constituting each polypeptide of antibody molecules. Further, Fc and Fc region of the present invention refers to a partial sequence and a partial structure of H chain constant region composed of hinge domain, CH2 domain and CH3 domain.
Further, CH is composed of CH1 domain, hinge domain, CH2 domain and CH3 domain from the N-terminus. The CH1 domain, hinge domain, CH2 domain, CH3 domain, and Fc region in the present invention can be identified by the number of amino acid residues from the N-terminus according to the EU index [Kabat et al., Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services (1991)].
Specifically, CH1 is identified by the amino acid sequence from positions 118 to 215 of the EU index, the hinge is identified by the amino acid sequence from positions 216 to 230 of the EU index, CH2 is identified by the amino acid sequence from positions 231 to 340 of the EU index, and CH3 is identified by the amino acid sequence from positions 341 to 447 of the EU index, respectively.
CL-Fc is composed of CL domain, hinge domain, CH2 domain and CH3 domain from the N-terminus. CL-Fc in the present invention can be identified by the number of amino acid residues from the N-terminus according to the EU index [Kabat et al., Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services (1991)].
Specifically, CL of CL-Fc is identified by the amino acid sequence from positions 108 to 214 of L chain defined by Kabat et al., Fc of CL-Fc is identified as the hinge of the amino acid sequence from positions 216 to 230 of the EU index, CH2 of the amino acid sequence from positions 231 to 340 of the EU index, and CH3 of the amino acid sequence from positions 341 to 447 of the EU index, respectively.
In the present invention, the antibody includes recombinant antibodies produced by a recombination technology as well as monoclonal antibodies obtained from hybridomas. The recombinant antibodies include a chimeric antibody that is prepared by binding a human antibody constant region to a non-human antibody variable region, a humanized antibody (or CDR-grafted antibody) that is prepared by grafting the complementarity determining region (hereinafter, abbreviated to CDR) of H chain and L chain of a non-human antibody variable region into a framework region (hereinafter, abbreviated to FR) of a human antibody variable region, and a human antibody that is prepared by using a human antibody-producing animal, or the like.
The chimeric antibody can be produced by obtaining cDNAs encoding VH and VL from a monoclonal antibody-producing hybridoma derived from a non-human animal, inserting them into an expression vector for animal cell having DNA encoding CH and CL of human antibody so as to construct a human chimeric antibody expression vector, and then introducing the vector into an animal cell so as to express the antibody.
The humanized antibody refers to an antibody in which the amino acid sequence of CDRs of VH and VL of a non-human animal antibody are grafted into the corresponding CDRs of VH and VL of a human antibody. The region other than CDRs of VH and VL is referred to as a framework region (hereinafter, referred to as FR).
The humanized antibody can be produced in the following manner: cDNA encoding an amino acid sequence of VH which consists of an amino acid sequence of CDR of VH of a non-human antibody and an amino acid sequence of FR of VH of any human antibody, and cDNA encoding an amino acid sequence of VL which consists of an amino acid sequence of CDR of VL of a non-human animal antibody and an amino acid sequence of FR of VL of any human antibody are constructed, these cDNAs are inserted respectively into expression vectors for animal cells having DNA encoding CH and CL of a human antibody so as to construct a humanized antibody expression vector, and this vector is introduced into animal cells so as to express the antibody.
The human antibody originally refers to an antibody naturally existing in the human body. However, the human antibody also includes antibodies that are obtained from a human antibody phage library, cloning of immortalized human peripheral blood lymphocytes, or human antibody-producing transgenic animals prepared according to the technical advancement in genetic engineering, cell engineering, and development engineering in recent years.
The human antibody can be obtained by immunizing a mouse having human immunoglobulin genes (Tomizuka K. et al., Proc Natl Acad Sci USA. 97, 722-7, 2000) with a desired antigen. In addition, by selecting a human antibody having a desired binding activity using a phage display library which is formed by antibody gene amplification from human B cells, it is possible to obtain human antibodies without performing immunization (Winter G. et al., Annu Rev Immunol. 12: 433-55. 1994).
Moreover, by immortalizing human B cells using an EB virus to prepare human antibody-producing cells having a desired binding activity, it is possible to obtain human antibodies (Rosen A. et al., Nature 267, 52-54. 1977).
The antibody existing in the human body can be purified in the following manner, for example; lymphocytes isolated from the human peripheral blood are immortalized by infection with the EB virus or the like, followed by cloning, whereby lymphocytes producing the antibody can be cultured and the antibody can be purified from the culture.
The human antibody phage library is a library of phages which are caused to express antibody fragments such as Fab and scFv on the surface thereof by insertion of antibody genes prepared from the human B cells into the gene of the phage. From this library, it is possible to recover phages which express antibody fragments having a desired antigen binding activity, by using binding activity with respect to an antigen-immobilized substrate as an index. The antibody fragments can be also converted into a human antibody molecule consisting of two complete H chains and two complete L chains by genetic engineering technique.
The human antibody-producing transgenic animal refers to an animal obtained by integration of the human antibody gene into chromosomes of a host animal. Specifically, the human antibody gene is introduced to mouse ES cells, the ES cells are grafted to the early embryo of another mouse, and then the embryo is developed, whereby the human antibody-producing transgenic animal can be prepared.
As a method of preparing human antibodies from the human antibody-producing transgenic animal, a human antibody-producing hybridoma is obtained by a normal hybridoma preparation method which is implemented using a mammal other than a human being, followed by culture, whereby human antibodies can be produced and accumulated in the culture.
The amino acid sequences of VH and VL bound to the heterodimer protein of the present invention can be any one of amino acid sequences of VH and VL of a human antibody, amino acid sequences of VH and VL of a non-human animal antibody, amino acid sequence of a humanized antibody that is prepared by grafting CDR of a non-human animal antibody into the framework of a human antibody, and amino acid sequences of VH and VL derived from a human antibody.
Specifically, it can include amino acid sequences of VH and VL of a non-human animal antibody, a humanized antibody, and a human antibody that are produced by hybridomas or antibody-producing cells.
The amino acid sequence of CL in the heterodimer protein of the present invention can be any one of the amino acid sequence of human antibody or the amino acid sequence of non-human animal antibody. The amino acid sequence of Cκ or Cλ of human antibody is preferred.
CH in the heterodimer protein of the present invention can be any one belonging to immunoglobulin. Preferably, any of γ1(IgG1), γ2(IgG2), and γ4(IgG4) belongs to human IgG class can be used.
In the present invention, the antibody fragment can include Fab, Fab′, F(ab′)2, scFv, diabody, dsFv, a peptide comprising plural CDRs, and preferably, a peptide comprising 6 CDRs of an antibody, or the like.
Fab refers to an antibody fragment having about a half H-chain of the N-terminus and a full L-chain which are bound to each other via a disulfide bond (S—S bond), a molecular weight of about 50000 and an antigen binding activity, among fragments (cleaved at position 224 of the amino acid residue of the H-chain) which are obtained by treating the IgG antibody with a protease papain.
F(ab′)2 refers to an antibody fragment which is slightly longer than Fab bound to each other via a S—S bond of the hinge region and has a molecular weight of about 100,000 and an antigen binding activity, among fragments (cleaved at position 234 of the amino acid residue of the H-chain) which are obtained by treating IgG with a protease pepsin.
Fab′ is an antibody fragment which is obtained by cleaving the S—S bond of the hinge region of the F(ab′)2 and has a molecular weight of about 50,000 and an antigen binding activity.
scFv is an antibody fragment having an antigen binding activity, which is a VH-P-VL or VL-P-VH polypeptide obtained by linking one VH to one VL by using an appropriate peptide linker (P), such as a linker peptide prepared by linking an arbitrary number of linker (G4S) consisting of 4 Gly residues and 1 Ser residue.
Diabody is an antibody fragment as a dimer formed of scFVs showing the same or different antigen binding specificity, and this antibody fragment has a divalent antigen binding activity with respect to the same antigen or has 2 types of specific antigen binding activity with respect to different types of antigens.
dsFv is one in which 1 amino acid residue in each of VH and VL is substituted with a cystine residue, and the polypeptides are linked through a S—S bond between these cysteine residues.
The peptide comprising CDR is constituted with at least one or more regions of CDR of VH or VL. In the peptide comprising plural CDRs, the CDRs can be bound to each other directly or via an appropriate peptide linker.
It can be prepared by constructing DNAs encoding CDRs of VH and VL of the heterodimer protein of the present invention, inserting these DNAs into an expression vector for prokaryote or eukaryote, and introducing this expression vector into prokaryote or eukaryote for expression. The peptide comprising CDR can be also prepared by chemical synthesis method such as an Fmoc method or a tBoc method.
The heterodimer protein of the present invention can be any one of a heterodimer protein, in which two antibody variable regions formed by the first polypeptide and the second polypeptide bind to two different epitopes, and a heterodimer protein, in which two antibody variable regions bind to the same epitope, respectively.
Further, a heterodimer protein comprising a binding protein that is further bound at least one of the C-terminus of the above described CH and CL-Fc and binding to two or more epitopes is also included in the present invention.
2. Control of Heterodimer Protein Activity
(1) Control of Effector Activity
Since the heterodimer of the present invention has Fc region composed of hinge domain, CH2 domain and CH3 domain, an effector activity depending on the Fc region of the heterodimer protein can be also provided. The effector activity of the heterodimer of the present invention can be controlled by various methods.
The effector activity refers to an antibody-dependent activity that is mediated by the Fc region of an antibody. As the effector activity, antibody-dependent cellular cytotoxicity activity (ADCC activity), complement-dependent cytotoxicity activity (CDC activity), and antibody-dependent phagocytosis (ADP activity) caused by phagocytes such as macrophages, dendritic cells or the like are known. In the present invention, the ADCC and CDC activities can be measured using known measurement methods [Cancer Immunol. Immunother., 36, 373 (1933)].
The ADCC activity refers to an activity in which an antibody bound to an antigen on a target cell binds to an Fc receptor of an immunocyte via the Fc region of the antibody, thereby activating the immunocyte (a natural killer cell or the like) and damaging the target cell.
The Fc receptor (hereinafter, referred to as FcR in some cases) refers to a receptor binding to the Fc region of an antibody, and induces various types of effector activity due to the binding of an antibody.
FcR corresponds to antibody subclasses, and IgG, IgE, IgA, and IgM specifically bind to FcγR, FcεR, FcαR, and FcμR respectively. FcγR has subtypes including FcγRI(CD64), FcγRII(CD32) and FcγRIII(CD16), and the subtypes respectively have isoforms including FcγRIA, FcγRIB, FcγRIC, FcγRIIA, FcγRIIB, FcγRIIC, FcγRIIIA, FcγRIIIB. These different types of FcγR exist on different cells [Annu Rev. Immunol. 9:457-492 (1991)].
In human beings, FcγRIIIB is specifically expressed in neutrophils, and FcγRIIIA is expressed in monocytes, Natural Killer cells (NK cells), and a portion of T cells. The antibody binding caused via FcγRIIIA induces NK cell-dependent ADCC activity.
The CDC activity refers to an activity in which an antibody bound to an antigen on a target cell activates a series of cascades (complement activation pathways) consisting of a group of complement-related proteins in the blood, thereby damaging the target cell. By the protein fragments generated due to the complement activation, it is possible to induce migration and activation of immunocytes.
When C1q having a binding domain for the Fc region of an antibody binds to the Fc region, and C1r and C1s as two serine proteases bind thereto, a C1 complex is formed, whereby the cascade of CDC activity begins.
The method for controlling the effector activity of the heterodimer protein of the present invention can be exemplified as follows.
Examples of methods of controlling the effector activity of the heterodimer protein can include a method of controlling the amount of fucose (also referred to as core fucose) which forms α1,6-bound to N-acetylglucosamine (GlcNAc) present in a reducing end of a complex type N-linked sugar chain (hereinafter, simply abbreviated to complex sugar chain in some cases) bound to Asn at position 297 of the EU index using the amino acid sequence of Fc of IgG1 subclass as Fc of the heterodimer protein of the present invention (WO 2005/035586, WO 2002/31140, WO 00/61739), or a method of controlling the activity by substituting amino acid residues of Fc region of the antibody.
1) Control of Effector Activity by Modification of Sugar Chains
The effector activity of the heterodimer protein can be increased or decreased by controlling the content of fucose that is added to N-acetylglucosamine in the reducing end of the complex sugar chain bound to the Fc region of the heterodimer protein.
The method for decreasing the content of fucose binding to the complex-type N-linked sugar chain bound to the Fc region of the heterodimer protein can be the method to obtain the heterodimer protein with no fucose binding thereto by expressing an antibody using CHO cell from which α1,6-fucosyltransferase gene (FUT8) is deleted. The heterodimer protein with no fucose binding thereto has high ADCC activity.
On the other hand, the method for increasing the content of fucose binding to the complex-type N-linked sugar chain bound to the Fc region of the heterodimer protein can be the method to obtain the heterodimer protein with fucose binding thereto by expressing the heterodimer protein using a host cell in which α1,6-fucosyltransferase gene is introduced. The heterodimer protein with fucose binding thereto has lower ADCC activity than the heterodimer protein with no fucose binding thereto.
In the Fc region of the heterodimer protein of the present invention, the N-linked sugar chain is bound to the Asn residue at position 297 of the EU index, but there is no report that sugar chain is bound to the Asn residue of other Fc region. Therefore, two N-glycoside linked sugar chains are typically bound to one molecule of the heterodimer protein.
The known N-linked sugar chains are high mannose type, complex type and hybrid type sugar chains. As long as the N-linked sugar chain has no fucose binding thereto, it has higher ADCC activity than the sugar chain with fucose binding thereto.
The complex-type sugar chain bound to the Fc region of the heterodimer protein of the present invention can include a sugar chain in which one or more of N-acetylglucosamine (GlcNAc) or galactose-N-acetylglucosamine (hereinafter, referred to as Gal-GlcNAc) are α1-2- or α1-4-linked to mannose (Man) at the non-reducing end of the core structure (tri-mannosyl core structure).
It can also include a complex-type sugar chain having sialic acid, bisecting N-acetylglucosamine (hereinafter, referred to as bisecting GlcNAc), or the like at the non-reducing end of Gal-GlcNAc.
In the present invention, the core-fucose or α1,6-fucose refers to a sugar chain structure in which the 1-position of fucose (hereinafter, referred to as Fuc in some cases) is bound to the 6-position of N-acetylglucosamine (hereinafter, referred to as GlcNAc in some cases) in the reducing end through α-bond of a complex type N-glycoside-linked sugar chain. Further, those having no core fucose bound to N-acetylglucosamine in the reducing end of the complex type N-glycoside-linked sugar chain are simply referred to as sugar chains with no fucose or no core fucose.
In the present invention, the core structure or the tri-mannosyl core structure refers to a Manα1-6(Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc structure.
As the sugar chain bound to the heterodimer protein of the present invention, a biantennary N-glycoside linked complex sugar chain (also called biantennary complex sugar chain) is represented by the following Chemical Formula.




