ABM BINDING MOLECULE ABM ANTIGEN BINDING MOLECULES ISOLATED POLYPEPTIDE VARIANT HUMANIZED ANTIGEN BI

专利摘要:
antigen binding molecule (abm), anti-cea antibody, antibody that specifically binds to cea, polynucleotide, vector, transgenic microorganism, method of producing an abm, composition, method for in vitro diagnosis of disease, use of abm, use of the antibody and use of the composition The present invention relates to antigen binding molecules (abms). in specific embodiments, the present invention pertains to recombinant monoclonal antibodies, including chimeric, primatized, humanized antibodies or variants thereof specific for membrane or cell surface bound human cea. further, the present invention relates to nucleic acid molecules encoding such abms and vectors and host cells comprising such nucleic acid molecules. the present invention further pertains to methods of producing abms as defined in the present invention and to methods of using such abms in the treatment of disease. further, the present invention relates to glycosylated modified abms that have improved therapeutic properties, including antibodies with increased fc receptor binding and increased effector function.
公开号:BR112012003983A2
申请号:R112012003983-0
申请日:2010-08-27
公开日:2021-09-14
发明作者:Thomas U. HOFER；Ekkehard Moessener；Pablo Umana；Ralf Hosse
申请人:Roche Glycart Ag；
IPC主号:

专利说明:

