U.S. patent application number 12/796496 was filed with the patent office on 2010-11-04 for anti-ephb2 antibodies and methods using same.
This patent application is currently assigned to Genentech, Inc.. Invention is credited to Weiguang Mao, Paul Polakis.
Application Number | 20100278842 12/796496 |
Document ID | / |
Family ID | 36341431 |
Filed Date | 2010-11-04 |
United States Patent
Application |
20100278842 |
Kind Code |
A1 |
Mao; Weiguang ; et
al. |
November 4, 2010 |
ANTI-EPHB2 ANTIBODIES AND METHODS USING SAME
Abstract
The invention provides anti-EphB2 antibodies, immunoconjugates,
and compositions comprising and methods of using these antibodies
and immunoconjugates.
Inventors: |
Mao; Weiguang; (San Mateo,
CA) ; Polakis; Paul; (Mill Valley, CA) |
Correspondence
Address: |
GENENTECH, INC.
1 DNA WAY
SOUTH SAN FRANCISCO
CA
94080
US
|
Assignee: |
Genentech, Inc.
South San Francisco
CA
|
Family ID: |
36341431 |
Appl. No.: |
12/796496 |
Filed: |
June 8, 2010 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11831787 |
Jul 31, 2007 |
7767205 |
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12796496 |
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PCT/US2006/003502 |
Jan 31, 2006 |
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11831787 |
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60648541 |
Jan 31, 2005 |
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60756844 |
Jan 5, 2006 |
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Current U.S.
Class: |
424/172.1 ;
435/320.1; 435/325; 435/69.6; 514/44R; 536/23.53 |
Current CPC
Class: |
A61K 47/6849 20170801;
A61P 35/00 20180101; C07K 16/2866 20130101; A61K 47/6809 20170801;
C07K 7/06 20130101; C07K 2317/92 20130101; C07K 2317/77 20130101;
C07K 7/08 20130101; A61K 2039/505 20130101; A61K 47/6803
20170801 |
Class at
Publication: |
424/172.1 ;
536/23.53; 435/320.1; 435/325; 435/69.6; 514/44.R |
International
Class: |
A61K 39/395 20060101
A61K039/395; C07H 21/04 20060101 C07H021/04; C12N 15/63 20060101
C12N015/63; C12N 5/10 20060101 C12N005/10; C12P 21/00 20060101
C12P021/00; A61K 31/7088 20060101 A61K031/7088; A61P 35/00 20060101
A61P035/00 |
Claims
1. An isolated polynucleotide encoding an anti-EphB2 antibody
comprising: at least one, two, three, four, five, and/or six
hypervariable region (HVR) sequences selected from the group
consisting of: (a) HVR-L1 comprising sequence KSSQSLLNSGNQENYLA
(SEQ ID NO:1); (b) HVR-L2 comprising sequence GASTRES (SEQ ID
NO:2); (c) HVR-L3 comprising sequence QNDHSYPFT (SEQ ID NO:3); (d)
HVR-H1 comprising sequence SYWMH (SEQ ID NO:4); (e) HVR-H2
comprising sequence FINPSTGYTDYNQKFKD (SEQ ID NO:5); and (f) HVR-H3
comprising sequence RLKLLRYAMDY (SEQ ID NO:6), wherein the antibody
specifically binds human EphB2.
2. The polynucleotide of claim 1, wherein the antibody comprises a
light chain comprising at least one, at least two, or all three of
HVR sequences selected from the group consisting of
KSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and
QNDHSYPFT (SEQ ID NO:3).
3. The polynucleotide of claim 1 or 2, wherein the antibody
comprises a heavy chain comprising at least one, at least two or
all three of HVR sequences selected from the group consisting of
SYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), and
RLKLLRYAMDY (SEQ ID NO:6).
4. The polynucleotide of claim 1, wherein the antibody comprises
(a) a heavy chain comprising at least one, at least two or all
three of HVR sequences selected from the group consisting of SYWMH
(SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), and RLKLLRYAMDY
(SEQ ID NO:6); and (b) a light chain comprising at least one, at
least two or all three of CDR sequences selected from the group
consisting of KSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID
NO:2), and QNDHSYPFT (SEQ ID NO:3).