The heterodimer protein composition of the present invention is a heterodimer protein molecule having the Fc region in which the complex-type sugar chain is bound to Asn at position 297 of the heterodimer protein molecule, and as long as it has the above sugar structure, it can be composed of heterodimer protein molecules having a single or plural different sugar chains.
In other words, the heterodimer protein composition of the present invention means a composition that is composed of heterodimer protein molecules having a single or plural different sugar chains, and specifically, a heterodimer protein, in which the sugar chain with no fucose bound to N-acetylglucosamine at the reducing end of the sugar chain among the total N-glycoside linked sugar chains bound to the Fc region included in the heterodimer protein is 20% or more.
The ratio of the sugar chain with no core fucose can be any ratio in the heterodimer protein composition, as long as ADCC activity of the heterodimer protein is increased. The ratio can be preferably 20% or more, more preferably 51%-100%, much more preferably 80%-100%, particularly preferably 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, and most preferably 100%.
The heterodimer protein composition having 50% of the ratio of the sugar chain with no core fucose can be any of a heterodimer protein composition comprising 100% of molecules with no fucose at one sugar chain of the N-glycoside linked sugar chains bound to the first and second polypeptides of the heterodimer protein molecule, and a heterodimer protein composition comprising 50% of molecules with no fucose at both sugar chains of the N-glycoside linked sugar chains bound to the first and second polypeptides of the heterodimer protein molecule and 50% of molecules with fucose at both sugar chains of the N-glycoside linked sugar chains bound to the first and second polypeptides of the heterodimer protein molecule.
In the present invention, the sugar chain with no fucose can have any structure of the sugar chain at the non-reducing end, as long as fucose does not bind to N-acetylglucosamine at the reducing end in the above Chemical Formula.
In the present invention, no fucose (no core fucose) bound to N-acetylglucosamine at the reducing end of the sugar chain means that fucose is not substantially bound. The heterodimer protein composition in which “fucose is not substantially bound” means a heterodimer protein composition in which fucose cannot be substantially detected in the sugar chain analysis described below. The “fucose cannot be substantially detected” means that it is below the detection limit. The heterodimer protein composition with no core fucose in all of the sugar chains has the highest ADCC activity.
The ratio of heterodimer protein molecules having sugar chains with no fucose contained in the composition which is composed of a heterodimer protein molecule having the Fc region bound with complex-type N-glycoside-linked sugar chains can be determined by releasing the sugar chains from the heterodimer protein molecule using a known method such as hydrazinolysis or enzyme digestion [Biochemical Experimentation Methods 23—Method for Studying Glycoprotein Sugar Chain (Japan Scientific Societies Press), edited by Reiko Takahashi (1989)], carrying out fluorescence labeling or radioisotope labeling of the released sugar chains and then separating the labeled sugar chains by chromatography.
Also, the ratio of heterodimer protein molecules bound with sugar chains with no fucose contained in the composition which is composed of a heterodimer protein molecule having the Fc region bound with complex-type sugar chains can be determined by analyzing the released sugar chains with the HPAED-PAD method [J. Liq. Chromatogr., 6, 1577 (1983)].
2) Control of Effector Activity by Substitution of Amino Acid Residues
The ADCC, ADCP, and CDC activities of the heterodimer protein of the present invention can be increased or decreased by changing antibody subclass of Fc constituting the heterodimer protein or by substituting the amino acid residues of Fc.
For example, CDC activity of the antibody can be increased by using the amino acid sequence of the Fc region, which is described in US Patent Application Publication No. 2007/0148165. Also, ADCC activity or CDC activity of the heterodimer protein can be increased or decreased by carrying out substitution of the amino acid residues, which is described in U.S. Pat. Nos. 6,737,056, 7,297,775, and 7,317,091.
Specific amino acid residue substitution for increasing ADCC activity may include P247I, A339D, F243L, R292P, Y300L, P396L, T393A, H433P, S239D, S298A, A330L, I332E, E333A, K334A or the like. Meanwhile, specific amino acid residue substitution for reducing ADCC activity can include L235E, P238A, N297A, K322A, P331S or the like.
Specific amino acid residue substitution for increasing CDC activity can include at least one amino acid residue substitution selected from K326A, S267E, H268F, S324T, K274Q, N276K, Y296F, Y300F, K326W, K326Y, E333A, E333S, A339T, D356E, L358M, N384S, K392N, T394F, T394Y, V397M and V422I.
CDC activity can be increased in combinations of two or more of amino acid residue substitutions, and amino acid residues to be substituted can be increased depending on the purpose. Preferably, the amino acid residue substitution for increasing CDC activity can include at least one amino acid residue substitution selected from N276K, A339T, T394F and T394Y, amino acid residue substitutions of N276K and A339T, and amino acid residue substitutions of K274Q, N276K, Y296F, Y300F, A339T, D356E, L358M, N384S, V397M and V422I, or the like. Meanwhile, specific amino acid residue substitution for reducing CDC activity can include L235E, N297A, K322A, P329A and P331S or the like.
The blood half-life can be also prolonged by introduction of amino acid mutations of T250Q, M428L, M252Y, S254T, T256E, or the like, into Fc of human IgG1 subclass. Cell cytotoxicity such as ADCC activity, ADCP activity, CDC activity can be also reduced by using Fc in which N-linked sugar chain is removed by introduction of amino acid mutation at position N297, Fc of human IgG2 or IgG4 subclass, chimeric Fc of IgG2 and IgG4, or the like.
Further, binding activity for the inhibitory Fc receptor FcγRIIb can be increased by introduction of amino acid mutation of G236D, L328F, S239D, S267E, or the like into human IgG1.
The heterodimer protein of the present invention includes any of the heterodimer proteins having increased or reduced effector activity described above.
Specifically, the IgG1-type heterodimer protein of the present invention can be a heterodimer protein composed of the first polypeptide comprising CH of IgG1 antibody and the second polypeptide comprising Fc and CL of IgG1, and also any one of IgG1-type heterodimer proteins of the following (1) to (9).
(1) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes a substitution of H435R
(2) a heterodimer protein, in which the first polypeptide includes no amino acid substitution and the second polypeptide includes substitutions of C214S and H435R of the EU index
(3) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes substitutions of C214S and H435R
(4) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes substitutions of C220S, C214S and H435R
(5) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes substitutions of C214S and H435R and a deletion of EPKSC of 216-220 of the EU index
(6) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes substitutions of C214S, H435R and Y436F
(7) a heterodimer protein, in which the first polypeptide includes a substitution of C220S of the EU index and the second polypeptide includes substitutions of C214S, H435R, Y436F and a deletion of EPKSC of 216-220 of the EU index
(8) a heterodimer protein, in which the first polypeptide includes substitutions of C220S, K322A and P331S of the EU index and the second polypeptide includes substitutions of C214S, K322A, P331S, H435R, Y436F and a deletion of EPKSC of 216-220 of the EU index
(9) a heterodimer protein, in which the first polypeptide includes substitutions of C220S and I332E of the EU index and the second polypeptide includes substitutions of C214S, I332E, H435R and Y436F and a deletion of EPKSC of 216-220 of the EU index
Specifically, the IgG4-type heterodimer protein of the present invention can be a heterodimer protein composed of the first polypeptide comprising CH of IgG4 antibody and the second polypeptide comprising Fc and CL of IgG4 and also any one of IgG4-type heterodimer proteins of the following (1) to (10).
(1) a heterodimer protein, in which the first polypeptide includes a substitution of C131S of the EU index and the second polypeptide includes substitutions of C214S and H435R
(2) a heterodimer protein, in which the first polypeptide includes a substitution of C131S of the EU index and the second polypeptide includes substitutions of C214S, H435R and Y436F
(3) a heterodimer protein, in which the first polypeptide includes substitutions of C131S and R409K of the EU index and the second polypeptide includes substitutions of C214S, R409K, H435R and Y436F
(4) a heterodimer protein, in which the first polypeptide includes substitutions of C131S, S228P and R409K of the EU index and the second polypeptide includes substitutions of C214S, S228P, R409K, H435R and Y436F
(5) a heterodimer protein, in which the first polypeptide includes substitutions of C131S, S228P, L235E and R409K of the EU index and the second polypeptide includes substitutions of C214S, S228P, L235E, R409K, H435R and Y436F
(6) a heterodimer protein, in which the first polypeptide includes substitutions of C131S and R133K of the EU index and the second polypeptide includes substitutions of C214S and H435R
(7) a heterodimer protein, in which the first polypeptide includes substitutions of C131S and R133K of the EU index and the second polypeptide includes substitutions of C214S, H435R and Y436F.
(8) a heterodimer protein, in which the first polypeptide includes substitutions of C131S, R133K and R409K of the EU index and the second polypeptide includes substitutions of C214S, R409K, H435R and Y436F
(9) a heterodimer protein, in which the first polypeptide includes substitutions of C131S, R133K, S228P and R409K of the EU index and the second polypeptide includes substitutions of C214S, S228P, R409K, H435R and Y436F
(10) a heterodimer protein, in which the first polypeptide includes substitutions of C131S, R133K, S228P, L235E and R409K of the EU index and the second polypeptide includes substitutions of C214S, S228P, L235E, R409K, H435R and Y436F
(2) Control of Binding Activity of Heterodimer Protein
The heterodimer protein of the present invention can be prepared into a heterodimer protein having a monovalent to tetravalent binding activity by connecting a molecule-specific binding protein to the N-terminus and C-terminus of each polypeptide of CH and CL-Fc (hereinafter, heterodimer scaffold protein; referred to as HSP in some cases) constituting the heterodimer molecule.
Therefore, the heterodimer protein of the present invention can be a heterodimer protein comprising HSP composed of CH and CL-Fc, in which at least one binding protein is bound to HSP (FIGS. 2A and 2B).
The heterodimer protein having a monovalent binding domain of the present invention (hereinafter, referred to as monovalent antibody or monomeric antibody in some cases) can include a monovalent antibody composed of a first polypeptide and a second polypeptide, in which VH and VL are bound to the N-terminus of CH and CL-Fc, respectively, and a monovalent antibody composed of a first polypeptide in which scFv is bound to the N-terminus of CH and a second polypeptide of CL-Fc.
The heterodimer protein having a divalent binding domain of the present invention (hereinafter, referred to as bispecific antibody or divalent antibody in some cases) can include a bispecific antibody composed of a first polypeptide and a second polypeptide, in which a first scFv and a second scFv are bound to the N-terminus of CH and CL-Fc, respectively, and a bispecific antibody composed of a first polypeptide in which VH is bound to the N-terminus of CH and scFv is bound to the C-terminus thereof, and a second polypeptide in which VL is bound to the N-terminus of CL-Fc (FIG. 2B). Further, it can include a heterodimer protein having a divalent binding activity in which scFv is bound to the N-terminus of the above described monovalent antibody.
The heterodimer protein having a trivalent or tetravalent binding domain of the present invention (hereinafter, referred to as trivalent or tetravalent antibody in some cases) can include a trivalent or tetravalent antibody in which three to four scFvs are bound to the N-terminus and C-terminus of CH and CL-Fc. Further, it can include a heterodimer protein having a trivalent binding activity in which the first scFv and the second scFv are bound to the N-terminus of the above described monovalent antibody.
Because the monovalent antibody of the present invention binds to one epitope, it does not cause the effect such as cross-linkage of antigens and does not cause unnecessary activities related to antigen cross-linkage.
Hereinafter, the preparation method of the heterodimer protein composition of the present invention will be described in detail.
3. Preparation Method of Heterodimer Protein Composition
The preparation method of the heterodimer protein of the present invention can be a preparation method comprising the following processes of (i) to (iii).
(i) a process of introducing into cells a vector including DNA encoding the first polypeptide comprising CH and a vector including DNA encoding the second polypeptide comprising CL-Fc having a reduced binding activity for the CH binder.
(ii) a process of culturing the cells and recovering the culture supernatant.
(iii) a process of binding the heterodimer protein to the CH binder for purification.
More specifically, for example, in the process of preparing the production cells for preparing the heterodimer protein of (1) described above, a process of adding a substitution of C131S of the EU index to the first polypeptide and adding any one selected from a substitution of C214S, a substitution of C220S, and substitutions of H435R and Y436F, of the EU index to the second polypeptide is properly performed according to the subclass of the antibody constant region included in the heterodimer protein.
More specifically, a process of adding a substitution of C131S of the EU index to the first polypeptide and a substitution of H435R of the EU index to the second polypeptide, adding substitutions of C214S and H435R of the EU index, substitutions of C220S and H435R of the EU index, or substitutions of C214S, H435R and Y436F of the EU index to the second polypeptide can be exemplified.
Further, the preparation method of the heterodimer protein of the present invention can include the following processes of (i) to (v).
(i) a process of reducing or deleting the binding activity of the second polypeptide for the CH binder in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of deleting or substituting the Cys residues involved in disulfide bonds between CH and CL of the heterodimer protein.
(iii) a process of introducing into cells the vector including DNA encoding the first polypeptide comprising CH and the vector including DNA encoding the second polypeptide comprising CL-Fc having a reduced binding activity for the CH binder.
(iv) a process of culturing the cells and recovering the culture supernatant.
(v) a process of binding the heterodimer protein to the CH binder for purification.
The heterodimer protein composition of the present invention can be obtained by expressing it in a host cell using the methods described in Molecular Cloning, Second Edition Current protocols in molecular biology, Antibodies, A Laboratory manual, Cold Spring Harbor Laboratory, 1988, Monoclonal Antibodies: principles and practice, Third Edition, Acad. Press, 1993, Antibody Engineering, A Practical Approach, IRL Press at Oxford University Press, 1996 or the like, for example, in the following manner.
(1) Construction of Expression Vector for Heterodimer Protein Composition of the Present Invention
The expression vector for heterodimer protein composition of the present invention is an expression vector for animal cells into which genes encoding the first polypeptide and the second polypeptide of the heterodimer protein molecule included in the heterodimer protein composition of the present invention are introduced.
The vector for expressing the heterodimer protein composition can be constructed by cloning each of the genes encoding the first and second polypeptides of the heterodimer protein molecule included in the heterodimer protein composition into an expression vector for animal cells.
The gene encoding the first polypeptide constituting the heterodimer protein molecule included in the heterodimer protein composition of the present invention can be prepared by preparing an amino acid sequence in which an amino acid sequence of the desired binding protein is linked to the N-terminus or C-terminus of antibody H chain constant region (CH).
In the same manner, the gene encoding the second polypeptide can be prepared by preparing an amino acid sequence in which an amino acid sequence of the desired binding protein is linked to the N-terminus or C-terminus of CL-Fc prepared by fusion of antibody L chain constant region (CL) and Fc.
Also, the total DNA can be synthesized by using synthetic DNAs and synthesis using polymerase chain reaction (PCR) is also possible (Molecular Cloning, Second Edition). Furthermore, the gene encoding the heterodimer protein can be produced in combinations of plural these techniques.
Specifically, when an IgG4-type monovalent antibody having a monovalent binding domain is prepared as the heterodimer protein of the present invention, an amino acid sequence is designed by adding amino acid substitutions of C131S/R133K/S228P/L235E/R409K to the amino acid sequence of CH of human IgG4 antibody, and the amino acid sequence of VH is linked to the N-terminus of the amino acid sequence of IgG4-CH to prepare an amino acid sequence of the first polypeptide.
Meanwhile, an amino acid sequence is designed by adding amino acid substitutions of C214S/S228P/L235E/R409K/H435R/Y436F to IgG4-CL-Fc that is prepared by linking the amino acid sequence of human CLκ and the amino acid sequences of hinge domain, CH2 domain and CH3 domain of human IgG4 antibody, and an amino acid sequence of the second polypeptide in which the amino acid sequence of VL is linked to the N-terminus of the amino acid sequence thereof, is prepared. Nucleotide sequences of DNA encoding the prepared amino acid sequences of the first and second polypeptides are prepared and inserted into an expression vector for animal cells, thereby preparing an expression vector for the monovalent antibody of the present invention.
When an animal cell is used as a host, any expression vector can be used as long as it exhibits its functions in animal cells, and examples thereof can include pcDNAI, pAGE107 [Japanese Patent Publication No. H3-22979; Cytotechnology, 3, 133 (1990)], pAS3-3 (Japanese Patent Publication No. H2-227075), pCDM8 [Nature, 329, 840 (1987)], pcDNAI/Amp (manufactured by Invitrogen), pcDNA 3.1 (manufactured by Invitrogen), pREP4 (manufactured by Invitrogen), pAGE103 [J. Biochemistry, 101, 1307 (1987)], pAGE210, pME18SFL3, pKANTEX93 (WO 97/10354), N5KG1val (U.S. Pat. No. 6,001,358), To12 transposon vector (WO 2010/143698) or the like.
As a promoter, any promoter can be used as long as it exhibits its functions in animal cells, and examples thereof may include the promoter of immediate early (IE) gene of cytomegalovirus (CMV), the SV40 early promoter, the promoter of a retrovirus, the metallothionein promoter, the heat shock promoter, the SRα promoter, the promoter or enhancer of Moloney murine leukemia virus. The enhancer of IE gene of human CMV may be also used in combination with the promoter.
The expression vector for the heterodimer protein composition of the present invention can be either of a type in which the gene encoding the antibody H chain and L chain exist on separate vectors or a type in which they exist on the same vector (hereinafter, referred to as tandem type).
(2) Acquisition of cDNA Encoding Variable Region of Antibody
cDNAs encoding VH and VL of any antibody can be obtained in the following manner.
A cDNA is synthesized by using mRNA as a template, which is extracted from a hybridoma cell producing any antibody. The synthesized cDNA is inserted into a vector such as a phage or a plasmid to obtain a cDNA library.
Each of a recombinant phage or recombinant plasmid having a cDNA encoding VH and a recombinant phage or recombinant plasmid having a cDNA encoding VL is isolated from the above library by using DNA encoding the constant region or variable region of a known antibody as the probe. Full length nucleotide sequences of VH and VL of the desired antibody on the recombinant phage or recombinant plasmid are determined, and full length amino acid sequences of VH and VL are deduced from the nucleotide sequences.
Hybridoma cells producing any non-human animal antibody can be obtained by immunizing a non-human animal with an antigen to be bound by the antibody and hybridomas are prepared from antibody-producing cells of the immunized animal and myeloma cells according to a known method [Molecular Cloning, Second Edition Current protocols in molecular biology, Antibodies, A Laboratory manual, Cold Spring Harbor Laboratory, 1988, Monoclonal Antibodies: principles and practice, Third Edition, Acad. Press, 1993, Antibody Engineering, A Practical Approach, IRL Press at Oxford University Press, 1996]. Subsequently, single cell cloned hybridomas are selected, cultured and the antibody is purified from the culture supernatant.
As the non-human animal, any animal can be used as long as hybridoma cells can be prepared from the animal such as mouse, rat, hamster, rabbit or the like.
The methods for preparing total RNA from a hybridoma cell may include, for example, the guanidine thiocyanate-cesium trifluoroacetate method [Methods in Enzymol., 154, 3 (1987)] and an RNeasy kit (manufactured by QIAGEN). The methods for preparing mRNA from the total RNA may include the oligo (dT) immobilized cellulose column method [Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Lab. Press New York, 1989] or the like.
Further, examples of the kits for preparing mRNA from a hybridoma cell may include a Fast Track mRNA Isolation Kit (manufactured by Invitrogen), a Quick Prep mRNA Purification Kit (manufactured by Pharmacia) or the like.
The methods for synthesizing the cDNA and preparing the cDNA library may include conventional methods (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Lab. Press New York, 1989; Current Protocols in Molecular Biology, Supplement 1-34], or methods using commercially available kits, for example, SuperScript (registered trade name) Plasmid System for cDNA Synthesis and Plasmid Cloning (manufactured by GIBCO BRL), ZAP-cDNA Synthesis Kit (manufactured by Stratagene) or the like.
In preparation of the cDNA library, the vector for integrating the cDNA that is synthesized using the mRNA extracted from a hybridoma cell as a template may be any vector as long as the cDNA can be integrated.
For example, ZAP Express (Strategies, 5, 58, 1992), pBluescript II SK(+) (Nucleic Acids Research, 17, 9494, 1989), λZAP II (manufactured by Stratagene), λgt10, λgt11 (DNA Cloning: A Practical Approach, I, 49, 1985), Lambda BlueMid (manufactured by Clontech), λExCell, pT7T3 18U (manufactured by Pharmacia), pcD2 (Mol. Cell. Biol., 3, 280, 1983), pUC18 (Gene, 33, 103, 1985) or the like may be used.
As Escherichia coli for introducing the cDNA library constructed with a phage or plasmid vector, any one can be used as long as the cDNA library can be introduced, expressed and maintained.
For example, XL1-Blue MRF (Strategies, 5,81,1992), C600 (Genetics, 39, 440, 1954), Y1088, Y1090 (Science, 222, 778, 1983), NM522 (Journal of Molecular Biology; J. Mol. Biol., 166, 1, 1983), K802(J. Mol. Biol., 16, 118, 1966), JM105(Gene, 38, 275, 1985) or the like may be used.
The methods for selecting the cDNA clones encoding VH and VL of a non-human animal antibody from the cDNA library can include colony hybridization or plaque hybridization (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Lab. Press New York, 1989) using an isotope- or fluorescence-labeled probe.
It is also possible to prepare the cDNAs encoding VH and VL by preparing primers and carrying out PCR (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Lab. Press New York, 1989; Current Protocols in Molecular Biology, Supplement 1-34) using the cDNA or cDNA library as a template.
The nucleotide sequences of the cDNAs selected by the above methods can be determined by cleaving the cDNAs with appropriate restriction enzymes, cloning it into a plasmid such as pBluescript II SK(−) (manufactured by Stratagene), and then analyzing it by generally employed nucleotide sequence analyzing methods, for example, the dideoxy method of Sanger, et al. (Proc. Natl. Acad. Sci., U.S.A., 74, 5463, 1977) or by use of nucleotide sequence autoanalyzers, for example, ABI PRISM 377 DNA Sequencer (manufactured by Applied Biosystems).
The full length of amino acid sequences of VH and VL are deduced from the determined nucleotide sequences and compared with the full length of amino acid sequences of VH and VL of a known antibody (Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, 1991), whereby it can be confirmed whether the obtained cDNAs encode amino acid sequences which completely include VH and VL of the antibody comprising secretory signal sequences.
Further, when the amino acid sequence of an antibody variable region or the nucleotide sequence of DNA encoding the variable region is already known, it can be obtained by the following methods.