"ANTIGEN BINDING MOLECULE (ABM), ANTI-CEA ANTIBODY, ANTIBODY THAT SPECIFICALLY BINDS CEA, POLYNUCLEOTIDE, VECTOR, TRANSGENIC MICRO-ORGANISM, METHOD OF PRODUCTION OF AN ABM, COMPOSITION, METHOD FOR 5 IN V/TRO DIAGNOSIS DISEASE, ABM USE, ANTIBODY USE AND COMPOSITION USE" BACKGROUND OF THE INVENTION
FIELD OF THE INVENTION The present invention relates to antigen binding molecules (ABMs). In specific embodiments, the present invention relates to recombinant monoclonal antibodies, including chimeric, primatized, or humanized antibodies specific for human carcinoembryonic antigen (CEA). Furthermore, the present invention relates to nucleic acid molecules encoding such ABMs and vectors and host cells comprising such nucleic acid molecules. The present invention further relates to methods of producing the ABMs in accordance with the present invention and to methods of using such ABMs in the treatment of disease. Furthermore, the present invention relates to glycosylated modified ABMs that have improved therapeutic properties, including antibodies with increased Fc receptor binding and increased effector function, such as ADCC.
BACKGROUND ART Carcinoembryonic antigen (CEA) and anti-CEA antibodies: Carcinoembryonic antigen (CEA, also known as CEACAM-5 or CD66e) is a glycoprotein that has a molecular weight of about 180 kDa. CEA is a member of the immunoglobulin superfamily and contains seven domains that are linked to the cell membrane via a glycosylphosphatidylinositol (GPI) anchor (Thompson, J.A., J. Clin. Lab. Anal. 5:344-366, 1991). The seven domains include a single N-terminal Ig variable domain and six domains (A1-81-A2-82-A3-83) homologous to the Ig constant domain (Hefta, L J. et al., Cancer Res. 52:5647 -5655, 1992).
The human CEA family contains 29 genes, of which 18 are expressed: seven belonging to the CEA subgroup and eleven to the pregnancy-specific glycoprotein subgroup 5. Several CEA subgroup members are believed to possess cell adhesion properties. CEA is believed to play a role in innate immunity (Hammarström, S., Semin.
Cancer Biol. 9(2):67-81 (1999)). Due to the existence of closely related proteins to CEA, it can be challenging to raise anti-CEA antibodies that are specific for CEA with minimal cross-reactivity to the other closely related proteins.
CEA has long been identified as a tumor-associated antigen (Gold and Freedman, J. Exp. Med., 121: 439-462, 1965; Berinstein, N.L., J.
Clinic Oncol., 20: 2197-2207, 2002). Originally classified as a protein expressed only in fetal tissue, CEA has now been identified in several normal adult tissues. These tissues are primarily epithelial in origin, including cells from the gastrointestinal, respiratory, and urogenital tracts, and cells from the colon, cervical, sweat glands, and prostate (Nap et al., TumourBiol., 9(2-3): 145-53, 1988; Nap et al., Cancer Res., 52(8): 2329-23339, 1992).
Tumors of epithelial origin, as well as their metastases, contain CEA as a tumor-associated antigen. Although the presence of CEA itself does not indicate transformation into a cancer cell, the distribution of CEA is indicative. In normal tissue, CEA is usually expressed on the apex surface of the cell (Hammarström, S., Semin. Cancer Biol. 9(2): 67-81 (1999)), making it inaccessible to antibody in the blood stream. Unlike normal tissue, CEA tends to be expressed over the entire surface of cancer cells (Hammarström, S., Semin. Cancer Biol. 9(2): 67-81 (1999)). This change in expression pattern makes CEA accessible to antibody binding in cancer cells. In addition, CEA expression increases in cancer cells.
Additionally, increased expression of CEA promotes increased intercellular adhesions, which can lead to metastasis (Marshall, J., Semin. Oncol., 30 (a Suppl. 8): 30-6, 2003 ).
5 CEA is easily broken down from the cell surface and cut off in the blood stream from tumors, either directly or via the lymphatic pathway.
Because of this property, the serum CEA level has been used as a clinical marker of cancer diagnosis and selection in search of recurrence of cancers, particularly colorectal cancer (Goldenberg, OM, The /ntemational Journal of Bio / ogica / Markers, 7: 183-188, 1992; Chau, I. et al., J. Clin. Oncol., 22: 1420-1429, 2004; Flamini et al., C/in. Cancer Res. 12 (23): 6985-6988, 2006) . This property also represents one of the challenges of using CEA as a target, as serum CEA binds to most of the anti-CEA antibodies currently available, preventing them from reaching their target on the cell surface and limiting potential clinical effects.
Various monoclonal antibodies have been raised against CEA for research purposes, as diagnostic tools, and for therapeutic purposes (such as in Nap et al., Cancer Res., 52(8): 2329-23339, 1992; Sheahan et al., Am. J
Clinic Path. 94: 157-164, 1990; Sakurai et al., J. Surg. Oncol., 42: 39-46, 1989; Goldenberg, D.M., The Internationale/Journal of Biological Markers, 7: 183-188, 1992; Ledermann, J.A., Br.J. Cancer, 58:654, 1988; Ledermann, J.A., Br.J. Cancer, 68: 69-73, 1993; Pedley, R.B. et al., Br.J. Cancer, 68:69-73, 1993; Boxer, G.M. et al., Br.J. Cancer, 65: 825-831, 1992). Chester et al isolated a single-stranded anti-CEA antibody from a phage display library to be used in radioimmunodetection and radioimmunotherapy (U.S. Patent No. 5,876,691) and the antibody was then humanized (U.S. Patent No. 7,232). .888).
Anti-CEA antibodies have been isolated from human phage display libraries (U.S. Patent No. 5,872,215).
Mouse monoclonal antibody PR1A3 was elevated by fusion of NS1 myeloma cells (P3/NS1/I-Ag-4-1) with spleen cells from mice immunized with normal colorectal epithelium (Richman, Pl and 8odmer, WF, Int. J. Cancer, 39: 317-328, 1987). PR1A3 reacts strongly to well- and poorly-differentiated colorectal carcinomas and has advantages over other colorectal epithelial-reactive antibodies in that its antigen is apparently attached to the tumor and is not found in the lymphatics or normal lymph nodes that drain a tumor (Granowska, M. et al., Eur. J. Nucl. Med., 20: 690-698, 1989). PR1A3 reacted, for example, with 59/60 colorectal tumors (Richman, P.I.
and 8odmer, W.F., Int. J. Cancer, 39: 317-328, 1987}, while the CEA 872.3 reactive antibody reacted with only 75% of colorectal tumors (Mansi, L. et al, Int. J.
Rad. App. lnstrum. B., 16(2): 127-35, 1989).
Epitope mapping of PR1A3 demonstrates that the antibody targets domain 83 and the GPI anchor of the CEA molecule (Durbin, H. et al., Proc.
natl. academy Know. U.S.A., 91:4313-4317, 1994). Consequently, the PR1A31 antibody binds only to the membrane-bound CEA and not to the soluble form of CEA that can be found in the blood streams of cancer patients. Due to this binding property, the PR1A3 antibody is unlikely to be sequestered by serum CEA; on the other hand, it can direct expressed CEA on cancer cells. The epitope bound by PR1A3 is a conformational epitope, not a linear epitope, which is believed to contribute to the loss of binding of PR 1A3 to soluble CEA (Stewart et al., Cancer Immunol. Immunother., 47: 299-06, 1999). ).
The PR1A3 antibody was previously humanized by grafting the CDRs from the parent antibody! in the heavy chain backbone regions 1 to 3 of the human antibody RF-TS3'CL (which retains the murine backbone chain 4 of PR1A3) and the light chain backbone regions of the REI antibody. (Stewart et al., Cancer/mmunol. Immunother., 47: 299-06, 1999). This humanized version of PR1A3 retained specificity for surface expressed CEA with similar affinity to that of the murine antibody (Stewart et al., Cancer Immunol.
Immunother., 47: 299-06, 1999; U.S. Patent No. 5,965,710).
A humanized PR1A3 (hPR1A3) has been shown to induce targeted killing of 5 colorectal cancer cell lines (Conaghhan, P.J. et al., Br.J. Cancer, 98(7): 1217-1225). The affinity of hPR1A3 for CEA, however, is relatively low.
Radiolabeled anti-CEA antibodies have been used in clinical trials in patients with colorectal cancer. A 123-labeled chimeric minibody 1T84.66 (cT84.66), for example, was used in a pilot clinical study in patients with colorectal cancer. The radiolabeled minibody was able to target cancer cells (Wong, J.Y. et al., Clin. Cancer Res. 10 (15): 5014-21, (2004)).
In another example, (131)1-labetuzumab, a radiolabeled humanized anti-CEA antibody, was tested in adjuvant radioimmunotherapy in patients with liver metastases from colorectal cancer and concluded that it provides a promising survival advantage (Liersch, T et al., Am. Surg. Onco/. 14 (9): 2577-90, (2007)).
GLYCOSYLATION OF ANTIBODIES: The oligosaccharide component can significantly affect properties relevant to the effectiveness of a therapeutic glycoprotein, including physical stability, resistance to protease attack, interactions with the immune system, pharmacokinetics, and specific biological activity. These properties may depend not only on the presence or absence, but also on the specific structures of oligosaccharides. Some generalizations can be made between oligosaccharide structure and glycoprotein function. Certain oligosaccharide structures mediate, for example, the rapid release of the glycoprotein from the blood stream through interactions with specific carbohydrate-binding proteins, while others can be bound by antibodies and trigger unwanted immune reactions (Jenkins et al., Nature Biotechnol. 14). : 975-81, 1996).
Mammalian cells have been the preferred hosts for the production of therapeutic glycoproteins, due to their ability to glycosylate proteins in the most compatible form for human application. (Cumming et al., Glycobiolog 1:115-30, 1991; Jenkins et al., Nature Biotechnol. 14:975-981, 1996). Bacteria glycosylate proteins very rarely and, like other common host types such as yeasts, filamentous fungi, and plant and insect cells, generate glycosylation patterns associated with rapid release from the blood stream, undesirable immune interactions, and, in some specific cases, reduced of biological activity. Among mammalian cells, Chinese hamster ovary (CHO) cells have been most commonly used during the last two decades. In addition to providing appropriate glycosylation patterns, these cells allow for the consistent generation of highly productive and genetically stable clonal cell lines. They can be grown at high densities in simple bioreactors using serum-free media and allow the development of safe and reproducible bioprocesses. Other commonly used animal cells include baby hamster kidney (BHK) cells and NSO and SP2/0 mouse myeloma cells. More recently, production from transgenic animals has also been tested (Jenkins et al., Nature Biotechno. 14: 975-81, 1996).
All antibodies contain carbohydrate structures in conserved positions in the heavy chain constant regions, where each isotype has a distinct set of N-linked carbohydrate structures that variably affect protein assembly, secretion, or functional activity. A. and Morrison, SL, Trends Biotech. 15: 26-32, 1997). The structure of the attached N-linked carbohydrate varies considerably, depending on the degree of processing, and can include high mannose, multiple branching, and also biantenate complex oligosaccharides (Wright, A. and Morrison, SL, Trends Biotech. 15: 26-32, 1997). ). Typically, there is heterogeneous processing of the core oligosaccharide structures linked at a specific glycosylation site, such that even monoclonal antibodies exist in the multi-glycoform population form. Similarly, major differences in antibody glycosylation have been shown to occur between cell lines and even small differences are observed for a given cell line grown under different culture conditions (Lifely, MR et al., Glycobiology 5 (8): 813 -22, 1995).
One way to obtain large increases in potency, while maintaining a simple production process and potentially avoiding significant undesirable side effects, is to improve the natural cell-mediated effector functions of monoclonal antibodies by projecting their oligosaccharide component as described. in Umana, P. et al, Nature Biotechnol. 17: 176-180 (1999); and US Patent No. 6,6082,84, the contents of which are incorporated herein by reference in their entirety. IgG1-like antibodies, the antibodies most commonly used in cancer immunotherapy, are glycoproteins that have a conserved N-linked glycosylation site at Asn297 in each CH2 domain. The two complex biantenate oligosaccharides linked to Asn297 are buried between the CH2 domains, forming extensive contacts with the polypeptide backbone, and their presence is essential for the antibody to mediate effector functions such as antibody-dependent cellular cytotoxicity (ADCC) (Lifely, MR et al., Gycobiology 5: 813-822 (1995); Jefferis, R. et al. Immunol. Rev. 163: 59-76 (1998); Wright, A and Morrison, SL, Trends Biotechnol. 15: 26- 32 (1997)).
Umaria et al have previously observed that overexpression in Chinese hamster ovary (CHO) cells of β(1,4)-N-acetylglucosaminyltransferase 111 ("GnTIII"), a glycosyltransferase that catalyzes the formation of bisected oligosaccharides, significantly increases ADCC activity in vitro of an anti-neuroblastoma chimeric monoclonal antibody (chCE7) produced by engineered CHO cells (see Umafia, P. et al., Nature Biotechnol. 17: 176-180 (1999) and International Patent No. 5 WO 99 /54342, the full content of which is incorporated herein by reference). The chCE7 antibody belongs to a large class of unconjugated mAbs that have high affinity and tumor specificity, but have too little potency to be clinically useful when produced in standard industrial cell lines that do not contain the GnTIII enzyme (Umana, P. et al. , Nature Biotechnol. 17: 176-180 (1999)). This study was the first to demonstrate that large increases in ADCC activity could be obtained by projecting antibody-producing cells to express GnTIII, which also generated an increase in the proportion of bisected oligosaccharides associated with the constant region (Fc), including bisected non-fucosylated oligosaccharides, above levels found in naturally occurring antibodies.
There remains a need for improved therapeutic approaches targeting CEA, particularly membrane-bound CEA for the treatment of cancers in primates, including, but not limited to, humans.
BRIEF DESCRIPTION OF THE INVENTION Recognizing the tremendous therapeutic potential of antigen binding molecules (ABMs) that possess the binding specificity of the PRIA3 antibody and that have been affinity matured and/or glycoengineered to increase the binding affinity of the Fc receptor and/or its effector function, the present inventors provided these ABMs. In one aspect, the present invention relates to variant ABMs and/or affinity matured ABMs that are capable of competing with the PR1A3 antibody for antigen binding. The effectiveness of these ABMs is further enhanced by projecting the glycosylation profile of the antibody Fc region.
In one aspect, the present invention also relates to an antigen-binding molecule (ABM) that comprises an affinity-matured, humanized antigen-binding domain comprising one or more 5 complementarity determining regions (CDRs), wherein said antigen-binding domain specifically binds to membrane-bound human carcinoembryonic antigen (CEA) and wherein said antigen-binding domain binds to the same epitope or is capable of competing for binding with the murine monoclonal antibody PR1A3. The present invention further relates to an ABM according to the present invention, wherein said ABM contains modified oligosaccharides. In one embodiment, the modified oligosaccharides have reduced fucosylation compared to unmodified oligosaccharides. In other embodiments, the modified oligosaccharides are hybrids or complexes. In another aspect, the present invention also relates to polypeptides, polynucleotides, host cells and expression vectors relating to ABMs. In a further aspect, the present invention relates to methods of projecting ABMs. In a further aspect, the present invention relates to methods of using ABMs, particularly for the treatment of diseases relating to abnormal expression of CEA, such as cancer.
BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 shows a schematic diagram of the CEA antigen (CEACAM-5, CD66e). The PRIA3 antibody specifically binds to domain 83 of the antigen when it is bound to the cell membrane.
Figure 2 displays enhanced ADCC activity of a glycoengineered chimeric PR1A3 antibody with human PBMCs as effectors.
Figure 3 displays antigen binding activity of a humanized PR1A3 antibody comprising a heavy chain variable region construct, CH7 A, and a light chain variable region construct, CL 1A.
Figure 4 shows randomization sites to generate an antibody library for affinity maturation of humanized PR1A3 antibody light chain. Positions marked with X were randomized.
Figure 5 shows randomization sites to generate a library of 5 antibodies for humanized PR1A3 antibody heavy chain affinity maturation. Positions marked with X were randomized.
Figure 6 shows binding activity of affinity matured anti-CEA antibodies derived from a humanized PR1A3 antibody comprising a CH7 ArF9 heavy chain variable region construct and a CL 1ArH11 light chain variable region construct.
Figure 7 shows the results of an efficacy study in SCID/bg mice that received intrasplenic administration of LS174T human colorectal carcinoma cells in order to have an orthotopic tumor model.
Antibody therapy was started seven days later by injecting the antibodies at a dose of 25 mg/kg body weight, followed by two additional weekly injections. "CH7A" represents a humanized antibody comprising the CDRs of PR1A3 as described herein. "SM3E" designates a previously generated anti-CEA antibody. "GA201" represents a humanized anti-EGF antibody used as a positive control. "PBS" refers to phosphate-buffered saline, which was used as a negative control. Survival was measured according to termination criteria defined by the Swiss regulatory authority.
Figure 8 shows the results of an efficacy study in SCID/bg mice that received intravenous injection with A549 lung carcinoma cells, in which the tumor is grafted into the animals' lungs.
Antibody therapy was started seven days later by injecting the antibodies at a dose of 25 mg/kg body weight, followed by two additional weekly injections. "CH7A", "SM3E" and "GA201" are as defined for Figure 7, above. The designation "CH7ArF9 CL 1A rH11" represents a CH7A antibody variant with affinity matured light and heavy chains.
The designation "ge" indicates that the antibody was glycoengineered to have reduced amounts of fucosylated oligosaccharides in the Fc region. "Vehicle" designates the negative control. A549 lung carcinoma cells are strongly positive for EGFR expression and weakly positive for CEA expression.
Figure 9 shows the results of an efficacy study in SCID/bg mice that received intrasplenic administration of MKN45 gastric carcinoma cells, which metastasizes tumors to the animals' liver. The designations "CH7ArF9 CL 1A rH11", "SM3E", "ge" and "PBS" are as defined for Figures 7 and 8 above.
Figure 10 shows kinetic analysis of affinity matured clones: (a) shows a sensorgram of anti-CEA Fabs with an affinity matured heavy chain CH7A H4E9 SEQ 10 No. 199) together with unmatured light chain CL 1A (SEQ 10 No 105); an affinity matured light chain CL 1A pAC18 (SEQ 10 No. 209) combined with unmatured heavy chain CH7A; and one of their combinations, CH7A H4E9 and CL 1A pAC18 (SEQ 10 NO. 199 and 209); (b) summary of kinetic analysis of affinity matured clones.
Figure 11 shows a schematic overview of the randomization of COR 1 and CDR2 of the humanized anti-CEA CH7 A antibody heavy chain.
Figure 12 shows a schematic overview of the randomization of CDR1 and CDR2 from the humanized anti-CEA CL 1A antibody light chain.
Figure 13 shows a schematic overview of the CDR3 randomization of the humanized anti-CEA CH7A antibody heavy chain.
Figure 14 shows a schematic overview of the CDR3 randomization of the humanized anti-CEA CL 1A antibody light chain.
Figure 15 shows binding affinity of anti-CEA antibodies for membrane-bound CEA on MKN45 target cells. Humanized anti-CEA antibodies with an affinity matured light chain (Table A, CH A, CL 1ArH7 or CH A, CL 1ArH11) or affinity matured light and heavy chains 5 (Table B, CH A rB9, CL 1A rH11 G2(1)) that have been converted to lgG exhibit enhanced binding compared to the control antibody (CH A, CL 1A).
Figure 16 displays the results of an antibody-dependent cellular cytotoxicity (ADCC) assay for affinity matured antibodies (CH7ArB9, CL1A rH11G2(1), CH7Arf9, CL1A rH11G2(1) and CH A, CL1A rH11 G2(1) ) compared to control antibodies (CH A, CL 1A G2(R2)).
DETAILED DESCRIPTION OF THE INVENTION Definitions: The terms are used herein as generally used in the art, unless otherwise defined as follows.
As used herein, the term "antigen-binding molecule" means, in its broadest sense, a molecule that specifically binds to an antigenic determinant. A non-limiting example of an antigen-binding molecule is an antibody or fragment thereof that maintains specific antigen binding. More specifically, as used herein, an antigen-binding molecule that binds to membrane-bound human carcinoembryonic antigen (CEA) is an ABM that specifically binds to CEA, more specifically to membrane-bound or cell-surface CEA and not the soluble CEA that is broken down from the cell surface. By "binds specifically" is meant that the binding is selective for the antigen and can be discriminated against undesired and non-specific interactions.
As used herein, the term "antibody" is intended to include entire antibody molecules, including monoclonal, polyclonal, and multispecific (such as bispecific) antibodies, as well as antibody fragments that possess an Fc region and retain binding specificity. , and fusion proteins that include a region equivalent to the Fc region of an immunoglobulin and retain binding specificity. Antibody fragments that retain binding specificity are also encompassed, including, but not limited to, VH fragments, VL fragments, Fab fragments, F(ab')2 fragments, scFv fragments, Fv fragments, minibodies, diabodies, triabodys and tetrabodys (see, for example, Hudson and Souriau, Nature Med. 9: 129-134 (2003 )).
As used herein, the term "antigen-binding domain" means the portion of an antigen-binding molecule comprising the area that specifically binds, in whole or in part, an antigen and is complementary thereto. When an antigen is large, an antigen-binding molecule can only bind to a specific portion of the antigen, which is called an epitope. An antigen-binding domain can be provided, for example, by one or more antibody variable domains.
Preferably, an antigen binding domain comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).
As used herein, the term "affinity matured" in the context of antigen-binding molecules (such as antibodies) means an antigen-binding molecule that is derived from a reference antigen-binding molecule, such as through mutation, it binds to the same antigen, preferably binds to the same epitope, of the reference antibody; and has a higher affinity for the antigen than that of the reference antigen-binding molecule. Affinity maturation usually involves the modification of one or more amino acid residues in one or more CDRs of the antigen-binding molecule.
Typically, the affinity matured antigen binding molecule binds to the same epitope as the initial reference antigen binding molecule.
As used herein, "binding affinity" is usually expressed in terms of equilibrium association or dissociation constants (Ka or Kd, respectively), which are, in turn, reciprocal ratios of dissociation and association rate constants. (kd and ka, respectively). In this way, equivalent affinities can comprise different rate constants, as long as the ratio between the rate constants remains the same.
As used herein, the term "Fc region" designates a C-terminal region of an IgG heavy chain. Although the boundaries of the Fc region of an IgG heavy chain may vary slightly, the Fc region of a human IgG heavy chain is normally defined as extending from the amino acid residue at position Cys226 to the carboxyl terminus.
As used herein, the term "region equivalent to the Fc region of an immunoglobulin" is intended to include naturally occurring allelic variants of the Fc region of an immunoglobulin, as well as variants that have alterations that produce substitutions, additions, or deletions, but that do not substantially reduce the immunoglobulin's ability to mediate effector functions (such as antibody-dependent cellular cytotoxicity). One or more amino acids can be deleted, for example, from the N-terminus or C-terminus of the Fc region of an immunoglobulin without substantial loss of biological function.
Such variants may be selected according to general rules known in the art so as to have minimal effect on activity (see, for example, Bowie, J.U. et al, Science 247: 1306-10 (1990).
As used herein, the term "membrane-bound human CEA" means human carcinoembryonic antigen (CEA) which is bound to a membrane portion of a cell or to the surface of a cell, specifically the surface of a tumor cell. The term "membrane-bound human CEA" can, in certain circumstances, designate CEA that is not bound to the membrane of a cell, but which has been constructed in such a way as to preserve the epitope to which the PR1A3 antibody binds. The term "soluble CEA" designates human carcinoembryonic antigen that is not bound or cleaved from a cell membrane or cell surface (such as a tumor cell surface) and/or that typically does not preserve the conformational epitope that is bound. by the PR1A3 antibody. Soluble CEA can be found, for example, in the blood or lymph stream of a cancer patient.
As used herein, the term "absence of substantial 1st cross-reactivity against soluble CEA" indicates that a molecule (such as an antigen-binding molecule) does not specifically recognize or bind soluble CEA, particularly in comparison to CEA bound to membrane. An antigen-binding molecule may bind, for example, less than about 10% to less than about 5% soluble CEA or it may bind soluble CEA in an amount selected from the group consisting of less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.2% or 0.1%, preferably less than about 2%, 1% or 0.5% soluble CEA and more preferably less than about 0.2% or 0.1% soluble CEA.
As used herein, the terms "fusion" and "chimeric", when used with reference to polypeptides such as ABMs, designate polypeptides that comprise amino acid sequences derived from two or more heterologous polypeptides, such as portions of antibodies from different species. For chimeric ABMs, for example, the non-antigen binding components can be derived from a wide variety of species, including primates such as chimpanzees and humans. The constant region of chimeric ABM is generally substantially identical to the constant region of a natural human antibody; the chimeric antibody variable region generally comprises a sequence that is derived from a recombinant anti-CEA antibody that contains the amino acid sequence of the murine variable region PR1A3. Humanized antibodies are a particularly preferred form of fusion or chimeric antibody.
As used herein, the term "humanized" is used to denote an antigen-binding molecule derived, in part, from a non-human antigen-binding molecule, such as a murine antibody, that retains or substantially retains the properties binding of antigens from the parent molecule! but which is less immunogenic in humans. This can be achieved through a variety of methods (hereinafter referred to as "humanization") which include, but are not limited to, (a) grafting entire non-human variable domains onto human constant regions to generate chimeric antibodies, (b) grafting only the CDRs non-human (such as donor antigen binding molecule) over human backbone (such as receptor antigen binding molecule) and constant regions with or without retention of critical backbone residues (such as those that are important for retention of good antigen-binding affinity or antibody functions) or (c) transplanting the entire non-human variable domains, but "disguising" them with a human-like section by replacing surface residues. Such methods are described in Jones et al., Morrison et al., Proc. natl. academy Sci., 81:6851-6855 (1984); Morrison and Oi, Adv. Immunol., 44: 65-92 (1988); Verhoeyen et al., Science, 239: 1534-1536 (1988); Padlan, Molec.
Immun., 28:489-498 (1991); Padlan, Molec.lmmun., 31(3): 169-217 (1994), all of which are incorporated herein by reference in their entirety. There are generally three complementarity determining regions or CDRs (COR 1, CDR2 and CDR3) in each of the light and heavy chain variable domains of an antibody, which are flanked by four main chain subregions (i.e. FR1, FR2, FR3 and FR4) in each of the light and heavy chain variable domains of an antibody: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4. A discussion of humanized antibodies can be found, among others, in U.S. Patent No. 6,632,927 and U.S. Application Published No. 2003/0175269, both of which are fully incorporated herein by reference. Humanization can also be achieved by transplanting truncated CORs that contain only the specificity-determining amino acid residues for a given COR onto a selected main chain. By "specificity determination residues" are denoted residues that are directly involved in specific interaction with antigen and/or that are required for specific antigen binding. Generally, only about one-fifth to one-third of the residues in a given COR participate in antigen binding. Specificity determination residues at a specific COR can be identified, for example, by computing interatomic contacts by three-dimensional modeling and determining sequence variability at a given residue position according to the methods described in Padlan et al. FASEB J. 9(1): 133-139 (1995), the contents of which are fully incorporated herein by reference.
In some cases, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. In addition, humanized antibody binding molecules can comprise residues that are not found in the recipient antibody or the donor antibody. These modifications are made to further refine the performance of the antigen binding molecule. Generally, the humanized antigen-binding molecule will comprise substantially all of at least one, typically two, variable domains, wherein at least one, substantially all or all of the hypervariable regions correspond to those of a non-human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antigen binding molecule will also optionally comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. See, for example, Jones et al., Nature 321: 522-525 (1986); Riechmann et al., Nature 332: 323-329 (1988); and Presta, Curr. Op. Struct.
5 Biol. 2: 593-596 (1992).
Similarly, as used herein, the term "primatized" is used to denote an antigen-binding molecule derived from a non-primate antigen-binding molecule, such as a murine antibody, that retains or substantially retains the binding properties of antigens from the parent molecule!, but which is less immunogenic in primates.
As used herein, the term "variant" (or analogous) polypeptide or polynucleotide means a polynucleotide or polypeptide other than a polypeptide or polynucleotide in accordance with the present invention specifically indicated by means of insertions, deletions and substitutions, created using, for example, example, recombinant DNA methods.
Specifically, recombinant variants encoding these same or similar polypeptides can be synthesized or selected using "redundancy" in the genetic code. Various codon substitutions, such as silent changes that produce multiple restriction sites, can be introduced to optimize cloning into a plasmid or viral vector or expression in a specific prokaryotic or eukaryotic system. Mutations in the sequence of polynucleotides can be reflected in the polypeptide or domains of other peptides added to the polypeptide to modify the properties of any portion of the polypeptide, alter characteristics such as ligand binding affinities, inter-chain affinities, or degradation/yield rate.
As used herein, the term "variant anti-CEA antigen binding molecule" means a molecule that differs in amino acid sequence from a "parent!" by virtue of the addition, deletion and/or substitution of one or more amino acid residues in the parent antibody sequence I. In a specific embodiment, the variant comprises one or more amino acid substitutions in one or more hypervariable regions or light chain CDRs and/or weight of the parent antigen binding molecule. The variant may comprise, for example, at least one, such as at least about one to about ten (i.e., about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10) and preferably about two to about five substitutions in one or more hypervariable regions or CDRs (i.e., one, two, three, four, five or six hypervariable regions or CDRs) of the parent antigen-binding molecule.
A variant anti-CEA antigen binding molecule may also comprise one or more additions, deletions and/or substitutions in one or more main chain regions of the heavy or light chain. Typically, the variant will contain an amino acid sequence that has at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% amino acid sequence identity. with the light chain or heavy chain variable domain sequences of the parent antigen binding molecule, typically at least about 80%, 90%, 95%, or 99%. Sequence identity is defined herein as the percentage of possible amino acid residues in the sequence that are identical to parental antibody residues, after aligning the sequences and introducing gaps, if necessary, to achieve maximum percent identity. of sequences. None of the N-terminal, C-terminal or internal extensions, deletions or insertions in the antibody sequence should be interpreted as affecting sequence homology or identity. The variant antigen-binding molecule retains the binding ability of membrane-bound human CEA, binding, for example, the same epitope as the parent antigen-binding molecule! and preferably has properties that are superior to those of the parent antigen-binding molecule. The variant may have, for example, stronger binding affinity and greater ability to induce antibody-mediated cellular cytotoxicity in vitro and in vivo. To analyze these properties, one should generally compare a variant antigen-binding molecule and the parent antigen-binding molecule! in the same format; a Fab form of the variant antigen-binding molecule with a Fab form of the parent antigen-binding molecule I, for example, or a full-length form of the variant antigen-binding molecule 1o with a full-length form of the binding molecule of parental antigen!. The variant antigen binding molecule of specific interest in the present is one that has an increase of at least about two-fold, three-fold, four-fold, five-fold, six-fold, seven-fold, eight-fold, nine-fold, ten-fold, eleven-fold times, twelve times, thirteen times, fourteen times, fifteen times, sixteen times, seventeen times, eighteen times, nineteen times or twenty times the biological activity compared to the parent antigen binding molecule!.
The term "parent!" designates an ABM that is used as a starting point or basis for variant preparation.
In a specific embodiment, the parent antigen-binding molecule! has a human backbone region and, when present, has human antibody constant region(s). The parent antibody! it can be, for example, a human or humanized antibody.
Amino acid "substitutions" can result in the replacement of one amino acid with another amino acid that has similar chemical and/or structural properties, such as conservative amino acid substitutions.
"Conservative" amino acid substitutions may be made based on similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphiphatic nature of the residues involved. Non-polar (hydrophobic) amino acids include, for example, alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine; polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine and glutamine; the positively charged (basic) 5 amino acids include arginine, lysine and histidine; and negatively charged amino acids (acids) include aspartic acid and glutamic acid.
"Insertions" or "exclusions" are generally in the range of about one to about twenty amino acids, more specifically about one to about ten amino acids, and even more specifically, about two to about five amino acids. Non-conservative substitutions will cause a member of one of these classes to be replaced by another class. Amino acid substitutions can also result, for example, in replacing one amino acid with another amino acid that has different chemical and/or structural properties, for example replacing one amino acid of one group (such as polar) with another amino acid of a group different (such as basic). The allowable variation can be determined experimentally by systematically designing insertions, deletions, or substitutions of amino acids in a polypeptide molecule using recombinant DNA methods and testing the resulting recombinant variants of activity.
As used herein, the term "single-stranded Fv" or "scFv" means an antibody fragment comprising a VH domain and a VL domain in the form of an isolated polypeptide chain. Typically, the VH and VL domains are linked by a linker sequence. See, for example, Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds. Springer-Verlag, New York, p. 269-315 (1994).
As used herein, the term "minibody" means a bivalent homodimeric scFv derivative that contains a constant region, typically the CH3 region of an immunoglobulin, preferably IgG, more preferably IgG1, as the dimerization region. Generally, the constant region is connected to the scFv via a hinge region and/or a linkage region. Examples of minibody proteins can be found in Hu et al (1996), Cancer Res. 56: 3055-61.
5 As used herein, the term "diabody" designates small antibody fragments with two antigen-binding sites, which comprise a heavy chain variable domain (VH) connected to a light chain variable domain (VL) in the same polypeptide chain (VH-VL).
Using a linker that is too short to allow pairing between the two domains on the same strand, the domains are forced to pair with the complementary domains of another strand and create two antigen binding sites. Diabodys are described more fully, for example, in EP 404,097, WO 93/11161 and Hollinger et al., Proc. natl. academy Know. U.
S.A., 90: 6444-6448 (1993). A triabody results from the formation of a trivalent trimer of three scFvs, generating three binding sites, and a tetrabody is a tetravalent tetramer of four scFvs, resulting in four binding sites.