5. The polynucleotide of claim 1, wherein the antibody comprises a
light chain variable domain having the sequence: TABLE-US-00010
(SEQ ID NO: 7) DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPG
QPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC
QNDHSYPFTFGAGTKVEIKR.
6. The polynucleotide of claim 1 or 5, wherein the antibody
comprises a heavy chain variable domain having the sequence:
TABLE-US-00011 (SEQ ID NO: 8
QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEW
IGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYY
CTRRLKLLRYAMDYWGQGTTLTVSA.
7. An isolated polynucleotide encoding an antibody comprising at
least one hypervariable sequence comprising a sequence selected
from the group consisting of HVR-L1, HVR-L2, HVR-L3, HVR-H1,
HVR-H2, and HVR-H3 of the antibody produced by hybridoma cell line
having American Tissue Type Culture (ATCC) No. PTA-6606, wherein
said isolated antibody specifically binds human EphB2.
8. An isolated polynucleotide encoding an antibody comprising heavy
and/or light chain variable domain of the antibody produced by
hybridoma cell line having American Tissue Type Culture (ATCC) No.
PTA-6606, wherein said isolated antibody specifically binds human
EphB2.
9. An isolated polynucleotide encoding an antibody that binds to a
same epitope on human EphB2 as the antibody produced by hybridoma
cell line having American Tissue Type Culture (ATCC) No.
PTA-6606.
10. An isolated polynucleotide encoding an antibody that competes
with an antibody produced by hybridoma cell line having American
Tissue Type Culture (ATCC) No. PTA-6606 for binding to human
EphB2.
11. An isolated polynucleotide encoding an antibody encoded by
antibody coding sequences of hybridoma cell line having American
Tissue Type Culture (ATCC) No. PTA-6606
12. The polynucleotide of claim 1, 9 or 10, wherein the antibody is
a monoclonal antibody.
13. The polynucleotide of claim 1, 9 or 10, wherein the antibody is
selected from the group consisting of a chimeric antibody, a
humanized antibody, an affinity matured antibody, a human antibody,
and a bispecific antibody.
14. The polynucleotide of claim 1, 9 or 10, wherein the antibody is
an antibody fragment.
15. A vector comprising the polynucleotide of claim 1, 9 or 10.
16. The vector of claim 15, wherein the vector is an expression
vector.
17. A host cell comprising a vector of claim 15 or 16.
18. The host cell of claim 17, wherein the host cell is
prokaryotic.
19. The host cell of claim 17, wherein the host cell is
eukaryotic.
20. The host cell of claim 17, wherein the host cell is
mammalian.
21. A method for making an anti-EphB2 antibody, said method
comprising culturing a host cell comprising polynucleotide encoding
the antibody of claim 1, 9 or 10 so that the polynucleotide is
expressed, and optionally, recovering the antibody from the
culture.
22. A method for making an anti-EphB2 immunoconjugate, said method
comprising culturing a host cell comprising polynucleotide encoding
the antibody of claim 1, 9 or 10 so that the polynucleotide is
expressed, and optionally, recovering the antibody from the
culture.
23. The method of claim 21 or 22, wherein the host cell is
prokaryotic.
24. The method of claim 21 or 22, wherein the host cell is
eukaryotic.
25. The method of claim 21, further comprising recovering the
antibody from the host cell culture.
26. The method of claim 25, where in the antibody is recovered from
the host cell culture medium.
27. The method of claim 25, further comprising combining the
recovered antibody with a pharmaceutically acceptable carrier,
excipient, or carrier to prepare a pharmaceutical formulation
comprising the antibody.
28. A composition comprising a polynucleotide of claim 14, 15 or
16.
29. The composition of claim 28, wherein the composition further
comprises a carrier.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a Divisional of U.S. application Ser.
No. 11/831,787, filed Jul. 31, 2007 which is a continuation of
International Application No. PCT/US2006/003502, filed Jan. 31,
2006, which claims the benefit under 35 USC .sctn.119 to 35 USC
.sctn.119 to U.S. Provisional Application 60/648,541, filed Jan.
31, 2005, and U.S. Provisional Application 60/756,844, filed Jan.
5, 2006, the entire contents of which are hereby incorporated by
reference.
FIELD OF THE INVENTION
[0002] The present invention relates generally to the fields of
molecular biology. More specifically, the invention concerns
anti-EphB2 antibodies, and uses of same.