When the amino acid sequence is known, the DNA can be obtained by designing a nucleotide sequence of DNA encoding the variable region taking into consideration the frequency of codon usage (Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, 1991), synthesizing several synthetic DNAs composed of approximately 100 to 150 bases based on the designed nucleotide sequence of DNA, and carrying out PCR using them or synthesizing complete length of DNA sequence. When the nucleotide sequence is known, the DNA can be obtained by the same method described above based on the information.
(3) Analysis of Amino Acid Sequence of Variable Region of Antibody
By comparing the full length of amino acid sequences of VH and VL of the antibody comprising secretory signal sequences with the amino acid sequences of VH and VL of a known antibody (Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, 1991), it is possible to deduce the length of the secretory signal sequences and the N-terminus amino acid sequences and further to know the subgroup to which the antibody belongs. In addition, the amino acid sequences of CDRs of VH and VL can be determined in a similar manner.
(4) Construction of cDNA Encoding Variable Region of Humanized Antibody
cDNAs encoding VH and VL of the humanized antibody can be constructed in the following manner. First, amino acid sequences of framework regions (hereinafter, referred to as FR) of VH and VL of the human antibody for grafting CDRs of VH and VL of the desired non-human animal antibody are selected. The amino acid sequences of FRs of VH and VL of the human antibody can be any of those from human antibodies.
Examples thereof can include the amino acid sequences of FRs of VHs and VLs of human antibodies registered at databases such as Protein Data Bank, the amino acid sequences common to subgroups of FRs of VHs and VLs of human antibodies (Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, 1991) or the like.
In order to prepare the humanized antibody having a sufficient activity among them, it is preferred to select amino acid sequences having a homology as high as possible (at least 60% or more) with the amino acid sequences of FRs of VH and VL of the desired non-human animal antibody.
Next, the amino acid sequences of CDRs of VH and VL of the desired non-human animal antibody are grafted to the selected amino acid sequences of FRs of VH and VL of the human antibody to design amino acid sequences of VH and VL of the humanized antibody. The designed amino acid sequences are converted into nucleotide sequences of DNA taking into consideration the codon usage in the nucleotide sequences of antibody genes (Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services, 1991), and nucleotide sequences of DNA encoding the amino acid sequences of VH and VL of the humanized antibody are designed. The designed DNA sequences are fully synthesized.
Cloning into the expression vector for the heterodimer protein composition of the present invention constructed in the above 3(1) can be easily carried out by introducing recognition sequences for appropriate restriction enzymes to the 5′-terminals of synthetic DNAs present on both ends. After PCR, the amplification products are cloned into a plasmid such as pBluescript II SK(−) (manufactured by Stratagene) and the nucleotide sequences are determined by the method described in the above 3(2) to obtain a plasmid having the nucleotide sequences of DNA that encode the amino acid sequences of VH and VL of the desired humanized antibody.
(5) Modification of Amino Acid Sequence of Variable Region of Humanized Antibody
It is known that a humanized antibody prepared merely by grafting only CDRs of VH and VL of a non-human animal antibody to FRs of VH and VL of a human antibody has a reduced antigen-binding activity, compared with the original non-human animal antibody (BIO/TECHNOLOGY, 9, 266, 1991).
This is probably because in VH and VL of the original non-human animal antibody, not only CDRs but also some of the amino acid residues in FRs are involved directly or indirectly in the antigen-binding activity, and such amino acid residues are changed to different amino acid residues of FRs of VH and VL of the human antibody by CDR grafting.
In order to solve this problem, attempts have been made with regard to a humanized antibody to raise the lowered antigen-binding activity by identifying the amino acid residues in the amino acid sequences of FRs of VH and VL of the human antibody which are directly relating to the binding to an antigen or which are indirectly relating to it through interaction with amino acid residues of CDRs or maintenance of the conformation of the antibody, and modifying such amino acid residues to those derived from the original non-human animal antibody (BIO/TECHNOLOGY, 9, 266, 1991).
In the preparation of the humanized antibody, it is most important to efficiently identify the amino acid residues of FR which are relating to the antigen-binding activity. The conformations of antibodies have been generated and analyzed by X ray crystallography (J. Mol. Biol., 112, 535, 1977), computer modeling (Protein Engineering, 7, 1501, 1994) or the like.
Such information of the conformations of antibodies have provided much useful information for the preparation of humanized antibodies. However, there is no established method for preparing a humanized antibody that is adaptable to any type of antibodies. At present, it is still necessary to make trial-and-error approaches, e.g., preparation of several variants for each antibody and examination of the correlation with the antigen-binding activity among antibody variants.
Modification of the amino acid residues in FRs of VH and VL of a human antibody can be achieved by PCR as described in the above 3(4) using synthetic DNAs for modification. The nucleotide sequence of the PCR amplification product is determined by the method described in the above 3(2) to confirm that the desired modification has been achieved.
(6) Expression of Heterodimer Protein
Transformants capable of transiently or stably producing the heterodimer protein can be obtained by introducing the heterodimer protein expression vectors of the above 3(1) into appropriate animal cells.
The heterodimer protein of the present invention is a protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc, in which Cys residues involved in disulfide bonds between CL and CH1 are deleted or substituted, and the amount of the multimers of the heterodimer protein is remarkably reduced in the host cells introduced with the expression vector. Therefore, the heterodimer protein of the present invention is a molecule that can efficiently form a heterodimeric structure composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
Further, the present invention includes a method for reducing multimers of heterodimer protein by deleting or substituting Cys residues involved in disulfide bonds between CL and CH1 in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(6-a) Transient Expression of Heterodimer Protein
The heterodimer protein expression vectors obtained in (3) and (6) or expression vectors obtained by modifying those vectors are used for transient expression of the heterodimer protein. In this manner, it is possible to efficiently evaluate the antigen binding activity of the various types of prepared heterodimer proteins.
Any type of cell can be used as the host cell to which the expression vector is introduced, as long as it is a host cell which can express the heterodimer protein, and for example, COS-7 cell [American Type Culture Collection (ATCC) No. CRL1651] can be used (Methods in Nucleic Acids Res., CRC press, 283, 1991).
For introducing an expression vector to COS-7 cell, a DEAE dextran method (Methods in Nucleic Acids Res., CRC press, 1991), a lipofection method [Proc. Natl. Acad. Sci. USA, 84, 7413 (1987)], or the like is used.
After the introduction of the expression vector, the expression amount and the antigen binding activity of the heterodimer protein in the culture supernatant are measured by ELISA (Monoclonal Antibodies-Principles and practice, Third edition, Academic Press (1996), Antibodies—A Laboratory Manual, Cold Spring Harbor Laboratory (1988), Manual for Monoclonal Antibody Experiment, Kodansha Scientific Ltd. (1987) or the like.
(6-b) Stable Expression of Heterodimer Protein
Transformants capable of stably expressing the heterodimer protein can be obtained by introducing the heterodimer protein expression vectors obtained in (1) into appropriate host cells.
Any method can be used as the method of introducing the expression vector into the host cell as long as it is the method of introducing a DNA into host cells. Examples thereof can include electroporation (Cytotechnology, 3, 133 (1990)), a calcium phosphate method (Japanese Patent Publication No. H2-227075), a lipofection method (Proc. Natl. Acad. Sci. U.S.A., 84, 7413, 1987), an injection method [Manipulating the Mouse Embryo A Laboratory Manual], a method using a particle gun (gene gun) (Japanese Patent Nos. 2606856 and 2517813), a DEAE-dextran method [Biomanual Series 4-Methods of Gene Transfer, Expression and Analysis (Yodosha), edited by Takashi Yokota and Kenichi Arai (1994)] and a virus vector method (Manipulating Mouse Embryo, Second Edition) or the like.
The host cells introduced with the heterodimer protein expression vector can be any cells as long as they are able to express the heterodimer protein. Human leukemia cell Namalwa cells, monkey COS cells, Chinese hamster CHO cells, HBT5637 (Japanese Patent Publication No. S63-299), rat myeloma cells, mouse myeloma cells, cells derived from Syrian hamster kidney, embryonic stem cells, fertilized egg cells, or the like can be used.
Specific examples thereof can include PER.C6, CHO-K1 (ATCC CCL-61), DUKXB11 (ATCC CCL-9096), Pro-5 (ATCC CCL-1781), CHO-S (Life Technologies, Cat #11619), Lec13 cell, rat myeloma cell YB2/3HL.P2.G11.16Ag. 20 (ATCC NO. CRL1662, or also called YB2/0), mouse myeloma cell NS0, mouse myeloma cell SP2/0-Ag14 (ATCC NO. CRL1581), mouse P3X63-Ag8.653 cell (ATCC NO. CRL1580), dihydroforate reductase gene (hereinafter, referred to as dhfr)-deficient CHO cell (CHO/DG44) [Proc. Natl. Acad. Sci. USA, 77, 4216 (1980)], Syrian Hamster cell BHK, HBT563 cell, substrains of the above cell lines and cells prepared by adapting the above cell lines, in serum free medium or under non-adhesion culture conditions, or the like.
In the present invention, as a cell used for the production of the heterodimer protein, a cell reducing or deleting the amount of core fucose of the sugar chain bound to Asn at position 297 of the EU index in the Fc region can be used. Specifically, cells in which an enzyme relating to the synthesis of GDP-L-fucose, an enzyme relating to transport of GDP-L-fucose to Golgi body, or an enzyme relating to the binding of a core fucose is reduced or deleted can be selected, or cells obtained by various artificial methods can be used as host cells.
Specifically, a cell in which a core fucose is controlled can be prepared by a method for decreasing or deleting an enzyme activity relating to the sugar chain modification of a core fucose, a method for increasing an activity of a core fucose cleavage enzyme, or the like.
Examples of the enzyme relating to the sugar chain modification of a core fucose can include an enzyme relating to the synthesis or transport of GDP-L-fucose, and an enzyme relating to the binding of a core fucose to a complex type N-glycoside-linked sugar chain.
Specific examples of the enzyme relating to the synthesis of GDP-L-fucose or the transport to Golgi body can include GDP-mannose 4,6-dehydratase (hereinafter referred to as GMD), GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase (hereinafter referred to as Fx), GDP-beta-L-fucose pyrophosphorylase (GFPP), fucokinase, GDP-L-fucose transporter or the like.
Examples of the enzymes relating to the binding of core fucose can include α1,6-fucosyltransferase (hereinafter referred to as FUT8), or the like.
The cell for producing the heterodimer protein of the present invention can include a cell in which one of the above enzyme activities is decreased or deleted or a cell in which plural enzyme activities in the above are decreased or deleted.
The method for decreasing or deleting the above enzyme activity can include
(a) technique of gene disruption targeting a gene of the enzyme;
(b) technique of introducing a dominant-negative mutant of the gene of the enzyme;
(c) technique of introducing a mutation into the enzyme;
(d) technique of suppressing transcription or translation of the gene of the enzyme;
(e) technique of electing a cell line resistant to a lectin which recognizes a sugar chain structure in which 1-position of fucose is bound to 6-position of N-acetylglucosamine at the reducing end of a N-glycoside-linked sugar chain through α-bond; or the like.
The lectin can include lectin binding to α1,6 fucose, such as lentil lectin LCA (lentil agglutinin derived from Lens culinaris), pea lectin PSA (pea lectin derived from Pisum sativum), broad bean lectin VFA (agglutinin derived from Vicia faba), Aleuria aurantia lectin AAL (lectin derived from Aleuria aurantia) or the like.
Specific examples of the cell can include FUT8 gene-deficient CHO cell (WO 2005/035586, WO 2002/31140, WO 2000/061739), lectin resistance-acquired Lec13 (Somatic Cell and Molecular genetics, 12, 55, 1986), GDP-fucose transporter gene-deficient cell (WO 2003/085102), GDP-mannose 4,6-dehydratase (GMD) gene-deficient cell (WO 2002/31140), WGA lectin resistant cell, LCA lectin resistant cell (WO 2002/31140) or the like.
In addition to the above described method, the heterodimer protein composition in which high mannose type N-linked sugar chain binds and the amount of core fucose is reduced can be expressed by inhibiting an enzyme relating to N-linked sugar chain synthesis system, such as mannosidase I, mannosidase II or the like.
Further, by using a host cell overexpressing N-acetylglucosamine transferase III (GnTIII), the heterodimer protein composition to which a bisecting GlcNAc-binding complex and hybrid sugar chains bind, and in which the amount of core fucose is reduced, can be produced.
After introduction of the expression vector, transformants that stably express the heterodimer protein are selected by culturing them in a medium for animal cell culture containing an agent such as G418 sulfate (hereinafter, referred to as G418), cycloheximide (hereinafter, abbreviated to CHX), methotrexate (hereinafter, abbreviated to MTX) or the like (Japanese Patent Publication No. H2-257891).
The medium for animal cell culture can include RPMI1640 medium (manufactured by Invitrogen), GIT medium (manufactured by NIHON PHARMACEUTICAL CO.), EX-CELL301 medium, EX-CELL302, EX-CELL325 medium (manufactured by JRH), IMDM medium (manufactured by Invitrogen), Hybridoma-SFM medium (manufactured by Invitrogen), media obtained by adding various additives such as fetal bovine serum (hereinafter abbreviated to FBS) to these media, or the like.
The heterodimer protein can be expressed and accumulated in a culture supernatant by culturing the obtained transformants in a medium. The expression amount and antigen binding activity of the heterodimer protein in the culture supernatant can be measured by ELISA or the like. Also, the expression amount of the heterodimer protein produced by the transformant can be increased by using a dhfr gene amplification system or the like (Japanese Patent Publication No. H2-257891).
The method for expressing the heterodimer protein composition using an animal cell as the host has been described, but the heterodimer protein composition can also be produced in yeast, an insect cell, a plant cell, an animal individual or a plant individual in the same manner as in the animal cell based on the known technology.
When yeast is used as the host cell, a microorganism belonging to Saccharomyces, Schizosaccharomyces, Kluyveromyces, Trichosporon, Schwanniomyces or the like, for example, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces lactis, Trichosporon pullulans, Schwanniomyces alluvius or the like can be exemplified.
Introduction of the recombinant vector can be carried out by any of the methods for introducing DNA into yeast, for example, electroporation (Methods Enzymol., 194, 182 (1990)), the spheroplast method (Proc. Natl. Acad. Sci. USA, 84, 1929 (1978)), the lithium acetate method (J. Bacteriology, 153, 163 (1983)), the method described in Proc. Natl. Acad. Sci. USA, 75, 1929 (1978) or the like.
When an insect cell is used as the host cell, the heterodimer protein can be expressed by, for example, the methods described in current Protocols in Molecular Biology; Baculovirus Expression Vectors, A Laboratory Manual, W.H. Freeman and Company, New York, 1992), Bio/Technology, 6,47,1988 or the like.
Therefore, if the host cell has an ability to express the heterodimer protein molecule, the heterodimer protein composition of the present invention can be produced by introducing the gene of the heterodimer protein into the host cells described below, culturing the cells and then purifying the desired heterodimer protein composition from the culture.
Further, the heterodimer protein composition can be produced using an animal individual into which a gene is introduced (non-human transgenic animal) or a plant individual into which a gene is introduced (transgenic plant), which is constructed by redifferentiating the animal or plant cells into which genes are introduced.
When the transformant is an animal individual or a plant individual, the heterodimer protein composition can be produced by rearing or cultivating them in a usual manner, allowing the heterodimer protein composition to form and accumulate therein, and collecting the heterodimer protein composition from the animal individual or plant individual.
Examples of the production method of the heterodimer protein composition using an animal individual can include a method of producing the desired heterodimer protein composition in an animal constructed by introducing the gene according to known methods [American Journal of Clinical Nutrition, 63, 639S, 1996; American Journal of Clinical Nutrition, 63, 627S, 1996; Bio/Technology, 9, 830, 1991].
In the case of an animal individual, the heterodimer protein composition can be produced, for example, by raising a non-human transgenic animal into which DNA encoding the heterodimer protein molecule is introduced, allowing the heterodimer protein composition to form and accumulate in the animal, and collecting the heterodimer protein composition from the animal.
The places for formation and accumulation in the animal can include, for example, milk (Japanese Patent Publication No. S63-309192), egg or the like of the animal. As the promoter in this process, any promoters capable of expressing it in an animal can be used. For example, mammary gland cell-specific promoters such as α casein promoter, β casein promoter, β lactoglobulin promoter, whey acidic protein promoter or the like are preferably used.
Examples of the production method of the heterodimer protein composition using a plant individual can include a method of cultivating a transgenic plant into which DNA encoding the heterodimer protein molecule is introduced according to known methods [Tissue Culture, 20 (1994); Tissue Culture, 21 (1995); Trends in Biotechnology, 15, 45 (1997)], allowing the heterodimer protein composition to form and accumulate in the plant, and collecting the heterodimer protein composition from the plant.
(7) Purification of Heterodimer Protein
When the host cells introduced with the heterodimer protein expression vector are cultured, homodimer proteins composed of the two second polypeptides and heterodimer proteins composed of the first polypeptide and the second polypeptide are produced. The heterodimer protein of the present invention is a protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc, in which the second polypeptide is also a polypeptide having a reduced or no binding activity for the CH-binder, and therefore, the heterodimer protein including the first polypeptide binding to the CH binder can be only specifically separated and purified.
Therefore, the purification method used in the present invention includes a process of binding the heterodimer protein to the CH binder and a process of eluting the heterodimer protein. That is, the purification method of the heterodimer protein of the present invention can be a purification method comprising the following processes of (i) to (iii).
(i) a process of reducing or deleting the binding activity of the second polypeptide for the CH binder in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of binding the heterodimer protein to the CH binder.
(iii) a process of eluting the heterodimer protein.
More specifically, for example, in the process of preparing the cells for production of the heterodimer protein of (i) described above, a process of adding any one selected from a substitution of C214S, a substitution of C220S, a substitution of H435R and a substitution of Y436F, of the EU index to the second polypeptide can be properly performed according to the subclass of the antibody constant region included in the heterodimer protein.
Specific examples thereof can include a process of adding substitutions of C214S and H435R of the EU index, substitutions of C220S and H435R of the EU index, or substitutions of C214S, H435R and Y436F of the EU index to the second polypeptide, or the like.
Further, the purification method of the heterodimer protein of the present invention can be a purification method comprising the following processes of (i) to (iv).
(i) a process of reducing or deleting the binding activity of the second polypeptide for the CH binder in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of deleting or substituting Cys residues involved in disulfide bonds between CH and CL of the heterodimer protein.
(iii) a process of binding the heterodimer protein to the CH binder.
(iv) a process of eluting the heterodimer protein.
In the present invention, the formation of halfmers and/or multimers of the heterodimer protein of the present invention can be reduced by deleting or substituting Cys residues involved in disulfide bonds between CH and CL during the above described production process (i).
The method for reducing the formation of halfmers of the heterodimer protein of the present invention can be a method for reducing the formation of halfmers of the heterodimer protein comprising the following processes of (i) to (iii).
(i) a process of introducing a substitution of R409K of the EU index in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of binding the heterodimer protein to the CH binder.
(iii) a process of purifying the heterodimer protein.
The present invention can include a method for reducing the formation of multimers of the heterodimer protein comprising the following processes of (i) to (iii).
(i) a process of deleting or substituting Cys residues involved in disulfide bonds between CH and CL in the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of binding the heterodimer protein to the CH binder.
(iii) a process of purifying the heterodimer protein.
The method for reducing the formation of halfmers and multimers of the heterodimer protein of the present invention may be a method for reducing the formation of halfmers of the heterodimer protein comprising the following processes of (i) to (iv).
(i) a process of deleting or substituting Cys residues involved in disulfide bonds between CH and CL of the heterodimer protein composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc.
(ii) a process of introducing a substitution of R409K of the EU index.
(iii) a process of binding the heterodimer protein to the CH binder.
(iv) a process of purifying the heterodimer protein.
More specifically, for example, in the process of preparing the cells for production of the heterodimer protein of (i) or (ii) described above, a process of adding any one selected from substitution of C214S of the EU index, substitution of C220S, substitution of R409K, and substitution of H435R to the second polypeptide can be properly performed according to the subclass of the antibody constant region included in the heterodimer protein.
More specifically, for example, a process of adding substitutions of C214S, R409K and H435R of the EU index, substitutions of C220S, R409K and H435R of the EU index, or substitutions of C214S, R409K, H435R and Y436F of the EU index to the second polypeptide can be performed.
The heterodimer protein of the present invention can be purified in the following manner. The heterodimer protein composition that is prepared by the transformant introduced with the gene encoding the heterodimer protein molecule can be obtained as follows. For example, when the heterodimer protein composition is expressed as a soluble protein within the cells, the cells are recovered by centrifugation after culturing is completed, suspended in an aqueous buffer and then disrupted using a ultrasonicator, a French press, a Manton Gaulin homogenizer, a dynomill or the like to obtain a cell-free extract.
From the supernatant that is obtained by centrifugation of the cell-free extract, a purified product of the heterodimer protein composition can be obtained by general enzyme isolation and purification techniques such as solvent extraction, salting-out using ammonium sulfate or the like, desalting, precipitation using an organic solvent, anion exchange chromatography using a resin such as diethylaminoethyl (DEAE) sepharose or DIAION HPA-75 (manufactured by Mitsubishi Chemical Corporation), cation exchange chromatography using a resin such as S-Sepharose FF (manufactured by Pharmacia), hydrophobic chromatography using a resin such as butyl-sepharose or phenyl-sepharose, gel filtration using a molecular sieve, affinity chromatography, chromatofocusing, electrophoresis such as isoelectric focusing electrophoresis, or the like which can be used alone or used in combination.