If there were two or more definitions of a term that is used and/or accepted in the art, the definition of the term as used herein is intended to include all such meanings unless explicitly stated otherwise. A specific example is the use of the term "complementarity determining region" ("COR") to describe the non-contiguous antigen combining sites (also known as antigen-binding regions) found in the variable region of light and heavy chain polypeptides. . CDRs are also called "hypervariable regions" and that term is used interchangeably in the present with the term "COR" with reference to the portions of the variable region that form the antigen-binding regions. This specific region has been described by Kabat et al, US Department of Health and Human Services, Sequences of Proteins of Immunological Interest (1983) and by Chothia et al, J. Moi. Biol. 196: 901-917 (1987), which are incorporated herein by reference wherein the definitions include the overlap or subsets of amino acid residues in comparison to each other. The application of any definition to refer to a COR of an antibody or its variants is, however, intended to be within the scope of the expression as defined and used herein. Appropriate amino acid residues that encompass the CORs as defined by any of the aforementioned references are described below in Table I by way of comparison. The exact numbers of residues that encompass a specific COR 1o will vary depending on the sequence and size of the COR. Those skilled in the art can routinely determine which residues comprise a specific COR by considering the amino acid sequence of the antibody variable region.
TABLE 1 1
CDR DEFINITIONS COLOR Kabat Chothia AbM 2 COR1 VH 31-35 26-32 26-35 COR2 VH 50-65 52-58 50-58 COR3 VH 95-102 95-102 95-102 COR1 VL 24-34 26-32 24 -34 COR2 VL 50-56 50-52 50-56 COR3 VL 89-97 91-96 89-97 The numbering of all COR definitions in Table 1 is in accordance with the numbering conventions established by Kabat et al (see below). 2 Lowercase "AbM" with "b" as used in Table 1 designates the CORs as defined by Oxford Molecular's "AbM" antibody modeling software.
Kabat et al also defined a numbering system for variable domain sequences that is applicable to any antibody. Those of ordinary skill in the art can unambiguously assign this "Kabat numbering" system to any variable domain sequence, without relying on any experimental data other than the sequence itself. As used herein, "Kabat numbering" means the numbering system described by Kabat et al, US Department of Health and Human Services, Sequences of Proteins of Immunology/Interest (1983). Unless otherwise specified, references to the numbering of specific amino acid residue positions in an ABM are in accordance with the Kabat numbering system. Sequences in the Sequence Listing (ie SEQ ID No 1 to SEQ ID No 216) are not numbered according to the Kabat numbering system. Those of ordinary skill in the field are, however, familiar with how to convert the sequences in the Sequence Listing into Kabat numbering.
By nucleic acid or polynucleotide having a nucleotide sequence, for example, at least 95% "identical" to a reference nucleotide sequence in accordance with the present invention, the nucleotide sequence of the polynucleotide is intended to be identical to the sequence reference, except that the polynucleotide sequence can include up to five point mutations for every hundred nucleotides of the reference nucleotide sequence. In other words, to obtain a polynucleotide that has a nucleotide sequence that is at least 95% identical to a reference nucleotide sequence, up to 5% of the nucleotides in the reference sequence can be deleted or replaced by another nucleotide or a number of nucleotides from up to 5% of the total nucleotides in the reference sequence can be inserted into the reference sequence.
Practically, one can conventionally determine whether any specific polypeptide or nucleic acid molecule is at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to a nucleotide sequence. or polypeptide sequence according to the present invention using known computer programs. A method of determining the best overall match between a query sequence (a sequence according to the present invention) and an object sequence, also called global sequence alignment, can be chosen using the FASTDB computer program based on the algorithm of Brutlag et al, Comp. App. Bíoscí.
6:237-245 (1990). In a sequence alignment, the query and object sequences are both DNA sequences. An RNA sequence can be compared by converting Us to Ts. The result of said global sequence alignment is in percent identity. The preferred parameters used in a FASTDB alignment of DNA sequences to calculate percent identity are: Array = Single, multiple k = 4, mismatch penalty=1, join penalty=30, randomization group length =O , cut evaluation=1, gap penalty=5, gap size penalty=0.05, window size=500, or the length of the object nucleotide sequence, whichever is shorter.
If the object string is shorter than the query string due to 5' or 3' exclusions, not due to internal exclusions, manual correction of the results must be performed. This is because the FASTDB program does not consider 5' and 3' truncations of the object sequence when calculating the percent identity. For object sequences truncated at the 5' or 3' ends, with respect to the query string, the percent identity is corrected by calculating the number of bases in the query string that are 5' and 3' of the object string, that are not matched/aligned, as a percentage of the total bases in the query string. Whether a nucleotide is matched/aligned is determined by FASTDB sequence alignment results. This percentage is then subtracted from the percent identity, calculated by the FASTDB program above using the specified parameters, to arrive at a final percent identity rating. This corrected assessment is used for the purposes of the present invention. Only bases outside the 5', 5' and 3' bases of the object sequence, as displayed by the FASTDB alignment, that are not matched/aligned with the query string, are calculated for the purpose of manually adjusting the percent identity assessment.
An object sequence of 90 bases is aligned, for example, with a query sequence of 100 bases to determine the percent identity.
Deletions occur at the 5' end of the object sequence and therefore the FASTDB alignment does not exhibit an alignment/match of the first ten bases at the 5' end. The ten mismatched bases represent 10% of the sequence (number of bases at the 5' and 3' ends mismatched/total number of bases in the query sequence), such that 10% is subtracted from the percent identity assessment calculated by the FASTDB program. If the remaining ninety bases were perfectly matched, the final percent identity would be 90%. In another example, an object sequence of ninety bases is compared with a query sequence of one hundred bases.
At this point, the exclusions are internal exclusions such that there are no bases on the 5' or 3' of the object sequence that are not matched/aligned with the query. In this case, the identity percentage calculated by FASTDB is not manually corrected. Again, only 5' and 3' bases of the object sequence that are not matched/aligned with the query sequence are manually corrected. No other manual corrections should be made for the purposes of the present invention.
For a polypeptide that has an amino acid sequence, for example, at least 95% "identical" to a query amino acid sequence in accordance with the present invention, the amino acid sequence of the subject polypeptide is intended to be identical to the sequence of query, except that the object polypeptide sequence can include up to five amino acid changes for every 100 amino acids in the query amino acid sequence. In other words, to obtain a polypeptide that has an amino acid sequence at least 95% identical to a query amino acid sequence, up to 5% of the amino acid residues in the object sequence can be inserted, deleted, or replaced by another amino acid.
These changes to the reference sequence may occur at the amino- or carboxy-terminal positions of the reference amino acid sequence or at any point between those terminal positions, interspersed individually between residues in the reference sequence or in one or more contiguous groups in the reference sequence.
Practically, one can conventionally determine whether any specific polypeptide is at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identical to a reference polypeptide using known computer programs. . A method of determining the best overall match between a query sequence (a sequence according to the present invention) and an object sequence, also called global sequence alignment, can be chosen using the FASTDB computer program based on the Brutlag algorithm. et al., Comp. App. Biosci. 6: 237-245 (1990). In a sequence alignment, the object and query sequences are either nucleotide sequences or amino acid sequences. The result of said global sequence alignment is in percent identity. The preferred parameters used in a FASTDB amino acid alignment are: Matrix=PAM 0, multiple k=2, mismatch penalty=1, join penalty=20, randomization group length=0, cutoff score=1, window size = string length, gap penalty = 5, gap size penalty =
0.05, window size=500 or the length of the object amino acid sequence, whichever is shorter.
If the object string is shorter than the query string due to N or C terminal exclusions, not due to internal exclusions, 5 manual correction of the results must be performed. This is because the FASTDB program does not represent N and C terminal truncations of the object sequence when calculating the percent global identity. For object sequences truncated at the N and C terminals, with respect to the query string, the percent identity is corrected by calculating the number of residues of the query string that are N and C terminals of the object string, which are not matched/ aligned with a corresponding object residue, in the form of a percentage of the total bases of the query string. Whether a residue is matched/aligned is determined by FASTDB sequence alignment results. This percentage is then subtracted from the percent identity, calculated by the FASTDB program above using the specified parameters, to arrive at a final percent identity rating. This final percent identity assessment is used for the purposes of the present invention. Only residues from the N and C ends of the object sequence, which are not matched/aligned with the query sequence, are considered for the purpose of manually adjusting the percent identity assessment. This means only query residue positions outside the most distant N and C terminal residues of the object sequence.
A ninety amino acid residue object sequence is aligned, for example, with a one hundred residue query sequence to determine percent identity. The deletion occurs at the N-terminus of the object sequence and therefore the FASTDB alignment does not exhibit a match/alignment of the first ten residues at the N-terminus. The ten unpaired residues represent 10% of the sequence (number of residues at the N- and C-terminus mismatches/total number of residues in the query string), such that 10% is subtracted from the percent identity assessment calculated by the FASTDB program. If the remaining ninety residues were perfectly coincident, the final percentage of identity would be 90%.
In another example, a ninety-residue object sequence is compared to a hundred-residue query sequence. At this point, the excludes are inner excludes such that there are no residues at the N or C ends of the object sequence that are not matched/aligned with the query. In this case, the identity percentage calculated by FASTDB is not manually corrected. Again, only positions of residues outside the N- and C-terminal ends of the object sequence, as displayed in the FASTDB alignment, which are not coincident/aligned with the object sequence, are manually corrected. No other manual corrections should be made for the purposes of the present invention.
The percentage of identity of polynucleotides and/or polypeptides can also be determined using the BLAST programs available through the National Center for Biotechnology Information (NCBI), with the default parameters indicated in the programs.
As used herein, a nucleic acid that "hybridizes under stringent conditions" to a nucleic acid sequence in accordance with the present invention means a polynucleotide that hybridizes under specified conditions, such as an overnight incubation at 42°C. in a solution comprising 50% formamide, 5x SSC (750 mM NaCl, 75 mM sodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate and 20 µg/ml denatured cut salmon sperm DNA, followed by washing the filters in 0.1x SSC at about 65°C. As used herein, the expression "polypeptide having GnTIII activity" designates polypeptides that are capable of catalyzing the addition of an N-acetylglucosamine residue (GicNAc) in 13-1-4 linkage to the 13-linked mannoside of the trimannosyl nucleus. of N-linked oligosaccharides. This includes fusion polypeptides that exhibit similar, but not necessarily identical, enzyme activity to an activity of 13(1,4)-N-5 acetylglucosaminyltransferase 111, also known as 13-1,4-mannosyl glycoprotein 4 -beta-N-acetylglucosaminyltransferase (EC 2.4.1.144), according to the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), as measured in a specific biological assay, with or without dose dependence. If there is indeed a dose dependence, it need not be identical to that of GnTIII, but substantially similar to the dose dependence on a given activity compared to GnTIII (i.e., the possible polypeptide will exhibit activity greater than or not more than about 25-fold). lower, preferably not more than about ten times less activity and preferably not more than about three times less activity with respect to Gn Til I).
As used herein, the term "Golgi localization domain" refers to the amino acid sequence of a Golgi resident polypeptide which is responsible for anchoring the polypeptide to a site in the Golgi complex. Generally, localization domains comprise the amino-terminal "tails" of an enzyme.
As used herein, the term "effector function" refers to biological activities that can be attributed to the Fc region (native sequence Fc region or Fc region with amino acid sequence variation) of an antibody. Examples of antibody effector functions include, but are not limited to, Fc receptor binding affinity, antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), cytokine secretion, immune complex-mediated antigen uptake by cells that present antigens, down-regulation of cell surface receptors, etc.
As used herein, the terms "projection, projecting, projection", particularly with the prefix "glyco", as well as the expression "projection by glycosylation", are considered to include any manipulation of the pattern of glycosylation of a recombinant polypeptide or of natural occurrence or fragment thereof. Design by glycosylation includes metabolic design of a cell's glycosylation machinery, including genetic manipulations of oligosaccharide synthesis processes to achieve altered glycosylation of glycoproteins expressed in cells. Furthermore, projection by glycosylation includes the effects of mutations and the cellular environment upon glycosylation. In one embodiment, projection by glycosylation is an alteration of glycosyltransferase activity. In a specific embodiment, the projection results in alteration of glucosaminyltransferase activity and/or fucosyltransferase activity.
As used herein, the term "host cell" covers any type of cellular system that can be designed to generate the polypeptides and antigen-binding molecules of the present invention. In one embodiment, the host cell is designed to allow the production of an antigen-binding molecule with modified glycoforms.
In a preferred embodiment, the antigen-binding molecule is an antibody, antibody fragment, or fusion protein. In certain embodiments, host cells have been further manipulated to express higher levels of one or more polypeptides that have GnTIII activity. Host cells include cultured cells, such as cultured mammalian cells, such as CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or cells of hybridoma, yeast cells, insect cells, and plant cells, to name just a few, but also cells comprised in a transgenic animal, transgenic plant, or cultured animal or plant tissue.
As used herein, the term "Fc-mediated cellular cytotoxicity" includes antibody-dependent cellular cytotoxicity (ADCC) and cellular cytotoxicity mediated by a soluble Fc fusion protein that contains a human Fc region. It is an immunological mechanism that generates lysis of "directed cells" by "human immune effector cells".
As used herein, the term "human immune effector cells" refers to a population of leukocytes that display Fc receptors on their surfaces, through which they bind to the Fc region of antigen-binding molecules or fusion proteins of Fc and perform effector functions. This population may include, but is not limited to, peripheral blood mononuclear cells (PBMC) and/or natural killer (NK) cells.
As used herein, the term "target cells" means cells to which antigen binding molecules comprising an Fc region (such as antibodies or fragments thereof which comprise an Fc region) or Fc fusion proteins specifically bind. Antigen binding molecules or Fc fusion proteins bind to target cells via the portion of the protein that is N-terminal to the Fc region.
As used herein, the expression "increased Fc-mediated cellular cytotoxicity" is defined as an increase in the amount of "target cells" that are lysed at a given time, at a given concentration of antigen-binding molecule or protein of Fc fusion in the medium around the target cells, via the mechanism of Fc-mediated cellular cytotoxicity defined above and/or reduction of the concentration of antigen-binding molecule or Fc fusion protein, in the medium around the target cells, necessary to achieve the lysis of a certain number of "target cells", in a certain time, by the mechanism of cellular cytotoxicity mediated by Fc. Enhanced Fc-mediated cellular cytotoxicity refers to cellular cytotoxicity mediated by the same antigen-binding molecule or Fc fusion protein produced by the same type of host cells, using the same standard methods of production, purification, formulation, and storage (which are known to those skilled in the art), but which has not been produced by engineered host cells to have an altered glycosylation pattern (such as to express glycosyltransferase, GnTIII, or other glycosyltransferases) by the methods described herein.
By "antigen-binding molecule that has the highest antibody-dependent cellular cytotoxicity (ADCC)" is meant an antigen-binding molecule, as that expression is defined herein, that has the highest ADCC as determined by by any suitable method known to those of ordinary skill in the art. An accepted in vitro ADCC assay is as follows: 1) the assay uses target cells that are known to express the target antigen recognized by the antigen binding region of the antibody; 2) the assay uses human peripheral blood mononuclear cells (PBMCs), isolated from the blood of a randomly selected healthy donor, as effector cells; 3) the assay is conducted according to the following protocol: i) PBMCs are isolated using standard density centrifugation procedures and suspended at 5 x 10 6 cells/ml in RPMI cell culture medium; ii) target cells are cultured using standard tissue culture methods, harvested from the exponential growth phase with viability of more than 90%, washed in RPMI cell culture medium, labeled with 100 microCuries of 51 Cr, washed twice times with cell culture medium and resuspended in cell culture medium at a density of 105 cells/ml;
iii) 100 microliters of the above final target cell suspension is transferred to each well of a 96-well microtiter plate; iv) the antibody is serially diluted from 4000 ng/ml to 0.04 ng/ml in cell culture medium and 50 microliters of the resulting antibody solutions 5 are added to the target cells in the 96-well microtiter plate, testing in three copies various concentrations of antibodies that cover the entire concentration range above; v) for the maximum release (MR) controls, three additional wells on the plate containing the labeled target cells receive 50 microliters of a 2% aqueous solution (VN) of nonionic detergent (Nonidet, Sigma, St.
Louis) instead of the antibody solution (point iv above); vi) for spontaneous release (SR) controls, three additional wells in the plate containing the labeled target cells receive 50 microliters of RPMI cell culture medium in place of the antibody solution (point iv above); vii) the 96-well microtiter plate is then centrifuged at 50 X g for one minute and incubated for one hour at 4°C; viii) 50 microliters of the PBMC suspension (point i above) is added to each well to generate an effector:target ratio of 25:1 and the plates are placed in an incubator under a 5% CO2 atmosphere at 37°C for four o'clock; ix) cell-free supernatant from each well is harvested and experimentally released radioactivity (ER) is quantified using a gamma counter; x) the percentage of specific lysis is calculated for each antibody concentration according to the formula (ER-MR)/(MR-SR) x 100, where ER is the quantified mean radioactivity (see point ix above) for that antibody concentration, MR is the quantified mean radioactivity (see point ix above) for the MR controls (see point v above) and SR is the quantified mean radioactivity (see point ix above) for the SR controls (see point v above) saw above); 4) "ADCC increase" is defined as an increase in the maximum percentage of specific lysis observed in the antibody concentration range 5 tested above and/or a reduction in the antibody concentration required to reach half the maximum percentage of specific lysis observed in the range of antibody concentration tested above. The increase in ADCC is relative to ADCC, as measured with the above assay, mediated by the same antibody, produced by the same type of host cells, using the same standard methods of production, purification, formulation and storage, which are known to those skilled in the art, but which were not produced by host cells designed to overexpress GnTIII.
ANTI-CEA ANTIGEN BINDING MOLECULES: CEA has long been used as a cancer marker for diagnostic purposes. It is abnormally expressed (such as over-expressed and/or distributed in a different pattern in the cell) in many tumor tissues compared to non-tumor tissues of the same cell type. As CEA is usually broken down from the surface of tumor cells and most of the available anti-CEA antibodies also bind to soluble CEA, however, unconjugated antibodies to CEA are generally not used for therapeutic purposes. Anti-CEA antibodies currently in pilot trials are administered, for example, as radio conjugates (Wong et al, 2004; Liersch et al, 2007).
Several mechanisms are involved in the therapeutic efficacy of anti-CEA antibodies, including antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Increased expression of CEA promotes increased intercellular adhesion, which can lead to metastasis of cancer cells (Marshall, J., Semin. Oncol. 30 (3), Suppl. 8: 30-
36). In this way, anti-CEA antigen binding molecules may also play a role in inhibiting CEA-mediated cell adhesion and cancer cell metastasis.
In one aspect, the present invention relates to an antigen-binding molecule (such as an antibody or fragment thereof) that comprises one or more (such as one, two, three, four, five or six) CDRs of the murine antibody PR1A3, in which at least one of the CDRs has substitution of at least one amino acid residue compared to the corresponding COR of PR1A3, and in which the antigen-binding molecule has enhanced affinity for CEA, preferably membrane-bound CEA compared to with a parent PR1A3 antigen-binding molecule. Such one or more CDRs may be truncated CDRs and will contain at least the specificity determining residues (SDRs), as that term is defined herein, for a given COR. In one embodiment, the antigen binding molecule comprises at least one (such as one, two, three, four, five or six) of the CDRs described in Table 2 below, which comprises residues of the CDRs that will retain specific binding.
In another embodiment, the antigen binding molecule comprises at least one (such as one, two, three, four, five or six) CDRs described in Table 2 below, or one of its variants or truncated forms that contain at least the residues determinants of specificity for said COR and comprises a sequence derived from a heterologous polypeptide. In a specific embodiment, when the antigen-binding molecule comprises a heavy chain CDR1 variant of PR1A3, the HCDR1 has a glutamate substituted for a valine at Kabat position 31. In one embodiment, the antigen-binding molecule comprises three CDRs of heavy chain (such as HCDR1, HCDR2 and HCDR3) and/or three light chain CDRs (such as LCDR1, LCDR2 and LCDR3) from Table 2 or variants or truncated forms thereof that contain at least the specificity determining residues for each of the said three CDRs. In a more specific embodiment, the antigen binding molecule comprises three heavy chain CDRs (such as HCDR 1, HCDR2 and HCDR3) and/or three light chain CDRs (such as LCDR 1, LCDR2 and LCDR3) from Table 2 In another embodiment, the antigen binding molecule comprises the variable region(s) of an antibody light and/or heavy chain, preferably a light and heavy chain variable region. In a more specific embodiment, the light chain and/or heavy chain region is selected from the light and/or heavy chain variable region of Table 4 or a combination thereof, wherein the light and heavy chain region is not a combination of SEQ ID No 99 and SEQ ID No 103 or SEQ ID No 100 and SEQ ID No
104. In one embodiment, the antigen-binding molecule is a chimeric antibody, and more specifically, a humanized antibody. In another embodiment, the antigen binding molecule comprises an Fc region. In another embodiment, the antigen binding molecule is affinity matured. In another embodiment, the antigen binding molecule has higher ADCC activity compared to PR1A3. In one embodiment, the increase in ADCC of the antigen-binding molecule is due to an increase in the affinity of the antigen-binding molecule for membrane-bound CEA, such as through affinity maturation or other affinity-enhancing methods ( see Tang et al., J. Immuno/. 2007, 179: 2815-2823, the entire contents of which are incorporated herein by reference). In another embodiment, the antigen binding molecule comprises an Fc region that is glycoengineered. In another aspect, the present invention also relates to methods of designing such antigen-binding molecules and their use in the treatment of diseases, particularly disorders of cell proliferation in which CEA is expressed, particularly in which CEA is abnormally expressed (such as overexpressed or expressed in a different pattern in the cell) compared to normal tissue of the same cell type. These disorders include, but are not limited to, colorectal cancer, NSCLC (non-small cell lung cancer), gastric cancer, pancreatic cancer, and breast cancer. CEA expression levels can be determined by methods known in the art and those described herein (such as by immunohistochemical assay, immunofluorescence assay, enzyme immunoassay, ELISA, flow cytometry, radioimmunoassay, Western Blot, ligand binding, kinase activity, etc.).
In another aspect, the present invention also relates to an isolated polynucleotide comprising a sequence encoding a 1st polypeptide comprising one or more (such as one, two, three, four, five or six) antibody complementarity determining regions. murine PR1A3 or variants or truncated forms thereof which contain at least specificity-determining residues for said complementarity-determining regions. Typically, these isolated polynucleotides encode one or more fusion polypeptides that form an antigen-binding molecule. In one embodiment, the polynucleotide comprises a sequence encoding one or more (such as one, two, three, four, five or six) of the CDRs described in Table 2 below, which comprises residues of the CDRs that will retain specific binding. In one embodiment, the polynucleotide comprises a sequence encoding at least three heavy chain CORs (such as HCDR1, HCDR2 and HCOR3) and/or three light chain CDRs (such as LCDR1, LCDR2 and LCDR3) of Table 2 or variants thereof or truncated forms that contain at least the specificity-determining residues for each of said three complementarity-determining regions. In a more specific embodiment, the polynucleotide encodes a polypeptide comprising three heavy chain CDRs (such as HCDR 1, HCDR2 and HCDR3) and three light chain CDRs (such as LCDR1, LCDR2 and LCDR3) of Table 2. In another embodiment, the polynucleotide encodes a polypeptide comprising the region(s)
variable(s) of an antibody light and/or heavy chain.
Polynucleotides encoding light and heavy chain variable region polypeptides can be expressed in one or more expression vectors.
In a more specific embodiment, the polynucleotide encoding a light chain variable region and/or
5 is selected from the group of polynucleotides shown in Table 5 or one of their combinations, wherein the light and heavy chain variable regions are not encoded by a combination of SEQ 10 No. 11 and SEQ
10 No. 115 or SEQ 10 No. 112 and SEQ 10 No. 116. In one embodiment, the light and heavy chain variable region polypeptides encoded by the
1st polynucleotides combine to form a chimeric antibody, more specifically a humanized antibody.
In a specific embodiment, wherein the polynucleotide comprises a sequence encoding PR1A3 heavy chain COR 1 or one of its variants, said polynucleotide encodes a valine substituted glutamate at Kabat position 31. In another embodiment, the polynucleotide comprises a sequence that encodes a region
fc.
The present invention further relates to the polypeptides encoded by such polynucleotides.
In one embodiment, the polypeptide encoded by the aforementioned polynucleotides comprises an Fc region.
In a more specific embodiment, the polypeptides encoded by the polynucleotides are glycoengineered to have an altered pattern of glycosylation in the Fc region.
In a specific embodiment, the affinity for membrane-bound CEA of the polypeptides encoded by the polynucleotides increases compared to the antibody
PR1A3 parent!. In another embodiment, the polypeptide encoded by the polynucleotide exhibits increased ADCC activity.
In one embodiment, the increase in ADCC of the polypeptide encoded by the polynucleotide is due to an increase in the affinity of the polypeptide for membrane-bound CEA, such as through affinity maturation or other affinity enhancement methods.
In another aspect, the present invention also relates to the use of the polypeptides
(such as antigen-binding molecules) encoded by the polynucleotides in the treatment of diseases, particularly disorders of cell proliferation where CEA is expressed, particularly where CEA is abnormally expressed (such as overexpressed or expressed in a different pattern in the cell) in 5 compared to normal tissue of the same cell type. These disorders include, but are not limited to, colorectal cancer, NSCLC (non-small cell lung cancer), gastric cancer, pancreatic cancer, and breast cancer. CEA expression levels can be determined by methods known in the art and those described herein (such as by immunohistochemical assay, immunofluorescence assay, enzyme immunoassay, ELISA, flow cytometry, radioimmunoassay, Western Blot , ligand binding, kinase activity, etc.).
In a specific embodiment, the present invention relates to a humanized antigen-binding molecule or a portion thereof or membrane-bound CEA-specific fragments comprising a heavy chain variable region comprising the sequence of any one of SEQ 10 No 101, 107 or 188-206. In another embodiment, the present invention relates to a humanized antigen-binding molecule or a portion thereof or membrane-bound CEA-specific fragments comprising a light chain variable region comprising the sequence of any one of SEQ 10 No 105, 108 or 207-216. In a specific embodiment, the humanized antigen-binding molecule or a portion thereof or membrane-bound CEA-specific fragments comprises a heavy chain variable region comprising the sequence of any one of SEQ 10 No. 101, 107, or 188-206 and a light chain variable region comprising the sequence of any one of SEQ 10 No. 105, 108, or 207-216. In one embodiment, the humanized antigen binding molecule further comprises a human heavy chain constant region and/or a human light chain constant region. Such constant regions are described herein and known in the art. In a more specific embodiment, the humanized antigen binding molecule comprises an Fc region, more specifically an Fc region that has been glycoengineered.
5 Methods of humanizing non-human antibodies are well known in the art. Humanized ABMs in accordance with the present invention can be prepared, for example, by the methods according to U.S. Patent No. 5,225,539 to Winter, U.S. Patent No. 5,225,539 to Winter.
6,180,370 to Queen et al or U.S. Patent No. 6,632,927 to Adair et al, the contents of which are incorporated herein by reference in their entirety.
Preferably, the humanized antibody contains one or more amino acid residues introduced into it from a non-human source. These non-human amino acid residues are often called "import" residues, which are typically taken from an "import" variable domain. Humanization can essentially be carried out following the method of Winter and co-workers (Jones et al., Nature, 321: 522-525 (1986); Riechmann et al., Nature, 332: 323-327 (1988); Verhoeyen et al. Science, 239: 1534-1536 (1988)) by replacing hypervariable region sequences with corresponding human antibody sequences. Consequently, these "humanized" antibodies are chimeric antibodies (U.S. Patent No.
4,816,567), wherein substantially less than an intact human variable domain has been replaced by the corresponding non-human species sequence.
Typically, humanized antibodies are human antibodies in which some hypervariable region residues and possibly some FR residues are replaced by residues from analogous sites in non-human (such as rodent) antibodies. The humanized anti-CEA antibodies of the present will optionally comprise constant regions of a human immunoglobulin.
The selection of human light and heavy chain variable domains for projecting the humanized antibodies is very important to reduce antigenicity. According to the so-called "best match" method, the variable domain sequence of a donor antibody (such as from a rodent) is selected against the entire library of known human variable domain sequences. The human sequence that is closest to that of the donor (such as rodent) is then accepted as the human framework region (FR) for the humanized antibody (Sims et al., J. Immuno/., 151: 2296 (1993); Chothia et al, J.
Mo/. Biol., 196: 901 (1987)). Another method of human backbone sequence selection is sequence comparison of each individual subregion of the complete donor (such as rodent) backbone (i.e., FR1, FR2, FR3, and FR4) or some combination of the individual subregions ( such as FR1 and FR2) against a library of known human variable region sequences that correspond to that main chain subregion (as determined by Kabat numbering) and selection of the human sequence for each subregion or combination that is closest to the rodent (Leung, US Patent Application published No. 2003/0040606A 1, published February 27, 2003). Another method uses a specific main chain region derived from the consensus sequence of all human antibodies of a specific subgroup of light or heavy chains (Carter et al, Proc. Natl.
academy Know. U.S.A., 89: 4285 (1992); Presta et al., J. Immunol., 151: 2623 (1993)).
In one embodiment, the human backbone regions are selected from a series of human germ lineage sequences. These series of human germ line sequences can be found in databases such as IMGT or VBase. Main chain regions can be selected individually (the FR1-3 selected for the receptor for the light and/or heavy chain variable regions of humanized anti-CEA ABMs, for example, can be encoded by genes from different germ lineages)
or as part of the same germ lineage. In a more specific embodiment, heavy chain FR1-3 is encoded by the human immunoglobulin germ lineage gene sequence IGHV7_4_1*02 (Accession No. X62110, SEQ 10 NO:114). In another specific embodiment, light chain FR1-3 is encoded by the human immunoglobulin germ lineage gene sequence IMGT_hVK_1_39 (Accession No. X59315, SEQ 10 NO: 118).
In another specific embodiment, heavy chain FR4 is encoded by the JH6 germ lineage gene sequence (see GenBank Accession M63030). In another specific embodiment, light chain FR4 is encoded by the JK2 germ lineage gene sequence (see GenBank Accession X61584).
It is generally desirable that antigen-binding molecules, such as antibodies and fragments thereof, be humanized with retention of high affinity for the antigen and other favorable biological properties.
Accordingly, in one embodiment, humanized antibodies are prepared by analyzing the parental sequences and various conceptual humanized products using three-dimensional models of the parental sequences! and humanized. Three-dimensional immunoglobulin models are commonly available and familiar to those skilled in the art. Computer programs are available that illustrate and display likely three-dimensional conformational structures of possible selected immunoglobulin sequences. Analysis of these displays helps elucidate the likely role of residues in the functioning of the possible immunoglobulin sequence, as does analysis of residues that influence the ability of the possible immunoglobulin to bind its antigen.
In this way, FR residues can be selected and combined from the recipient and imported sequences to achieve the desired antibody characteristic, such as increased affinity for the target antigen(s). Generally, the hypervariable region residues are directly and most substantially involved in influencing antigen binding.
In one aspect, the present invention relates to humanized, affinity matured and/or variant anti-CEA antigen binding molecules with desirable properties and characteristics that include, but are not limited to: strong binding affinity for the CEA antigen (particularly, membrane-bound CEA), although it has substantially no cross-reactivity against soluble CEA; an ability to induce cell lysis of cells expressing CEA in vitro and ex vivo, preferably in a dose-dependent manner; an ability to inhibit CEA-mediated cell adhesion in vitro; an ability to inhibit tumor tissue growth and/or induce tumor tissue regression (as demonstrated, for example, in tumor models (such as mouse xenograft)).
As described herein, in some embodiments, antigen-binding molecules according to the present invention have increased binding affinity, due, for example, to affinity maturation of a parent antibody. which comprises one or more CDRs of the PR1A3 antibody. The affinity of the antigen-binding molecules of the present invention can be determined by methods known in the art and as described herein. In a specific embodiment, humanized anti-CEA antigen binding molecules or variants according to the present invention bind human CEA, preferably membrane-bound CEA, with a monovalent affinity constant (Ko) value of no more than about from 1 µM to about 0.001 nM, more specifically not more than about 800 nM to about 1 nM, and even more specifically not more than about 550 nM to about 10 nM. In a specific embodiment, the variant anti-CEA antigen binding molecule is an affinity matured antibody or membrane-bound CEA-binding fragment thereof with a monovalent affinity constant (Ko) value of less than about 100 nM at about 10 nM.