BACKGROUND OF THE INVENTION
[0003] The EphB2 receptor ("EphB2" or "EphB2R") is a member of the
eph receptor family, which constitutes the largest family of
tyrosine kinase receptors in the human genome (reviewed in Dodelet,
Oncogene, 19: 5614-5619, 2000). The human eph receptor tyrosine
kinases are categorized by sequence identity into an A class and a
B class with corresponding A-type and B-type ligands referred to as
ephrins. Signaling can occur in a forward manner, in which the
receptor tyrosine kinase is activated by the ligand, and in a
reverse manner, in which the transmembrane ephrinB ligands are
activated by interaction with receptors. Eph receptor ligand
interactions have been implicated in a wide range of biological
functions including axon guidance, tissue border formation,
vasculogenesis, and cell motility (Kullander et al. Nat. Rev. Mol.
Cell. Biol., 3: 475-486, 2002; Cheng et al. Cytokine Growth Factor
Rev., 13: 75-85, 2002; Coulthard et al. Int. J. Dev. Biol., 46:
375-384, 2002).
[0004] The EphB2 receptor has an extracellular region with a
cysteine-rich motif extending over its amino-terminal half followed
by two fibronectin type II motifs. There is an intracellular domain
featuring a conserved kinase region and a transmembrane domain.
EphB2 binds ligands such as ephrin-B1, ephrin-B2, and ephrin-B3.
The cytoplasmic regions of the activated EphB2 receptor has been
reported to interact with myriad familiar signaling molecules such
as Src, Grb2, and Abl (Holland et al., EMBO J., 16: 3877-3888,
2001). The EphB2 receptor tyrosine kinase down-regulates the
ras/mitogen-activated protein (MAP) kinase signaling pathway and
also inhibits the abl tyrosine kinase in endothelial and neuronal
cells (Yu et al., Oncogene, 20: 3995-4006, 2001; Kim et al., FASEB
J., 16: 1126-1128, 2002; Elowe et al. Mol. Cell. Biol., 21:
7429-7441, 2001).
[0005] Upregulation of both ephrin ligand and Eph receptor family
members has been described in a range of human tumors and cell
lines. For instance, EphB2 is reported to be over-expressed in
small cell lung cancer (Tang et al., Clin Cancer Res 1999;
5:455-60), neuroblastomas, (Tang et al., Med Pediatr Oncol 2001;
36:80-2), melanoma (Vogt et al. Clin Cancer Res 1998; 4:791-7),
breast carcinoma (Wu et al., Pathol Oncol Res 2004; 10:26-33),
colorectal cancer (CRC) (Jubb et al., co-owned, co-pending U.S.
patent application no. 60/642,164, filed Jan. 6, 2005, and Cairns
et al., WO2003/000113) and hepatocellular carcinoma (Hainer et al.,
Clin Chem 2004; 50:490-9).
[0006] Antibody-based therapy has proved very effective in the
treatment of various disorders. For example, HERCEPTIN.TM. and
RITUXAN.TM. (both from Genentech, S. San Francisco), have been used
successfully to treat breast cancer and non-Hodgkin's lymphoma,
respectively. HERCEPTIN.TM. is a recombinant DNA-derived humanized
monoclonal antibody that selectively binds to the extracellular
domain of the human epidermal growth factor receptor 2 (HER2)
proto-oncogene. HER2 protein overexpression is observed in 25-30%
of primary breast cancers. RITUXAN.TM. is a genetically engineered
chimeric murine/human monoclonal antibody directed against the
CD.sub.2O antigen found on the surface of normal and malignant B
lymphocytes. Both these antibodies are produced in CHO cells.
[0007] The use of antibody-drug conjugates (ADC), i.e.
immunoconjugates, for the local delivery of agents such as
cytotoxic or cytostatic agents to kill or inhibit tumor cells in
the treatment of cancer (Syrigos and Epenetos (1999) Anticancer
Research 19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drug
Del. Rev. 26:151-172; U.S. Pat. No. 4,975,278) allows targeted
delivery of the drug moiety to tumors, and intracellular
accumulation therein, where systemic administration of these
unconjugated drug agents may result in unacceptable levels of
toxicity to normal cells as well as the tumor cells sought to be
eliminated (Baldwin et al (1986) Lancet pp. (Mar. 15, 1986):603-05;
Thorpe, (1985) "Antibody Carriers Of Cytotoxic Agents In Cancer
Therapy: A Review," in Monoclonal Antibodies '84: Biological And
Clinical Applications, A. Pinchera et al (eds), pp. 475-506).