In the present invention, as the affinity chromatography, affinity chromatography using a CH binder is used (Monoclonal Antibodies-Principles and practice, Third edition, Academic Press (1996), Antibodies—A Laboratory Manual, Cold Spring Harbor Laboratory, 1988).
Further, when the heterodimer protein composition is expressed within cells by forming an inclusion body, the cells are recovered, disrupted and centrifuged in the same manner, and the inclusion body of the heterodimer protein composition is recovered as a precipitation fraction. The recovered inclusion body of the heterodimer protein composition is solubilized with a protein denaturing agent. The heterodimer protein composition is made into a normal conformation by diluting or dialyzing the solubilized solution, and then a purified product of the heterodimer protein composition is obtained by the same isolation and purification method as above.
When the heterodimer protein composition is secreted extracellularly, the heterodimer protein composition or the derivative thereof can be recovered from the culture supernatant. That is, the culture is treated by a method such as centrifugation in the same manner as above to obtain a culture supernatant, a purified product of the heterodimer protein composition can be obtained from the culture supernatant by the same isolation and purification method as above.
Specifically, the CH binder or Fc binder can be any one as long as it binds to CH or Fc, such as proteins, resins or the like, and examples thereof can include Fc-binding proteins, antibodies bound to H chain constant region (CH) of an antibody or the like.
Specific example of the Fc-binding protein can include Staphylococcus Aureus-derived Protein A, hemolytic Streptococcus-derived Protein G, Fc receptor, the subclasses (FcγRI, IIA, IIB, IIIA, IIIB), binding fragments thereof, or the like.
Examples of the CH-binding antibody can include antibodies binding to CH1 domain, hinge domain, CH2 domain or CH3 domain.
In the present invention, the CH binder can include more preferably Protein A, Protein G, anti-CH1 antibody and binding fragments thereof.
As the purification method of the heterodimer protein of the present invention, for example, the supernatant obtained by culturing the transformed cell line prepared in 3(6) is loaded on Protein A column or Protein G column, and then this column is washed with phosphate buffer saline, (hereinafter, abbreviated to PBS).
Thereafter, the heterodimer protein is eluted from the column using a citrate buffer of low pH (pH 2.0 to 6.0) or the like, the eluate was neutralized with alkaline Tris buffer or the like. The neutralized eluate was subjected to dialysis using a sufficient amount of PBS, or the like, to obtain the purified heterodimer protein.
The molecular weight of the purified heterodimer protein molecule can be measured by polyacrylamide gel electrophoresis [Nature, 227, 680 (1970)], Western blotting [Monoclonal Antibodies—Principles and practice, Third edition, Academic Press (1996), Antibodies—A Laboratory Manual, Cold Spring Harbor Laboratory (1988)] or the like.
4. Evaluation of Activity of Heterodimer Protein Composition
The protein amount, FcR binding activity, C1q binding activity, antigen binding activity or cytotoxic activity, such as ADCC activity and CDC activity of the purified heterodimer protein composition can be measured using the known methods, for example, described in Molecular Cloning 2nd Edition, Current Protocols in Molecular Biology, Antibodies, A Laboratory manual, Cold Spring Harbor Laboratory, 1988, Monoclonal Antibodies: principles and practice, Third Edition, Acad. Press, 1993, Antibody Engineering, A Practical Approach, IRL Press at Oxford University Press, 1996 or the like.
Specifically, the binding activity of the heterodimer protein composition to an antigen or an antigen-positive cultured cell line can be measured by ELISA, the fluorescent antibody technique (Cancer Immunol. Immunother, 36, 373, 1993) or the like. The cytotoxic activity to the cultured cell line which is antigen-positive can be evaluated by measuring CDC activity, ADCC activity, or the like [Cancer Immunol. Immunother, 36, 373, 1993, US Patent Application Publication No. 2004/0259150].
The FcR binding activity of the heterodimer protein composition of the present invention can be confirmed by producing a recombinant FcγRIIIA protein or a recombinant neonatal Fc receptor (FcRn) and then measuring a binding activity (US Patent Application Publication No. 2004/0259150).
Example of the method for measuring ADCC activity can include a method in which a target cell labeled with a radioisotope, a fluorescent substance, a dye or the like is allowed to contact with the heterodimer protein and an effector cell, and then the activity of the labeled substance released from the injured target cell is measured or the biological activity of an enzyme released therefrom is measured.
Example of the method for measuring CDC activity can include a method in which a target cell labeled with a radioisotope, a fluorescent substance, a dye or the like is allowed to contact with the heterodimer protein and a biological sample such as serum containing a complement component, and then the activity of the labeled substance released from the injured target cell or the biological activity of an enzyme released therefrom is measured.
5. Sugar Chain Analysis of Heterodimer Protein Composition
The sugar chain structure of the heterodimer protein molecule expressed in various cells can be analyzed according to general methods of analyzing the sugar chain structure of glycoprotein. For example, a sugar chain bound to an IgG molecule consists of neutral sugars such as galactose (Gal), mannose (Man), or fucose (Fuc), amino sugars such as N-acetylglucosamine (GlcNAc), and acidic sugars such as sialic acid (Sial), and can be analyzed by techniques such as sugar chain structure analysis using sugar composition analysis and two-dimensional sugar chain mapping.
(1) Analysis of Neutral Sugar and Amino Sugar Compositions
The sugar chain composition of the heterodimer protein composition can be analyzed by carrying out acid hydrolysis of sugar chains with trifluoroacetic acid or the like to release neutral sugars or amino sugars and by analyzing the composition ratio.
Specifically, the analysis can be carried out, for example, by a method using a sugar composition analysis device manufactured by Dionex. BioLC is a device for analyzing the sugar composition by HPAEC-PAD (high performance anion-exchange chromatography-pulsed amperometric detection) (J. Liq. Chromatogr., 6, 1577 (1983)].
Further, the composition ratio can also be analyzed by the fluorescence labeling method using 2-aminopyridine. Specifically, the composition ratio can be calculated by fluorescence labeling an acid-hydrolyzed sample by 2-aminopyridylation according to a known method [Agric. Biol. Chem., 55(1), 283-284 (1991)] and then analyzing the composition by HPLC.
(2) Analysis of Sugar Chain Structures
The sugar chain structures of the heterodimer protein composition can be analyzed by two-dimensional sugar chain mapping [Anal. Biochem., 171, 73, 1988, Biochemical Experimentation Methods 23—Methods of Studies on Glycoprotein Sugar Chains (Japan Scientific Societies Press) Reiko Takahashi (1989)]. The two-dimensional sugar chain mapping is a method of deducing a sugar chain structure, for example, by plotting the retention time or elution position of a sugar chain by reversed phase chromatography as the X axis and the retention time or elution position of the sugar chain by normal phase chromatography as the Y axis, respectively, and comparing them with the results of known sugar chains.
Specifically, a sugar chain is released from the heterodimer protein by hydrazinolysis of the heterodimer protein and subjected to fluorescence labeling with 2-aminopyridine (hereinafter, abbreviated to PA) (J. Biochem., 95, 197, 1984). After being separated from an extra PA-treating reagent by gel filtration, the sugar chain is subjected to reversed phase chromatography. Then, each peak of the fractionated sugar chain is subjected to normal phase chromatography. The sugar chain structure can be deduced by plotting the obtained results on a two-dimensional sugar chain map and comparing them with the spots of a sugar chain standard (manufactured by TaKaRa) or those in the document (Anal. Biochem., 171, 73, 1988).
Further, the structure deduced by the two-dimensional sugar chain mapping can be confirmed by carrying out mass spectrometry, e.g., MALDI-TOF-MS, of each sugar chain.
The portion to which a sugar chain is bound in Fc region of the heterodimer protein can be confirmed by treating the heterodimer protein that is subjected to reductive alkylation with endoprotease such as trypsin, pepsin, Lys-C or Asp-N, and separating it using reverse phase chromatography (LC) to analyze them using a mass spectrometer (MS).
Namely, it can be confirmed whether a sugar chain is actually bound or not by checking if the molecular weights of obtainable peptides by protease treatment and the molecular weight of peptide to which a sugar chain is bound correspond to analysis values of MS based on the amino acid sequence of the objective Fc region of the heterodimer protein.
6. Method for Determining Sugar Chain Structure of Heterodimer Protein Molecule
The heterodimer protein composition is composed of heterodimer protein molecules that are different in sugar chain structures bound to Asn at position 297 in the Fc region of the heterodimer protein. The heterodimer protein composition in which the ratio of sugar chains with no core fucose among the total complex-type N-glycoside-linked sugar chains which bind to Fc of the heterodimer protein composition of the present invention is 20% or more, shows high ADCC activity. Such a heterodimer protein composition can be determined using the method for analyzing the sugar chain structure of the heterodimer protein molecule described in the above 5. Further, it can also be determined by an immunological quantitative method using lectins.
Determination of the sugar chain structure of the heterodimer protein molecule by an immunological quantitative method using lectins can be made according to the immunological quantitative method such as Western staining, RIA (radioimmunoassay), VIA (viroimmunoassay), EIA (enzyme immunoassay), FIA (fluoroimmunoassay) and MIA (metalloimmunoas say) described in the document [Monoclonal Antibodies: Principles and Applications, Wiley-Liss, Inc. (1995); Enzyme Immunoassay, 3rd Ed., IGAKU-SHOIN Ltd. (1987); Enzyme Antibody Technique, Revised Edition, Gakusai Kikaku (1985)], for example, in the following manner.
A lectin recognizing the sugar chain structure of the heterodimer protein molecule included in the heterodimer protein composition is labeled, and the labeled lectin is subjected to the reaction with the sample heterodimer protein composition, followed by measurement of the amount of a complex of the labeled lectin with the heterodimer protein molecule.
Examples of the lectin used for identifying the sugar chain structure of the heterodimer protein molecule can include WGA (T. vulgaris-derived wheat-germ agglutinin), ConA (C. ensiformis-derived concanavalin A), RIC (R. communis-derived toxin), L-PHA (P. vulgaris-derived leukoagglutinin), LCA (L. culinaris-derived lentil agglutinin), PSA (P. sativum-derived Pea lectin), AAL (Aleuria aurantia Lectin), ACL (Amaranthus caudatus Lectin), BPL (Bauhinia purpurea Lectin), DSL (Datura stramonium Lectin), DBA (Dolichos biflorus Agglutinin), EBL (Elderberry Balk Lectin), ECL (Erythrina cristagalli Lectin), EEL (Euonymus europaeus Lectin), GNL (Galanthus nivalis Lectin), GSL (Griffonia simplicifolia Lectin), HPA (Helix pomatia Agglutinin), HHL (Hippeastrum Hybrid Lectin), Jacalin, LTL (Lotus tetragonolobus Lectin), LEL (Lycopersicon esculentum Lectin), MAL (Maackia amurensis Lectin), MPL (Maclura pomifera Lectin), NPL (Narcissus pseudonarcissus Lectin), PNA (Peanut Agglutinin), E-PHA (Phaseolus vulgaris Erythroagglutinin), PTL (Psophocarpus tetragonolobus Lectin), RCA (Ricinus communis Agglutinin), STL (Solanum tuberosum Lectin), SJA (Sophora japonica Agglutinin), SBA (Soybean Agglutinin), UEA (Ulex europaeus Agglutinin), VVL (Vicia villosa Lectin), WFA (Wisteria floribunda Agglutinin).
Lectin specifically recognizing the core fucose is preferably used, and specific examples thereof can include lentil lectin LCA (lentil agglutinin derived from Lens culinaris), pea lectin PSA (pea lectin derived from Pisum sativum), broad bean lectin VFA (agglutinin derived from Vicia faba), Aleuria aurantia lectin AAL (lectin derived from Aleuria aurantia) or the like.
7. Use of Heterodimer Protein Composition of the Present Invention
With respect to the heterodimer protein composition of the present invention, the heterodimer proteins having monovalent to tetravalent binding activity can be prepared by connecting a molecule-specific binding protein to the N-terminus and the C-terminus of the CH and CL-Fc (heterodimer scaffold protein; HSP) constituting the heterodimer protein molecule.
Therefore, the heterodimer protein composition of the present invention can be used as a heterodimer protein drug, because it can be tailored to have a molecular shape for the target antigen.
For example, if the heterodimer protein of the present invention is a monovalent antibody having a monovalent binding domain, it binds to one epitope of the target at 1:1, and thus does not cause cross-linkage of the antigen and is able to inhibit antigen activation and antigen activity.
Further, if the heterodimer protein of the present invention is a divalent antibody (also called bispecific antibody) having a divalent binding activity, it binds to two epitopes, thereby causing cross-linkage of two antigens or it binds to two antigens expressed on different cells, thereby causing cell-cell cross-linkage.
Further, when the heterodimer protein of the present invention causes cell-cell cross-linkage, immune cells can be collected around the target cells and activated by cross-linking an antigen on the target cell with an antigen on the surface of cells such as cytotoxic T cells (CTL), B cells, NK cells, macrophages, neutrophils, eosinophils, basophilis, and mast cells.
The antigen binding to the heterodimer protein of the present invention may be any antigen, and preferably include antigen molecules associated with cancer, immune diseases, allergic diseases or cardiovascular diseases. Examples thereof may include cytokines, chemokines, growth factors and receptors thereof, CD antigens or the like.
Examples of the cytokines or the growth factors can include interferon (hereinafter, referred to as IFN)-α, IFN-β, IFN-γ, interleukin (hereinafter, referred to as IL)-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-12, IL-13, IL-15, IL-17, IL-18, IL-21, IL-23, IL-27, granulocyte colony-stimulating factor (G-CSF), granulocyte/macrophage colony stimulating factor(GM-CSF), macrophage colony stimulating factor (M-CSF), receptors thereof, or the like.
Examples of the chemokines can include SLC, ELC, I-309, TARC, MDC, MIP-3α, CTACK and receptors of these chemokines.
Examples of growth factors can include Epidermal Growth Factor (EGF), vascular endothelial growth factor (VEGF), angiopoietin, fibroblast growth factor (FGF), hepatocyte growth factor (HGF), platelet-derived growth factor (PDGF), insulin-like growth factor (IGF), erythropoietin (EPO), TGFβ, ephrin, angiopoietin, Frizzled ligand, SDF-1, receptors thereof, or the like.
Examples of cluster of differentiation (hereinafter, referred to as CD) antigens can include CD2, CD3, CD4, CD7, CD10, CD14, CD16, CD19, CD20, CD21, CD22, CD23, CD24, CD28, CD32, CD37, CD40, CD44, CD52, CD64, CD53, CD56, CD72, CD73, CD74, CDw75, CDw76, CD77, CDw78, CD79a, CD79b, CD80 (B7.1), CD81, CD82, CD83, CDw84, CD85, CD86 (B7.2), CD98, human leukocyte antigen (HLA)-Class II, HLA-I, or the like.
Further, examples of the antigen involved in formation of pathologic state of tumor or the antigen for the antibody which regulates immunological function can include ganglioside GM1, GM2, GD2, GD3, Lewis X, Lewis Y, CD3, CD4, CD40, CD40 ligand, B7 family molecules (e.g., CD80, CD86, CD274, B7-DC, B7-H2, B7-H3, or B7-H4), ligand of B7 family molecules (e.g., CD28, CTLA-4, ICOS, PD-1, or BTLA), OX-40, OX-40 ligand, CD137, tumor necrosis factor (TNF) receptor family molecules (e.g., DR3, DR4, DR5, TNFR1, or TNFR2), TNF-related apoptosis-inducing ligand receptor (TRAIL) family molecules, receptor family of TRAIL family molecule (e.g., TRAIL-R1, TRAIL-R2, TRAIL-R3, or TRAIL-R4), receptor activator of nuclear factor kappa B ligand (RANK), RANK ligand, CD25, folate receptors, Mesothelin, cytokines [e.g., IL-1α, IL-1β, IL-4, IL-5, IL-6, IL-10, IL-13, transforming growth factor (TGF) β, or TNFα, or the like.], receptors of these cytokines, chemokines (e.g., SLC, ELC, I-309, TARC, MDC, or CTACK, or the like.), or receptors of these chemokines.
The proper target molecule of the monovalent antibody is exemplified by antigens that can be activated by dimerization or agglutination. Examples of the molecule having this property can include enzyme-linked receptors, cell adhesion molecules or the like. The enzyme-linked receptors can include receptor tyrosine-kinase, tyrosine-kinase-associated receptor, receptor serine-threonine kinase, and receptor guanylate cyclase.
Examples of the receptor tyrosine-kinase can include EGF receptor, insulin receptor, IGF-1 receptor, NGF receptor, PDGF receptor, M-CSF receptor, FGF receptor, VEGF receptor, Eph receptor or the like. Examples of the tyrosine-kinase-associated receptor can include cytokine receptor, Fc receptor or the like. Further, examples of the cell adhesion molecules can include cadherin, integrin or the like.
Specific examples thereof can include interleukin-1 receptor 1 (IL-1R1), interleukin-1 receptor accessory protein (IL-1RAP), hepatocyte growth factor receptor (c-Met), macrophage stimulating 1 receptor (RON), platelet-derived growth factor receptor (PDGFR), junctional adhesion molecule-like (JAML), nectin-like protein 5 (Necl-5), tumor necrosis factor receptor 1 (TNF-R1), tumor necrosis factor receptor 2 (TNF-R2), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1), TNF-related apoptosis-inducing ligand receptor 2 (TRAIL-R2), death receptor 3 (DR3), death receptor 6 (DR6), receptor activator of NF-kB (RANK), nerve growth factor receptor (NGFR), lymphotoxin-beta receptor (LTβR), OX40 (TNFRSF4), Fas (TNFRSF6), 4-1BB (TNFRSF9), Fn14 (TNFRSF12A), TACI (TNFRSF13B), BAFF-R (TNFRSF13C), HVEM (TNFRSF14), BCMA (TNFRSF17), GITR (TNFRSF18), TROY (TNFRSF19), ectodysplasin A1 receptor (EDAR), ectodysplasin A2 receptor (XEDAR), receptor expressed in lymphoid tissues (RELT), CD3, CD27, CD30, CD40, FcαRI, FcγRIII, FcεRI, or the like.
A drug comprising the heterodimer protein composition of the present invention can be administered alone as a therapeutic agent. However, it is preferably mixed with one or more pharmaceutically acceptable carriers and provided as a pharmaceutical preparation produced by an arbitrary method well known in the technical field of pharmaceutics.
It is preferable to use the administration route that is most effective for the treatment. Examples thereof can include oral administration and parenteral administration such as intraoral administration, intratracheal administration, intrarectal administration, subcutaneous administration, intramuscular administration and intravenous administration. In the case of a heterodimer protein preparation, intravenous administration is preferred.
Examples of the administration form can include spray, capsules, tablets, granules, syrup, emulsion, suppository, injection, ointment, tape, or the like.
Examples of the preparations suitable for oral administration can include emulsions, syrups, capsules, tablets, powders, granules or the like.
Liquid preparations such as emulsions and syrups can be prepared using, as additives, water, sugars such as sucrose, sorbitol, fructose, glycols such as polyethylene glycol, propylene glycol, oils such as sesame oil, olive oil, soybean oil, antiseptics such as p-hydroxybenzoate esters, flavors such as strawberry flavor, peppermint, or the like.
Capsules, tablets, powders, granules or the like can be prepared using, as additives, excipients such as lactose, glucose, sucrose, mannitol, disintegrating agents such as starch, sodium alginate, lubricants such as magnesium stearate, talc, binders such as polyvinyl alcohol, hydroxypropyl cellulose, gelatin, surfactants such as fatty acid esters, plasticizers such as glycerin, or the like.
Examples of the preparations suitable for parenteral administration can include injections, suppositories, sprays or the like.
Injections can be prepared using carriers comprising a salt solution, a glucose solution, or a mixture thereof, or the like. Alternatively, it is also possible to prepare powder injections by freeze-drying the heterodimer protein composition according to a conventional method and adding sodium chloride thereto.
Suppositories can be prepared using carriers such as cacao butter, hydrogenated fat, carboxylic acid or the like.
Sprays can be prepared using the heterodimer protein composition as it is, or using a carrier which does not stimulate the buccal or airway mucous membrane of the recipient and can facilitate absorption of the heterodimer protein composition by dispersing it as fine particles, or the like.
Specific examples of the carriers can include lactose, glycerin or the like. It is also possible to prepare aerosols, dry powders, or the like according to the properties of the heterodimer protein composition and the carriers used. For these parenteral preparations, the above-mentioned additives for the oral preparations can also be added.
The dose and administration frequency will vary depending on the desired therapeutic effect, the administration route, the period of treatment, age, body weight, or the like. However, a dose of the active ingredient for an adult person is generally 10 μg/kg to 20 mg/kg per day.
Furthermore, the anti-tumor effect of the heterodimer protein composition against various tumor cells can be examined by in vitro tests such as CDC activity measurement and ADCC activity measurement. In addition, examples of in vivo tests can include anti-tumor experiments using tumor systems in an experimental animal such as mice.
EXAMPLES
Example 1 Construction of Heterodimer Protein Expression Vector
(1) Introduction of Amino Acid Modification into H Chain Constant Region
The amino acid sequences, IgG1-CH and IgG4-CH (SEQ ID NOs: 6 and 8) (FIGS. 3A and 3B) were respectively designed by connecting 6 histidine residues (hereinafter, referred to as His tag) to the C-terminus of the amino acid sequences (SEQ ID NOs: 2 and 4) (nucleotide sequence of DNA: SEQ ID NOs: 1 and 3) of human IgG1 CH (Mol. Immunol., 2000; 37: 1035) and human IgG4 CH (J. Immunol. Methods, 2005; 306: 151), and the nucleotide sequences of DNA (SEQ ID NOs: 5 and 7) encoding the amino acid sequences were prepared. The recognition sequences for the restriction enzymes ApaI and BamHI were introduced into the 5′- and 3′-terminals of the nucleotide sequences of DNA so as to prepare DNA fragments of IgG1-CH and IgG4-CH.
The prepared IgG1-CH fragment and IgG4-CH fragment and a plasmid pBluescript SK-(manufactured by Stratagene) were treated with the restriction enzymes, ApaI and BamHI, and then ligation was performed, respectively. Each fragment was inserted into the pBluescript SK-vector to prepare an IgG1-CH vector and an IgG4-CH vector.
CH comprising an amino acid residue substitution was prepared by using the prepared IgG1-CH and IgG4-CH vectors as templates and a QuikChange (registered trade name) II XL Site-Directed Mutagenesis Kit (manufactured by Stratagene). Thus, IgG1-CH vectors and IgG4-CH vectors, each including the amino acid residue substitutions shown in Table 1, were prepared. Cys residue at position 220 present in the hinge domain of IgG1 is known to form an intermolecular disulfide bond with Cys residues of L chain. Thus, it was substituted with Ser to remove the disulfide bond.
Meanwhile, Cys residue at position 131 present in the CH1 domain of IgG4 is known to form an intermolecular disulfide bond with Cys residue of L chain. On the basis of this fact that Ser and Lys residues are located at positions 131 and 133 of IgG1, the partial sequences of C131/R133 including Cys residue involved in the disulfide bond between CH1-CL were substituted with C131S/R133K in the IgG4-type monovalent antibody to be made for IgG1-type sequence, in order to remove the disulfide bond and to reduce antigenicity.
Further, Ser residue at position 228 of the hinge domain of IgG4 and Arg residue at position 409 of the CH3 domain of IgG4 are known to be involved in IgG4-specific Fab-arm exchange. Because Pro and Lys are located at positions 228 and 409 of IgG1, respectively, amino acid residue substitutions of S228P and R409K were added to H chain of the IgG4-type monovalent antibody, in order to inhibit Fab-arm exchange. Further, amino acid residue substitution of L235E in IgG4 can reduce the effector activity.
Hereinafter, unless otherwise particularly mentioned, the amino acid sequence was represented as 1 letter based on the EU index of Kabat et al. [Sequences of Proteins of Immunological Interest, US Dept. Health and Human Services (1991)]. In addition, the amino acid residue before substitution was described before a number, and the amino acid residue after substitution was described after the number. The nucleotide sequences of DNA of IgG H chain are represented by SEQ ID NOs: 9, 11, 13, 15, 17 and 19, respectively.