In one embodiment, the antigen-binding molecule according to the present invention typically binds to the same epitope as recognized by mouse antibody PR 1A3 or is capable of competing with antibody PR1A for binding to membrane-bound CEA. To select 5 antibodies that bind to the epitope on human CEA bound by an antibody of interest (such as those that block PR1A3 antibody binding to human CEA), a routine cross-blocking assay can be performed as described above. in Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, Ed.
Harlow and Lane (1988). Alternatively, epitope mapping can be performed, as described in Champe et al., J. Biol. Chem. 270: 1388-1394 (1995) to determine whether the antibody binds an epitope of interest. In one embodiment, human CEA-specific variant antigen binding molecules are engineered from a parent anti-CEA antigen binding molecule! which comprises at least one COR of the monoclonal antibody PR1A3, wherein the anti-CEA antibody is parent! binds to the same epitope as the PR1A3 antibody and is able to compete with PR1A3 for antigen binding. In one embodiment, the parental antigen-binding molecule comprises at least one, two, or typically three PR1A3 antibody heavy chain CDRs; in another embodiment, the parent antigen-binding molecule I comprises at least one, two, or typically three light chain CDRs of the PR1A3 antibody; in another embodiment, the parent antigen-binding molecule! comprises the three heavy chain CDRs and the three light chain CDRs of the PR1A3 antibody. Preferably, when the antigen binding molecule comprises HCDR1 of PR1A3, said HCDR1 comprises a substitution of glutamate for valine at position Kabat 31. The variant ABMs typically have a higher affinity for CEA than the parent. In one embodiment, the variant ABM comprises an Fc region. In one embodiment, the variant ABM is glycoengineered. In one embodiment, the variant ABM has higher AOCC activity compared to the parent ABM!. In a specific embodiment, the higher AOCC is the result of the higher affinity achieved, for example, through affinity maturation of the parent ABM! to generate the variant ABM. In a more specific embodiment, the increase in AOCC is at least about 40% to about 100% compared to said parent antigen-binding molecule. In another specific embodiment, variant ABM increases AOCC by at least about 10% to about 100% in an in vitro cytotoxicity assay. In a more specific embodiment, the variant ABM is at least about ten-fold to about a thousand-fold more potent in the 1st induction of AOCC at a given concentration compared to the murine antibody PR1A3. In another specific embodiment, the increase in AOCC activity is a result of Fc region glycoprojection. In another specific embodiment, the increase in AOCC activity is the result of a combination of increased affinity and glycoprojection.
In one embodiment, the variant antigen binding molecules according to the present invention comprise one or more amino acid substitutions in at least one COR. The number of amino acid substitutions can range from one to ten (such as one, two, three, four, five, six, seven, eight, nine or ten), preferably from two to five (such as two, three, four or ten). five). In one embodiment, at least one heavy chain COR comprises one or more amino acid substitutions. In another embodiment, at least one light chain COR comprises one or more amino acid substitutions. In another embodiment, at least one heavy chain COR comprises one or more substitutions and at least one light chain COR comprises one or more substitutions. Preferably, when the antigen binding molecule comprises HCOR1 of PR1A3, said HCOR1 comprises a substitution of glutamate for valine at position Kabat 31.
Substantial modifications of the biological properties of the antigen-binding molecules are achieved through the selection of substitutions that differ significantly in effect on the maintenance (a) of the polypeptide backbone structure in the area of substitution, such as in sheet form or in helical conformation; (b) the charge or hydrophobicity of the molecule at the desired location; or (c) the volume of the side chain. Variant antigen-binding molecules that comprise amino acid substitutions may have improved biological activities, such as improved antigen-binding affinity and improved ADCC, compared to the parent antigen-binding molecule. Amino acid substitutions can be introduced by various methods known in the art, which include, but are not limited to, site-directed mutagenesis and/or affinity maturation of the parent antigen-binding molecule, for example, via phage display.
In order to identify possible sites such as hypervariable region residues for modification, alanine scanning mutagenesis can be performed to find residues that significantly contribute to antigen binding. Alternatively or additionally, it may be beneficial to analyze a crystal structure of the antigen and antibody complex to identify points of contact between the antibody and human CEA. These contact residues and neighboring residues are candidates for substitution according to methods known in the art and/or described herein. After generating such variants, the pool of variants can be selected by methods known in the art and/or described herein and antibodies with superior properties in one or more relevant assays can be selected for further development.
Phage display can be used to generate a repertoire of hypervariable region sequences from a parent antigen-binding molecule that contains random amino acid mutation(s). Several hypervariable region sites (such as six to seven sites) are mutated, for example, to generate all possible amino substitutions at each site.
Alternatively, random mutagenesis can be performed on light and/or heavy chain variable regions. Mutations can be generated by methods known in the art, including, but not limited to, the use of mutagenesis primers, control of the number of cycles, and use of mutagenic nucleotide analogues 8-oxo-dGTP and dPTP during PCR amplification. Antibody variants generated in this way are displayed novelly from filamentous phage particles as fusions to the M13 111 gene product packaged in each particle. The phage displayed variants are then selected for their biological activities (such as binding affinity) as described herein and candidates that have one or more enhanced activities will be used for further development.
Methods of screening phage display libraries can be found in Huse et al., Science, 246: 1275-1281 (1989); process natl. academy Know. U.S.A., 88: 4363-4366 (1991), the contents of which are incorporated herein by reference. An alternative method of identifying affinity matured antigen binding molecules can be found, for example, in U.S. Patent No. 7,432,063 to Balint et al, the contents of which are incorporated herein by reference in their entirety.
In some embodiments, the antigen binding molecules of the present invention comprise an Fc region, preferably a human Fc region. The sequences and structures of Fc regions are known in the art and have been characterized. In a specific embodiment, the human constant region is IgG1, as described in SEQ 10 Nos. 121 and 122 and detailed below.
lgG1 Nucleotide Sequence (SEQ ID NO 121) ACCAAGGGCCCATCGGTCTTCCCCCTGGCACCCTCCTCCAAGAGCACCTCTG GGGGCACAGCGGCCCTGGGCTGCCTGGTCAAGGACTACTTCCCCGAACCGG TGACGGTGTCGTGGAACTCAGGCGCCCTGACCAGCGGCGTGCACACCTTCC CGGCTGTCCTACAGTCCTCAGGACTCTACTCCCTCAGCAGCGTGGTGACCGT
GCCCTCCAGCAGCTTGGGCACCCAGACCTACATCTGCAACGTGAATCACAAG 5 CCCAGCAACACCAAGGTGGACAAGAAAGCAGAGCCCAAATCTTGTGACAAAA CTCACACATGCCCACCGTGCCCAGCACCTGAACTCCTGGGGGGACCGTCAG TCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACCCCT GAGGTCACATGCGTGGTGGTGGACGTGAGCCACGAAGACCCTGAGGTCAAG TTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGC GGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCC TGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAA AGCCCTCCCAGCCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCC CGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAGCTGACCAAG AACCAGGTCAGCCCTGACCTGCCTGGTCAAAGGCTTCTATCCCAGCGACATCG CCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGC CTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGT GGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCAT GAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTA
AATGA Amino Acid Sequence lgG1 (SEQ 10 No 122) TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSVVNSGALTSGVHTFPAVL QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSCDKTHTCPPC PAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNVVYVDGVEV HNAKTKPREEQYNSTYRWSVLTVLHQDVVLNGKEYKCKVSNKALPAPIEKTISKA KGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEVVESNGQPENNYKT
TPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK Human Fc region variants and isoforms are also, however, encompassed by the present invention. Suitable variant Fc regions for use in the present invention can be produced, for example, according to the methods taught in U.S. Patent No. 6,737,056 to Presta (Fc region variants with altered effector function due to one or more amino acid modifications ); or US Patent Applications 60/439,498, 560/456,041, 60/514,549 or WO 2004/063351 (variant Fc regions with increased binding affinity due to amino acid modifications); or in US Patent Application No. 10/672,280 or WO 2004/099249 (Fc variants with altered binding to FcγR due to amino acid modifications), the contents of which are fully incorporated herein by reference. In a specific 1st embodiment, the anti-CEA ABMs and variant ABMs comprise an Fc region that has been glycoengineered to alter ABM effector function activity (e.g. reduce fucosylation, increase Fc receptor binding affinity, increase ADCC etc.). Glycoprojection methods that can be used are described in detail below and are known in the art).
In one embodiment, the antigen binding molecule according to the present invention is conjugated to an additional moiety, such as a radiolabel or a toxin. Such conjugated antigen-binding molecules can be prepared by a variety of methods that are well known in the art. Anti-CEA ABM conjugates according to the present invention are described in detail below in the chapter entitled "Anti-CEA Antigen Binding Molecule Conjugates".
ANTt-CEA ABM POLYPEPTIDES AND POLYNUCLEOTIDES In one aspect, the present invention relates to antigen binding molecules and polypeptides that have the same binding specificity as the murine antibody PR1A3 (such as binding to the same membrane-bound epitope of CEA). and which has improved or comparable biological activities (such as increased affinity for membrane-bound CEA and/or enhanced ADCC). In one embodiment, the antigen binding molecule comprises one or more of the CDRs described in Table 2 below. In a more specific embodiment, the antigen binding molecule comprises three heavy chain CDRs from Table 2 below. In another specific embodiment, the antigen binding molecule comprises three light chain CDRs from Table 2 below.
In another specific embodiment, the present invention relates to a membrane-bound human CEA-specific antigen binding molecule comprising: (a) a heavy chain CDR1 sequence selected from the group consisting of: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11 and SEQ ID No 12; (b) a heavy chain CDR2 sequence selected from the group consisting of: SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO: 19, SEQ 10 NO: 20, SEQ 10 NO: 21, SEQ 10 NO: 22, SEQ ID NO: 23, and SEQ 10 NO: 24; and (c) a heavy chain CDR3 sequence selected from the group consisting of: SEQ ID NO 25, SEQ ID NO 26, SEQ ID NO 27, SEQ ID NO 28, SEQ 10 NO 29, SEQ 10 NO 30, SEQ ID NO: 31, SEQ 10 NO: 32, SEQ 10 NO: 33, SEQ 10 NO: 34, and SEQ 10 NO: 35. In another specific embodiment, the present invention relates to an antigen binding molecule specific for human CEA bound to the membrane, comprising: (a) a light chain CDR1 sequence selected from the group consisting of: SEQ 10 NO: 36, SEQ 10 NO: 37, SEQ ID NO: 38, SEQ 10 NO: 39, SEQ 10 NO: 40, SEQ 10 #41, SEQ 10 #42, SEQ 10 #43, SEQ 10 #44 and SEQ ID #45; (b) a light chain COR sequence selected from the group consisting of: SEQ ID NO:46, SEQ ID NO:47, SEQ ID NO:48, SEQ ID NO:49, SEQ ID NO:50, SEQ ID NO:51, SEQ 10 #52, SEQ 10 #53, SEQ 10 #54 and SEQ 10 #55; and (c) a light chain CDR3 of SEQ 10 No.
56. In a specific embodiment, the antigen binding molecule lacks substantial cross-reactivity against soluble human CEA. In another embodiment, the antigen binding molecule comprises a human light and/or heavy chain constant region. In one embodiment, for example, the antigen binding molecule comprises an Fc region. In a more specific embodiment, the antigen binding molecule comprises an Fc region that has been glycoengineered. The present invention also relates to polynucleotides encoding any of the antigen-binding molecules according to the present invention specific for membrane-bound human CEA.
In one aspect, the present invention relates to a membrane-bound human CEA-specific antigen binding molecule comprising a heavy chain variable region and/or a light chain variable region. In one embodiment, the heavy chain variable region comprises a polypeptide having the sequence of SEQ ID No. 101. In another embodiment, the heavy chain variable region comprises a polypeptide having at least about 80%, 85%, 90 %, 95%, 96%, 97%, 98% or 99% identity to the sequence of SEQ ID No 101. In one embodiment, the light chain variable region comprises a polypeptide having the sequence of SEQ ID No 105.
In another embodiment, the heavy chain variable region comprises a polypeptide that has at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequence of SEQ ID No 105.
In one embodiment, the membrane-bound human CEA-specific antigen binding molecule comprises a heavy chain variable region and/or a light chain variable region. In a specific embodiment, the heavy chain variable region comprises a polypeptide having the sequence of SEQ ID No. 4 as follows: 1 2 3 4
QVQLVQSGSELKKPGASVKVSCKASGYTFTEX X MX WVRQAPGQGLEWMGX 8 9 INTKX5 GEAX 6YX7 EEFKGRFVFSLDTSVSTAYLQISSLKAEDTAVYYCARWDX X X 1oyx11X12X13X14DYWGQGTTVTVSS 4 where X 1is You F; X 2is Sou G; X 3 is N or S; X is Wou Y; X is N, T 5 or S·' X6 is T or N·, X7 is V or 1·, X8 is F or A ' X9 is Y ' A , V ' F or S·' X10 is O' H, W ' E or Y; X11 is V, L or F; X12 is E, K or Q; X13 is A or T; and X14 is M or L.
In a specific embodiment, the light chain variable region comprises a polypeptide having the sequence of SEQ 10 No 11 as follows: OIQMTQSPSSLSASVGORVTITCKASX 15X16X17 X18X19X20VAWYQQKPGKAPKX 21 L IYX22ASX 23X24 X25 X26 GVPSRFSGSGSGTOFTLTISSLQPEOFATYFCHQYYTY
TFGQGTKLEIK wherein X15 is Q, A, K or H; X16 is N, A, Y, I, K, T or F; X17 is V, A, G or M; X18 is G, S, T or L; X19 is T, N, P or A; X20 is N or Y; X21 is P or L; X22 is S, L or W; X23 is Y, N or H; X24 is R, L, P or H; X25 is Y, S, Q, K, E, F or P; and X26 is S, G, I or R.
In another specific embodiment, the heavy chain variable region comprises a polypeptide having the sequence of SEQ 10 No 107.
In another specific embodiment, the heavy chain variable region comprises a polypeptide that has a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to sequence of SEQ 10 No. 107. In another specific embodiment, the antigen light chain variable region comprises a polypeptide having the sequence of SEQ 10 No. 108.
In another specific embodiment, the light chain variable region comprises a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to the sequence of SEQ 10 No. 108. In one embodiment, the antigen binding molecule comprises a heavy chain polypeptide that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100 % identical to a sequence selected from the group consisting of: SEQ 10 No. 101, 107 and 188 to 206 and a light chain polypeptide that is at least about 80%, 85%, 90%, 95%, 96% , 97%, 98%, 99% or 100% identical to a sequence selected from the group consisting of: SEQ 10 No. 105, 108 and
207 to 216. An antigen binding molecule comprising the light and/or heavy chain variable region is specific for CEA, particularly membrane-bound CEA. In one embodiment, an antigen binding molecule comprising the light and/or heavy chain variable region has substantially no cross-reactivity against soluble CEA. In another embodiment, the heavy chain additionally comprises an Fc region. In a specific embodiment, the Fc region was glycoengineered to have reduced fucosylation of the N-linked oligosaccharides as described in detail below.
In one aspect, the present invention also relates to an isolated polypeptide comprising one or more CORs described in Table 2.
In one embodiment, the isolated polypeptide comprises: heavy chain COR 1 sequence selected from the group consisting of: SEQ 10 #1, SEQ 10 #2, SEQ 10 #3, SEQ 10 #5, SEQ 10 #6, SEQ 10 #7, SEQ 10 #8, SEQ 10 #9, SEQ 10 #10, SEQ 10 #11 and SEQ 10 #12; (b) a heavy chain CDR2 sequence selected from the group consisting of: SEQ 10 #13, SEQ 10 #14, SEQ 10 #15, SEQ 10 #16, SEQ 10 #17, SEQ 10 #18, SEQ 10 #19, SEQ 10 #20, SEQ 10 #21, SEQ 10 #22, SEQ 10 #23 and SEQ 10 #24; and (c) a heavy chain COR3 sequence selected from the group consisting of: SEQ 10 #25, SEQ 10 #26, SEQ 10 #27, SEQ 10 #28, SEQ 10 #29, SEQ 10 #30, SEQ 10 #31, SEQ 10 #32, SEQ 10 #33, SEQ 10 #34 and SEQ 10 #35; In one embodiment, the isolated polypeptide comprises a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to the sequence of SEQ 10 No 107 In another embodiment, the present invention relates to a polypeptide comprising: (a) a light chain CDR1 sequence selected from the group consisting of: SEQ 10 No. 36, SEQ 10 No. 37, SEQ ID No. 38, SEQ 10 #39, SEQ 10 #40, SEQ 10 #41, SEQ 10 #42, SEQ 10 #43, SEQ 10 #44 and SEQ 10 #45; (b) a light chain COR sequence selected from the group consisting of: SEQ 10 #46, SEQ 10 #47, SEQ 10 #48, SEQ 10 #49, SEQ 10 #50, SEQ 10 #51, SEQ 10 #52, SEQ 10 #53, SEQ 10 #54 and SEQ 10 #55; and (c) a light chain CDR3 of SEQ 10 No. 56. In one embodiment, the isolated polypeptide comprises a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence of SEQ 10 No. 108. In another aspect, the present invention also relates to polynucleotides encoding any such polypeptide and antigen-binding molecules comprising any such polypeptide. An antigen-binding molecule comprising the polypeptide is specific for CEA, particularly membrane-bound CEA. In one embodiment, the antigen binding molecule lacks substantial cross-reactivity against soluble human CEA. In one embodiment, the polypeptide further comprises a light and/or heavy chain constant region. In another embodiment, the polypeptide comprises an Fc region, more specifically a glycoengineered Fc region. In a specific embodiment, the Fc region has been glycoengineered to have reduced fucosylation of the N-linked oligosaccharides as described in detail below.
In another aspect, the present invention further relates to isolated polynucleotides encoding membrane-bound human CEA-specific antigen binding molecules. In one embodiment, the isolated polynucleotide comprises one or more of the COR sequences shown in Table 3 below, or one of their combinations, wherein the polynucleotide encodes a polypeptide that, as part of an antigen-binding molecule, specifically binds CEA. , particularly membrane-bound CEA. In one embodiment, the isolated polynucleotide comprises a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to one or more of the sequences from variable region shown in Table 5. In one embodiment, the present invention pertains to a composition comprising a first isolated polynucleotide comprising a sequence that is at least about 80%, 85%, 90%, 95%, 96% , 97%, 98%, 99% or 100% identical to a sequence selected from the group consisting of SEQ 10 Nos. 113, 119 and 159-177 and an isolated second polynucleotide comprising a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to a sequence selected from the group consisting of SEQ ID Nos. 117, 120 and 178-187. In one embodiment, the polynucleotide encodes a heavy chain comprising a variable region and a constant region (such as an IgG constant region or fragment thereof, particularly an IgG constant region comprising an Fc region). In one embodiment, the polynucleotide encodes a light chain comprising a variable region and a constant region (such as a kappa or lambda constant region). In one embodiment, antigen binding molecules encoded by these isolated polynucleotides lack substantial cross-reactivity against soluble human CEA.
In another embodiment, the present invention also encompasses an isolated polynucleotide that comprises a sequence encoding a polypeptide that contains a sequence that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98 %, 99% or 100% identical to a sequence selected from the group consisting of: SEQ 10 No. 101, 105, 107, 108 and 188-216 with conservative amino acid substitutions, wherein an antigen binding molecule comprising the polypeptide (an antigen-binding molecule comprising a polypeptide, for example, that is at least about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or 100% identical to a sequence selected from the group consisting of: SEQ 10 No. 101, 107 and 188 to 206 and a polypeptide that is at least about 80%,85%,90%,95%,96%,97%,98 %, 99% or 100% identical to a sequence selected from the group consisting of SEQ 10 No. 105, 108 and 207-216) specifically binds CEA, particularly membrane-bound CEA. In one embodiment, the polypeptide further comprises a human constant region. In a specific embodiment, the polypeptide comprises a human Fc region. In a more specific embodiment, the Fc region is a glycoengineered IgG Fc region.
In one embodiment, the present invention relates to a polynucleotide comprising: (a) a sequence encoding a heavy chain CDR1 from the group consisting of SEQ 10 Nos. 57-59 and 61, (b) a sequence of Heavy chain CDR2 selected from the group consisting of SEQ 10 Nos. 62-66 and (c) a heavy chain CDR3 sequence selected from the group consisting of SEQ 10 Nos. 67-77. In another embodiment, the present invention relates to a polynucleotide comprising: (a) a light chain COR 1 sequence selected from the group consisting of SEQ 10 No. 78-88, (b) a CDR2 sequence chain selected from the group consisting of SEQ 10 No. 89-97 and (c) a light chain CDR3 sequence of SEQ 10 No. 98.
TABLE2 COLOR Amino Acid Sequence SEQIDW EFGMN 1 EYGMN 2 Kabat EYSMN 3 CDR1 EFGMS 5 from GYTFTEF 6 Chothia chain GYTFTEY 7 heavy GYTFTEFGMN 8 GYTFTEYGMN 9 AbM GYTFTEYSMN 10 GYTFTEFGMS 12
COR Amino Acid Sequence SEQIDW
WINTKTGEATYVEEFKG 13 WINTKTGEATYIEEFKG 14 Kabat WINTKSGEATYVEEFKG 15 YINTKNGEANYVEEFKG 16 CDR2 WINTKNGEATYIEEFKG 17 NTKTGEAT 18 chain Chothia NTKSGEAT 19 heavy NTKNGEAN 20 WINTKTGEAT 21 WINTKSGEAT 22 AbM YINTKNGEAN 23 WINTKNGEAT 24 WDFYDYVEAMDY 25 WDFYHYVEAMDY 26 WDFVDYVEAMDY 27 WDFYWYVEAMDY 28 CDR3 Kabat WDAFEYVKALDY 29 Chothia WDFFEYFKTMDY 30 chain eAbM WDFFYYVQTMDY 31 heavy WDFSYYVEAMDY 32 WDFAHYFQTMDY 33 WDFAYYFQTMDY 34
WDFAYYLEAMDY 35 KASQNVGTNVA 36 KASANVGNNVA 37 KASKNVGTNVA 38 KASAAVGTYVA 39 light chain CDR1 KASQYASTNVA 40 KASHNVGTNVA 41 KASQIMGPNVA 42 KASQIVGTNVA 43
43 ysshrys 53 yssashrys 51 ysshrys 51 yssashrys 51 ysshrys 53 ysshrys 53 ysshrys 53 ysshrys 53 yssashrps 53 ysyrys 54 ylishryr 55 chain cor3 hqyytyplft 56 light table 3 color sequence nucleotides seq 10 GGATACACCTTCACTGAGTTTGGAATGAAC 57 COR1 GGATACACCTTCACTGAGTATGGTATGAAC 58 of heavy chain GGATACACCTTCACTGAGTATTCTATGAAC GGATACACCTTCACTGAGTTTGGAATGAGC 59 61 62 TGGATAAACACCAAAACTGGAGAGGCAACATATGTTGA COR2 of AGAGTTT AAGGGA heavy chain TGGATAAACACCAAAACTGGAGAGGCAACATATATTGA 63 AGAGTTTAAGGGA 64 TGGATAAACACCAAAAGTGGAGAGGCAACATATGTTGA
AGAGTTTAAGGGA TATATAAACACCAAAAATGGAGAGGCAAACTATGTTGA 65
AGAGTTT AAGGGA TGGATAAACACCAAAAATGGAGAGGCAACATATATTGA 66
COR Nucleotide Sequence SEQIDW
AGAGTTTAAGGGA CDR3 TGGGACTTCTATGATTACGTGGAGGCTATGGACTAC 67 chain TGGGACTTCTATCATTACGTGGAGGCTATGGACTAC 68 heavy TGGGACTTCGTGGATTACGTGGAGGCTATGGACTAC 69 TGGGACTTCTATTGGTACGTGGAGGCTATGGACTAC 70 TGGGACGCCTTTGAGTACGTGAAGGCGCTGGACTAC 71 TGGGATTTCTTTGAGTATTTTAAGACTATGGACTAC 72 TGGGACTTTTTTTATTACGTGCAGACTATGGACTAC 73 TGGGATTTTTCTTATTACGTTGAGGCGATGGACTAC 74 TGGGACTTTGCTCATTACTTTCAGACTATGGACTAC 75 TGGGACTTCGCTTATTACTTTCAGACTATGGACTAC 76 TGGGATTTCGCGTATTACCTTGAGGCTATGGACTAC 77 CDR1 AAGGCCAGTCAGAATGTGGGTACTAATGTTGCC 78 chain AAGGCCAGTGCCAATGTGGGTAATAATGTTGCC 79 light AAGGCCAGTAAGAATGTGGGGACTAATGTTGCG 80 AAGGCCAGTGCGGCTGTGGGTACGTATGTTGCG 81 AAGGCCAGTCAGATAGCGAGTACTAATGTTGCC 82 AAGGCCAGTCACAATGTGGGTACCAACGTTGCG 83 AAGGCCAGTCAGATTATGGGTCCTAATGTTGCG 84 AAGGCCAGTCAAATTGTGGGTACTAATGTTGCG 85 AAGGCCAGTCAGAAGGTGCTTACTAATGTTGCG 86 AAGGCCAGTCAGACTGTGAGTGCTAATGTTGCG 87 CDR2 of TATTCGGCATCCTACCGCTACAGT 88 TATTTGGCCTCCAACCTCTCCGGT 89 light chain TACCTGGCATCCTACCCCCAGATT 90 TATTCGGCATCCTACCGCAAAAGG 91
COLOR Nucleotide Sequence SEQ TATTCGGCATCCCACCGGTACAGT 10 92 93 In TATTGGGCATCCTACCGCTATAGT TATTTGGCATCCTACCACGAAAGT TATTCGGCATCCCACCGTCCCAGT 94 95 96 TATTTGGCATCCTACCGCTACAGT TATTTGGCATCCTACCGCTACAGA CACCAATATTACACCTATCCTCTATTCACG 98 97 CDR3 light chain CONSTRUCTION TABLE 4 Peptide Sequence SEQ ID NO PR1A3 VH QVKLQQSGPELKKPGETVKISCKASGYTFTEFGMNWVK 99 QAPGKGLKWMGWINTKTGEATYVEEFKGRFAFSLETSA TTAYLQINNLKNEDTAKYFCARWDFYDYVEAMDYWGQG
TTVTVSS pEM1496 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 100 huPR1A3 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VH VSTA YLQISSLKADDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS CH A QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 101 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTA VYYCARWDFYDYVEAMDYWGQ
GTTVTVSS IGHV7-4- QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAMNWV 102 1*02 RQAPGQGLEWMGWI NTNTGNPTYAQGFTGRFVFSLDT
SVSTAYLQISSLKAEDTAVYYCAR PR1A3 VL DIVMTQSQRFMSTSVGDRVSVTCKASQNVGTNVAWYQ 103 QKPGQSPKALIYSASYRYSGVPDRFTGSGSGTDFTLTIS NVQSEDLAEYFCHQYYTYPLFTFGSGTKLEMKRT
CONSTRUCTION Peptide Sequence SEQIDW pEM1495 DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQ 104 huPR1A3 VL KPGKAPKLLIYSASYRYSGVPSRFSGSGSGTDFTFTISSL
QPEDIATYYCHQYYTYPLFSFGQGTKVEI KR CL1A DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQ 105 KPGKAPKLLIYSASYRYSGVPSRFSGSGSGTDFTLTISSL
QPEDF ATYYCHQYYTYPLFTFGQGTKLEI K IMGT_hVK DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQK 106 - 1_39 PGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQ
PEDFATYYCQQSYSTP CH7 rF9 QVQLVQSGSELKKPGASVKVSCKASGYTFTEYGMNWV 107 RQAPGQGLEWMGWINTKSGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS CLA1 rH11 DIQMTQSPSSLSASVGDRVTITCKASQTVSANVAWYQQ 108 KPGKAPKLLIYLASYRYRGVPSRFSGSGSGTDFTL TISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEIKRT PMS22 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 188 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS 1C8 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 189 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTA VYYCARWDFYHYVEAMDYWGQ
GTTVTVSS 3E1 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 190 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFVDYVEAMDYWGQ GTTVTVSS
CONSTRUCTION Peptide Sequence SEQIDW 207 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNVVV 191 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYWYVEAMDYWGQ
GTTVTVSS heavy chain QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNVVV 192 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS affinity matured VSTAYLQISSLKAEDTAVYYCARWDFAHYFQTMDYWGQ by GTTVTVSS heavy chain QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 193 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS affinity matured VSTAYLQISSLKAEDTAVYYCARWDFAYYFQTMDYWGQ GTTVTVSS heavy chain QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNVVV 194 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS affinity matured VSTAYLQISSLKAEDTAVYYCARWDFAYYLEAMDYWGQ GTTITVSS H3 Full (5) 195 19 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMSVVV RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDAFEYVKALDYWGQ
GTTVTVSS H3 Full (5) QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 196 8 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VSTA YLQISSLKAEDTAVYYCARWDFFEYFKTMDYWGQ
GTTVTVSS H3 Full (5) QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNVVV 197 28 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFFYYVQTMDYWGQ
GTTVTVSS H3 Full (5) QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNVVV 198 27 RQAPGQGLEWMGWI NTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFSYYVEAMDYWGQ GTTVTVSS
CONSTRUCTION Peptide Sequence SEQIDW Heavy Chain QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 199 RQAPGQGLEWMGWINTKTGEATYIEEFKGRFVFSLDTS H4E9 VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS pAC14 (89) QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 200 RQAPGQGLEWMGWI NTKSGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS pAC15 (F9) QVQLVQSGSELKKPGASVKVSCKASGYTFTEYGMNWV 201 RQAPGQGLEWMGWI NTKSGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS H1/H2 (5) 2 QVQLVQSGSELKKPGASVKVSCKASGYTFTEYSMNWV 202 RQAPGQGLEWMGYINTKNGEANYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS H1/H2 (5) 11 QVQLVQSGSELKKPGASVKVSCKASGYTFTEYGMNWV 203 RQAPGQGLEWMGWINTKNGEATYIEEFKGRFVFSLDTS VSTA YLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS H1/H2 (5) 13 QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMNWV 204 RQAPGQGLEWMGYINTKNGEANYVEEFKGRFVFSLDAS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS H1/H2 (5) 14 QVQLVQSGSELKKPGASVKVSCKASGYTFTEYGMNWV 205 RQAPGQGLEWMGYINTKNGEANYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDFYDYVEAMDYWGQ
GTTVTVSS H3 Full (5) QVQLVQSGSELKKPGASVKVSCKASGYTFTEFGMSWV 206 19 RQAPGQGLEWMGWINTKTGEATYVEEFKGRFVFSLDTS VSTAYLQISSLKAEDTAVYYCARWDAFEYVKALDYWGQ GTTVTVSS
CONSTRUCTION Peptide Sequence SEQIDW pAC21 (3A1) DIQMTQSPSSLSASVGDRVTITCKASANVGNNVAWYQQ 207 KPGKAPKLLIYLASNRSGGVPSRFSGSGSGTDFTLTISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEIKRT pAC19 (2C6) DIQMTQSPSSLSASVGDRVTITCKASKNVGTNVAWYQQ 208 KPGKAPKPLIYLASYPQIGVPSRFSGSGSGTDFTLTISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEI KRT pAC18 (2F1) DIQMTQSPSSLSASVGDRVTITCKASAAVGTYVAWYQQ 209 KPGKAPKLLIYSASYRKRGVPSRFSGSGSGTDFTLTISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEI KRT pAC23 DIQMTQSPSSLSASVGDRVTITCKASQIASTNVAWYQQK 210 (2F11) PGKAPKLLIYWASYRYSGVPSRFSGSGTDFTLTISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEI KRT Light Chain DIQMTQSPSSLSASVGDRVTITCKASQNVGTNVAWYQQ 211 of H4E9 KPGKAPKPLIYSASYRYSGVPSRFSGSGSGTDFTLTI SSL
QPEDF ATYYCHQYYTYPLFTFGQGTKLEI KRT L2D2 DIQMTQSPSSLSASVGDRVTITCKASHNVGTNVAWYQQ 212 KPGKAPKLLIYSASHRYSGVPSRFSGSGSGTDFTLTISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEIKRT pAC6 (C1) DIQMTQSPSSLSASVGDRVTITCKASQIMGPNVAWYQQ 213 KPGKAPKLLIYLASYH ESGVPSRFSGSGSGTDFTLTISSL
QPEDF ATYYCHQYYTYPLFTFGQGTKLEI KRT pAC7 (E1 O) DIQMTQSPSSLSASVGDRVTITCKASQIVGTNVAWYQQK 214 PGKAPKLLIYSASHRPSGVPSRFSGSGSGTDFTLTISSLQ
PEDFATYYCHQYYTYPLFTFGQGTKLEIKRT pAC12 (H ) DIQMTQSPSSLSASVGDRVTITCKASQKVLTNVAWYQQK 215 PGKAPKLLIYLASYRYSGVPSRFSGSGSGTDFTLTISSLQ PEDFATYYCHQYYTYPLFTFGQGTKLEIKRT
CONSTRUCTION Peptide Sequence SEQIDW pAC13 (H11) DIQMTQSPSSLSASVGDRVTITCKASQTVSANVAWYQQ 216 KPGKAPKLLIYLASYRYRGVPSRFSGSGSGTDFTL TISSL
QPEDFATYYCHQYYTYPLFTFGQGTKLEIKRT TABLE 5 CONSTRUCTION Nucleotide Sequence SEQIDW PR1A3 VH CAGGTGAAGCTGCAGCAGTCAGGACCTGAGTTGAAGA 111 AGCCTGGAGAGACAGTCAAGATCTCCTGCAAGGCTTC TGGATATACCTTCACAGAATTCGGAATGAACTGGGTGA AGCAGGCTCCTGGAAAGGGTTTAAAGTGGATGGGCTG GATAAAACACCAAAACTGGAGAGGCAACATATGTTGAAG AGTTTAAGGGACGGTTTGCCTTCTCTTTGGAGACCTCT GCCACCACTGCCTATTTGCCAGATCAACAACCTCAAAAA TGAGGACACGGCTAAATATTTCTGTGCTCGATGGGATT TCTATGACTATGTTGAAGCTATGGACTACTGGGGCCAA
GGGACCACCGTGACCGTCTCCTCA pEM1496 CAGGTGCAGCTGGTGCAATCTGGGTCTGAGTTGAAGA 112 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGACGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA CH7A CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 113 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC CAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW IGHV -4-1 *02 CAGGTGCAGCTGGTGCAATCTGGGTCTGAGTTGAAGA 114 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTAGCTATGCTATGAATTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATCAACACCAACACTGGGAACCCAACGTATGCCCA GGGCTTCACAGGACGGTTTGTCTTCTCCTTGGACACCT CTGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAA
GGCTGAGGACACTGCCGTGTATTACTGTGCGAGA PR1A3 VL GATATCGTGATGACCCAGTCTCAAAGATTCATGTCCAC 115 ATCAGTAGGAGACAGGGTCAGCGTCACCTGCAAGGCC AGTCAGAATGTGGGTACTAATGTTGCCTGGTATCAACA GAAACCAGGACAATCCCCTAAAGCACTGATTTACTCGG CATCCTACCGGTACAGTGGAGTCCCTGATCGCTTCACA GGCAGTGGATCTGGGACAGATTTCACTCTCACCATCA GCAATGTACAGTCTGAAGACTTGGCGGAGTATTTCTGT CACCAATATTACACCTATCCTCTATTCACGTTCGGCTC
GGGGACAAAGTTGGAAATGAAACGTACG pEM1495 GACATCCAGATGACTCAGAGCCCAAGCAGCCTGAGCG 116 CCAGCGTGGGTGACAGAGTGACCATCACCTGTAAGGC CAGTCAGAATGTGGGTACTAATGTTGCCTGGTACCAGC AGAAGCCAGGTAAGGCTCCAAAAGCTGCTGATCTACTC GGCATCCTACCGGTACAGTGGTGTGCCAAGCAGATTC AGCGGTAGCGGTAGCGGTACCGACTTCACCTTCACCA TCAGCAGCCTCCAGCCAGAGGACATCGCCACCTACTA CTGCCACCAATATTACACCTATCCTCTATTCAGCTTCG
GCCAAGGGACCAAGGTGGAAATCAAACGT CL 1A GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 117 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGAATGTGGGTACTAATGTTGCCTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTCG GCATCCTACCGCTACAGTGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA GGGCACCAAGCTCGAGATCAAG
CONSTRUCTION Nucleotide Sequence SEQIDW IMGT_hVK_1 GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 118 - 39 ATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCA AGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCA GAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCT GCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTG
TCAACAGAGTTACAGTACCCCT CH7 rF9 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 119 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTATGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACGAAATCTGGAGAGGCAACCTATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCAGCTAGC CLA1 rH11 GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 120 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGACTGTGAGTGCTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTACTTG GCATCCTACCGCTACAGAGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG PMS22 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 159 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC CAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW 1C8 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 160 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATCATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA 3E1 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 161 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCGTGGATTACGTGGAGGCTATGGACTACTGGGG
CCAAGGGACCACGGTCACCGTCTCCTCA 207 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 162 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATTGGTACGTGGAGGCTATGGACTACTGGGG CCAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW Heavy Chain CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 163 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC matured by TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC affinity GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTTGCTCATTACTTTCAGACTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 164 heavy chain AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC matured by TGGATACACCCTTCACTGAGTTTGGAATGAACTGGGTGC affinity GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCGCTTATTACTTTCAGACTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 165 heavy chain AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC matured by TGGATACACCCTTCACTGAGTTTGGAATGAACTGGGTGC affinity GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ATTTCGCGTATTACCTTGAGGCTATGGACTACTGGGGC CAAGGGACCACGATCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW H3 Full (5) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 166 19 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAGCTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCTGTGTATTACTGTGCGAGATGGG ACGCCTTTGAGTACGTGAAGGCGCTGGACTACTGGGG
CCAAGGGACCACGGTCACCGTCTCCTCA H3 Full (5) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 167 8 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ATTTCTTTGAGTATTTTAAGACTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA H3 Full (5) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 168 28 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTTTTTTATTACGTGCAGACTATGGACTACTGGGGC CAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW H3 Full (5) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 169 27 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ATTTTTCTTATTACGTTGAGGCGATGGACTACTGGGGC
CAAGGGACCACAGTCACCGTCTCCTCA Heavy Chain CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 170 AGCCTGGGGCTCAGTGAAGGTTTCCTGCAAGGCTTC H4E9 TGGATACACCTTCACTGAGTTTGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAATACCAAAACTGGAGAGGCAACTTATATTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA pAC14 (89) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 171 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAAGTGGAGAGGCAACCTATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC CAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQ ID No pAC15 (F9) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 172 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTATGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACGAAATCTGGAGAGGCAACCTATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA H1/H2 (5) 2 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 173 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTATTCTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATA CATAAACACCAAAAATGGAGAGGCAAACTATGTTGAAG AGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTCT GTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAGG CTGAAGACACTGCCGTGTATTACTGTGCGAGATGGGA CTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA H1/H2 (5) 11 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 174 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTATGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAACACCAAAAATGGAGAGGCAACCTATATTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCCGTGTATTACTGTGCGAGATGGG ACTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC CAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW H1/H2 (5) 13 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 175 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATA TATAAAACCCAAAAATGGAGAGGCAAACTATGTTGAAG AGTTTAAGGGACGGTTTGTCTTCTCCTTGGACGCCTCT GTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAGG CTGAAGACACTGCCGTGTATTACTGTGCGAGATGGGA CTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA H1/H2 (5) 14 CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 176 AGCCTGGGGCCTAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTATGGTATGAACTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATA TATAAAACCCAAAAATGGAGAGGCAAACTATGTTGAAG AGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTCT GTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAGG CTGAAGACACTGCCGTGTATTACTGTGCGAGATGGGA CTTCTATGATTACGTGGAGGCTATGGACTACTGGGGC