TABLE 1







Amino acid substitution introduced in CH















DNA
Protein







Sequence
SEQ ID
SEQ ID


name
NO:
NO:
Subclass
CH1
Hinge
CH2
CH3

















1H0
9
10
IgG1
—
—
—
—


1H1
11
12
IgG1
—
C220S
—
—


4H0
13
14
IgG4
—
—
—
—


4H1
15
16
IgG4
C131S/R133K
—
—
—


4H2
17
18
IgG4
C131S/R133K
S228P
—
R409K


4H3
19
20
IgG4
C131S/R133K
S228P
L235E
R409K









(2) Introduction of Amino Acid Modification into Artificial Constant Region Prepared by Fusion of Human κ Chain Constant Region (CL) and IgG Antibody Fc
The C-terminus of the human κ chain constant region (SEQ ID NOs: 57 and 58) was bound with the hinge domain, CH2 domain and CH3 domain of the constant region of human IgG1 or human IgG4 in this order to design the amino acid sequence of CL-Fc (hereinafter, referred to as IgG1-L and IgG4-L) (SEQ ID NO: 22 and SEQ ID NO: 26) (FIGS. 4A and 4B). Then, nucleotide sequences of DNA (SEQ ID NO: 21 and SEQ ID NO: 25) encoding the amino acid sequences were prepared. Hereinafter, the second polypeptide comprising CL-Fc is referred to as L chain in some cases.
Meanwhile, a hinge domain having a deletion of the amino acid residues EPKSC at positions from 216 to 220 of the EU index corresponding to 5 amino acid residues from the N-terminus of the hinge domain was used in the IgG1-L (FIG. 4A). As described above, Cys residues involved in intermolecular disulfide bond with L chain exist in the hinge domain of IgG1. To remove this, EPKSC was deleted.
Subsequently, a gene sequences was prepared by linking 3′-untranslated region (UTR) of L light chain included in pKANTEX93 vector (J. Immunol. Methods, 2005; 306: 151) and a recognition sequence for the restriction enzyme KpnI to the 3′-terminus of the CL-Fc, and linking a recognition sequence for the restriction enzyme BsiWI to the 5′-terminus thereof.
The prepared BsiWI-KpnI gene fragment was cloned into a pTA2 vector (manufactured by TOYOBO) included in a Target Clone-Plus-kit (manufactured by TOYOBO) so as to prepare an IgG1-L vector and an IgG4-L vector.
Because the Cys residue at position 214 of human κ chain is known to form an intermolecular disulfide bond with Cys residue of H chain, it was substituted with Ser, thereby removing the disulfide bond. Further, His residue at position 435 and Tyr residue at position 436 of the CH3 domain of IgG1 and IgG4 are known to be involved in Protein A binding of an antibody.
Arg and Phe exist at positions 435 and 436 of IgG3 having no Protein A-binding activity. Thus, amino acid residue substitutions of H435R and Y436F were introduced into the L chain to reduce the Protein A-binding activity of the CL-Fc chain of the monovalent antibody.
CL-Fc including the amino acid substitution shown in Table 2 was prepared by using the IgG1-L vector and IgG4-L vector as templates and the QuikChange (registered trade name) IIXL Site-Directed Mutagenesis Kit (manufactured by Stratagene). The nucleotide sequences of DNA of each CL-Fc were represented by SEQ ID NOs: 21, 23, 25, 27, 29, 31 and 33, respectively.







TABLE 2







Amino acid substitution introduced in CL-Fc















DNA
Protein







Sequence
SEQ
SEQ ID


name
ID NO:
NO:
Subclass
CH1
Hinge
CH2
CH3





1L0
21
22
IgG1
—
Deletion
—
—







(216-220)


1L1
23
24
IgG1
C214S
Deletion
—
H435R/Y436F







(216-220)


4L0
25
26
IgG4
—
—
—
—


4L1
27
28
IgG4
C214S
—
—
—


4L2
29
30
IgG4
C214S
—
—
H435R/Y436F


4L3
31
32
IgG4
C214S
S228P
—
R409K/H435R/Y436F


4L4
33
34
IgG4
C214S
S228P
L235E
R409K/H435R/Y436F









(3) Construction of Monovalent Antibody Expression Vector
A heterodimer protein having a monovalent binding domain (hereinafter, abbreviated to monovalent antibody) in which the H chain variable region (VH) and L chain variable region (VL) of IgG antibody were linked to CH and CL-Fc prepared in Example 1(1) and (2) was prepared in the following manner. Hereinafter, the first polypeptide is referred to as H chain and the second polypeptide is referred to as L chain in some cases.
As the binding proteins to be bound with CH and CL-Fc, the variable regions of anti-CD20 antibody humanized B-Lyl (B-HH2 and B-KV1, hereinafter, referred to as GA101) (Japanese Patent Publication No. 2010-81940) and anti-HER2 antibody humAb4D5-8 (hereinafter, referred to as 4D5) (Proc. Natl. Acad. Sci. U.S.A., 1992; 89: 4285) were used. As the nucleotide sequences of DNA and amino acid sequences, GA101-VH (SEQ ID NOs: 35 and 36), GA101-VL (SEQ ID NOs: 37 and 38), 4D5-VH (SEQ ID NOs: 39 and 40) and 4D5-VL (SEQ ID NOs: 41 and 42) were used.
The recognition sequence for the restriction enzyme NotI was introduced into the 5′-terminals of the nucleotide sequences of DNA encoding the amino acid sequences of VHs of GA101 antibody and 4D5 antibody, and the recognition sequence for the restriction enzyme ApaI was introduced into the 3′-terminals thereof so as to prepare nucleotide sequences of DNA, which were inserted into the NotI-ApaI site of a pKANTEX93 vector (J. Immunol. Methods, 2005; 306: 151).
Consequently, an expression vector pKANTEX93/GA101-VH including anti-CD20 humanized antibody VH and an expression vector pKANTEX93/4D5-VH including anti-HER2 humanized antibody VH were prepared.
Subsequently, the recognition sequence for the restriction enzyme BsiWI was introduced into the 5′-terminals of the nucleotide sequences of DNA encoding the amino acid sequences of VLs of GA101 antibody and 4D5 antibody and the recognition sequence for the restriction enzyme KpnI was introduced into the 3′-terminals thereof so as to prepare nucleotide sequences of DNA, each was inserted into the NotI-ApaI site of the pKANTEX93/GA101-VH vector or the pKANTEX93/4D5-VH vector, respectively.
Consequently, an anti-CD20 humanized antibody GA101 expression vector pKANTEX93/GA101, and an anti-HER2 humanized antibody expression vector pKANTEX93/humAb4D5-8 were obtained.
CHs included in the ApaI-BamHI site of anti-CD20 humanized antibody GA101 expression vector pKANTEX93/GA101 and anti-HER2 humanized antibody expression vector pKANTEX93/humAb4D5-8 were substituted with a variety of IgG1-CH or IgG4-CH prepared in Example 1 (1) above.
Subsequently, CL included in the BsiWI-KpnI site of the expression vectors was substituted with a variety of CL-Fc that was prepared by fusion of hinge domain, CH2 domain and CH3 domain with the CL prepared in Example 1(2) above.
Consequently, a variety of monovalent antibody expression vectors composed of the first polypeptide comprising VH-CH and the second polypeptide comprising VL-CL-Fc were prepared (Table 3). Further, the structures of various monovalent antibody molecules are shown in FIG. 5.







TABLE 3







Combination list of variable region, CH and


CL-Fc of various monovalent antibodies












Variable region
CH
CL-Fc
Expression vector






humAb4D5-8
1H0
1L0
pKANTEX93/mvG1-1



GA101
1H1
1L1
pKANTEX93/mvG1-2



humAb4D5-8
4H0
4L0
pKANTEX93/mvG4-1



humAb4D5-8
4H1
4L1
pKANTEX93/mvG4-2



humAb4D5-8
4H1
4L2
pKANTEX93/mvG4-3



humAb4D5-8
4H2
4L3
pKANTEX93/mvG4-4



humAb4D5-8
4H3
4L4
pKANTEX93/mvG4-5









Example 2 Construction of Bispecific Heterodimer Protein Expression Vector
In order to construct a heterodimer protein having a divalent binding domain (hereinafter, referred to as bispecific antibody), a bispecific antibody was designed to be composed of the first polypeptide having VH linked at the N-terminus of CH and the second polypeptide having VL linked at the N-terminus of CL-Fc and a single chain Fv (scFv)-type variable region linked at the C-terminus thereof (FIGS. 6 and 7).
The bispecific antibody has a divalent binding activity, in which the binding domain composed of VH-VL specifically binds to CD74 and the scFv linked at the C-terminus of the second polypeptide specifically binds to Her2 or CD20. The bispecific antibody was prepared in the following manner.
(1) Construction of Anti-CD74 Antibody Expression Vector
As the anti-CD74 antibody, the known anti-CD74 humanized antibody hLL1 (U.S. Pat. No. 7,312,318) (SEQ ID NOs: 43 to 46) was used. The recognition sequence for a restriction enzyme was linked at the 5′- and 3′-terminals of VH and VL of the anti-CD74 humanized antibody hLL1 in the same manner as in Example 1(3) above, which was inserted into a pKANTEX93 vector, thereby preparing an anti-CD74 humanized antibody expression vector, pKANTEX93/hLL1.
(2) Construction of Anti-CD74 IgG4-Type Monovalent Antibody Expression Vector
In the same manner as in Example 2(1), DNA fragments of VH and VL of the anti-CD74 humanized antibody hLL1 antibody were prepared, and inserted into the NotI-ApaI site and the EcoRI-BsiWI site of the pKANTEX93/mvG4-4 vector prepared in Example 1(3). Consequently, an anti-CD74 IgG4-type monovalent antibody expression vector, pKANTEX93/G4-4/hLL1 was prepared.
(3) Construction of CD74-HER2 Bispecific Antibody and CD74-CD20 Bispecific Antibody Expression Vectors
In order to prepare CD74-HER2 bispecific antibody and CD74-CD20 bispecific antibody which was prepared by fusion of anti-HER2scFv or anti-CD20 scFv at the C-terminus of the second polypeptide of the anti-CD74 IgG4-type monovalent antibody prepared in Example 2(2) above, CL-Fc and scFv were linked to each other via a linker composed of 15 amino acid residues of [Ser-Gly-Gly-Gly-Gly]×3 (hereinafter, referred to as GS linker) (SEQ ID NOs: 47 and 48) so as to design CL-Fc-linker-VH-linker-VL (FIGS. 6 and 7). Further, each scFv was prepared in the following manner.
The VH and VL sequences of anti-HER2 humanized antibody 4D5-8 described in Example 1(3) above were used in the anti-HER2 antibody, and the VH and VL sequences (SEQ ID NOs:49-52) of anti-CD20 antibody 2F2 (US Patent Application Publication No. 2004/0167319) was used for the anti-CD20 antibody.
A stop codon of CL-Fc of the anti-CD74 IgG4-type monovalent antibody expression vector pKANTEX93/G4-4/hLL1 was deleted, and subsequently, the nucleotide sequences of DNA of CD74VL-CL-Fc-2F2scFv and CD74VL-CL-Fc-4D5scFv which were prepared by linking the nucleotide sequence of DNA encoding the GS linker, DNA encoding VH, DNA encoding the linker composed of 15 amino acid residues of [Gly-Gly-Gly-Gly-Ser]×3, and DNA encoding VL were designed (SEQ ID NOs: 53 to 56).
Subsequently, anti-HER24D5-8scFv or anti-CD20 2F2scFv was inserted into the anti-CD74 IgG4-type monovalent antibody expression vector, pKANTEX93/G4-4/hLL1 to prepare pKANTEX93/G4-4/hLL1-4D5-8scFv and pKANTEX93/G4-4/hLL1-2F2scFv, respectively.
Example 3 Production of Heterodimer Protein
(1) Expression of Heterodimer Protein
Cell culture was performed at 37° C. in a 5% CO2 incubator. In order to express a variety of monovalent antibodies and bispecific antibodies, introduction of the expression vectors was performed in the following manner.
8 μg of various monovalent antibody expression vectors or bispecific antibody expression vectors were added to 4×106 of Chinese hamster ovary cell CHO/DG44 cell (Somatic Cell Mol. Genet., 12, 555, 1986) or α1,6-fucosyltransferase gene (FUT8)-knockout CHO/DG44 cell (hereinafter, abbreviated to CHO/FUT8KOcell) (U.S. Pat. No. 6,946,292), and gene was introduced by electroporation method [Cytotechnology, 3,133 (1990)]. The names of the host cells, expression vectors, and heterodimer proteins to be produced are summarized in Table 4.
The heterodimer protein composition prepared by CHO cells has fucose binding to N-acetylglucosamine included in the reducing end of the N-glycoside sugar chain bound to Fc, but the heterodimer protein composition prepared by CHO/FUT8KO cells has no fucose binding thereto at the sugar chain. Hereinafter, F (fucosylated) and DF (defucosylated) were added to the sample name of the heterodimer protein composition prepared by each cell.
After gene introduction, each cell was cultured in an IMDM medium (manufactured by GIBCO) [hereinafter, abbreviated to IMDM-(10)] containing 10% dialyzed fetal bovine serum (hereinafter, abbreviated to dFBS) for 2 days, and then the medium was replaced with IMDM-(10) [hereinafter, abbreviated to IMDM-(10G)] containing 0.5 mg/mL G418 sulfate (NACALAI TESQUE, INC.) to continue the culture, thereby obtaining a G418 resistant cell line.
3×105 cell/mL of G418 resistant cell line was suspended in IMDM-(10G) and cultured for 3 days, and then the medium was replaced with Excell302 (manufactured by SAFC Biosciences) to perform the culture for 7 to 11 days and then culture supernatant was recovered.







TABLE 4







List of combination and sample name of vector and host cell









Host cell









Expression vector
CHO/DG44
CHO/FUT8KO





pKANTEX93/humAb4D5-8
—
4D5/IgG1 DF


pKANTEX93/GA101
GA101/IgG1 F
GA101/IgG1 DF


pKANTEX93/mvG1-1
—
4D5/mvG1-1 DF


pKANTEX93/mvG1-2
GA101/mvG1-2 F
GA101/mvG1-2 DF


pKANTEX93/mvG4-1
—
4D5/mvG4-1 DF


pKANTEX93/mvG4-2
—
4D5/mvG4-2 DF


pKANTEX93/mvG4-3
—
4D5/mvG4-3 DF


pKANTEX93/mvG4-4
4D5/mvG4-4 F
4D5/mvG4-4 DF


pKANTEX93/mvG4-5
4D5/mvG4-5 F
—


pKANTEX93/hLL1
hLL1/IgG1 F



pKANTEX93/G4-4/hLL1
hLL1/mvG4-4 F
—


pKANTEX93/G4-4/hLL1-
hLL1-4D5/
—


4D5-8scFv
mvG4-4 F



pKANTEX93/G4-4/hLL1-
hLL1-2F2/
—


2F2scFv
mvG4-4 F









(2) Purification of Heterodimer Protein
The culture supernatants of the various monovalent antibodies and bispecific antibodies obtained in Example 3(1) above were passed through a column packed with ProSep-vA High Capacity (manufactured by MILLIPORE) carrier at a flow rate of 0.5 to 1.0 mL/min. The column was washed with phosphate buffer saline (PBS), and then proteins were eluted using 0.1 M citrate buffer of pH 5.0 to pH 3.0, and immediately neutralized with 2 M Tris-hydrochloric acid buffer (pH 8.0).
Purification of 4D5/mvG4-3 DF and 4D5/mvG4-4 DF was also performed using a Protein G carrier. The culture supernatant was passed through the column packed with ProSep-G (manufactured by MILLIPORE) carrier at a flow rate of 0.5 to 1.0 mL/min. The column was washed with PBS, and then protein was eluted using 0.1 M citrate buffer of pH 5.0 to pH 2.5, and immediately neutralized with 2 M Tris-hydrochloric acid buffer (pH 8.0).
The elution fraction showing a high protein concentration was dialyzed against a buffer (hereinafter, abbreviated to citrate buffer) containing 10 mM citric acid, of which pH was adjusted to 6.0 with sodium hydroxide, and 150 mM sodium chloride. The sample was recovered, and a low-concentration sample was concentrated by an ultrafiltration filter (manufactured by MILLIPORE), and sterilized using a 0.22 um filter (manufactured by MILLIPORE). The protein concentration was calculated from absorbance at 280 nm (OD280).
The sample was further purified by gel filtration chromatography, and used in the in vitro activity test. A Superdex 200 10/300 GL column (GE Healthcare) was connected to a High speed liquid chromatography system AKTA explore 10S (GE Healthcare), and the citrate buffer was used as a running buffer, and the sample was passed through the column at a flow rate of 0.5 mL/min. The fractions detected as peaks around 25 to 30 minutes were recovered, and used for analysis.
(3) SDS-PAGE Analysis of Heterodimer Protein
The various monovalent antibodies purified using Protein A were subjected to SDS-PAGE analysis. The samples were adjusted with a buffer (hereinafter, abbreviated to sample buffer) containing 10% sodium dodecyl sulfate, 50% glycerol, and 0.3 M Tris hydrochloric acid (pH 6.8) containing 0 mM dithiothreitol (DTT) (non-reducing conditions) or 10 mM DTT (reducing conditions), and treated at 100° C. for 5 minutes, and 1 μg/lane thereof was loaded in a polyacrylamide gel (ATTO catalog No. E-T520L) for electrophoresis. As a molecular weight marker, Precision plus protein all blue standards (Bio-Rad Laboratories Inc.) were used and added in an amount of 5 μL/lane. After gel recovery, staining was performed using Quick CBB (Wako Pure Chemical Industries, Ltd.) according to the product procedure manual.
As a result, both H chain and L chain of the monovalent antibody had a molecular weight of approximately 50 kDa. In the SDS-PAGE under the non-reducing conditions, plural bands at 250 kDa or greater which were predicted as a multimer, a band around approximately 100 kDa which was predicted as a monomer composed of two polypeptide chains, and a band around approximately 50 kDa which was predicted as a halfmer composed of one polypeptide chain were recognized (FIGS. 8A (a) and (b), 8B).
In anti-HER2 IgG4-type monovalent antibody 4D5/mvG4-1 DF, plural bands of 250 kDa or greater which were predicted as a multimer were detected, it was indicated that plural multimers were formed. However, in 4D5/mvG4-2 DF composed of H chain including C131S/R133K substitutions and L chain including C214S substitution, multimers were hardly detected (FIG. 8A).
Therefore, it was found that in the heterodimer protein composed of the first polypeptide comprising IgG4-CH and the second polypeptide comprising IgG4-L, substitution of H chain C131S/R133K, substitution of L chain C214S, and substitutions of H chain C131S/R133K and L chain C214S deleting Cys residue involved in disulfide bonds between IgG4-CH and Cκ are able to inhibit multimer formation caused by intermolecular disulfide bonds.
Similarly, bands of multimers were not detected in 4D5/mvG4-3 DF, 4D5/mvG4-4 DF, 4D5/mvG4-4 F, and 4D5/mvG4-5 F having substitutions of H chain C131S/R133K and L chain C214S. Further, the multimers were clearly detected in 4D5/mvG1-1 DF, but not detected in GA101/mvG1-2 DF and GA101/mvG1-2 F including substitutions of H chain C220S and L chain C214S.
Therefore, it was found that in the heterodimer protein composed of the first polypeptide comprising IgG1-CH and the second polypeptide comprising IgG1-L, substitution of H chain C220S, substitution of L chain C214S, and substitutions of H chain C220S and L chain C214S deleting Cys residues involved in disulfide bonds between IgG1-CH and Cκ are able to inhibit multimer formation.
On the other hand, in 4D5/mvG4-1 DF, 4D5/mvG4-2 DF and 4D5/mvG4-3 DF, bands around approximately 50 kDa which was predicted as a halfmer were detected. However, in 4D5/mvG4-4 DF, 4D5/mvG4-4 F and 4D5/mvG4-5 F including substitutions of S228P/R409K in both H chain and L chain, halfmer bands were not recognized. Therefore it was indicated that substitution of S228P, substitution of R409K and substitutions of S228P/R409K in H chain and L chain are able to inhibit halfmer formation (FIG. 8B).
These results suggest that the heterodimer protein composition of the present invention is a composition having reduced amounts of multimer, halfmer, and multimer/halfmer generated during production of the heterodimer protein.
Example 4 Component Analysis of Monovalent Antibody
(1) Component Separation by Cation Exchange Chromatography
In order to perform a detailed component analysis of anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-2 DF that was purified by affinity purification using the Protein A column in Example 3 described above, cation exchange chromatography was performed. 4D5/mvG4-2 DF is an IgG4 type monovalent antibody including amino acid residue substitution of C214S in CL and amino acid residue substitutions of C131S/R133K in CH1 and having no fucose that is bound to N-acetylglucosamine included in the reducing end of N-glycoside sugar chain bound to Fc.
A WCX-10 (manufactured by DIONEX) column was connected to High Performance Liquid Chromatography (HPLC) analysis equipment (LC-10Avp series, SHIMADZU Corporation), and a buffer of 10 mM sodium phosphate at pH 6.2 (hereinafter, abbreviated to Buffer A) was used as a staring buffer, and a buffer of 10 mM sodium phosphate and 500 mM sodium chloride at pH 6.2 (hereinafter, abbreviated to Buffer B) was used as an elution buffer.
After applying the sample, buffer A was applied at a flow rate of 1 mL/min, and analysis was performed for 30 minutes with 1% increase of the ratio of buffer B per minute. Then, the running buffer was replaced with buffer B, and analysis was performed for 10 minutes.
The results of cation exchange chromatography of 4D5/mvG4-2 DF showed that three peak groups of (1), (2) to (6) and (7) to (10) were separated as shown in FIG. 9, indicating that plural components are included in the Protein A-purified protein. Therefore, the peaks (1) to (10) were further fractionated and analysis of each peak was performed.
(2) Classification of Components by Western Blot Analysis
In the same manner as in Example 3(3) above, 40 ng was added per lane under non-reducing conditions to perform SDS-PAGE electrophoresis, and a PVDF membrane and a gel were put between filter papers soaked in a transfer buffer containing 0.1 M Tris, 0.2 M glycine and 20% methanol, and proteins were blotted on the PVDF membrane (2.5 mA/cm2, for 40 minutes). Thereafter, PBS containing 1% bovine serum albumin (BSA) (hereinafter, abbreviated to BSA-PBS) was used to block the protein-transferred PVDF membrane.
As a detection antibody, 1000-fold diluted peroxidase (hereinafter, abbreviated to HRP)-labeled anti-His tag antibody (NACALAI TESQUE, INC., Cat. No. 04546-34) for H chain detection, 5000-fold diluted peroxidase-labeled anti-human κ chain antibody (SIGMA, Cat. No. 7164) for L chain detection, and 5000-fold diluted peroxidase-labeled anti-human IgG antibody (American Qualex, Cat. No. A 110PD) for IgG detection were used, and reacted at room temperature for 1 hour.
Thereafter, the PVDF membrane was washed with PBS containing 0.1% Tween 20 (hereinafter, abbreviated to Tween-PBS), and reacted with a SuperSignal West Dura Extended Duration Substrate (manufactured by Thermo Scientific), followed by detection using an image analyzer (manufactured by FUJI FILM).
The results of Western blot analysis (FIG. 10) of the peaks (1) to (10) detected in the cation exchange chromatography (FIG. 9) of 4D5/mvG4-2 DF showed that bands around 100 kDa predicted as a monomer composed of two polypeptide chains were detected in the peaks (1) and (3). It reacted with both anti-human κ chain antibody and anti-hIgG antibody but did not react with anti-His tag antibody, indicating L chain-L chain homodimer monomer (hereafter, abbreviated to LL form) comprising only L chain and no H chain including His tag.
Further, bands around 100 kDa predicted as a monomer were detected in the peaks (8) and (9). It reacted with all detection antibodies of anti-human κ chain antibody, anti-His tag antibody, and anti-hIgG antibody, indicating HL heterodimer monomer (hereafter, abbreviated to HL form) comprising L chain and H chain including His tag (FIG. 10).
Further, the detection results by peroxidase-labeled anti-hIgG antibody showed that components of peaks (1), (3) and peaks (8), (9) were different in the molecular weight, and can be separated by SDS-PAGE. The samples of other peaks (2), (4) to (7) and (10) were below the detection limits of Western blot analysis, and thus their components could not be identified.
(3) Separation of Heterodimer and Homodimer from Mixture
In the above section, it was suggested that HL and LL forms were included in 4D5/mvG4-2 DF purified by Protein A. Subsequently, in order to obtain standard products of HL and LL forms, each of the fractions obtained by changing elution pH during the protein A purification was analyzed by cation exchange chromatography. As a result, fraction X, which was one of the fractions eluted at pH 3.5 during the Protein A purification, was identified to have peaks (8) and (9) as a main component. Fraction Y, which was eluted at pH 5.0 during the Protein A purification, was identified to have peak (1) as a main component.
As shown in Table 5, the content of HL form in fraction X was 74.9% or more, and the content of LL form in fraction Y was 93.8% or more. In the subsequent analysis, fraction X was used as a control of the sample including HL form as the main component, and fraction Y was used as a control of the sample including LL form as the main component. Further, the values of Table 5 represent an area ratio (%), and ┌n.d.┘ represents “unanalyzed”.







TABLE 5







Component analysis of each fractions of mvG4-2


DF by cation exchange chromatography










mvG4-2 DF











Peak no.
Component
Fraction X
Fraction Y













(1)
LL
1
88.6 


(2)
unidentified
n.d.
1.5


(3)
LL
n.d.
5.2


(4)
unidentified
n.d.
1.3


(5)
unidentified
n.d.
2.1


(6)
unidentified
5.7
1.3


(7)
unidentified
10.3
n.d.


(8)
HL
24.2
n.d.


(9)
HL
49.9
n.d.


(10) 
unidentified
8.8
n.d.


Total (%)
LL
1
93.8 



HL
74.1
n.d.