CAAGGGACCACGGTCACCGTCTCCTCA H3 Full (5) CAGGTGCAATTGGTGCAATCTGGGTCTGAGTTGAAGA 177 19 AGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCTTC TGGATACACCTTCACTGAGTTTGGAATGAGCTGGGTGC GACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAT GGATAAAACACCAAAACTGGAGAGGCAACATATGTTGAA GAGTTTAAGGGACGGTTTGTCTTCTCCTTGGACACCTC TGTCAGCACGGCATATCTGCAGATCAGCAGCCTAAAG GCTGAAGACACTGCTGTGTATTACTGTGCGAGATGGG ACGCCTTTGAGTACGTGAAGGCGCTGGACTACTGGGG CCAAGGGACCACGGTCACCGTCTCCTCA
CONSTRUCTION Nucleotide Sequence SEQIDW pAC21 (3A1) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 178 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTGCCAATGTGGGTAATAATGTTGCCTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTTGG CCTCCAACCGCTCCGGTGGAGTCCCATCAAGGTTCAG TGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCA GCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTGT CACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC19 (2C6) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 179 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTAAGAATGTGGGGACTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCCCCTGATCTACCTG GCATCCTACCCCCAGATTGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCCCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC18 (2F1) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 180 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTGCGGCTGTGGGTACGTATGTTGCGTGGTATCAGC AGAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTCG GCATCCTACCGCAAAAGGGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC23 (2F11) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 181 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGATAGCGAGTACTAATGTTGCCTGGTATCAGCA GAAACCAGGGAAAAGCACCTAAGCTCCTGATCTATTGG GCATCCTACCGCTATAGTGGAGTCCCATCAAGGTTCAG TGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCA GCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTGT CACCAATATTACACCTATCCTCTATTCACGTTTGGCCA GGGCACCAAGCTCGAGATCAAGCGTACG
CONSTRUCTION Nucleotide Sequence SEQIDW Light Chain GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 182 of H4E9 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGAATGTGGGTACTAATGTTGCCTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCCCCTGATCTATTCG GCATCCTACCGCTACAGTGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG L2D2 GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 183 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCACAATGTGGGTACCAACGTTGCGTGGTATCAGC AGAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTCG GCATCCCACCGGTACAGTGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC6 (C1) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 184 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGATTATGGGTCCTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTTGG CATCCTACCACGAAAGTGGAGTCCCATCAAGGTTCAGT GGCAGTGGATCTGGGACAGATTTCACTCTCACCATCA GCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTGT CACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC7 (E1 O) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 185 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAAATTGTGGGTACTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTCG GCATCCCACCGTCCCAGTGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA GGGCACCAAGCTCGAGATCAAGCGTACG
CONSTRUCTION Nucleotide Sequence SEQIDW pAC12 (H7) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 186 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGAAGGTGCTTACTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTATTTGG CATCCTACCGCTACAGTGGAGTCCCATCAAGGTTCAGT GGCAGTGGATCTGGGACAGATTTCACTCTCACCATCA GCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTGT CACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG pAC13(H11) GATATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGC 187 ATCTGTGGGAGACAGAGTCACCATCACTTGCAAGGCC AGTCAGACTGTGAGTGCTAATGTTGCGTGGTATCAGCA GAAACCAGGGAAAGCACCTAAGCTCCTGATCTACTTG GCATCCTACCGCTACAGAGGAGTCCCATCAAGGTTCA GTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATC AGCAGTCTGCAACCTGAAGATTTCGCAACTTACTACTG TCACCAATATTACACCTATCCTCTATTCACGTTTGGCCA
GGGCACCAAGCTCGAGATCAAGCGTACG EXPRESSION VECTORS AND HOST CELLS: In one aspect, the present invention relates to an expression vector and/or a host cell comprising one or more isolated polynucleotides in accordance with the present invention. The host cell or expression vector comprises, for example, any one or more of the polynucleotides or polynucleotides encoding the polypeptides, ABMs and/or variant ABMs described above in the chapters entitled "Anti-CEA Antigen Binding Molecules" and " Polypeptides and Polynucleotides of Anti-CEA ABMs".
In another aspect, the present invention relates to a method of producing ABM that specifically binds membrane-bound human CEA, wherein the method comprises: culturing the host cell comprising one or more isolated polynucleotides according to present invention or an expression vector comprising one or more isolated polynucleotides according to the present invention in a medium under conditions allowing the expression of said one or more polynucleotides, wherein said one or more polynucleotides encode one or more polypeptides that are part of the ABM; and recovering said ABM, wherein said ABM or a portion thereof binds to the same epitope or is capable of competing for binding with the murine monoclonal antibody PR1A3.
Generally, any type of cultured cell line can be used to express ABM in accordance with the present invention. In a preferred embodiment, CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, other mammalian cells, cells yeast, insect cells or plant cells are used in the background cell line to generate the designed host cells in accordance with the present invention.
In a specific embodiment, the host cell or expression vector comprises one or more polynucleotides that encode an ABM that is a variant antibody or one of the fragments thereof that have the binding specificity of the murine antibody PR1A3; the ABM binds, for example, the same epitope as PR1A3 or is able to compete with the PR1A3 antibody for antigen binding. In a preferred embodiment, the antibody is affinity matured. The affinity matured antibody generally has improved binding affinity over that of the reference antibody from which the affinity matured antibody was derived. In another preferred embodiment, the antibody has desirable therapeutic properties that include, but are not limited to: strong binding affinity for the CEA antigen (particularly, membrane-bound CEA), while having substantially no cross-reactivity against soluble CEA; an ability to induce cell lysis of cells expressing CEA in vitro and ex vivo, preferably in a dose-dependent manner; an ability to inhibit CEA-mediated cell adhesion in vitro; an ability to inhibit tumor growth and/or induce tumor tissue regression in tumor models in mice (such as mouse xenograft 5). In another preferred embodiment, the variant antibody or fragment thereof comprises human Fc.
In one embodiment, one or more polynucleotides encoding an ABM in accordance with the present invention may be expressed under the control of a constitutive promoter or, alternatively, a regulated expression system.
Suitable regulated expression systems include, but are not limited to, tetracycline-regulated expression system, ecdysone-inducible expression system, lac key expression system, glucocorticoid-inducible expression system, temperature-inducible promoter system, and temperature-inducible expression system. metallothionein. If several different nucleic acids encoding an ABM according to the present invention are comprised within the host cell system, some of them may be expressed under the control of a constitutive promoter, while others are expressed under the control of a regulated promoter. The maximum expression level is considered the highest possible level of stable polypeptide expression that has no significant adverse effect on cell growth rate and will be determined using routine experimentation. Expression levels are determined by methods generally known in the art, including Western Blot analysis, using an antibody specific for ABM or an antibody specific for a peptide tag fused to ABM; and Northern Blot analysis. In a further alternative, the polynucleotide may be operably linked to a reporter gene; expression levels of an ABM described herein are determined by measuring a signal correlated to the level of expression of the reporter gene. The reporter gene may be transcribed together with the nucleic acid(s) encoding said ABM as a single mRNA molecule; their corresponding coding sequences can be linked by an internal ribosome entry site (IRES) or by a cap-independent translation enhancer (CITE). The reporter gene can be translated together with at least one nucleic acid encoding an ABM described herein to form a single polypeptide chain. Nucleic acids encoding an ABM in accordance with the present invention can be operatively linked to the reporter gene under the control of a single promoter, such that the nucleic acid encoding the ABM and the reporter gene are transcribed into one RNA molecule. which is alternatively split into two separate messenger RNA (mRNA) molecules; one of the resulting mRNAs is translated into said reporter protein and the other is translated into ABM.
Methods that are well known to those skilled in the art can be used to construct expression vectors that contain the coding sequence of an ABM that binds to the same epitope of the murine antibody PR1A3 along with appropriate transcriptional/translational control signals. These methods include in vitro recombinant DNA methods, synthetic methods and genetic recombination/in vivo recombination. See, for example, the methods described in Maniatis et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1989) and Ausubel et al, Current Protocols in Molecular Biology, Greene Publishing and Wiley lnterscience, New York ( 1989).
Various host expression vector systems can be used to express the coding sequence of the ABMs in accordance with the present invention. Preferably, mammalian cells are used as host cell systems which have been transfected with cosmid DNA or recombinant plasmid DNA expression vectors that contain the coding sequence for the protein of interest and the coding sequence for the fusion polypeptide. More preferably, CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, other mammalian cells, yeast, insect cells or plant cells 5 are used as host cell systems. Some examples of expression systems and selection methods are described in the following references and in the references referred to therein: Borth et al., Biotechnol. Bioeng. 71 (4): 266-73 (2000-2001), in Werner et al., Arzneimittelforschung/Drug Res. 48 (8): 870-80 (1998), in Andersen and Krummen, Curr. Op. Biotechno/. 13: 117-123 (2002), in Chadd and Chamow, Curr. Op. Biotechnol. 12: 188-194 (2001) and in Giddings, Curr. Op.
Biotechnol. 12: 450-454 (2001).
In alternative embodiments, other eukaryotic host cell systems may be used, including yeast cells transformed with recombinant yeast expression vectors that contain the coding sequence of an ABM in accordance with the present invention, such as the expression systems taught in US Patent Application No. 60/344,169 and WO 03/056914 (methods of producing a human-like glycoprotein in a non-human eukaryotic host cell) (the contents of which are fully incorporated by reference); insect cell systems infected with recombinant virus expression vectors (such as bacilloviruses) that contain the coding sequence of an ABM that binds to the same epitope as the murine antibody PR1A3 or is capable of competing with PR1A3 for antigen binding; plant cell systems infected with recombinant virus expression vectors (such as cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (such as Ti plasmid) that contain the ABM coding sequence according to the present invention, including, but not limited to, the expression systems taught in U.S. Patent No.
6,815,184 (methods of expression and secretion of biologically active polypeptides from genetically engineered Lemnaceae); WO 2004/057002 (production of glycosylated proteins in bryophytic plant cells by means of the introduction of a glycosyl transferase gene) and WO 2004/024927 (methods of 5th generation of extracellular heterologous non-plant protein in moss protoplast); and US Patent Applications Nos. 60/365,769, 60/368,047 and WO 2003/078614 (Glycoprotein processing in transgenic plants comprising a functional mammalian GnTIII enzyme) (the contents of which are fully incorporated herein by reference); or animal cell systems infected with recombinant virus expression vectors (such as adenovirus, vaccinia virus), including cell lines designed to contain multiple copies of the DNA encoding a chimeric ABM that binds to the same epitope as the murine PR1A3 antibody, either stably amplified (CHO/dhfr) or unstable amplified on small double chromosomes (such as murine cell lines). In one embodiment, the vector comprising the polynucleotide(s) encoding ABM according to the present invention is polycistronic. Furthermore, in one embodiment, the ABM discussed above is an antibody or fragment thereof. In a preferred embodiment, the ABM is an affinity matured antibody.
Stable expression is generally preferred over transient expression as it typically achieves more reproducible results and is also more prone to large scale production; it is, however, within the skill of the art how to determine whether transient expression is best for a specific situation. Instead of using expression vectors that contain viral origins of reproduction, host cells can be transformed with the corresponding coding nucleic acids controlled by appropriate expression control elements (such as promoter sequences, enhancers, transcription terminals, polyadenylation sites etc. .) and a selectable bookmark. After the introduction of external DNA, the engineered cells can be allowed to grow for one to two days in enriched medium and then switched to a selective medium. The selectable marker on the recombinant plasmid confers resistance to selection and allows for the selection of 5 cells that have stably integrated the plasmid into their chromosomes and grow to form foci which, in turn, can be linked and expanded into cell lines.
Various selection systems can be used, including, but not limited to, herpes simplex virus thymidine kinase (Wigler et al., Ce// 11:10 223 (1977), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, Proc. Natl. Acad Sci. USA 48: 2026 (1962)) and adenine phosphoribosyltransferase genes (lowy et al, Ce/1 22: 817 (1980)), which can be employed in tk-, hgprr or aprr cells, respectively. Antimetabolite resistance is used based on selection for dhfr, which confers resistance to methotrexate (Wigler et al., Natl. Acad. Sci. USA 77: 3567 (1989); O'Hare et al, Proc. Natl. Acad. Sci. USA 78: 1527 (1981)); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA
78: 2072 (1981)); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin et al., J. Mo/. Biol. 150:1 (1981)); and hygro, which confers resistance to hygromycin genes (Santerre et al., Gene 30: 147 (1984)).
Recently, additional selectable genes have been described, namely trpB, which allow cells to utilize indole in place of tryptophan; hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. U.S.A. 85:8047 (1988)); the glutamine synthase system; and ODC (ornithine decarboxylase), which confers resistance to the ornithine decarboxylase inhibitor, 2-(difluoromethyl)-DL-ornithine, DFMO (McConlogue, in Current Communications in Molecular Biology, Cold Spring Harbor Laboratory, Ed. (1987)) .
The present invention further relates to a method of modifying the glycosylation profile of ABMs according to the present invention that are produced by a host cell, which comprises expressing in said host cell a nucleic acid encoding an ABM according to the present invention. with the
The present invention and a nucleic acid encoding a polypeptide having glycosyltransferase activity or a vector comprising such nucleic acids.
Genes with glycosyltransferase activity include ~(1,4)-N-acetylglucosaminyltransferase
111 (GnTII), α-mannosidase 11 (ManII), ~(1,4)-galactosyltransferase (GaiT), ~(1,2)-N-
acetylglucosaminyltransferase I (GnTI) and ~(1,2)-N-acetylglucosaminyltransferase 11
(GnTII). In one embodiment, a combination of genes with glycosyltransferase activity is expressed in the host cell (such as GnTIII and Man 11). Similarly, the method also encompasses the expression of one or more polynucleotides encoding ABM in a host cell in which a glycosyltransferase gene has been disrupted or otherwise inactivated (such as a host cell in which the activity of the gene encoding a1 -6 core fucosyltransferase was knocked out). In another embodiment, the ABMs according to the present invention can be produced in a host cell that additionally expresses a polynucleotide encoding a polypeptide that has GnTIII activity to modify the glycosylation pattern.
In a specific embodiment, the polypeptide having GnTIII activity is a fusion polypeptide comprising the Golgi localization domain of a Golgi resident polypeptide.
In another preferred embodiment, expression of the ABMs according to the present invention in a host cell that expresses a polynucleotide encoding a polypeptide that has GnTIII activity results in ABMs with higher Fc receptor binding affinity and increased effector function. .
Accordingly, in one embodiment, the present invention relates to a host cell comprising (a) an isolated nucleic acid comprising a sequence encoding a polypeptide having GnTIII activity; and (b) an isolated polynucleotide that encodes an ABM in accordance with the present invention, such as a chimeric, primatized or humanized antibody that binds human CEA. In a preferred embodiment, the polypeptide having GnTIII activity is a fusion polypeptide comprising the catalytic domain of GnTIII and the Golgi localization domain is the mannosidase localization domain 11. Methods of generating such fusion polypeptides and their use to produce antibodies with enhanced effector functions are described in US Provisional Patent Application No. 60/495,142 and published US Patent Application No. 2004/0241817 , the entire contents of which are expressly incorporated herein by reference. In a specific embodiment, the modified ABM produced by the host cell has an IgG constant region or one of the fragments thereof that comprises the Fc region. In another specific embodiment, the ABM is a humanized antibody or one of the fragments thereof that comprises an Fc region.
The alteard glycosylation ABMs produced by the host cells in accordance with the present invention typically exhibit increased Fc receptor binding affinity and/or increased effector function as a result of host cell modification (such as through expression of a glycosyltransferase gene). ). Preferably, the increase in Fc receptor binding affinity is the increase in binding to an Fcγ activating receptor, such as the FcγRIIIa receptor. The highest effector function is preferably an increase in one or more of the following: increased antibody-dependent cellular cytotoxicity, increased antibody-dependent cellular phagocytosis (ADCP), increased cytokine secretion, increased immune complex-mediated antigen uptake by antigen-presenting cells, increased Fc-mediated cellular cytotoxicity, increased binding to NK cells, increased binding to macrophages, increased binding to polymorphonuclear cells (PMNs), increased binding to monocytes, increased cross-linking of antibodies bound to target, increased direct signaling-inducing apoptosis, increased maturation of dendritic cells, and increased priming of T cells. GENERATION AND USE OF ABMS THAT HAVE IMPROVED EFFECTIVE FUNCTION,
INCLUDING ANTIBODY DEPENDENT CELL CYTOTOXICITY In one aspect, the present invention provides glycoforms of ABMs (such as variant ABMs) that bind the same epitope as the murine antibody PR1A3 and that have enhanced effector function, including antibody-dependent cellular cytotoxicity. Glycosylation projection of antibodies has been described previously. See, for example, U.S. Patent No. 6,602,684, incorporated herein by reference in its entirety. Methods of producing ABMs from host cells that have altered activity of genes involved in glycosylation are also described in detail herein (see, for example, the previous chapter entitled "Expression Vectors and Host Cells"). Increases in ADCC of the ABMs according to the present invention are also achieved by increasing the affinity of the antigen-binding molecule for membrane-bound CEA, such as through affinity maturation or other affinity-enhancing methods (see Tang et al., J. Immunol. 2007, 179: 2815-2823). Combinations of these approaches are also encompassed by the present invention.
Clinical trials of unconjugated monoclonal antibodies (mAbs) for the treatment of some types of cancer have recently generated encouraging results. Dillman, Cancer Biother. & Radiopharma. 12: 223-25 (1997); Deo et al. Immunology Today 18: 127 (1997). Chimeric unconjugated IgG1 is approved for low-grade or follicular B-cell non-Hodgkin's lymphoma. Dillman, Cancer Biother. & Radiopharma. 12: 223-25 (1997), while another unconjugated mAb, a humanized IgG1 targeting solid breast tumors, also showed promising results in phase 111 clinical trials. Deo et al. /mmunology Today 18: 127 (1997). The antigens of these two mAbs are highly expressed on their corresponding tumor cells and the antibodies mediate the destruction of potent tumors by effector cells in vitro and in vivo. On the other hand, many other unconjugated mAbs with fine tumor specificities cannot trigger effector functions with sufficient potency to be clinically useful. Frost et al., Cancer 80: 317-33 (1997); Surfus et al, J.
lmmunother. 19: 184-91 (1996). For some of these weaker mAbs, adjunctive cytokine therapy is currently being tested. The addition of cytokines can stimulate antibody-dependent cellular cytotoxicity (ADCC) by increasing the activity and number of circulating lymphocytes. Frost et al., Cancer 80: 317-33 (1997); Surfus et al, J. Immunother. 19: 184-91 (1996). ADCC, lytic attack on targeted cells, is triggered by binding of leukocyte receptors to the constant region (F c) of antibodies. Deo et al. Immunology Today 18: 127 (1997).
A different but complementary approach to increasing the ADCC activity of unconjugated IgG1s is the projection of the Fc region of the antibody. Protein projection studies have demonstrated that FcyRs interact with the lower hinge region of the CH2 domain of IgG. Lund et al., J.
Immunol. 157: 4963-69 (1996). The binding of FcyR also requires, however, the presence of covalently linked oligosaccharides in the Asn 297 conserved in the CH2 region. Lund et al., J. Immuno/. 157: 4963-69 (1996); Wright and Morrison, Trends Biotech. 15: 26-31 (1997), which suggests that oligosaccharide and polypeptide either contribute directly to the site of interaction or that oligosaccharide is required to maintain an active CH2 polypeptide conformation. Modification of the oligosaccharide structure can therefore be explored as a means of increasing the affinity of the interaction.
An IgG molecule carries two N-linked oligosaccharides in its Fc region, one on each heavy chain. Like any glycoprotein, an antibody is produced as a population of glycoforms that share the same polypeptide backbone but have oligosaccharides attached to glycosylation sites. The oligosaccharides normally found in the Fc region of serum IgG are of the complex biantennated type (Wormald et al., Biochemistry 36: 130-38 (1997), with a low level of terminal sialic acid and bisected N-5 acetylglucosamine (GicNAc) and a high degree of variable terminal galactosylation and central fucosylation Some studies suggest that the minimal carbohydrate structure required for FcγR binding lies within the oligosaccharide core Lund et al, J. Immunol 157: 4963-69 (1996).
Rat or hamster-derived cell lines used in industry and academia for the production of unconjugated therapeutic mAbs normally bind the necessary oligosaccharide determinants to Fc sites. IgGs expressed in these cell lines do not, however, have the bisected GlcNAc found in low amounts in serum IgGs.
Lifely et al., Glycobiology 318: 813-22 (1995). On the other hand, it was recently observed that a humanized IgG1 produced by mouse myeloma (CAMPATH-1 H) carried a bisected GlcNAc in some of its glycoforms. Lifely et al., Glycobiology 318: 813-22 (1995). The mouse cell-derived antibody achieved similar maximal in vitro ADCC activity as CAMPATH-1 H antibodies produced in standard cell lines, but at significantly lower antibody concentrations.
The CAMPATH antigen is normally present at high levels on lymphoma cells and this chimeric mAb has high ADCC activity in the absence of bisected GlcNAc. Lifely et al., Glycobiology 318: 813-22 (1995).
In the N-linked glycosylation process, a bisected GlcNAc is added by GnTIII. Schachter, Biochem. Ce/1 Biol. 64: 163-81 (1986).
Previous studies used an antibody-producing CHO cell line that was previously engineered to express, in an externally regulated manner, different levels of a cloned GnTIII enzyme gene.
(Umaria P. et al., Nature Biotechnol. 17:176-180 (1999)). This approach established for the first time a rigorous correlation between the expression of a glycosyltransferase (such as GnTIII) and the ADCC activity of the modified antibody. Thus, the present invention contemplates a variant ABM (such as an affinity matured ABM) that binds to the same epitope as the murine antibody PR1A3, which comprises an Fc region or region equivalent to an Fc region that has altered glycosylation resulting from the change. the level of expression of a glycosyltransferase gene in the ABM-producing host cell.
In a specific embodiment, the change in the level of gene expression is an increase in GnTIII activity. The increase in GnTIIII activity results in an increase in the percentage of bisected oligosaccharides, as well as a reduction in the percentage of fucose residues, in the Fc region of ABM. This antibody or fragment thereof has the highest Fc receptor binding affinity and highest effector function.
The present invention also relates to a method of producing an ABM according to the present invention which has modified oligosaccharides, which comprises (a) culturing a host cell designed to express at least one nucleic acid encoding a polypeptide having activity of glycosyltransferase under conditions permitting the production of an ABM in accordance with the present invention, wherein said polypeptide having glycosyltransferase activity is expressed in an amount sufficient to modify oligosaccharides in the Fc region of said ABM produced by said host cell; and (b) isolating said ABM. In one embodiment, the polypeptide having glycosyltranserase activity is GnTIII. In another embodiment, there are two polypeptides that have glycosyltransferase activity. In a specific embodiment, the two peptides that possess glycosyltransferase activity are GnTIII and ManII. In another embodiment, the polypeptide having glycosyltransferase activity is a fusion polypeptide comprising the catalytic domain of GnTIII. In a more specific embodiment, the fusion polypeptide further comprises the Golgi localization domain of a Golgi resident polypeptide. Preferably, the Golgi localization domain is the mannosidase II or GnTI localization domain. Alternatively, the Golgi localization domain is selected from the group consisting of: the mannosidase I localization domain, the GnTII localization domain and the core α1-6 fucosyltransferase localization domain. ABMs produced by the methods according to the present invention have enhanced Fc receptor binding affinity and/or enhanced effector function.
1st Generally, increased effector function is one or more of the following: increased Fc-mediated cellular cytotoxicity (including increased antibody-dependent cellular cytotoxicity), increased antibody-dependent cellular phagocytosis (ADCP), increased cytokine secretion, increased immune complex-mediated uptake of antigen by antigen-presenting cells, increased binding to NK cells, increased binding to macrophages, increased binding to monocytes, increased binding to polymorphonuclear cells, increased direct signaling-inducing apoptosis, increased cross-linking of target-bound antibodies, increased maturation of dendritic cells, and increased priming of T cells. The increase in Fc receptor binding affinity is preferably increased binding to activating Fc receptors, such as FcyRIIIa. In a particularly preferred embodiment, the ABM is a humanized antibody or fragment thereof.
In one embodiment, the percentage of bisected N-linked oligosaccharides in the Fc region of the ABM is at least from about 10% to about 100%, specifically at least about 50%, more specifically at least about 60%, at least about 70%, at least about 80%, or at least about 90 to 95% of the total oligosaccharides. In yet another embodiment, the antigen-binding molecule produced by the methods according to the present invention has a higher proportion of non-fucosylated oligosaccharides in the Fc region as a result of modification of its oligosaccharides by the methods according to the present invention. .
In one embodiment, the percentage of non-fucosylated oligosaccharides is at least
5 from about 20% to about 100%, specifically at least about 50%,
at least about 60% to about 70%, and more specifically, at least about 75%. Non-fucosylated oligosaccharides can be of the hybrid or complex type.
In yet another embodiment, the antigen binding molecule produced by the methods according to the present invention has a higher proportion of oligosaccharides bisected in the Fc region as a result of modification of its oligosaccharides by the methods according to the present invention.
In one embodiment, the percentage of bisected oligosaccharides is at least from about 20% to about 100%,
specifically at least about 50%, at least about 60% to about
70% and more specifically at least about 75%. In a particularly preferred embodiment, the ABM produced by the host cells and methods according to the present invention has a higher proportion of bisected non-fucosylated oligosaccharides in the Fc region.
Bisected non-fucosylated oligosaccharides can be hybrid or complex.
Specifically, the methods according to the present invention can be used to produce antigen-binding molecules in which at least about 10% to about 100%, specifically at least about
15%, more specifically at least about 20% to about 50%, more specifically at least about 20% to about 25%, and more specifically at least about 30% to about 35% of the oligosaccharides in the region Fc of the antigen-binding molecule are bisected and not fucosylated.
ABMs according to the present invention may also comprise an Fc region in which at least about 10% to about 100%,
specifically at least about 15%, more specifically at least about 20% to about 25%, and more specifically at least about 30% to about 35% of the oligosaccharides in the Fc region of the ABM are bisected non-fucosylated hybrids.
In another embodiment, the present invention relates to an antigen-binding molecule (such as variant ABM) that is capable of competing with the PR 1A3 antibody for membrane-bound human CEA designed to have enhanced effector function and/or enhanced Fc receptor binding affinity produced by the methods according to the present invention. Enhanced effector function may include, but are not limited to, one or more of the following: increased Fc-mediated cellular cytotoxicity (including increased antibody-dependent cellular cytotoxicity), increased antibody-dependent cellular phagocytosis (ADCP), increased secretion cytokine activity, increased immune complex-mediated antigen uptake by antigen-presenting cells, increased binding to NK cells, increased binding to macrophages, increased binding to monocytes, increased binding to polymorphonuclear cells, increased signaling-inducing apoptosis increase in cross-linking of target-bound antibodies, increase in dendritic cell maturation, or increase in T cell priming. In a preferred embodiment, the increase in Fc receptor binding affinity is the increase in binding to an activating receptor of Fc, preferably higher than FcyRIIIa. In one embodiment, the antigen-binding molecule is an antibody, antibody fragment that contains the Fc region, or a fusion protein that includes a region equivalent to the Fc region of an immunoglobulin. In a particularly preferred embodiment, the antigen binding molecule is a humanized affinity matured antibody.
The present invention further provides methods of generating and using host cell systems for the production of glycoforms of the
ABMs according to the present invention, which have enhanced Fc receptor binding affinity, preferably enhanced binding to Fc activating receptors, and/or which have enhanced effector functions, including antibody-dependent cellular cytotoxicity. The glycoprojection methodology that can be used with ABMs in accordance with the present invention has been described in more detail in U.S. Patent No. 6,602,684, U.S. Patent Application Published No. 2004/0241817 A 1, Patent Application US Published No. 2003/0175884 A 1, US Provisional Patent Application No. 60/441,307 and WO 2004/065540, the contents of which are hereby fully incorporated by reference. ABMs in accordance with the present invention may alternatively be glycoengineered to have reduced fucose residues in the Fc region according to the methods described in U.S. Patent Application published 2003/0157108 (Genentech) or in EP 1,176,195 A 1, WO 03/084570, WO 03/085119 and US Patent Applications published 2003/0115614, 2004/093621, 2004/110282, 2004/110704 and 2004/132140 (Kyowa). The contents of each of these documents are fully incorporated herein by reference. Glycoengineered ABMs in accordance with the present invention can also be produced in expression systems that produce modified glycoproteins, such as those taught in U.S. Patent Application published No. 60/344,169 and WO 03/056914 (GiycoFi, Inc.) or in WO 2004/057002 and WO 2004/024927 (Grenovation), the contents of which are fully incorporated herein by reference. GENERATION OF CELL LINES FOR THE PRODUCTION OF PROTEINS WITH
ALTERED GLYCOSYLATION PATTERN In one aspect, the present invention provides host cell expression systems for generating the ABMs in accordance with the present invention that have modified glycosylation patterns. Particularly, the present invention provides host cell systems for generating glycoforms of the ABMs in accordance with the present invention that have enhanced therapeutic value. The present invention therefore provides host cell expression systems selected or designed to express a polypeptide that has glycosyltransferase activity. In a specific embodiment, the glycosyltransferase activity is a GnTIII activity. In one embodiment, the polypeptide having GnTIII activity is a fusion polypeptide comprising the Golgi localization domain of a heterologous Golgi resident polypeptide. Specifically, such host cell expression systems can be designed to comprise a recombinant nucleic acid molecule encoding a GnTIII-bearing polypeptide operably linked to a constitutive or regulated promoter system.
In a specific embodiment, the present invention provides a host cell that is designed to express at least one nucleic acid encoding a fusion polypeptide that has GnTIII activity and comprises the Golgi localization domain of a heterologous Golgi resident polypeptide. In one aspect, the host cell is engineered with a nucleic acid molecule that comprises at least one gene that encodes a fusion polypeptide that has GnTIII activity and comprises the Golgi localization domain of a heterologous Golgi resident polypeptide.
Generally, any type of cultured cell line, including the cell lines discussed above, can be used as a background to design the host cell lines in accordance with the present invention. In a preferred embodiment, CHO cells, BHK cells, NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6 cells or hybridoma cells, other mammalian cells, cells yeast, insect cells or plant cells are used in the background cell line to generate the designed host cells in accordance with the present invention.
It is contemplated that the present invention encompasses any engineered host cell that expresses a polypeptide that has glycosyltransferase activity, such as GnTIII activity, including a 5-fusion polypeptide that comprises the Golgi localization domain of a heterologous Golgi resident polypeptide as defined herein. .
One or more nucleic acids encoding a polypeptide that has glycosyltransferase activity, such as GnTIII activity, can be expressed under the control of a constitutive promoter or, alternatively, a regulated expression system. Such systems are well known in the art and include the systems discussed above. If several different nucleic acids that encode fusion polypeptides that have glycosyltransferase activity, such as GnTIII activity, and comprise the Golgi localization domain of a heterologous Golgi resident polypeptide are comprised in the host cell system, some of them may be expressed under the control of a constitutive promoter, while others are expressed under the control of a regulated promoter. Expression levels of fusion polypeptides that have glycosyltransferase activity, such as GnTIII activity, are determined by methods generally known in the art, including Western Blog analysis, Northern Blot analysis, analysis of reporter gene expression, or measurement of the activity of glycosyltransferase, such as GnTIII activity. Alternatively, one can employ a lectin that binds to GnTIII biosynthetic products, such as lectin E4 -PHA. Alternatively, a functional assay can be used that measures the enhancement of Fc receptor binding or the enhancement of antibody-mediated effector function produced by cells engineered with nucleic acid encoding a polypeptide with glycosyltransferase activity, such as GnTIII activity. IDENTIFICATION OF TRANSFERENTS OR TRANSFORMERS THAT EXPRESS THE
PROTEIN THAT HAS A MODIFIED GYCOSYLATION PATTERN Host cells that contain the coding sequence of a variant ABM (such as humanized and affinity matured ABM) that is capable of competing with the PR 1A3 antibody for antigen binding and expressing the gene products biologically active compounds can be identified by at least four general approaches: (a) DNA-DNA or DNA-RNA hybridization; (b) presence or absence of "marker" gene functions; (c) determining the level of transcription measured by expressing the corresponding mRNA transcripts in the host cell; and (d) detection of the gene product as measured by immunoassay or its biological activity.
In the first approach, the presence of the coding sequence of a variant ABM that is capable of competing with the PR1A3 antibody and/or the coding sequence of the polypeptide that has glycosyltransferase activity (such as GnTIII) can be detected by means of DNA hybridization. -DNA or DNA-RNA using probes comprising nucleotide sequences that are homologous to the corresponding coding sequences, respectively, or portions thereof or derivatives thereof.