unidentified
24.9
6.2









(4) Specific Purification of Heterodimer Protein
In order to confirm specific separation and purification of the heterodimer protein that includes the second polypeptide comprising CL-Fc having a reduced binding activity for the CH binder, Protein G and Protein A were used to perform purification, and purified proteins were compared.
Protein G is known to bind to any subclass of human IgG, and human IgG3 having no Protein A-binding activity is able to bind to Protein G. In the purification using Protein G, therefore, it is suggested that all antibody molecules can be purified irrespective of the presence or absence of amino acid residue substitution in this Example in the Protein A-binding site.
In this Example, a heterodimer protein (4D5/mvG4-3 DF) including CL-Fc having a reduced Protein A-binding activity was prepared by substituting His at position 435 and Tyr at position 436 of the EU index of IgG1, which are known to be involved in the protein A binding, with Arg and Phe that are amino acid residues of human IgG3 having no Protein A-binding activity, followed by analysis.
In the same manner as in Example 3(3) and Example 4(2) above, SDS-PAGE analysis under non-reducing conditions and Western blotting were performed.
In SDS-PAGE under non-reducing conditions, the results of performing the electrophoresis for a long time showed that X fraction of 4D5/mvG4-2 mainly including HL form had a band in the higher molecular weight region than Y fraction of 4D5/mvG4-2 DF mainly including LL form. Therefore it was found that the band in the high molecular weight region is the HL form and a band in the low molecular weight region is LL form. Further, as the electrophoresis time was prolonged, HL heteromonomer and LL homomonomer could be separated (FIG. 11).
Similarly, the results of Western blotting using anti-κ chain antibody also showed that X fraction of 4D5/mvG4-2 had a band in the higher molecular weight region than Y fraction of 4D5/mvG4-2 (FIG. 11).
Further, with respect to 4D5/mvG4-3 DF purified using Protein G or Protein A, each of the purified products was subjected to SDS-PAGE, and a comparison was performed.
First, the conditions for purifying 4D5/mvG4-3 DF using each carrier were examined, and as a result, all proteins were found to be eluted by Protein G at pH 2.5 and by Protein A at pH 3.0.
In 4D5/mvG4-3 DF (Protein G purified product) obtained by performing elution using Protein G at pH 2.5, both bands of HL and LL forms were observed, indicating that 4D5/mvG4-3 DF purified by Protein G includes both HL and LL forms, like 4D5/mvG4-2 DF (FIG. 11, SDS-PAGE). Therefore, it was found that both molecules of HL and LL are expressed in 4D5/mvG4-3 DF prepared by adding amino acid residue substitutions of H435R and Y436F to 4D5/mvG4-2.
Meanwhile, the results of SDS-PAGE of 4D5/mvG4-3 DF (Protein A purified product) obtained by eluting the same culture supernatant as in the Protein G purification at pH 3.0 using Protein A showed that the band of HL was observed, but the band of LL was hardly observed, and the results of Western blot analysis by anti-κ chain antibody also showed that the band of HL of the high molecular weight region was only observed (FIG. 11).
Therefore, it was found that cells expressing 4D5/mvG4-3 DF express HL heterodimer and LL homodimer in the culture supernatant, but HL heterodimer protein of 4D5/mvG4-3 DF can be selectively purified by Protein A purification (FIG. 11).
Meanwhile, LL form as well as HL form can be purified by Protein A from 4D5/mvG4-2 DF having no amino acid residue substitutions of H435R and Y436F in L chain. It was indicated that only HL form can be specifically purified from LL form having no Protein A-binding activity and HL form having Protein A-binding activity by adding amino acid substitutions of H435R and Y436F to L chain.
Example 5 Heterodimer Protein-Detection ELISA
(1) Sandwich ELISA of IgG4 Type Monovalent Antibody
For the detection of HL form, establishment of a sandwich enzyme-linked immunosorbent assay (ELISA) system was examined. The monovalent antibody prepared in this Example is a heterodimer protein that is composed of H chain having His tag at the C-terminus of CH and L chain prepared by fusion of Fc and Cκ (chain, as shown in the structure of FIG. 5, and thus, anti-His tag antibody could be used as the H chain-specific binding antibody and anti-human κ chain antibody could be used as the L chain-specific binding antibody.
The anti-His tag antibody (QIAGEN, Cat. No. 34670) was immobilized on an ELISA plate (2 μg/mL, 50 μL/well, 4° C., 16 hours), and washed with PBS, followed by blocking with BSA-PBS (100 μL/well, room temperature, 1 hour).
After the blocking solution was discarded, various concentrations of monovalent antibody 4D5/mvG4-2 DF fraction X, 4D5/mvG4-2 DF fraction Y, and 4D5/mvG4-3 DF, 4D5/mvG4-4 F and 4D5/mvG4-5 F purified by Protein A were reacted (50 μL/well, room temperature, 2 hours).
Subsequently, after washing with 0.05% Tween 20-containing PBS (hereinafter, abbreviated to Tween-PBS), 5000-fold diluted horseradish peroxidase (hereinafter, abbreviated to HRP)-labeled anti-human κ chain antibody (SIGMA, Cat. No. A7164) was reacted (50 μL/well, 2 hours).
Subsequently, after washing with Tween-PBS, 50 μl/well of ABTS chromogenic substrate [2.2-azinobis(3-ethylbenzothiazole-6-sulfonic acid)ammonium] solution [1 mmoL/L ABTS/0.1 moL/L citrate buffer (pH 4.2), 0.1% H2O2] was added to develop a color at room temperature for 15 minutes. The color development was terminated by addition of 50 μL/well of 5% SDS aqueous solution. Absorbance was determined on a plate reader at 415 nm with a reference at 490 nm. SoftMax Pro(Molecular Devices) was used for data analysis. The experiment was repeated three times.
In the binding ELISA system, fraction X composed of HL heterodimer of 4D5/mvG4-2 DF was used as a positive control, and fraction Y composed of LL homodimer of 4D5/mvG4-2 DF was used as a negative control.
As a result, 4D5/mvG4-3 DF, 4D5/mvG4-4 F and 4D5/mvG4-5 F obtained by Protein A purification equivalently bound to 4D5/mvG4-2 DF fraction X, but hardly bound to 4D5/mvG4-2 DF fraction Y (FIG. 12).
Therefore, it was found that all of the IgG4 type monovalent antibodies, 4D5/mvG4-3 DF, 4D5/mvG4-4 F and 4D5/mvG4-5 F are HL heterodimer proteins composed of the first polypeptide comprising CH-His tag and the second polypeptide comprising CL-Fc (FIG. 12).
Further, it was found that the HL heterodimer can be specifically purified from all of IgG4 type monovalent antibody 4D5/mvG4-3 DF prepared by further adding amino acid substitutions of H435Y and R436F to L chain in the HL heterodimer protein of IgG4 type monovalent antibody 4D5/mvG4-2 DF, 4D5/mvG4-4 F prepared by further adding amino acid substitutions of S228P/R409K, and 4D5/mvG4-5 F prepared by further adding amino acid substitution of L235E to 4D5/mvG4-4 F, by Protein A purification (FIG. 12).
Therefore, the effect that the HL heterodimer form can be specifically purified using Protein A by adding amino acid substitutions of H435Y and R436F to L chain is maintained, even though the amino acid substitutions of S228P/R409K and L235E are included.
(2) Sandwich ELISA of IgG1 Type Monovalent Antibody
In the same manner as in Example 5(1) described above, Protein A purified fractions of IgG1 type monovalent antibody 4D5/mvG1-1 DF were subjected to sandwich ELISA.
As a result, the fractions 1 to 4 that were eluted at each pH by Protein A purification showed different reactivities in sandwich ELISA, indicating that the contents of HL heterodimer in the fractions differ from each other (FIG. 13A).
Therefore, fraction showing the highest reactivity was used as 4D5/mvG1-1 DF in the subsequent in vitro activity test.
Meanwhile, IgG1 type monovalent antibody GA101/mvG1-2 F and GA101/mvG1-2 DF including amino acid residue substitutions of H435R and Y436F showed reactivity equivalent to that of the 4D5/mvG4-2 DF fraction X including HL heterodimer as a main component (FIG. 13B).
Therefore, it was shown that in the IgG1 type monovalent antibodies GA101/mvG1-2 F and GA101/mvG1-2 DF that were purified by use of Protein A, HL heterodimers were specifically purified (FIG. 13B).
These results suggest that in IgG1 type monovalent antibody as well as IgG4 type monovalent antibody, heterodimer proteins including amino acid residue substitutions of H435R/Y436F in L chain can be specifically purified by Protein A.
Example 6 Binding Activity of Heterodimer Protein for Cancer Cells
Binding activities of IgG1 type and IgG4 type monovalent antibodies for cancer cells were confirmed by binding inhibition experiment of each IgG 1 antibody. First, as a control antibody, anti-CD20 IgG1 antibody GA101/IgG1 F, anti-HER2 IgG1 antibody Herceptin (Proc. Natl. Acad. Sci. U.S.A., 1992; 89: 4285) and human IgG1 (manufactured by Millipore, AG502) were labeled with Alexa488 using an Alexa488 labeling kit (Invitrogen, A20181) to prepare GA101_Alx, Herceptin_Alx and hIgG1_Alx.
CD20-positive human lymphoma cell line Raji (7CRB9012) and HER2-positive human breast cancer cell line SK-BR-3(ATCC: HTB-30) were used to perform flow cytometry. The experiment was repeated twice. 1×105 cells were suspended in a PBS buffer containing 1% BSA, 0.02% ethylene diamine tetracetate (EDTA), and 0.05% sodium azide (hereinafter, abbreviated to FACS buffer), and 2.0 μg/mL of Alexa-labeled antibody and 210 nM to 1.68 nM of non-labeled IgG1 antibody or various monovalent antibodies were added to the suspension at the same time, and reacted at 4° C. under shading conditions for 1.5 hours.
Further, hIgG1_Alx was used as a negative control. After washing with FACS buffer, a flow cytometer Cytomics FC 500 MPL (Beckman Coulter) was used for measurement.
As a result, the negative control hIgG1 antibody did not inhibit the binding of anti-HER2 antibody Herceptin_Alx to SK-BR-3 cells, but anti-HER2 IgG1 antibody Herceptin, anti-HER2 IgG1 defucosylated antibody 4D5/IgG1 DF, anti-HER2 IgG1 type monovalent antibody 4D5/mvG1-1 DF, anti-HER2 IgG4 type monovalent antibody 4D5/mvG4-4 F and 4D5/mvG4-5 F inhibited the binding of Herceptin_Alx to SK-BR-3 in an antibody concentration dependent manner (FIG. 14A).
Therefore, anti-HER2 monovalent antibody was found to specifically bind to HER2. It was indicated that the heterodimer protein prepared on the basis of the heterodimer scaffold protein (HSP) composed of CH and CL-Fc is a heterodimer protein having a monovalent binding activity.
However, the inhibitory effect of the binding by the monovalent antibody per unit mol concentration was lower than those of anti-HER2 IgG1 antibody Herceptin and 4D5/IgG1 DF (FIG. 14A).
Meanwhile, in CD20-positive lymphoma cell line Raji, similarly, the negative control hIgG1 antibody did not inhibit the binding of GA101-Alx to Raji cells, but anti-CD20 IgG1 antibody GA101, anti-CD20 IgG1 defucosylated antibody GA101/IgG1 DF, anti-CD20 IgG1 type monovalent antibodies, GA101/mvG1-2 F and GA101/mvG1-2 DF inhibited the binding of GA101-Alx to Raji cells in an antibody concentration dependent manner (FIG. 14B).
Therefore, anti-CD20 monovalent antibody was found to specifically bind to CD20. Like HER2 antibody, the inhibitory effect of the binding by the monovalent antibody per unit mol concentration was lower than those of anti-CD20 IgG1 antibodies, GA101/IgG1 F and GA101/IgG1 DF (FIG. 14B).
Example 7 Antibody-Dependent Cytotoxicity of Heterodimer Protein
(1) Antibody-Dependent Cytotoxicity of Anti-HER2 Monovalent Antibody
ADCC activity of antibody was measured by the method described in WO 2007/011041, and repeated three times.
HER2-positive human breast cancer cell SK-BR-3 (ATCC: HTB-30), human breast cancer BT-20 (ATCC: HTB-19), CD20-positive human lymphoma cell Raji (JCRB9012), Burkitt lymphoma cell ST-486 (ATCC: CRL-1647) and chronic B cell leukemia cell MEC-1 (DSMZ: ACC-497) were used as target cells and peripheral blood mononuclear cells (PBMC) prepared from a healthy donor was used as an effector cell.
The experiment was performed at a ratio of the effector cell to the target cell of 1:25, and cytotoxicity (%) was calculated by the following Equation.

Cytotoxicity (%)=100×(S−Ab)/(Max−T)

S=absorbance of sample reaction well-absorbance of medium well
Ab=absorbance of non-antibody added well-absorbance of medium well
T=absorbance of target well-absorbance of medium well
Max=absorbance of 100% reaction well-absorbance of 100% reaction control well
hIgG1 was used as a negative control and anti-HER2 IgG1 antibody Herceptin and anti-HER2 IgG1 defucosylated antibody 4D5/IgG1 DF were used as positive controls, and PBMC prepared from another volunteer donor was used as effector cells. The well including target cells lysed in Triton X-100 was used as the 100% reaction well.
As a result, anti-HER2 monovalent antibody 4D5/mvG1-1 DF (Protein A purified fraction) showed high ADCC activity in an antibody concentration dependent manner, equivalent to that of anti-HER2 IgG1 antibody 4D5/IgG1 DF (FIG. 15A). In contrast, both of the anti-HER2 IgG4 type monovalent antibodies, mvG4-4F and mvG4-5F showed no ADCC activity (FIG. 15B).
Therefore, it was found that the heterodimer protein composed of the first polypeptide comprising IgG-CH and the second polypeptide comprising CL(IgG1-L) prepared by fusion of IgG1-Fc is able to impart ADCC activity and the heterodimer protein composed of the first polypeptide comprising IgG4-CH and the second polypeptide comprising CL(IgG4-L) prepared by fusion of IgG4-Fc is able to exclude ADCC activity.
Further, although IgG1 type monovalent antibody has an antigen binding site reduced from divalent to monovalent, compared to IgG1 antibody, it showed equivalent effects to that of IgG1 antibody under the same conditions, indicating that a monovalent antibody having the reduced unnecessary bivalent binding activity while retaining ADCC activity can be prepared.
(2) Antibody-Dependent Cytotoxicity of Anti-CD20 Monovalent Antibody
In the same manner as in Example 7(1) described above, hIgG1 was used as the negative control, and anti-CD20 IgG1 antibody GA101/IgG1 F and anti-CD20 IgG1 defucosylated antibody GA101/IgG1 DF were used as positive controls. All experiments were performed using PBMC prepared from one healthy donor.
As a result, anti-CD20 IgG1 type defucosylated monovalent antibody GA101/mvG1-2 DF showed a remarkably increased ADCC activity, compared to anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 F [FIGS. 16(a) to (c)].
It was known that removal of core fucose from human IgG increases ADCC activity. Removal of core fucose from IgG1 type monovalent antibody composed of the first polypeptide comprising CH and the second polypeptide comprising CL-Fc was also found to increase ADCC activity. That is, the ADCC activity of the heterodimer protein composed of the first polypeptide including CH and the second polypeptide comprising CL-Fc was found to be increased or decreased by changing the content of core fucose binding to Fc.
Further, induced potency of ADCC activity per unit mol concentration of anti-CD20 IgG1 type defucosylated monovalent antibody GA101/mvG1-2 DF was reduced, compared to anti-CD20 IgG1 defucosylated antibody GA101/IgG1 DF, but the maximum efficacy was almost equivalent. That is, although anti-CD20 IgG1 type monovalent antibody has an antigen binding site reduced from divalent to monovalent, compared to anti-CD20 IgG1 antibody, equivalent effects to that of IgG1 antibody can be obtained by increasing the number of monovalent antibody molecule under the same conditions.
Example 8 Preparation of Divalent Heterodimer Protein
(1) Preparation of Bispecific Antibody
As a divalent heterodimer protein, a bispecific antibody that is composed of a first polypeptide comprising CD74 antibody H chain and a second polypeptide comprising anti-CD20 scFv antibody or anti-HER2 scFv antibody bound to the C-terminus of CD74 antibody VLCL-Fc, and anti-CD74 IgG4 type monovalent antibody hLL1/mvG4-4 F were prepared.
The bispecific antibody expression vector of Example 2(3) was used to express and purify the bispecific antibodies in the same manner as in Example 3, thereby obtaining CD74-HER2 bispecific antibody, CD74-CD20 bispecific antibody and anti-CD74 IgG4 type monovalent antibody hLL1/mvG4-4 F.
The results of SDS-PAGE showed that hLL1/mvG4-4 F, hLL1-4D5/mvG4-4 F and hLL1-2 F2/mvG4-4 F compositions showed high purity, and included little impurities, degradation products and aggregates (FIG. 17).
(2) Evaluation of Binding Activity for Recombinant Human HER2 and CD74 by ELISA
In the assay, a 96-well plate for ELISA (Greiner) was used. 2 μg/mL of recombinant human HER2-Fc (R&D Systems) or 2 μg/mL of CD74 (Santa Cruz Biotechnology) was dispensed in an amount of 50 μL/well, and left at 4° C. overnight for adsorption. The plate was washed with PBS, and then 100 μL/well of BSA-PBS was added and left at room temperature for 1 hour to block the remaining active groups.
Thereafter, BSA-PBS was discarded, and various concentrations of anti-HER2 IgG1 antibody Herceptin F, anti-CD74 IgG1 antibody hLL1 F or CD74-HER2 bispecific antibody hLL1-4D5/mvG4-4 F were dispensed as primary antibodies in the plate at an amount of 50 μL/well, and left at room temperature for 1 hour.
The plate was washed with Tween-PBS, and then peroxidase-labeled goat anti-human κ chain antibody (Southern Biotech) was dispensed as a secondary antibody at an amount of 50 μL/well, and left at room temperature for 1 hour. The plate was washed with Tween-PBS, and 50 μL/well of ABTS colorimetric substrate [2.2-azinobis(3-ethylbenzothiazole-6-sulfonic acid)ammonium] solution [1 mmoL/L ABTS/0.1 moL/L citrate buffer (pH 4.2), 0.1% H2O2] was added for color development.
The reaction was terminated by addition of 50 μL/well of 5% sodium dodecyl sulfate (SDS) solution. Absorbance (OD415-490) was determined using a plate reader (SPECTRA Max 340PC, Molecular Devices) at a sample wavelength of 415 nm and a reference wavelength of 490 nm.
As a result, CD74-HER2 bispecific antibody hLL1-4D5/mvG4-4 F bound to HER2 protein, like anti-HER2 IgG1 antibody Herceptin F. Further, hLL1-4D5/mvG4-4 F bound to CD74 protein, like anti-CD74 IgG1 antibody hLL1 F [FIGS. 18 (a) to (b)].
Therefore, CD74-HER2 bispecific antibody hLL1-4D5/mvG4-4 F prepared on the basis of the heterodimer scaffold protein (HSP) composed of CH and CL-Fc was found to be a heterodimer protein having a divalent binding activity.
Example 9 Complement-Dependent Cytotoxicity (CDC Activity) of Heterodimer Protein
CDC activity of the monovalent antibody composed of two polypeptides of H chain and CL-Fc chain prepared in Example 3 was measured according to the method described in WO 2011/108502. The experiment was repeated three times. CD20-positive Burkitt lymphoma cell line ST-486 (ATCC: CRL-1647) was used as a target cell.
50 μL of the target cells diluted by 1.0×106/mL using RPMI1640 (Wako Pure Chemical Industries, Ltd.) containing 10% FBS (JRH), 50 μL of the antibody solution adjusted to 3-fold of the final concentration, and 50 μL of 2-fold diluted human complement (SIGMA) were dispensed in each well of 96-well flat-bottom plate (Sumitomo Bakelite Co., Ltd.). hIgG1 was used as a negative control and anti-CD20 antibody GA101/IgG1 F and anti-CD20 defucosylated antibody GA101/IgG1 DF were used as positive controls.
Further, the well containing no antibody was prepared as a 0% reaction well, and the well containing no target cell was prepared as a 100% reaction well. The cells were cultured at 37° C. (5% CO2) for 2 hours, and then 15 μL of WST-1 (ROCHE) was added to each reaction well, and cultured at 37° C. (5% CO2) for 3 hours.
After completing the reaction, OD450 of each well was measured and cytotoxicity (%) was calculated using the following Equation.

Cytotoxicity (%)=100×{1−(absorbance of reaction well−absorbance of 100% reaction well)/(absorbance of 0% reaction well−absorbance of 100% reaction well)}