In the second approach, the host and recombinant expression vector system can be identified and selected based on the presence or absence of certain "marker" gene functions (such as thymidine kinase activity, antibiotic resistance, methotrexate resistance, phenotype of transformation, formation of occlusion body in bacillovirus, etc.). If the coding sequence of the ABM according to the present invention or one of the fragments thereof and/or the coding sequence of the polypeptide having glycosyltransferase activity (such as GnTIII) are inserted into a marker gene sequence of the vector, for example For example, recombinants that contain the corresponding coding sequences can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed together with the coding sequences under the control of the same promoter used to control the expression of the coding sequences or a different promoter. Expression of the marker in response to induction or selection indicates expression of the ABM coding sequence according to the present invention and/or the coding sequence of the polypeptide having glycosyltransferase activity (such as GnTIII).
In the third approach, the transcriptional activity for the coding region of the ABM according to the present invention or one of the fragments thereof and/or the coding sequence of the polypeptide having glycosyltransferase activity (such as GnTIII) can be determined by through hybridization assays. RNA can be isolated and analyzed by means of Northern Blot using, for example, a probe homologous to the coding sequences of the ABM according to the present invention or one of the fragments thereof and/or the coding sequence of the polypeptide having activity of glycosyltransferase (such as GnTIII) or specific portion thereof.
Alternatively, total host cell nucleic acids can be extracted and tested to determine hybridization in these probes.
In the fourth approach, the expression of the protein products can be tested immunologically, such as by Western Blot, immunoassays such as radioimmunoprecipitation, enzyme-linked immunoassays, and the like.
The final test of the success of the expression system, however, involves the detection of the biologically active gene products. THERAPEUTIC APPLICATIONS AND METHODS OF USE OF ANTI-CEA MOLECULES
ANTIGEN BINDING The present invention also relates to a method of targeting cells in vivo or in vitro that express CEA. Cells that express CEA can be targeted for therapeutic purposes (such as treating a disorder by targeting cells that express CEA for destruction by the immune system). In one embodiment, the present invention relates to a method of targeting cells that express CEA in a patient which comprises administering to the patient a composition comprising an ABM in accordance with the present invention. Cells that express CEA can also be targeted for diagnostic purposes (such as to determine whether they are expressing CEA, either normally or abnormally). Accordingly, the present invention also relates to methods of detecting the presence of CEA or a cell expressing CEA, either in vivo or in vitro. A method of detecting CEA expression according to the present invention comprises contacting a sample to be tested, optionally with a control sample, with an ABM according to the present invention, under conditions which allow the formation of a complex between ABM and CEA Complex formation is then detected (such as by ELISA or other methods known in the art). When using a control sample with the test sample, any statistically significant difference in the formation of ABM and CEA complexes when comparing the test and control samples is indicative of the presence of CEA in the test sample.
In one aspect, the ABMs according to the present invention may be target cells used in vivo or in vitro that express CEA. Cells expressing CEA can be targeted for diagnostic or therapeutic purposes. In one aspect, the ABMs according to the present invention can be used to detect the presence of CEA in a sample. CEA is abnormally expressed (as well as over-expressed) in many human tumors compared to non-tumor tissue of the same cell type. Thus, the ABMs according to the present invention are particularly useful in preventing tumor formation, eradicating tumors and inhibiting tumor growth or metastasis. The ABMs according to the present invention also act to arrest the cell cycle, cause apoptosis of target cells (such as tumor cells) and inhibit angiogenesis and/or differentiation of target cells. The ABMs according to the present invention can be used to treat any tumor that expresses CEA. Specific malignancies that can be treated with the ABMs according to the present invention include, but are not limited to, colorectal cancer, non-small cell lung cancer, gastric cancer, pancreatic cancer, and breast cancer.
The anti-CEA ABMs described herein can be used alone to inhibit tumor growth or kill tumor cells. Anti-CEA ABMs can bind, for example, CEA that is on the cell membrane or surface of cancer cells and allow, for example, ADCC or other effector-mediated killing of cancer cells. Anti-CEA ABMs can be humanized, specifically affinity matured, more specifically glycoengineered and affinity matured.
ABMs can alternatively be used to block CEA antigen activity, particularly through physical interference with its binding to another compound. Antigen binding molecules can be used, for example, to block CEA-mediated cell adhesion.
The anti-CEA ABMs of the present invention are administered to mammals, preferably humans, in a pharmaceutically acceptable dosage form such as those discussed below, including those that can be administered to humans intravenously in the form of a mixture or by continuous infusion over a period of time, intramuscularly, intraperitoneally, intracerebrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical or inhalation. ABMs are also appropriately administered by intratumoral, peritumoral, intralesional, or perilesional routes to exert local and systemic therapeutic effects. The intraperitoneal route is expected to be particularly useful, for example, in the treatment of colorectal tumors.
For the treatment of disease, the appropriate dosage of ABM will depend on the type of disease being treated, the severity and course of the disease, previous therapy, the patient's clinical history, antibody reaction, and the judgment of the attending physician. ABM is appropriately given to the patient once or over a series of treatments.
The present invention provides a method for selectively killing tumor cells that express CEA. This method comprises reacting the antigen-binding molecules or the conjugates (such as the immunotoxin) according to the present invention with said tumor cells. Such tumor cells may be from a human carcinoma which includes colorectal carcinoma, non-small cell lung carcinoma (NSCLC), gastric carcinoma, pancreatic carcinoma and breast carcinoma.
In one embodiment, the present invention provides a method for inhibiting CEA-mediated cell adhesion of a tumor cell. This method comprises contacting said tumor cell with antigen binding molecules or conjugates according to the present invention. These tumor cells can be human cells, including colorectal cancer cells, non-small cell lung cancer (NSCLC) cells, gastric cancer cells, pancreatic cancer cells, and breast cancer cells.
Furthermore, the present invention provides a method of treating carcinomas (such as human carcinomas) in vivo. This method comprises administering to a patient a pharmaceutically effective amount of a composition that contains at least one of the antigen-binding molecules or the immunoconjugates (such as the immunotoxin) according to the present invention.
In a further aspect, the present invention relates to a method of treating cancers characterized by overexpression of CEA, including, but not limited to, colorectal cancer cells, NSCLC (non-small cell lung cancer), gastric cancer, pancreatic cancer cells and breast cancer cells, by administering a therapeutically effective amount of the humanized and affinity matured antigen binding molecules or variant antigen binding molecules described herein.
In a further embodiment, the present invention relates to a method of inducing tumor tissue regression in a patient using the humanized and affinity matured antigen binding molecules or variant antigen binding molecules described herein. Non-limiting examples of tumor tissue include colorectal tumor, non-small cell lung tumor, gastric tumor, pancreatic tumor and breast tumor. In a specific embodiment, the tumor tissue is a colorectal tumor.
Pursuant to the practice of the present invention, the patient may be a human, equine, porcine, bovine, murine, canine, feline and avian patient. Other warm blooded animals are also included in the present invention.
The present invention further provides methods of inhibiting tumor cell growth, treating tumors in patients, and treating proliferative-type diseases in patients. These methods comprise administering to the patient an effective amount of the composition of the present invention.
In another aspect, the present invention relates to the use of the affinity matured and humanized antigen binding molecules or variant antigen binding molecules described herein for the manufacture of a medicament for the treatment of a disease related to CEA expression. not normal. In a specific embodiment, the disease is a cancer that overexpresses CEA, including, but not limited to, colorectal tumor, non-small cell lung tumor, gastric tumor, pancreatic tumor, and breast tumor. In a specific embodiment, the tumor is a colorectal tumor.
COMPOSITIONS, FORMULATIONS, DOSAGES AND ROUTES OF ADMINISTRATION: In one aspect, the present invention pertains to pharmaceutical compositions comprising the ABMs of the present invention and a pharmaceutically acceptable carrier. The present invention further relates to the use of such pharmaceutical compositions in the method of treating diseases such as cancer or in the manufacture of a medicament for the treatment of diseases such as cancer. Specifically, the present invention relates to a method of treating disease, and more specifically, treating cancer, wherein the method comprises administering a therapeutically effective amount of the pharmaceutical composition according to the present invention.
In one aspect, the present invention encompasses pharmaceutical compositions, combinations and methods of treating human carcinomas, such as colorectal carcinoma. The present invention includes, for example, pharmaceutical compositions for use in the treatment of human carcinomas which comprise a pharmaceutically effective amount of an antibody according to the present invention and a pharmaceutically acceptable carrier.
The ABM compositions of the present invention can be administered using conventional modes of administration that include, but are not limited to, intravenous, intraperitoneal, oral, intralymphatic, or direct administration to the tumor. Intravenous administration is preferred.
In one aspect of the present invention, therapeutic formulations containing the ABMs of the present invention are prepared for storage by mixing an antibody having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients, or stabilizers (Remington's Pharmaceutica/ Sciences, 16th edition, Osol, A.
Ed. (1980)), in the form of lyophilized formulations or aqueous solutions. Acceptable carriers, excipients, or stabilizers are non-toxic to patients at the dosages and concentrations employed.
Formulations to be used for in vivo administration must be sterile. This is easily achieved by filtering through sterile filter membranes.
The most effective mode of administration and dosage regimen for the pharmaceutical compositions in accordance with the present invention depends on the severity and course of the disease, the health of the patient, the reaction to treatment 1 and the judgment of the attending physician. Accordingly, the dosages of the compositions should be titrated to the individual patient. An effective dose of the compositions of the present invention will generally, however, be in the range of about 0.01 to about 2000 mg/kg.
The molecules described herein can be found in a variety of dosage forms which include, but are not limited to, liquid suspensions or solutions, tablets, pills, powders, suppositories, polymeric microcapsules or microbubbles, liposomes, and injectable or infusible solutions. The preferred form depends on the mode of administration and the therapeutic application.
The composition comprising an ABM in accordance with the present invention will be formulated, dosed and administered in a manner consistent with good medical practice. Factors for consideration in this context include the specific disease or disorder being treated, the specific mammal being treated, the clinical condition of the individual patient, the cause of the disease or disorder, the site of delivery of the agent, the method of administration, the schedule of administration. and other factors known to medical practitioners. The therapeutically effective amount of the antagonist to be administered will be governed by these considerations.
The examples below explain the present invention in more detail. The following examples and preparations are provided to enable those skilled in the art to more clearly understand and practice the present invention.
The present invention is not limited in scope, however, by the exemplified embodiments, which are intended to be only illustrations of isolated aspects of the present invention and methods that are functionally equivalent are within the scope of the present invention. Indeed, various modifications of the present invention, in addition to those described herein, will become apparent to those skilled in the art from the above specification and the accompanying figures.
These modifications are intended to fall within the scope of the appended claims.
EXAMPLES Unless otherwise specified, references to the numbering of specific amino acid residue positions in the Examples below are in accordance with the Kabat numbering system.
EXAMPLE 1 Generation of Affinity Maturation Libraries: H1/H2 Library For the generation of an affinity maturation library randomized in the HCDR1 and HCDR2 region, triplets encoding positions F32 G33 in COR 1 and positions W50 N52 T52a K52b T54 E56 T58 in CDR2 were randomized. In a first step, a DNA fragment (fragment 1) was amplified using pMS22 as a template and the primers MS-43 and EAB-679 that contain the randomized CDR1 positions (Fig. 11 and Table 6). Using the same template, primers MS-56 and MS-52 amplified a second fragment (fragment 2) that has a region overlapping with the 3' end of fragment 1. The amplification conditions included an initial incubation step at 94°C for five minutes followed by 25 cycles,
each consisting of denaturation at 94°C for one minute, combination at 55°C for one minute and an elongation step at 72°C for twenty seconds and fifty seconds for fragment 1 and fragment 2, respectively.
Finally, a final incubation step was performed at 72 °C for ten minutes. 5 The two fragments were purified on an agarose gel. Overlapping extension PCR with fragment 1 and fragment 2 using primers MS-43 and EAB-680, which harbored randomized positions of CDR2, generated a fragment with the two randomized CDRs (fragment 3). For the assembly of fragments 1 and 2, equimolar amounts of fragment 1 and fragment 2 were used. The amplification conditions included an initial incubation step at 94 oc for five minutes followed by five cycles without c for one minute, primers, in which each cycle consists of a 94° denaturing combination at 55°C for one minute and an elongation step at 72°C for forty seconds. After the addition of external primers, twenty additional cycles were performed using the same parameters. A fourth fragment (fragment 4) which overlaps the 3' region of fragment 3 was amplified by PCR again using pMS22 as a template and the primers MS-55 and MS-52.
After gel purification, a final overlap extension PCR using fragments 3 and 4 as templates and primers MS-43 and MS-52 generated a fragment that contains CL and VH portions. For this, equimolar amounts of fragment 3 and fragment 4 were used. The amplification conditions included an initial incubation step at 94°C for five minutes followed by five cycles without primers, in which each cycle consists of denaturation at 94°C for one minute , combination at 55°C for one minute and a stretch step at 72°C for eighty seconds. After the addition of the external primers, twenty additional cycles were performed using the same parameters. The resulting fragment was then gel purified and ligated with pMS22 after Ncoi/NheI digestion.
TABLES Prime r SEQ ID No Nucleotide Sequences of MS-43 H1/H2 Library Primers 123 CCAGCCGGCCATGGCCGATATCCAGATGACCCAGTCT
CCATC MS-52 124 GAAGACCGATGGGCCTTTGGTGCTAG MS-55 125 GCAACATATGTTGAAGAGTTTAAGGGACGG MS-56 126 ATGAACTGGGTGCGACAGGCCCCTG EAB-679 127 CAGGGGCCTGTCGCACCCAGTTCATMNNAWACTCAGT
GAAGGTGTATCCAGAAGCC EAB-680 128 CCGTCCCTTAAACTCTTCAACATAGGTTGCCTCTCCAG TTTTGGTGTTTATCCATCCCATCCACTCAAGCCCTTGTC
CAGG Randomization of EAB-679 and EAB-680 primers: Underline: 60% original base and 40% randomization as N L1/L2 library For the generation of a randomized affinity maturation library in the LCDR1 and LCDR2 region, triples encoding positions Q27, N28, V29, G30 T31 N32 in CDR1 and positions Y49 S50 Y53 R54 Y55 S56 in CDR2 were randomized. In a first step, a DNA fragment (fragment 1) was amplified using pMS22 as a template and the primers EAB-685 and EAB-681 that contain the randomized CDR1 positions (Fig. 12 and Table 6). Using the same template, primers EAB-686 and EAB-687 amplified a second fragment (fragment 2) that has a region overlapping with the 3' end of fragment 1. The amplification conditions included an initial incubation step at 94°C for five minutes followed by 25 cycles, each consisting of denaturation at 94°C for one minute, blending at 55°C for one minute and an elongation step at 72°C for sixty seconds for fragment 1 and fragment 2, respectively.
Finally, a final incubation step was carried out at 72
5 oc for ten minutes.
The two fragments were purified on an agarose gel.
Overlapping extension PCR with fragment 1 and 2 using primers EAB-685 and EAB-682, which harbored randomized positions of CDR2,
generated a fragment with the two randomized CDRs (fragment 3). For the assembly of fragments 1 and 2, equimolar amounts of fragment 1 and fragment 2 were used. The amplification conditions included an initial incubation step at 94°C for five minutes followed by five cycles without primers, in which each cycle consists of denaturation at 94c for one minute, the combination at 55oc for one minute and a stretch step at 72oc for sixty seconds.
After the addition of external primers, twenty additional cycles were performed using the same parameters.
a fourth fragment
(fragment 4) that overlaps the 3' region of fragment 3 was amplified by
PCR again using pMS22 as a template and primers EAB-688 and
EAB-687. After gel purification, a final overlapping extension PCR using fragments 3 and 4 as templates and the primers EAB-685 and EAB-
687 generated a fragment that contains both VL and CL portions.
For this, equimolar amounts of fragment 3 and fragment 4 were used. The amplification conditions included an initial incubation step at 94 oc for five minutes followed by 5 cycles without primers, in which each cycle oc for one minute, combination at 55 oc for one consists of denaturing at 94 minutes and an elongation step at 72 oc for eighty seconds.
After the addition of external primers, twenty additional cycles were performed using the same parameters.
This fragment was then ligated with pMS22 after Hindiii/Sacl digestion.
TABLE 7 Primer SEQ ID No Nucleotide Sequences of L1/L2 Libraries EAB-685 129 CAGCTATGACCATGATTACGCCAAGCTTGCATGCAA
ATTCTATTTCAAGG EAB-686 130 GTTGCGTGGTATCAGCAGAAACCAGGG EAB-687 131 GCTCTTTGTGAGGGGCGAGCTCAGGCCCTGATGG EAB-688 132 GGAGTCCCATCAAGGTTCAGTGGCAGTGGATCTGG EAB-681 133 CCTGGTTTCTGCTGATACCACGCAACATTAGTACCC
ACATTCTGACTGGCCTTGCAAGTGATGGTGACTC EAB-682 134 CTGCCACTGAACCTTTGATGGGACTCCACTGTAGCG GTAGGATGCCGAATAGATCAGGAGCTTAGGTGCTT
TCCCTGG Randomization of EAB-681 and EAB-682 primers: Underline: 60% original base and 40% randomization as N.
H3 Libraries For the generation of randomized affinity maturation libraries in the HCOR3 region, trios encoding positions W95, 096, F97, Y98, 099, Y100, V100a, E100b, A100c, and M100d were randomized in two different approaches: (1) randomization of the entire segment (complete H3 library) or (2) individual randomization of each position, resulting in ten sub-1st libraries. Sub-libraries containing clones with individually randomized positions were pooled after transformation into bacteria (pooled library H3). For randomization of the HCOR3 region, the fragments were amplified by PCR using a primer that was combined at the 3' end of CL and primers harboring the randomized sequences of HCOR3 (Fig. 13). Overlapping extension PCR was then performed with a second fragment that overlaps the 3' end of fragment 1 and comprises the VH end and the 5' region of CH 1. The pooled fragments were then ligated into pMS22 after ingestion of Saci!Nhel. For the generation of the pooled H3 library, ten 5 DNA fragments were PCR amplified separately using each of primers AC7-AC16 in combination with primer EAB-749. For the generation of the complete L3 library, primers AC17 and EAB-749 were used.
Plasmid pMS22 was used as a template. Amplification conditions included an initial incubation step at 94°C for five minutes followed by 25 cycles, each consisting of denaturation at 94°C for one minute, blending at 55°C for one minute, and an elongation step at 72°C for 36 seconds, followed by a final incubation step at 72°C for ten minutes. This resulted in fragments about 580 bp in length that were purified over agarose gel. For overlapping extension PCR, a second fragment was amplified using primer EAB-750 or EAB-751 in combination with EAB-
752. Although primer EAB-750 had an overlapping sequence with randomization primers AC7-11, EAB-751 shared sequence homologies with randomization primers AC12-17. Amplification conditions included an initial incubation step at 94°C for five minutes followed by 25 cycles, each consisting of denaturing at 94°C for one minute, blending at 55°C for one minute, and an elongation step at 72°C for twelve minutes. seconds, followed by a final incubation step at 72°C for ten minutes. The resulting fragments were about 180 bp in length. For the assembly of the two fragments, equimolar amounts of fragment 1 and the corresponding fragment 2 were used. Amplification conditions included an initial incubation step at 94 °C for five minutes followed by five cycles without oc for one minute, primers, where each cycle consists of denaturation at 94 combination at 55 °C for one minute and an extension step at 72 oc per
11 or sixty seconds. After the addition of external primers EAB-749 and EAB-752, twenty additional cycles were performed using the same parameters. Finally, a final incubation step was performed at 72 °C for ten minutes. The gel purified fragments were then ligated into pMS22 after Saci!Nhel digestion and the purified ligations were transformed into TG1 bacteria by electroporation. TABLE 8 Primer SEQIDW h3 Libraries - Nucleotide Sequence of Primer AC7 135 CCAGTAGTCCATAGCCTCCACGTAATCATAGAAGTCMNNTCTCGCA
CAGTAATACACGGCAGTG AC8 136 CCAGTAGTCCATAGCCTCCACGTAATCATAGAAMNNCCATCTCGCA
CAGTAATACACGGCAGTG AC9 137 CCAGTAGTCCATAGCCTCCACGTAATCATAMNNGTCCCATCTCGCA
CAGTAATACACGGCAGTG AC10 138 CCAGTAGTCCATAGCCTCCACGTAATCMNNGAAGTCCCATCTCGCA
CAGTAATACACGGCAGTG AC11 139 CCAGTAGTCCATAGCCTCCACGTAMNNATAGAAGTCCCATCTCGCA
CAGTAATACACGGCAGTG AC12 140 CGTGGTCCCTTGGCCCCAGTAGTCCATAGCCTCCACMNNATCATA
GAAGTCCCATCTCGCACAG AC13 141 CGTGGTCCCTTGGCCCCAGTAGTCCATAGCCTCMNNGTAATCATAG
AAGTCCCATCTCGCACAG AC14 142 CGTGGTCCCTTGGCCCCAGTAGTCCATAGCMNNCACGTAATCATA
GAAGTCCCATCTCGCACAG AC15 143 CGTGGTCCCTTGGCCCCAGTAGTCCATMNNCTCCACGTAATCATAG
AAGTCCCATCTCGCACAG AC16 144 CGTGGTCCCTTGGCCCCAGTAGTCMNNAGCCTCCACGTAATCATA
GAAGTCCCATCTCGCACAG AC17 145 CGTGGTCCCTTGGCCCCAGTAGTCCATAGCCTCCACGTAATCATAG
AAGTCCCATCTCGCACAGTAATACACGGCAG EAB- 146 CCATCAGGGCCTGAGCTCGCCCGTC 749
Primer SEQ 10 Libraries No. h3 - Primer Nucleotide Sequence EAB- 147 CGTGGAGGCTATGGACTACTGGGGCCAAGG 750 EAB- 148 GACTACTGGGGCCAAGGGACCACGGTCAC 751 EAB- 149 GGTCAGGGCGCCTGAGTTCCACG 752 Randomization of primer AC17: Bold and italic of original M. .
Underline: 60% original base and 40% randomization as N.
5 L3 Libraries For the generation of randomized affinity maturation libraries in the CDR3 region of the light chain, trios encoding positions Y91, Y92, T93, Y94, and L95a were randomized across the entire segment (L3 complete library) or resulted individually in five sub-libraries.
Sub-libraries containing clones with individually randomized positions were pooled after transformation into bacteria (L3 pooled library). For the generation of sub-libraries, five DNA fragments were amplified by PCR using each of primers AC 1-AC5 in combination with primer MS43. For the generation of the complete L3 library, primers AC6 and MS43 were used (Fig. 14). Plasmid pMS22 was used as a template. The five-minute amplification conditions included an initial incubation step at 94°C followed by 25 cycles, each of which consisted of denaturing at 94°C for 1 minute, blending at 55°C for 1 minute, and an elongation step at 72°C for 25°C. seconds, followed by a final incubation step at 72°C for ten minutes. The resulting fragments encompassing positions 1 to 104 of the VL domain were purified on an agarose gel and used as a template for further PCR amplification. All reactions were carried out with the primer
EAB-746, which has an overlapping sequence with the randomization primers and MS43 using the same conditions described above. Purified fragments, as well as pMS22, were digested with Ncoi/XhoI. For all five sub-libraries, 0.51Jg of insert was ligated with 0.51Jg of pAC16. For 5 the complete L3 library, ligation was performed with 9.81 µg of insert and 9.81 µg of pMS22. The purified bonds were transformed into TG1 bacteria by electroporation.
TABLE 9 Primer SEQ ID No L3 Libraries - Nucleotide Sequence of Primer AC1 150 GGTGCCCTGGCCAAACGTGAATAGAGGATAGGTGTAMNNTT
GGTGACAGTAGTAAGTTGC AC2 151 GGTGCCCTGGCCAAACGTGAATAGAGGATAGGTMNNATATT
GGTGACAGTAGTAAGTTGC AC3 152 GGTGCCCTGGCCAAACGTGAATAGAGGATAMNNGTAATATT
GGTGACAGTAGTAAGTTGC AC4 153 GGTGCCCTGGCCAAACGTGAATAGAGGMNNGGTGTAATATT
GGTGACAGTAGTAAGTTGC AC5 154 GGTGCCCTGGCCAAACGTGAAMNNAGGATAGGTGTAATATT
GGTGACAGTAGTAAGTTGC AC6 155 GGTGCCCTGGCCAAACGTGAATAGAGGATAGGTGTAATATT
GGTGACAGTAGTAAGTTGC EAB-746 156 CGCTTGATCTCGAGCTTGGTGCCCTGGCCAAACGTG MS-43 123 CCAGCCGGCCATGGCCGATATCCAGATGACCCAGTCTCCAT c AC6 primer randomization: Bold and italics: 60% original base and 40% randomization as M.
Underline: 60% original base and 40% randomization as N.
GENERATION OF ANTIGENS: Because murine PR1A3 and humanized antibodies recognize only membrane-bound but not particulate soluble human CEA, a recombinant chimeric protein was generated that contains the PR1A3 epitope for in vitro affinity maturation of humanized PR1A3 (SEQ 10 No. 7 and 8). Generation of this hybrid protein was performed as described in Steward et al.
1999. Briefly, the human biliary glycoprotein (8GP) domain 8 ONA sequence was replaced with the human CEA-83 domain sequence, which contains the epitope of PR1A3. As a result, the sequence encodes a hybrid protein comprising the N and A 1 domains of 8GP, the domain 83 of CEA and the A2 domain of 8GP (N-A1-83-A2, huNA8A). This fusion product was ligated to the Fc portion of human IgG1 (huNA8A-Fc) (Steward et al., Cancer Immunol.
/mmunother., 47: 299-306, 1999) or fused to a sequence encoding the precision protease cleavage site, an avi tag and a (His)6 tag (huNA8A-avi-his) (SEQ 10 No. 158 ). huNA8A-Fc was purified from the supernatant of a suitably transfected CHO cell line using a protein A column. huNA8A-avi-his was transiently transfected into HEK 293 cells, which stably express the E8V-derived protein EBNA. A concurrently cotransfected plasmid encoding a biotin ligase allowed specific biotinylation of the avi tag in vivo. The protein was then purified by immobilized metal affinity chromatography (IMAC) followed by gel filtration.
SEQ 10 No 158 (huNA8A-avi-his) pETR6592 QLTTESMPFNVAEGKEVLLLVHNLPQQLFGYSWYKGERVOGNRQIVGYAIGTQQ ATPGPANSGRETIYPNASLLIQNVTQNOTGFYTLQVIKSOLVNEEATGQFHVYPEL PKPSISSNNSNPVEOKOAMAFTCEPETQDTTYLWWINNQSLPVSPRLQLSNGNR TLTLLSVTRNDTGPYECEIQNPVSANRSOPVTLNVTYGPDTPTISPPDSSYLSGAN LNLSCHSASNPSPQYSWRINGIPQQHTQVLFIAKITPNNNGTYACFVSNLATGRN NSIVKSITVSALSPWAKPQIKASKTTVTGDKDSVNLTCSTNDTGISIRWFFKNQSL PSSERMKLSQGNITLSINPVKREDAGTYWCEVFNPISKNQSDPIMLNVNYNALPQ
ENLINVDLEVLFQGPGSGLNDIFEAQKIEWHEARAHHHHHH AFFINITY MATURATION OF HUMANIZED PR 1A3: Generation of affinity matured humanized PR1A3 Fabs was conducted by phage display using standard protocols (Silacci et al., Proteomics, 5(9): 2340-2350, 2005). Selections with all affinity maturation libraries were conducted in solution according to the following procedure: 1. binding of about 1012 phagemid particles from each affinity maturation library to 100 nM biotinylated huNABA-avi-his per half hour in a total volume of 1 ml; 2. capture of biotinylated huNABA-avi-his and specifically bound phage particles by adding 5.4 x 10 7 streptavidin-coated magnetic beads for ten minutes; 3.
bead washing using 5-10x 1 ml PBSffween 20 and 5-10x 1 ml PBS;
4. elution of phage particles by adding 1 ml of 100 mM TEA (triethylamine) for ten minutes and neutralizing by adding 500 IJI of 1 M Tris/HCl, pH 7.4; and 5. reinfection of exponentially growing Eco/i TG1 bacteria, infection with helper phage VCSM13 and subsequent PEG/NaCI precipitation of phagemid particles to be used in subsequent rounds of selection. Selections were conducted over three to five rounds using constant or decreasing antigen concentrations (from 1o-7M to 2x1o-9M). In round 2, the capture of antigen and phage complexes was performed using neutrovidin plates in place of streptavidin beads.
Specific binders were identified by ELISA as follows: 100 IJI of 10 nM biotinylated huNABA-avi-his per well were coated onto neutralvidin plates. Bacterial supernatants containing Fab and binding Fabs were detected using their markers
Flag using a secondary anti-Fiag/HRP antibody. ELISA positive clones were bacterially expressed as soluble Fab fragments in a 96-well format and the supernatants were subjected to a kinetic selection experiment by SP analysis using BIACORE T100. Clones 5 expressing Fabs with the constants of Higher affinity were identified and the corresponding phagemids were sequenced.
PURIFICATION OF FABS AND MEASUREMENT OF KINETIC PARAMETERS: For exact analysis of kinetic parameters, Fabs were purified from bacterial cultures. A 500 ml culture was inoculated and induced with 1 mM IPTG in 00600 of 0.9. Bacteria were incubated at 25°C overnight and collected by centrifugation. After incubating the suspended pellet for twenty minutes in 25 ml of PPB buffer (30 mM Tris-HCl, pH 8, 1 mM EDTA, 20% sucrose), the bacteria were centrifuged again and the supernatant was collected. This incubation step was repeated once with 25 ml of a 5 mM MgSO4 solution. Supernatants from the two incubation steps were pooled, filtered and loaded onto an IMAC column (His gravitrap, GE Healthcare). Then the column was washed with forty volumes.
After elution (500 mM NaCl, 500 mM imidazole, 20 mM NaH2PO4, pH 7.4), the eluate was buffered again using PD1 O(GE Healthcare) columns.
The kinetic parameters of the purified Fabs were then studied by means of SPR analysis in a dilution row that ranged from 200 nM to 6.25 nM.
EXEMPL02 The PR 1A3 antibody was chimerized to have a human IgG1/kappa constant region and expressed using the GylcoMab technology in order to have a high degree of sugars afucosylated on the Fc. Glycoengineered and non-glycoengineered antibodies were compared at an effector to target ratio of 25:1. The maximum amount of antibody-dependent target cell killing was doubled via Fc region glycoprojection (Figure 2). Further increase in cell death was achieved by increasing the effector to target ratio (Figure 2).
PR1A3 was humanized using structures identical to human germ lineage sequences. The sequence IMGT IGHV -4-1*02 (Accessed No. 5 X62110) was the humanized VH receptor and IMGT_hVK_1_39 (Accessed No. X59315) was the humanized VL receptor. A humanized PR1A3 antibody comprising a CH7 A heavy chain variable region construct and a CL 1A light chain variable region construct exhibited satisfactory binding to human colon carcinoma cells as measured by flow cytometry (Figure 3).
Affinity maturation of PR 1A3 by phage display was performed using standard protocols as described in detail in Example 1 hereof. The parent humanized PR1A3 antibody! which was used for affinity maturation comprises a CH7A heavy chain variable region construct and a CL 1A light chain variable region construct. Tables 3 to 6 below display the libraries used for affinity maturation. For the L 1/L2 library, the positions Valine 29, Alanine 50 or Serine 51 in the CDRs were held constant. For the H1/H2 library, the positions Isoleucine 51, Glycine 55 or Alanine 57 in the CDRs were held constant (Figures 4 and 5).
An affinity matured heavy chain variable region construct, CH7A rF9, and an affinity matured light chain variable region construct, CL 1A rH11, were paired with the parent light chain variable region construct! and heavy chain variable region construction, respectively, and with each other. All antibodies were converted to human IgG1/kappa and binding to the CEA MKN45 positive cell line was measured by flow cytometry. Antibodies comprising one affinity matured light or heavy chain variable region or both affinity matured light or heavy chain variable regions exhibited improved binding characteristics compared to the parent antibody! humanized (Figure 6). Figures 6, 10 and 15 show several examples where the matured light and heavy chains independently contribute to the increase in affinity. The parent antibody I CH7A CL 1A has the lowest signal strength as well as the highest EC50 value in Figures 6 and 15. The matured light chain replaces the EC50 values with lower numbers, while the matured heavy chains (rF9 in Figure 6 and rB9 in Figure 15) substitute for the total fluorescence signal intensity in a flow cytometry measurement. Figure 10 displays the individual light and heavy chain contributions measured using Biacore methodology. The combination of these two chains further increases the affinity.
The binding affinities of the affinity matured light and heavy chain CDRs were determined using Biacore and listed in Table 10 below.
TABLE 10 SEQ ID No CDR-H3 Affinity Construct (randomized residues are residues (determined by selected bold underlines) Biacore medium) 25 WDFYDYVEAMDY 3681 nM PMS22 26 WDFYHYVEAMDY 586 nM 1C8 27 WDFVDYVEAMDY 1893 nM 3E1 28 WDFYWYVEAMDY 3681 nM PMS22 26 WDFYHYVEAMDY 586 nM 1C8 27 WDFVDYVEAMDY 1893 nM 3E1 28 WDFYWYVEAMDY 3681 nM WDFYHYVEAMDY 586 nM 1C8 27 WDFVDYVEAMDY 1893 nM 3E1 28 WDFYWYVEAMDY 3QYFQ 3D 746 nM 59 nM affinity matured CDRH-3 34 WDFAYYFQTMD 44 nM affinity matured CDRH-3
35 WDFAYYLEAMD 69 nM affinity matured CDRH-3
29 W DA F E Y V K A L O Y 26 nM H3 total (5) 19
30 WDFFEYFKTMDY 51 nM H3 total (5) 8
31 WDFFYYVQTMDY 81 nM H3 total (5) 28
33 WDFSYYVEAMDY 132 nM H3 total (5) 27
CDR-H1 and CDR-H2
Randomized residues are underlined and selected residues in bold
1 and 13 EFGMN and WINTKTG_EAIYVEEFKG 3681 nM pMS22
1 and 14 EFGMN and WINTKTGEATYIEEFKG 402 nM H4E9
1 and 15 EFGMN and WINTKSGEATYVEEFKG pAC14 (89)
2 and 15 EYGMN and WINTKSGEATYVEEFKG pAC15 (F9)
3 and 16 EYSMN and YINTKNGEANYVEEFKG H1/H2 (5) 2
2 and 17 EYGMN and WINTKNGEATYIEEFKG H1/H2 (5) 11
1 and 16 EFGMN and YINTKNGEANYVEEFKG H1/H2(5)13
2 and 16 EYGMN and YINTKNGEANYVEEFKG H1/H2 (5) 14 and 13 EFGMS and WINTKTG_EAIYVEEFKG 26 nM H3 total (5) 19
COR-L 1 and CDR-L2
Randomized residues are underlined and selected residues in bold
36 and 46 QNVGTN and YSASYRYS 3681 nM pMS22
37 and 47 ANVGNN and YLASNLSG 250 nM pAC21 (3A1)
38 and 48 KNVGTN and YLASYPQI 700 nM pAC19 (2C6)
39 and 49 AAVGTY and YSASYRKR 220 nM pAC18 (2F1)
40 and 50 QYASTN and YWASYRYS 290 nM pAC23 (2F11)
36 and QNVGTN and PU-YSASYRYS 402 nM H4E9 - 41 and 51 HNVGTN and YSASHRYS 2255 nM L2D2
42 and 52 QIMGPN and YLASYHES pAC6 (C1)
43 and 53 QIVGTN and YSASHRPS pAC7 (E10)
COR-L 1 and CDR-L2
Randomized residues are underlined and selected residues in bold
44 and 54 QKVL TN and YLASYRYS pAC12 (H )
45 and 55 QTVSAN and YLASYRYR pAC13 (H11)
CDR-L3
Randomized residues are underlined and selected residues in bold
56 HQYYTYP_bFT pMS22
Table 11 below summarizes the affinity constants of the various affinity matured antibody sequences.
The parental antibody PR1A3 is listed, as well as various combinations of light chain and heavy chain of matured and unmatured sequences.
All values were obtained using Biacore technology by measuring the association (kon) and dissociation (kott) rate constants of the various Fab-format soluble antibody constructs on a Biacore chip with immobilized NABA-avi-his reagent (SEQ ID No 158) as an antigen.
The affinity constant is labeled with KD.
TABLE 11
KINETIC ANALYSIS OF AFFINITY MATURED CLONES Chain Name Affinity Monovalent Affinity Bivalent Clone PR1A3 wt!wt k0 n: 6.74x10 3 1/Ms; koff: 2.48x10" kon: 2.82x10 5 1/Ms; koff: 5.52x10" 4 2 1/s; KD 3681 x10" 9M 1/s; KD: 2x10"9M 1C8 hc/wt k0 n: 12.9x103 1/Ms; koff: 0.76x10" kan: 4.67x1 05 1/Ms; koff: 3.24x1 0"4 2 9 1/s; KD 586x10"M 1/s; 9 KD: 0.693x10"M H4E9 hc/wt k0 n: 5.22x103 1/Ms; kaff: 0.21 x 1 o·kon: 2.92 x 10 5 1/Ms; koff: 2.04x10" 3 2 9 1/s; KD 402x1 0" M 1/s; KD: 0.7x10 -9 M H3 Total hc/wt kan: 54.2x103 1/Ms; koff: 0.13x1 o·k0 n: 9.02x10 5 1/Ms; koff: 1.75x10 -4 2 (5) 19 1/s; KD 24x10 -9 M 1/s; 9 KD: O, 19x10" M H3 Total hc/wt k0 n: 27.3x10 3 1/Ms; koff: 0.14x10- N/A (5) 8 2 1/s·, KD 51x10-9 M 3A1 wt/lc kon: 46.8x103 1/ms; kaff: 1.17x1 o·kan: 2.42x105 1/ms; kaff: 3.64x10"4 29 1/s; KD 250x10"M 1/s; KD: 1.5x10"9M 5 4 2F1 wtJ lc k 0 n: 95.7x10 3 1/Ms; koff: 2.07x10" kan: 4.23x1 0 1/Ms; koff: 4.1 Ox1 0" 2 1/s; KD 220x1 0"9 M 1/s; KD: 0.952x1 0"9 M 5L 1A10 hc/wt k0 n: 15.6x10 3 1/Ms; koff: 0.09x10-N/A 2 1/s·, KD 59x10 -9 M 5HFF12 hc/wt k0 n: 20.8x10 3 1/Ms; koff: 0.09x10-N/A 2 1/s; KD 44x1 0"9 M M4F1 hc/wt kan: 25, 7x1 03 1/Ms; koff: 0, 17x1 o· N/A 2 1/s; KD 69x1 0-9M k0 n: 36.4x1 03 1/Ms koff: 0.35x1 o·4 H4E9x hcllc k0 n: 4.23x105 1/Ms; koff: 1.91x10" 29 2F1 1/s; KD 96x1 0" M 1/s; 9 KD: 0.452x1 0" M
Chain Name Monovalent Affinity Bivalent Affinity Clone
H4E9 X hc/lc N/D kon: 2.46x10 5 1/Ms; koff: 1.36x10 -4 3A1 1/s; KD: 0.55x10-9M 1C8 X 2F1 hc/lc kon: 68.1x103 1/Ms; koff: 0.87x1 o-kon: 9.68x10 5 1/Ms; koff: 6.36x10 -4 2 1/s; KD 128x10 -9 M 1/s; KD: 0.66x10-9 M 1C8 X 3A1 hc/lc N/D kon: 2.89x10 5 1/Ms; koff: 2.57x10 -4 1/s; KD: 0.888x10 -9 M kn: 1.76x10 -1 /Ms; koff: 2.84x10-46 H3 Total hc/lc k0n: 206x1031/Ms; koff: 0.25x10-(5)19X21/s; KD: 12.2x10 -9 M 1/s;
2F1 KD: O, 16x1 o-9 M
H3 Total hc/lc N/A kon: 9.93x10 5 ; 1/Ms; koff: 2.71x10 -4 (5) 8 X 2F1 1/s; KD: 0.28x1 o-9 M

权利要求:
Claims (28)
[1]
1. ANTIGEN BINDING MOLECULE (ABM), characterized in that it comprises a humanized, affinity-matured antigen binding domain, as compared to the murine monoclonal antibody PR1A3, which comprises one or more complementarity determining regions (CDRs), wherein said antigen-binding domain specifically binds to membrane-bound human carcinoembryonic antigen (CEA) with a KD value of less than about 100 nM, and wherein said antigen-binding domain binds to the same epitope or is capable of compete for binding with PR1A3.
[2]
2. ABM, according to claim 1, characterized in that said antigen binding domain comprises a heavy chain variable region comprising: a heavy chain COR 1 selected from the group consisting of SEQ 10 No 1 , SEQ 10 #2, SEQ 10 #3, SEQ 10 #5, SEQ 10 #6, SEQ 10 #7, SEQ 10 #8, SEQ 10 #9, SEQ 10 #10 and SEQ 10 #12; and a heavy chain CDR2 selected from the group consisting of SEQ ID NO 13, SEQ 10 NO 14, SEQ 10 NO 15, SEQ 10 NO 16, SEQ 10 NO 17, SEQ 10 NO 18, SEQ 10 NO 19, SEQ 10 #20, SEQ 10 #21, SEQ 10 #22, SEQ ID #23 and SEQ ID #24; and a heavy chain CDR3 selected from the group consisting of SEQ 10 #25, SEQ ID #26, SEQ 10 #27, SEQ 10 #28, SEQ 10 #29, SEQ 10 #30, SEQ 10 #31, SEQ 10 NO 32, SEQ 10 NO 33, SEQ ID NO 34 and SEQ 10 NO 35; and a light chain variable region comprising: a light chain COR 1 selected from the group consisting of SEQ 10 #36, SEQ 10 #37, SEQ ID #38, SEQ 10 #39, SEQ 10 #40, SEQ ID NO: 41, SEQ 10 NO: 42, SEQ 10 NO: 43, SEQ ID NO: 44, and SEQ 10 NO: 45; and a light chain CDR2 selected from the group consisting of SEQ ID NO 46, SEQ ID NO 47, SEQ ID NO 48, SEQ ID NO 49, SEQ ID NO 50, SEQ ID NO 51, SEQ ID NO 52, SEQ ID No. 53, SEQ ID No. 54 and SEQ ID No. 55; and a light chain CDR3 of SEQ ID NO 56.
[3]
5 3. ABM, according to claim 2, characterized in that said heavy chain variable region comprises: SEQ ID No 9; SEQ ID NO: 15; and SEQ ID NO:25; and wherein said light chain variable region comprises: SEQ ID NO 45; SEQ ID NO: 55; and SEQ ID NO 56.
[4]
4. ABM, according to claim 2, characterized in that said heavy chain variable region comprises: SEQ ID No 2; SEQ ID NO: 15; and SEQ ID NO:25; and wherein said light chain variable region comprises: SEQ ID NO 45; SEQ ID NO: 55; and SEQ ID NO 56.
[5]
5. ABM, according to one of claims 2 to 4, characterized in that said heavy chain variable region comprises the sequence of SEQ ID No. 107.
[6]
6. ABM, according to one of claims 2 to 4, characterized in that said light chain variable region comprises the sequence of SEQ ID No. 108.
[7]
7. ABM, according to one of claims 1 to 6, characterized in that said antigen-binding domain comprises a heavy chain variable region that comprises the sequence of SEQ ID No. 107, and a light chain variable region that comprises the sequence of SEQ 5 IDN°108.
[8]
8. ABM, according to claim 3 or 4, characterized in that said heavy chain variable region comprises a polypeptide that has at least 95% identity with the sequence of SEQ ID No 107, and said chain variable region light comprises a polypeptide that has at least 95% identity to the sequence of SEQ ID NO:108.
[9]
9. ABM, according to one of claims 1 to 8, characterized in that said ABM comprises an Fc region.
[10]
10. ABM, according to claim 9, characterized in that said Fc region is an Fc region of human IgG.
[11]
11. ABM, according to claim 9 or 10, characterized in that the Fc region is a glycoengineered Fc region.
[12]
12. ABM according to claim 11, characterized in that at least about 20% to about 100% of the N-linked oligosaccharides in said Fc region are non-fucosylated.
[13]
13. ABM, according to claim 11, characterized in that at least about 20% to about 100% of the N-linked oligosaccharides in said Fc region are bisected.
[14]
14. ABM according to claim 11, characterized in that at least about 20% to about 50% of the N-linked oligosaccharides in said Fc region are bisected, not fucosylated.
[15]
15. ABM, according to one of claims 11 to 14, characterized in that said ABM has at least one increased effector function compared to the murine antibody PR1A3.
[16]
16. ABM according to claim 15, characterized in that said at least one increased effector function is selected from the group consisting of: increased Fc receptor binding affinity, increased antibody-dependent cellular cytotoxicity (ADCC) , increased natural killer (NK) cell binding, increased macrophage binding, increased monocyte binding, increased polymorphonuclear cell binding, apoptosis-inducing direct signaling, increased dendritic cell maturation, and increased T cell priming.
[17]
17. ABM, according to claim 16, characterized in that said increased effector function is increased ADCC or increased NK cell binding.
[18]
18. ABM, according to one of claims 1 to 17, characterized in that said ABM is an antibody or a fragment thereof, selected from the group consisting of: a total antibody, an scFv fragment, an Fv fragment, an F(ab')2 fragment, a minibody, a diabody, a triabody and a tetrabody.
[19]
19. ABM according to one of claims 1 to 18, characterized in that said ABM is at least from about ten times to about a thousand times more potent in inducing ADCC at a given concentration compared to the murine antibody PR1A3.
[20]
20. ANTI-CEA ANTIBODY, characterized in that it comprises a heavy chain variable region comprising: SEQ 10 No. 2; SEQ 10 No. 15; and SEQ 10 No. 25; and a light chain variable region comprising: SEQ ID NO:45; SEQ ID NO: 55; and
SEQ 10 No 56.
[21]
21. ANTIBODY, according to claim 20, characterized in that the antibody comprises: (a) a heavy chain variable domain that has at least 595% sequence identity with the amino acid sequence of SEQ 10 No. 107 ; (b) a light chain variable domain that has at least 95% sequence identity to the amino acid sequence of SEQ 10 No. 108; or (c) a heavy chain variable domain as in (a) and a light chain variable domain as in (b).
[22]
22. ANTIBODY, according to claim 20, characterized in that the antibody comprises a heavy chain variable domain sequence of SEQ 10 No. 107.
[23]
23. ANTIBODY, according to claim 20, characterized in that the antibody comprises a light chain variable domain sequence of SEQ 10 No. 108.
[24]
24. ANTIBODY according to claim 20, characterized in that the antibody comprises a heavy chain variable domain sequence of SEQ ID No. 107 and a light chain variable domain sequence of SEQ 10 No. 108.
[25]
25. Membrane-bound ANTIBODY THAT SPECIFICALLY BINDING CEA, characterized in that said antibody comprises the heavy chain variable region of SEQ 10 No. 107 and the light chain variable region of SEQ 10 No. 108, wherein said antibody has AOCC increased compared to the murine PR1A3 antibody.
[26]
26. ANTIBODY, according to one of claims 20 to 25, characterized in that said antibody comprises an Fc region that has been glycoprojected.
[27]
27. ANTIBODY, according to one of claims 20 to 26, characterized in that said antibody increases ADCC by at least about 10% to about 100% in an in vitro cytotoxicity assay.
5
[28]
28. POLYNUCLEOTIDE, characterized in that it encodes ABM, as defined in one of claims 1 to 19, or the antibody, as defined in one of claims 20 to 27.
29. VECTOR, characterized in that it comprises the polynucleotide as defined in claim 28.
30. TRANSGENIC MICRO-ORGANISM, characterized in that it comprises the vector as defined in claim 29.
31. METHOD OF PRODUCTION OF AN ABM, which specifically binds to membrane-bound human CEA, characterized in that said method comprises: (a) culturing the transgenic microorganism, as defined in claim 30, in a medium under conditions allowing expression of said polynucleotide, wherein said polynucleotide encodes a polypeptide that forms part of said ABM; and (b) recovering said ABM; wherein said ABM or a portion thereof binds to the same epitope as, or is capable of competing for binding with, the murine monoclonal antibody PR1A3.
32. COMPOSITION, characterized in that it comprises the ABM as defined in one of claims 1 to 19, or the antibody as defined in one of claims 20 to 27, and a pharmaceutically acceptable carrier.
33. METHOD FOR IN VITRO DIAGNOSIS OF DISEASE, in a patient, characterized in that said method comprises administering to said patient an effective amount of a diagnostic agent, wherein said diagnostic agent comprises ABM as defined in a of claims 1 to 19, or the antibody as defined in one of claims 20 to 27, and a marker that allows detection of a complex of said diagnostic agent and CEA.
34. METHOD, according to claim 33, characterized by the fact that said marker is an image formation agent.
35. USE OF ABM, as defined in one of claims 1 to 19, characterized in that it is in the manufacture of a drug for the 1st treatment of a patient who has a cancer that expresses CEA abnormally.
36. USE OF THE ANTIBODY, as defined in one of claims 20 to 27, characterized by the fact that it is in the manufacture of a drug for the treatment of a patient who has a cancer that expresses CEA abnormally.
37. USE OF THE COMPOSITION, as defined in claim 32, characterized in that it is in the manufacture of a drug for the treatment of a patient who has a cancer that expresses CEA abnormally.
38. USE, according to one of claims 35 to 37, characterized in that said cancer is selected from the group consisting of colorectal cancer, non-small cell lung cancer (NSCLC), gastric cancer, pancreatic cancer and breast cancer.
39. USE OF ABM, as defined in one of claims 1 to 19, characterized in that it is in the manufacture of a drug to induce cell lysis in a tumor cell.
40. USE, according to claim 39, characterized in that said tumor cell is selected from the group consisting of colorectal cancer cells, non-small cell lung cancer (NSCLC), gastric cancer cells, of pancreatic cancer and breast cancer cells.
41. USE, according to claim 39, characterized in that said cell lysis is induced by antibody-dependent cellular cytotoxicity of said ABM.
42. USE, according to one of claims 35 to 41, characterized in that said drug also comprises a chemotherapeutic agent.
43. USE, according to one of claims 35 to 42, characterized in that said patient is a human being.
NH2 /..C Glycosylation site s s Disulfide bridge between cysteines Domain N
PR1A3 -- ~
~
Q)
extracellular
cell membrane
intracellular
Fig. 1
Lovo colon carcinoma as target cells for ADCC Release-LDH, 4-h analysis, huPBMC as effectors. ~ so r--- ·--·---·-----·-------------------~~---------- -----~-------·-- ------------~~-------------------- ---------------- - - ·- - - - - - - - - - - - - - - -------1 ~ I --*- chCEA Glycoproject (E:T"' 50.1} ~ 50 1 "'O
CD ! ::::~EA :~:oproj (E:T = 251)
I ::::J 1~~EA ~ 40 modified (E:T"=25:1) ::::J éD ~ lll ::::J .---+- o· 20 -· 30 t- ~------J~._
II i Ii' --
N~O> o..., "'O --....-~
I o -....-.. ~ 10- ~ 0 -~--- ---------------·------------- T·--·------------------ -,..--------------------,-- -----------------,.-- ••• ••••••-:• ••••-_,n~••~u• .r • 1o' 000 1'000 100 1o 1 0.1 Antibody concentration (ng/ml) Fig. 2
Binding to LoVo human colon carcinoma cells measured by FACS 6000 5000 ', -...Chimeric I ü: 4000 I ---6- Re-humanized , L___ I :::! 3000 w 2000 1000 -- _....lo.
o) the
0.01 0.1 1 10 100 Antibody concentration (ng/ml) Fig. 3
VL's Kabat V PR1A3-VL
YXT Y P L
L -- ~ ~ O>
Y Y X Y P L
YYTXPL
Y Y T Y X L
YYTYPX Fig. 4
VH's
Kabat VH PRIA3
-- 0'1 ~
THE)
Fig. 5
30000 r·-·······---·-····-··--~---------------- r. ------- ----- -- ___..;::::::·:-~::: --···· · :-:-···r ·-i - .... - ,;~ ~-,~~-~,_...,.u •• -e- CH7.A. rF9 CUA ~ I ~ 25000 'l·' . . . . ,._ ... ,7/'~------·-· ~ •• , ··••••o•_....,..._,._ .... _ , , , •• ~ : 'r·1 ·â 20000 l. . . . . . . . . :-:t_______ ,,, ................. ~------·' ...•. ,.,..........-: ! .......,._ CH7 A rF9 CL 1A rH11 !l ~ Ii ~CH7ACL1A llu ~ ·+i------ •••••• ••••...... OoOO "o •• ••--N--~-··--- ... ~ i L.
-- 15000 g,._ 10000
I.L. ...... ~ CH7A CI..1A rH11 I Q') .....lo. Q') l. . ., _ , 4 Q) ' -o Q) l ~ -g 5000 1 -"'- - . -oi ~~ -~ o L-~---------------- --------~-----------------------------------.----- ---------------~~------- ____::;::as:_______________________._ c 100 10 1 0.1 0.01 0.001 Antibody concentration (ng/ml) Fig. 6
Liver Metastasis Model LS174T
·----- ----------- --·----··--- ---------·
80 i-----·--· - ---------k!F&&&~~ ~··-E~OGG ' u · - - · -
~ i 70 _ _ _i ... -;:!2 o (I) ........ ·-------·1 60 ucl l ~ ~-- bE:!l . ---·t - -· -· - - - -· <(]) > -::;: (]) '-- _o o (f) 50
40 I - ~-- < -~-- ~::.c:)-Ç:+GQ -----1 l i -- -.J ~
The>
30 ................-------------y----· .-. :-----· . . . . -... ..... ~.-:___::______ . ...........- - ·-----~
20 1-- -B-GA201 -fr- CH7A ~~~y------- . .. . __ ----~--- -~ ..... --------------------~------------- --.1 l 10 1--- -e- SM3E ~~) __________ __~Ablb&-Lt~i-Yf.-l'sf-:.6/to 20 ~PBS 25 30 35 40 I---·········- -1 45 50 55 60 . ) . . _. J 65 70
study day
Fig. 7
Lung metastasis model A549
100 -e-GA201 90 ~Vehicle
80 ~SM3Ege
70 ~CH7A rF9 CL1A 0 . o rH11 (I) 60 --e-CH7A ge ··I uc <(]) > ·:;;: (]) .__ _Q 50 40 -- (X) ....-.. (j) the ({) 30
20 ~AfiXKX1~
10 or 40 50 60 70 80 90 100 110 120 130 140 Study day
Fig. 8
Liver Metastasis Model MKN45 100 .,_... --- ~--···- ---- : 90 ..... -·-·-·-" ........ 1------ I -a-PBS to Li.. ... -ts- CH7 ArF9 CL 1A ge 1------ 70 1----·-- 1 -··· --- -11--- SM3E ge 1--- ::R ! ~ so r· o I ··· - . - ,~ ·u ''> Q) -g,_ 40 ' so L-- -- i
I l'
I ··- . -----------------·---· m.& - 6 "' -- -- (O ~ O> (f) ' lb ' 30 l--- - ................ .. -~~-~-- ----~--- i 20 ~m -~ 10 - o 30 40 50 60 Day of study Fig. 9
Sensogram of anti-CEA Fabs ~ k0 n: 0.527 X 103 1201, :;) 80' /"'---··--------...• /~·=--=--- .. - 100 l ------------ CH7A H4E9 CLlA k0 ff: 0.0027 I l ~~ l ~;;~~~-:;= !; so KD: 518 nM "' o L .......,.. -20 100 200 300 400 o Time(s) ~ 250 ,.-.•----··'"'1 /'~-, o ... ._ k0 n: 9.57 104 l X _250 ~ 200 f/ "\ ~ CH7A CLlA pAC18 koff: 0.0206 ; 150 ~--___,,·,.;>. . O) f ~ v--------<~:~~~~;~~-- 1 KD: 216 nM - .....
- 5 0 ' - - - - - ~----------- o 100 200 300 400 500 Time(s) 450 375 k 0 n: 3.64 X 104 ~300 ;225 CH7A H4E9 CL lA pAC18 k0 ff: 0.0035 :;:-=~ i 7~~L-~~~~----~~-~ ;:;150 KD: 96 nM -==··==-==- ---- -----------====== -75 ' - - - - - - - - - - - - - - - - o 75 150 225 300 375 Time (s) Fig. 10
Randomization CDR1 and CDR2 VH (CH7A)
EAB-679 MS-43 ~ ( ){ ~
.- 1_ MS-56 ------ MS-52 ~ 1 1-- -- - - - - - - - -----~:..::....:::::__ - I
Ncol CH7 A N;;!l
PCR1 PCR2 EAB-680 & -~ ~ ~
~
1 MS-55
1 -- ~
~
THE)
PCR3 PCR4
~ ----7
PCR5 1 .----------- 1_
Ncol v A -------------- -----.I Nhel
Fig. 11
Randomization CDR1 and CDR2 VL (Cl 1A) EAB-681 EAB-685 ~ ( )( ~ EAB-687 I EAB-686 ~
I Hio;on -l CL1A l ""'I PCR1 PCR2 EAB-682 - .....Jo,.
-- ~ ~ EAB-688 N ~ I .....Jo,.
O) 1 PCR3 ! PCR4 ~ ~ PCR5 1 Hindll Saci Fig. 12
Randomization CDR3 VH (CH7 A) randprimer- EAB-749 ~ ---7 EAB-752 ~ ---7
I .-------- EAB-7501751 1 Sac l -, Nhel 1 PCR1 PCR2 ~ EAB-749 ---7
I 1 - - ------- - ----,.,- EAB-752 ~ -- (..V ~ O) 1 PCR3 L__ YJ - ------------ ---------- • -------,- Saci Nhel Fig. 13
Randomization CDR3 VL (Cl 1A) rand primer - MS43 ---7 CL1A ~
I l 1 Ncol PCR1 ~ MS43 ---7 EAB-746 1ir -- ~ ~ O') 1 PCR2 ,----- I ~ I Ncol Xhol Fig. 14
CEA binding target with MKN 45 target cells The affinity matured clone of ~ :~:fjfE;:!~:~.:;}········ /Z~;:=c:~::~ =~! light chain library has an affinity enhancement of a factor of 3 when converted to lgG. ~ 600 400 "l 1 ~~/Hno// ,A< .r:;-:::;;11 ~ 200 I i- uoHoo on•~ _,v..-/ . . ••• . 4V / ,.,··'-----··-------------~ ~ Q ~:-::f;_;_:_-7.:f~~~ ~:~.. --·:·-....:. 1 ! 1 1 ~ IIII! li' ! IIII 1 II
0.01 0.1 1 10 100 Antibody concentration (IJg/ml) .---------------------------------· -- Jo Binding of affinity matured and parental antibodies on MKN45 CEA target cells The affinity matured clone of the (J1....._ 30000 heavy chain library shows a --Jo. -.!t-CH7A 189 CL1AIH11 G2(1) · MI.,II'"S 25000 ~ strongly high signal, when O> . . - CH7A Cl1A G2(R2)· MNK45 20000 "ªô converted to lgG. 15000 ~ g 10000 ~ "O <D "O ·--- ---- 5000 "' "O g; o 2l
0.001 om ~ 1 m 100 E Antibody concentration (IJg/ml) 7 Antibody light and heavy chain, both contribute to the affinity of the whole antibody (Binding to the membrane-bound form is preserved after affinity maturation) Fig. 15
In vitro testing of ADCC on various affinity matured anti-CEA Abs compared to the unmatured parental antibody. 90r------------------------------------------ 80+----- -------------------------------------------------- -------------------------------~ ~ o -e-CH7ACL1AG2(R2) ;::+ 70 m -&- CH7Ar89 CL 1ArH11G2(1) ~~=·····=i·············-·----~
0.. {g 60 ~CH7ArF9 Cl1ArH11G2(1) I ---···-··········· m ~CH7ACL1ArH11 G2(1)
6.. m 50 -/ ::::::1 air 40 ~
0.. m ~ t E= -- m ::::::1 301------------------------------- ----·
I O) ~ i--------E ;;e~; ~ O) 20 10 LmuuuUu...: ; ; ; uOOuo u uU • ~ L-"····,=r-----··---·~T l Q __ .. ,. . . . . . . _: . -10 L ...
0.01 0.1 10 100 10000 concentration ab (ng/ml) Combined matured light~ heavy chains Combined matured only light chain ~ Improvement of affinity leads to improvement of ADCC Fig. 16