CDC activity per mol concentration of anti-CD20 IgG1 type monovalent antibody was shown in FIG. 19. As a result, the anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 F and anti-CD20 IgG1 type defucosylated monovalent antibody GA101/mvG1-2 DF showed increased CDC activity, compared to anti-CD20 antibody GA101/IgG1 F and GA101/IgG1 DF.
Example 10 C1q Binding Activity of Heterodimer Protein
Binding of IgG antibody, monovalent antibody and C1q bound to thereof on cell surface were measured by flow cytometry. CD20-positive tumor cell line Raji (JCRB9012) and ST-486 (ATCC: CRL-1647) were used as target cells. The target cells were adjusted to 4×106/mL using BSA-PBS (NACALAI TESQUE, INC.), and 1/20-diluted mouse serum (CEDARLANE) was further added, and left at room temperature for 5 minutes.
50 μL of this cell suspension was dispensed in each well of 96-well U plate (FALCON) and each 50 μL of 3-fold diluted concentration antibody solution (GA101/IgG1 F, GA101/mvG1-2 F, hIgG1) in BSA-PBS and 3-fold concentration of purified Clq (SIGMA, C1740) were added. Buffer was added as a negative control.
Each well was suspended, and left on ice for 1 hour. Then, the supernatant was discarded by centrifugation. 180 μL of BSA-PBS was added to each well, and the supernatant was also discarded by centrifugation. This manipulation was repeated twice for washing.
Thereafter, 30 μL of 10 μg/mL FITC-labeled anti-human IgG-Fc antibody (Abeam, ab99763) or FITC-labeled anti-C1q antibody (Dako, F0254) was added to each well, and left on ice under shading conditions for 30 minutes. Thereafter, the above described washing manipulation was repeated twice, and they were suspended in 180 μL of BSA-PBS to use as a measurement sample.
Mean Fluorescent Intensity (MFI) of each measurement sample was determined by flow cytometry. A ratio of MFI of the sample well to that of the negative control well was calculated as Relative Fluorescent Intensity (RFI). With respect to antibody concentration and RFI value, the binding amount of antibody to Raji cell and the binding amount of C1q to Raji cell are shown in FIGS. 20(a) and 20(b), respectively, and the binding amount of antibody to ST-486 cell and the binding amount of C1q to ST-486 cell are shown in FIGS. 21A and 21B, respectively.
In both Raji [FIGS. 20(a) and (b)] and ST-486 [FIGS. 21(a) and (b)], the binding amount of anti-IgG-Fc antibody was increased in monovalent antibody GA101/mvG1-2 F, compared to IgG1 antibody GA101/IgG1 F [FIGS. 20(a) and 21(a)], and the binding amount of anti-C1q antibody was increased in monovalent antibody GA101/mvG1-2 F, compared to IgG1 antibody GA101/IgG1 F [FIGS. 20(b) and 21(b)].
Meanwhile, it was already confirmed that affinities of anti-IgG-Fc antibody for GA101/IgG1 F and GA101/mvG1-2 F used in this experiment were equivalent (data not shown). These results suggest that the antigen binding activity of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 F was reduced, compared to that of anti-CD20 IgG antibody GA101/IgG1 F, but the C1q binding activity of anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 F was increased compared to anti-CD20 IgG antibody GA101/IgG1 F.
Example 11 Preparation of CDC Enhanced-Heterodimer Protein
In order to prepare a CDC enhanced-monovalent antibody as a CDC enhanced-heterodimer protein, a monovalent antibody expression vector including a CDC enhanced-Fc region (WO 2011/108502) was prepared in the following manner.
(1) Preparation of H Chain Vector
The amino acid sequence of Fc region of H chain constant region 1H1 described in Example 1 was substituted with the amino acid sequence of Fc region of the high CDC constant region represented by SEQ ID NO: 3, described in WO 2011/108502. The fragments of CH2 and CH3 regions of IgG1-CH vector 1H1 were digested with the restriction enzymes, BmgBI and EcoT22I.
In the same manner, the pKTX93/113 F-N392K vector (WO 2011/108502) containing CDC enhanced-Fc region was treated with the restriction enzymes, BmgBI and EcoT22I, and the digested BmgBI-EcoT22I fragment was inserted into the IgG1-CH vector 1H1. Consequently, a monovalent antibody H chain vector including CDC enhanced-Fc region (hereinafter, abbreviated to HCVcom) was obtained.
(2) Preparation of L Chain Vector
In the same manner as in (1), the amino acid sequence of Fc region of CL-Fc (1L1) described in Example 1 was substituted with the amino acid sequence of Fc region of the high CDC constant region represented by SEQ ID NO: 3, described in WO 2011/108502, so as to obtain a monovalent antibody L chain vector including CDC enhanced-Fc (hereinafter, abbreviated to LCVcom).
(3) Preparation of CDC Enhanced-Monovalent Antibody Expression vector
HCVcom and LCVcom obtained in (1) and (2) above were introduced into CH and CL regions of pKANTEX93/mvG1-2 described in Table 3 of Example 1 in the following manner. The ApaI site present at the 5′-terminus of CH1 region and the BamHI site present at the 3′-terminus of CH3 region of HCVcom were cleaved with each restriction enzyme and inserted into the corresponding site of pKANTEX93/mvG1-2, and subsequently, the BsiWI site present at the 5′-terminus of Cκ region and the PmaCI site present at the 3′-terminus of CH3 region of LCVcom were cleaved with each restriction enzyme and inserted into the corresponding site.
Consequently, a monovalent antibody expression vector including CDC enhanced-Fc (hereinafter, referred to as pKANTEX93/mvCom) was obtained. The amino acid sequences of the constant regions of H chain and L chain of the prepared pKANTEX93/mvCom are shown in FIGS. 22A and 22B.
Further, in order to prepare CDC enhanced anti-CD20 antibody GA101, DNAs encoding the amino acid sequences (SEQ ID NOs: 36 and 38) of GA101-VH and VL were inserted into the appropriate sites of pKTX93/113 F-N392K vector (WO 2011/108502) to prepare CDC enhanced anti-CD20 divalent antibody GA101/IgG1-Com expression vector.
(4) Production of CDC Enhanced-Monovalent Antibody
Production of CDC enhanced-monovalent and divalent antibodies was performed in the same manner as in Example 3, and anti-CD20 monovalent antibody expression vector pKANTEX93/mvG1-2 and CDC enhanced anti-CD20 monovalent antibody expression vector pKANTEX93/mvCom were introduced into CHO/FUT8KO cell, and the monovalent antibodies having no α1,6-fucose at the N-linked sugar chain, GA101/mvG1-2 DF and GA101/mvCom DF, or the divalent antibody GA101/IgG1-Com DF were expressed.
The purification of monovalent antibodies was performed in the same manner as in Example 2(2), except that Protein A purification was performed using a MabSelectSuRe (GE Healthcare) carrier, and 0.1 M citrate buffer of pH 3.9 was used as an elution buffer. The purified proteins were subjected to SDS-PAGE analysis in the same manner as in Example 2(3).
As shown in FIG. 23, the molecular weights of both of CL-Fc chain and H chain of the monovalent antibody were approximately 50 kDa, and a single band around 50 kDa was found under reducing conditions, and a single band around 100 kDa predicted as the heterodimer composed of two polypeptide chains of H chain and CL-Fc chain was recognized under non-reducing conditions. Therefore, the uniform monovalent antibodies, GA101/mvG1-2 DF and GA101/mvCom DF were purified.
These results suggest that not only IgG1 and IgG4 type monovalent antibodies, but also the CDC enhanced-monovalent antibodies including plural amino acid residue substitutions in the constant region can be specifically purified as heterodimer protein by Protein A with adding amino acid substitutions of H435Y/Y436F to CL-Fc chain.
That is, it was revealed that it is possible to prepare a heterodimer protein including plural amino acid residue substitutions in the first polypeptide and/or the second polypeptide.
Example 12 CDC Activity of CDC Enhanced-Heterodimer Protein
CDC activity of the monovalent antibody composed of two polypeptides of H chain and CL-Fc chain prepared in Example 11 was measured by the method described in WO 2011/108502. The experiment was performed three times. CD20-positive human lymphoma cell Raji (JCRB9012) and chronic B cell leukemia cell MEC-1 (DSMZ: ACC-497) were used as target cells. Hereinafter, CDC activity was measured in the same manner as in Example 9.
The results are shown in FIGS. 24(a) and (b). The CDC enhanced anti-CD20 monovalent antibody GA101/mvCom DF showed enhanced CDC activity, compared to anti-CD20 IgG1 type monovalent antibody GA101/mvG1-2 DF. Further, the CDC enhanced anti-CD20 high monovalent antibody GA101/mvCom DF showed equivalent CDC activity to the CDC enhanced divalent anti-CD20 antibody GA101/IgG1-Com DF in the high concentration range.
Therefore, it was also revealed that the CDC activity of monovalent antibody was increased by plural amino acid residue substitutions of the antibody constant region in the monovalent antibody which is a heterodimer protein composed of H chain and CL-Fc, like in the divalent IgG antibody.
Example 13 ADCC Activity of Heterodimer Protein
The ADCC activity of CDC enhanced anti-CD20 monovalent antibody GA101/mvCom DF which is the CDC enhanced-heterodimer protein prepared in Example 11 was measured in the same manner as in Example 7(2). CD20-positive human lymphoma cell Raji (JCRB9012) and chronic B cell leukemia cell MEC-1 (DSMZ: ACC-497) were used as target cells.
hIgG1 (Millipore, AG-502) was used as a negative control, anti-CD20 IgG1 type defucosylated monovalent antibody GA101/mvG1-2 DF was used as a positive control, and anti-CD20 IgG1 type fucosylated monovalent antibody GA101/mvG1-2 F was used as a comparison control.
The results are shown in FIGS. 25 (a) and (b). It was found that the CDC enhanced anti-CD20 defucosylated monovalent antibody GA101/mvCom DF showed high ADCC activity, equivalent to that of anti-CD20 IgG1 type defucosylated monovalent antibody GA101/mvG1-2 DF.
Though the present invention has been described in detail by using specific embodiments, a person skilled in the art knows clearly that the various changes and modifications can be made within a range which does not depart from the spirit and scope of the present invention. The present application is based on U.S. provisional application (No. 61/710,221) filed on Oct. 5, 2012, the entire content of which is incorporated herein as reference.
SEQ ID NO: 1—Nucleotide sequence of DNA of human IgG1CH
SEQ ID NO: 2—Amino acid sequence of human IgG1CH
SEQ ID NO: 3—Nucleotide sequence of DNA of human IgG4CH
SEQ ID NO: 4—Amino acid sequence of human IgG4CH
SEQ ID NO: 5—Nucleotide sequence of DNA of human IgG1CH-His
SEQ ID NO: 6—Amino acid sequence of human IgG1CH-His
SEQ ID NO: 7—Nucleotide sequence of DNA of human IgG4CH-His
SEQ ID NO: 8—Amino acid sequence of human IgG4CH-His
SEQ ID NO: 9—Nucleotide sequence of DNA of 1H0
SEQ ID NO: 10—Amino acid sequence of 1H0
SEQ ID NO: 11—Nucleotide sequence of DNA of 1H1
SEQ ID NO: 12—Amino acid sequence of 1H1
SEQ ID NO: 13—Nucleotide sequence of DNA of 4H0
SEQ ID NO: 14—Amino acid sequence of 4H0
SEQ ID NO: 15—Nucleotide sequence of DNA of 4H1
SEQ ID NO: 16—Amino acid sequence of 4H1
SEQ ID NO: 17—Nucleotide sequence of DNA of 4H2
SEQ ID NO: 18—Amino acid sequence of 4H2
SEQ ID NO: 19—Nucleotide sequence of DNA of 4H3
SEQ ID NO: 20—Amino acid sequence of 4H3
SEQ ID NO: 21—Nucleotide sequence of DNA of 1L0
SEQ ID NO: 22—Amino acid sequence of 1L0
SEQ ID NO: 23—Nucleotide sequence of DNA of 1L1
SEQ ID NO: 24—Amino acid sequence of 1L1
SEQ ID NO: 25—Nucleotide sequence of DNA of 4L0
SEQ ID NO: 26—Amino acid sequence of 4L0
SEQ ID NO: 27—Nucleotide sequence of DNA of 4L1
SEQ ID NO: 28—Amino acid sequence of 4L1
SEQ ID NO: 29—Nucleotide sequence of DNA of 4L2
SEQ ID NO: 30—Amino acid sequence of 4L2
SEQ ID NO: 31—Nucleotide sequence of DNA of 4L3
SEQ ID NO: 32—Amino acid sequence of 4L3
SEQ ID NO: 33—Nucleotide sequence of DNA of 4L4
SEQ ID NO: 34—Amino acid sequence of 4L4
SEQ ID NO: 35—Nucleotide sequence of DNA of GA101 VH
SEQ ID NO: 36—Amino acid sequence of GA101 VH
SEQ ID NO: 37—Nucleotide sequence of DNA of GA101 VL
SEQ ID NO: 38—Amino acid sequence of GA101 VL
SEQ ID NO: 39—Nucleotide sequence of DNA of 4D5 VH
SEQ ID NO: 40—Amino acid sequence of 4D5 VH
SEQ ID NO: 41—Nucleotide sequence of DNA of 4D5 VL
SEQ ID NO: 42—Amino acid sequence of 4D5 VL
SEQ ID NO: 43—Nucleotide sequence of DNA of CD74 VH
SEQ ID NO: 44—Amino acid sequence of CD74 VH
SEQ ID NO: 45—Nucleotide sequence of DNA of CD74 VL
SEQ ID NO: 46—Amino acid sequence of CD74 VL
SEQ ID NO: 47—Nucleotide sequence of DNA of GS linker
SEQ ID NO: 48—Amino acid sequence of GS linker
SEQ ID NO: 49—Nucleotide sequence of DNA of 2F2 VH
SEQ ID NO: 50—Amino acid sequence of 2F2 VH
SEQ ID NO: 51—Nucleotide sequence of DNA of 2F2 VL
SEQ ID NO: 52—Amino acid sequence of 2F2 VL
SEQ ID NO: 53—Nucleotide sequence of DNA of CD74VL-CL-Fc-2F2scFv
SEQ ID NO: 54—Amino acid sequence of CD74VL-CL-Fc-2F2scFv
SEQ ID NO: 55—Nucleotide sequence of DNA of CD74VL-CL-Fc-4D5scFv
SEQ ID NO: 56—Amino acid sequence of CD74VL-CL-Fc-4D5scFv
SEQ ID NO: 57—Nucleotide sequence of DNA of human Cκ
SEQ ID NO: 58—Amino acid sequence of human Cκ

## Claims

1. A heterodimer protein that is
(i) a heterodimer protein composed of
a first polypeptide comprising a heavy chain variable region (VH) and an immunoglobulin G (IgG)1 heavy chain constant region (CH), and
a second polypeptide comprising a light chain variable region (VL) and a fusion polypeptide (CL-Fc) prepared by fusion of a light chain constant region (CL) and an Fc region of IgG1,
wherein the heterodimer protein has a modification selected from the group consisting of:
(a-i) substitutions of C220S in the first polypeptide and H435R in the second polypeptide,
(b-i) substitutions of C214S and H435R in the second polypeptide,
(c-i) substitutions of C220S in the first polypeptide and C214S and H435R in the second polypeptide,
(d-i) substitutions of C220S in the first polypeptide and C220S, C214S and H435R in the second polypeptide,
(e-i) substitutions of C220S in the first polypeptide and C214S and H435R in the second polypeptide and a deletion of positions 216-220 in the second polypeptide,
(f-i) substitutions of C220S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(g-i) substitutions of C220S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide,
(h-i) substitutions of C220S, K332A and P331S in the first polypeptide, and C214S, K322A, P331S, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide, and
(j-i) substitutions of C220S and I332E in the first polypeptide and C214S, I332E, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide, numbering according to the EU index of Kabat (“the EU index”), or

(ii) a heterodimer protein composed of
a first polypeptide comprising a VH and an IgG4 CH, and
a second polypeptide comprising a VL and a CL-Fc prepared by fusion of a CL and an Fc region of IgG4,
wherein the heterodimer protein has a modification selected from the group consisting of:
(a-ii) substitutions of C131S in the first polypeptide and C214S and H435R in the second polypeptide,
(b-ii) substitutions of C131S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(c-ii) substitutions of C131S and R409K in the first polypeptide and C214S, R409K, H435R and Y436F in the second polypeptide,
(d-ii) substitutions of C131S, S228P and R409K in the first polypeptide and C214S, S228P, R409K, H435R and Y436F in the second polypeptide,
(e-ii) substitutions of C131S, S228P, L235E and R409K in the first polypeptide and C214S, S228P, L235E, R409K, H435R and Y436F in the second polypeptide,
(f-ii) substitutions of C131S and R133K in the first polypeptide and C214S and H435R in the second polypeptide,
(g-ii) substitutions of C131S and R133K in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(h-ii) substitutions of C131S, R133K and R409K in the first polypeptide and C214S, R409K, H435R and Y436F in the second polypeptide,
(j-ii) substitutions of C131S, R133K, S228P and R409K in the first polypeptide and C214S, S228P, R409K, H435R and Y436F in the second polypeptide, and
(k-ii) substitutions of C131S, R133K, S228P, L235E and R409K in the first polypeptide and C214S, S228P, L235E, R409K, H435R and Y436F in the second polypeptide, numbering according to the EU index of Kabat,

wherein in (i) and (ii), the VH of the first polypeptide and the VL of the second polypeptide forms a binding domain.

2. The heterodimer protein according to claim 1, wherein the heterodimer protein is the heterodimer protein of (ii).

3. The heterodimer protein according to claim 1, wherein the heterodimer protein of (ii) has a modification selected from the group consisting of (d-ii), (e-ii), (j-ii) and (k-ii).

4. The heterodimer protein according to claim 1, wherein the heterodimer protein of (ii) has a modification selected from the group consisting of (c-ii), (d-ii), (e-ii), (h-ii), (j-ii) and (k-ii).

5. The heterodimer protein according to claim 1, wherein the heterodimer protein of (ii) has a modification selected from the group consisting of (e-ii) and (k-ii).

6. The heterodimer protein according to claim 1, wherein the heterodimer protein is the heterodimer protein of (i).

7. The heterodimer protein according to claim 1, wherein the heterodimer protein of (i) has a modification selected from the group consisting of (e-i), (g-i), (h-i) and (j-i).

8. The heterodimer protein according to claim 1, wherein the Fc region in (i) and (ii) have N-glycoside linked sugar chains bound thereto, and a content of fucose-free sugar chains is 20% or more based on the total N-glycoside linked sugar chains of the heterodimer protein.

9. The heterodimer protein according to claim 1, wherein the first polypeptide in (i) or (ii) and/or the second polypeptide (i) or (ii) has one or more additional amino acid residue substitutions selected from the group consisting of P247I, F243L, R292P, Y300L, Y300F, P396L, T393A, H433P, S239D, S298A, A330L, I332E, E333A, K334A, L235E, P238A, N297A, K322A, P331S, K326A, S267E, H268F, S324T, K274Q, N276K, Y296F, K326W, K326Y, E333A, E333S, A339T, A339D, D356E, L358M, N384S, K392N, T394F, T394Y, V397M and V422I, numbering according to the EU Index.

10. The heterodimer protein according to claim 1, which further comprises one or more binding proteins bound at the N-terminus and/or the C-terminus of the CH of the first polypeptide in (i) or (ii) and the CL-Fc of the second polypeptide in (i) or (ii).

11. The heterodimer protein according to claim 10, wherein the one or binding proteins are selected from the group consisting of an antibody variable region, a single chain Fv and a single variable domain.

12. The heterodimer protein according to claim 1, which further comprises an immunoglobulin heavy chain variable region bound at the N-terminus and/or C-terminus of the CH of the first polypeptide in (i) and/or (ii), and an immunoglobulin light chain variable region bound at the N-terminus and/or C-terminus of the CL-Fc of the second polypeptide in (i) and/or (ii).

13. The heterodimer protein according to claim 1, which further comprises an immunoglobulin light chain variable region bound at the N-terminus and/or C-terminus of the CH of the first polypeptide in (i) and/or (ii), and an immunoglobulin heavy chain variable region bound at the N-terminus and/or C-terminus of the CL-Fc of the second polypeptide in (i) and/or (ii).

14. The heterodimer protein according to claim 11, wherein the heterodimer protein is selected from the group consisting of a monovalent antibody, a divalent antibody, a trivalent antibody and a tetravalent antibody.

15. The heterodimer protein according to claim 1, which further comprises a light chain variable region or a heavy chain variable region at the N-terminus and/or the C-terminus of the first polypeptide in (i) or (ii) and/or the second polypeptide in (i) or (ii).

16. The heterodimer protein according to claim 15, which is bispecific and binds to CD74 and Her2 or CD74 and CD20.

17. A heterodimer protein that is
(i) a heterodimer protein composed of
a first polypeptide comprising a light chain variable region (VL) and an IgG1 heavy chain constant region (CH), and
a second polypeptide comprising a heavy chain variable region (VH) and a fusion polypeptide (CL-Fc) prepared by fusion of a light chain constant region (CL) and an Fc region of IgG1,
wherein the heterodimer protein has a modification selected from the group consisting of:
(a-i) substitutions of C220S in the first polypeptide and H435R in the second polypeptide,
(b-i) substitutions of C214S and H435R in the second polypeptide,
(c-i) substitutions of C220S in the first polypeptide and C214S and H435R in the second polypeptide,
(d-i) substitutions of C220S in the first polypeptide and C220S, C214S and H435R in the second polypeptide,
(e-i) substitutions of C220S in the first polypeptide and C214S and H435R in the second polypeptide and a deletion of positions 216-220 in the second polypeptide,
(f-i) substitutions of C220S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(g-i) substitutions of C220S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide,
(h-i) substitutions of C220S, K332A and P331S in the first polypeptide, and C214S, K322A, P331S, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide, and
(j-i) substitutions of C220S and I332E in the first polypeptide and C214S, I332E, H435R and Y436F in the second polypeptide and a deletion of positions 216-220 in the second polypeptide, numbering according to the EU index of Kabat (“the EU index”), or

(ii) a heterodimer protein composed of
a first polypeptide comprising a VL and an IgG4 CH, and
a second polypeptide comprising a VH and a CL-Fc prepared by fusion of a CL and an Fc region of IgG4,
wherein the heterodimer protein has a modification selected from the group consisting of:
(a-ii) substitutions of C131S in the first polypeptide and C214S and H435R in the second polypeptide,
(b-ii) substitutions of C131S in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(c-ii) substitutions of C131S and R409K in the first polypeptide and C214S, R409K, H435R and Y436F in the second polypeptide,
(d-ii) substitutions of C131S, S228P and R409K in the first polypeptide and C214S, S228P, R409K, H435R and Y436F in the second polypeptide,
(e-ii) substitutions of C131S, S228P, L235E and R409K in the first polypeptide and C214S, S228P, L235E, R409K, H435R and Y436F in the second polypeptide,
(f-ii) substitutions of C131S and R133K in the first polypeptide and C214S and H435R in the second polypeptide,
(g-ii) substitutions of C131S and R133K in the first polypeptide and C214S, H435R and Y436F in the second polypeptide,
(h-ii) substitutions of C131S, R133K and R409K in the first polypeptide and C214S, R409K, H435R and Y436F in the second polypeptide,
(j-ii) substitutions of C131S, R133K, S228P and R409K in the first polypeptide and C214S, S228P, R409K, H435R and Y436F in the second polypeptide and
(k-ii) substitutions of C131S, R133K, S228P, L235E and R409K in the first polypeptide and C214S, S228P, L235E, R409K, H435R and Y436F in the second polypeptide, numbering according to the EU index of Kabat,

wherein in (i) and (ii), the VL of the first polypeptide and the VH of the second polypeptide forms a binding domain.