类似技术:

---

公开号 | 公开日 | 专利标题

---

US20220002441A1|2022-01-06|Anti-cea antibodies

---

US20200332012A1|2020-10-22|Antigen Binding Molecules That Bind EGFR, Vectors Encoding Same, and Uses Thereof

---

BR112012003983A2|2021-09-14|ABM BINDING MOLECULE ABM ANTIGEN BINDING MOLECULES ISOLATED POLYPEPTIDE VARIANT HUMANIZED ANTIGEN BINDING MOLECULE ISOLATED POLYNUCLEOTIDE ANTIBODY VECTOR COMPOSITION HOST CELL ABM PRODUCTION METHOD TUMOR CELL LYSIS INDUCTION METHOD, DIAGNOSTIC DIAGNOSIS METHOD OF TUMOR DIAGNOSIS METHOD CANCER METHOD OF INCREASE TIME OF SURVIVAL IN PATIENTS THAT HAVE A CANCER INDUCTION METHOD IN REGRESSION PATIENTS OF A ENGINE USE ABM AND INVENTION

---

AU2007282923B2|2012-09-13|Antigen binding molecules that bind EGFR, vectors encoding same, and uses thereof

同族专利:

---

公开号 | 公开日

---

MX339608B|2016-05-31|

---

SG178567A1|2012-04-27|

---

AR078111A1|2011-10-12|

---

CA2770174A1|2011-03-03|

---

RU2012112340A|2013-10-10|

---

KR20120060874A|2012-06-12|

---

ECSP12011698A|2012-03-30|

---

TW201121994A|2011-07-01|

---

CN102741293B|2015-04-01|

---

CL2012000551A1|2012-10-12|

---

HK1176951A1|2013-08-09|

---

JP5744872B2|2015-07-08|

---

CN102741293A|2012-10-17|

---

IL218038D0|2012-04-30|

---

EP2473532A1|2012-07-11|

---

WO2011023787A1|2011-03-03|

---

US20160075795A1|2016-03-17|

---

PE20121552A1|2012-11-26|

---

JP2013502913A|2013-01-31|

---

US9068008B2|2015-06-30|

---

AU2010288469A1|2012-03-01|

---

CR20120087A|2012-03-22|

---

EP2473532B1|2017-06-21|

---

KR101528013B1|2015-06-16|

---

CO6491105A2|2012-07-31|

---

MA33536B1|2012-08-01|

---

MX2012002461A|2012-03-14|

---

ZA201200954B|2014-07-30|

---

RU2570554C2|2015-12-10|

---

US20110104148A1|2011-05-05|

引用文献:

---

公开号 | 申请日 | 公开日 | 申请人 | 专利标题

---

---

US4816567A|1983-04-08|1989-03-28|Genentech, Inc.|Recombinant immunoglobin preparations|

---

US5225539A|1986-03-27|1993-07-06|Medical Research Council|Recombinant altered antibodies and methods of making altered antibodies|

---

US5530101A|1988-12-28|1996-06-25|Protein Design Labs, Inc.|Humanized immunoglobulins|

---

DE3920358A1|1989-06-22|1991-01-17|Behringwerke Ag|BISPECIFIC AND OLIGO-SPECIFIC, MONO- AND OLIGOVALENT ANTI-BODY CONSTRUCTS, THEIR PRODUCTION AND USE|

---

US5859205A|1989-12-21|1999-01-12|Celltech Limited|Humanised antibodies|

---

US5872215A|1991-12-02|1999-02-16|Medical Research Council|Specific binding members, materials and methods|

---

EP0617706B1|1991-11-25|2001-10-17|Enzon, Inc.|Multivalent antigen-binding proteins|

---

BR9207126A|1992-05-07|1995-08-29|Sterling Winthrop Inc|Radioactive labeling immunoreagent, image-forming composition, therapeutic composition, process for forming diagnostic image at a site in a patient and for treating disease sites in a patient, and, composition of matter|

---

GB9317423D0|1993-08-21|1993-10-06|Imp Cancer Res Tech|Monoclonal antibodies|

---

GB9324807D0|1993-12-03|1994-01-19|Cancer Res Campaign Tech|Tumour antibody|

---

US6001358A|1995-11-07|1999-12-14|Idec Pharmaceuticals Corporation|Humanized antibodies to human gp39, compositions containing thereof|

---

US6417337B1|1996-10-31|2002-07-09|The Dow Chemical Company|High affinity humanized anti-CEA monoclonal antibodies|

---

DK1071700T3|1998-04-20|2010-06-07|Glycart Biotechnology Ag|Glycosylation modification of antibodies to enhance antibody-dependent cellular cytotoxicity|

---

US6737056B1|1999-01-15|2004-05-18|Genentech, Inc.|Polypeptide variants with altered effector function|

---

EP2270147B2|1999-04-09|2020-07-22|Kyowa Kirin Co., Ltd.|Method for controlling the activity of immunologically functional molecule|

---

CA2417415C|2000-07-31|2012-10-09|Biolex, Inc.|Expression of biologically active polypeptides in duckweed|

---

US6946292B2|2000-10-06|2005-09-20|Kyowa Hakko Kogyo Co., Ltd.|Cells producing antibody compositions with increased antibody dependent cytotoxic activity|

---

US6815175B2|2001-03-16|2004-11-09|Cornell Research Foundation, Inc.|Anti-amyloid peptide antibody based diagnosis and treatment of a neurological disease or disorder|

---

US7321026B2|2001-06-27|2008-01-22|Skytech Technology Limited|Framework-patched immunoglobulins|

---

KR20040054669A|2001-08-03|2004-06-25|글리카트 바이오테크놀로지 아게|Antibody glycosylation variants having increased antibody-dependent cellular cytotoxicity|

---

DE60232265D1|2001-10-25|2009-06-18|Genentech Inc|GLYCOPROTEIN COMPOSITIONS|

---

US20040093621A1|2001-12-25|2004-05-13|Kyowa Hakko Kogyo Co., Ltd|Antibody composition which specifically binds to CD20|

---

EP1467615B2|2001-12-27|2017-03-22|GlycoFi, Inc.|Methods to engineer mammalian-type carbohydrate structures|

---

US7432063B2|2002-02-14|2008-10-07|Kalobios Pharmaceuticals, Inc.|Methods for affinity maturation|

---

US20070148171A1|2002-09-27|2007-06-28|Xencor, Inc.|Optimized anti-CD30 antibodies|

---

NZ534881A|2002-03-19|2006-09-29|Plant Res Internat B|Mammalian GnTIII expression in plants|

---

EP1498490A4|2002-04-09|2006-11-29|Kyowa Hakko Kogyo Kk|Process for producing antibody composition|

---

US20050031613A1|2002-04-09|2005-02-10|Kazuyasu Nakamura|Therapeutic agent for patients having human FcgammaRIIIa|

---

WO2003085119A1|2002-04-09|2003-10-16|Kyowa Hakko Kogyo Co., Ltd.|METHOD OF ENHANCING ACTIVITY OF ANTIBODY COMPOSITION OF BINDING TO FcϜ RECEPTOR IIIa|

---

JPWO2003085107A1|2002-04-09|2005-08-11|協和醗酵工業株式会社|Genome-modified cells|

---

AT503829T|2002-04-09|2011-04-15|Kyowa Hakko Kirin Co Ltd|CELL WITH REDUCED OR DELETED ACTIVITY OF A PROTEIN INVOLVED IN GDP FUCOSET TRANSPORT|

---

US7232888B2|2002-07-01|2007-06-19|Massachusetts Institute Of Technology|Antibodies against tumor surface antigens|

---

JP5138867B2|2002-08-01|2013-02-06|イミューノメディクス、インコーポレイテッド|α-fetoprotein Immu31 antibody and fusion protein and method of use thereof|

---

WO2004024927A1|2002-09-12|2004-03-25|Greenovation Biotech Gmbh|Protein production method|

---

US20040132101A1|2002-09-27|2004-07-08|Xencor|Optimized Fc variants and methods for their generation|

---

AU2003294912B2|2002-12-20|2009-06-04|Greenovation Biotech Gmbh|Production of heterologous glycosylated proteins in bryophyte cells|

---

JP2006524039A|2003-01-09|2006-10-26|マクロジェニクス，インコーポレーテッド|Identification and production of antibody containing mutant Fc region and use thereof|

---

NZ541503A|2003-01-22|2008-09-26|Glycart Biotechnology Ag|Fusion constructs and use of same to produce antibodies with increased Fc receptor binding affinity and effector function|

---

AU2004239065B2|2003-05-14|2008-05-15|Domantis Limited|A process for recovering polypeptides that unfold reversibly from a polypeptide repertoire|

---

JP6046642B2|2011-03-02|2016-12-21|ロシュ グリクアート アーゲー|CEA antibody|JPS5992710A|1982-11-16|1984-05-29|Kansai Electric Power Co|Method of laying shaft of direct water cooling line|

---

KR20040054669A|2001-08-03|2004-06-25|글리카트 바이오테크놀로지 아게|Antibody glycosylation variants having increased antibody-dependent cellular cytotoxicity|

---

TWI666027B|2011-02-10|2019-07-21|羅齊克雷雅公司|Mutant interleukin-2 polypeptides|

---

WO2012107416A2|2011-02-10|2012-08-16|Roche Glycart Ag|Improved immunotherapy|

---

JP6046642B2|2011-03-02|2016-12-21|ロシュ グリクアート アーゲー|CEA antibody|

---

EA201892619A1|2011-04-29|2019-04-30|Роше Гликарт Аг|IMMUNOCONJUGATES CONTAINING INTERLEUKIN-2 MUTANT POLYPETIPS|

---

WO2013026831A1|2011-08-23|2013-02-28|Roche Glycart Ag|Bispecific antigen binding molecules|

---

EA030147B1|2011-08-23|2018-06-29|Роше Гликарт Аг|Bispecific t cell activating antigen binding molecules|

---

WO2013054320A1|2011-10-11|2013-04-18|Tel Hashomer Medical Research Infrastructure And Services Ltd.|Antibodies to carcinoembryonic antigen-related cell adhesion molecule |

---

GB201213858D0|2012-08-03|2012-09-19|Mab Design Ltd|Method|

---

SG11201407580YA|2012-08-07|2014-12-30|Roche Glycart Ag|Composition comprising two antibodies engineered to have reduced and increased effector function|

---

US10087250B2|2012-10-08|2018-10-02|Roche Glycart Ag|Fc-free antibodies comprising two fab-fragments and methods of use|

---

WO2014131711A1|2013-02-26|2014-09-04|Roche Glycart Ag|Bispecific t cell activating antigen binding molecules|

---

CN105143270B|2013-02-26|2019-11-12|罗切格利卡特公司|Bispecific T cell activation antigen binding molecules|

---

WO2014131712A1|2013-02-26|2014-09-04|Roche Glycart Ag|Bispecific t cell activating antigen binding molecules|

---

EP3137502B1|2014-04-27|2020-07-29|FameWave Ltd.|Humanized antibodies against ceacam1|

---

SG11201700879WA|2014-08-04|2017-03-30|Hoffmann La Roche|Bispecific t cell activating antigen binding molecules|

---

SI3221355T1|2014-11-20|2021-01-29|F. Hoffmann-La Roche Ag|Combination therapy of t cell activating bispecific antigen binding molecules cd3 and folate receptor 1and pd-1 axis binding antagonists|

---

CA2990755A1|2015-10-02|2017-04-06|F. Hoffman-La Roche Ag|Bispecific anti-ceaxcd3 t cell activating antigen binding molecules|

---

KR20180085740A|2015-12-09|2018-07-27|에프. 호프만-라 로슈 아게|Type II anti-CD20 antibodies to reduce the formation of anti-drug antibodies|

---

KR20180097615A|2016-01-08|2018-08-31|에프. 호프만-라 로슈 아게|Methods for the treatment of CEA-positive cancers using PD-1 axis-binding antagonists and anti-CEA / anti-CD3 bispecific antibodies|

---

MA43724A|2016-03-22|2018-11-28|Hoffmann La Roche|BISPECIFIC MOLECULES OF PROTEASE ACTIVATED T CELLS|

---

CN107663240B|2016-07-29|2021-01-12|中国人民解放军第四军医大学|Single-chain antibody specifically bound by highly glycosylated CEA and application thereof in detection and treatment|

---

PL3519437T3|2016-09-30|2022-01-17|F. Hoffmann-La Roche Ag|Bispecific antibodies against p95her2|

---

CN114127123A|2019-06-26|2022-03-01|豪夫迈·罗氏有限公司|Fusion of CEA-binding antibodies to 4-1BBL|

---

CN113906053A|2019-06-26|2022-01-07|江苏恒瑞医药股份有限公司|anti-CEA antibodies and uses thereof|

---

CN110713539B|2019-09-23|2021-04-16|华道生物医药有限公司|Anti-carcinoembryonic antigen antibody and preparation method and application thereof|

---

CN110862456B|2019-09-23|2021-04-09|华道生物医药有限公司|Anti-carcinoembryonic antigen antibody and preparation method and application thereof|

法律状态:
2021-09-28| B06F| Objections, documents and/or translations needed after an examination request according [chapter 6.6 patent gazette]|

---

2021-10-13| B06U| Preliminary requirement: requests with searches performed by other patent offices: procedure suspended [chapter 6.21 patent gazette]|

---

2022-02-01| B11B| Dismissal acc. art. 36, par 1 of ipl - no reply within 90 days to fullfil the necessary requirements|

优先权:

---

申请号 | 申请日 | 专利标题

---

US23850509P| true| 2009-08-31|2009-08-31|

---

US61/238,505|2009-08-31|

---

PCT/EP2010/062527|WO2011023787A1|2009-08-31|2010-08-27|Affinity-matured humanized anti cea monoclonal antibodies|

---