[0008] It is clear that there continues to be a need for agents
that have clinical attributes that are optimal for development as
therapeutic agents. The invention described herein meets this need
and provides other benefits.
[0009] All references cited herein, including patent applications
and publications, are incorporated by reference in their
entirety.
SUMMARY OF THE INVENTION
[0010] The invention is in part based on the identification of a
variety of EphB2 binding agents (such as immunoconjugates,
antibodies, and fragments thereof). EphB2 presents as an important
and advantageous therapeutic target, and the invention provides
compositions and methods based on binding EphB2. EphB2 binding
agents of the invention, as described herein, provide important
therapeutic and diagnostic agents for use in targeting pathological
conditions associated with expression and/or activity of the
EphB2-EphB2 ligand pathways. Accordingly, the invention provides
methods, compositions, kits and articles of manufacture related to
EphB2 binding.
[0011] The present invention provides antibodies that bind to
EphB2.
[0012] In one aspect, the invention provides the antibody produced
by hybridoma cell line 2H9.11.14 having American Tissue Type
Culture (ATCC) No. PTA-6606, deposited on Feb. 24, 2005.
[0013] In one aspect, the invention provides an isolated antibody
comprising heavy and/or light chain variable domain(s) of the
antibody produced by hybridoma cell line 2H9.11.14 having American
Tissue Type Culture (ATCC) No. PTA-6606, wherein said isolated
antibody specifically binds human EphB2.
[0014] In one aspect, the invention provides an isolated antibody
comprising at least one (at least 2, at least 3, at least 4, at
least 5, and/or 6) hypervariable sequence(s) (HVR(s)) comprising a
sequence selected from the group consisting of HVR-L1, HVR-L2,
HVR-L3, HVR-H1, HVR-H2, and/or HVR-H3 of the antibody produced by
hybridoma cell line 2H9.11.14 having American Tissue Type Culture
(ATCC) No. PTA-6606, wherein said isolated antibody specifically
binds human EphB2.
[0015] In one aspect, the invention provides an isolated antibody
that binds to the same epitope on human EphB2 as the antibody
produced by hybridoma cell line 2H9.11.14 having American Tissue
Type Culture (ATCC) No. PTA-6606.
[0016] In one aspect, the invention provides an isolated antibody
that competes with the antibody produced by hybridoma cell line
2H9.11.14 having American Tissue Type Culture (ATCC) No. PTA-6606
for binding to human EphB2.
[0017] In one aspect, the invention provides an isolated anti-EphB2
antibody, wherein a full length IgG form of the antibody
specifically binds human EphB2 with a binding affinity of 70 pM or
better. As is well-established in the art, binding affinity of a
ligand to its receptor can be determined using any of a variety of
assays, and expressed in terms of a variety of quantitative values.
Accordingly, in one embodiment, the binding affinity is expressed
as Kd values and reflects intrinsic binding affinity (e.g., with
minimized avidity effects). Generally and preferably, binding
affinity is measured in vitro, whether in a cell-free or
cell-associated setting. Any of a number of assays known in the
art, including those described herein, can be used to obtain
binding affinity measurements, including, for example, Biacore,
radioimmunoassay (RIA) and ELISA.
[0018] In one aspect, the invention provides an isolated antibody
that binds a ligand binding region of EphB2. In some embodiments,
the isolated antibody binds a polypeptide comprising, consisting of
or consisting essentially of amino acids about 19 to about 208 of
human EphB2 (FIG. 12).
[0019] In one aspect, the invention provides an isolated anti-EphB2
antibody that competes with EphB2 ligand for binding of EphB2.
[0020] In one aspect, the invention provides an isolated anti-EphB2
antibody that inhibits, reduces, and/or blocks EphB2 activity. In
some embodiments, EphB2 autophosphorylation is inhibited, reduced,
and/or blocked.
[0021] In one aspect, the invention provides an anti-EphB2 antibody
comprising: at least one, two, three, four, five, and/or six
hypervariable region (HVR) sequences selected from the group
consisting of: (a) HVR-L1 comprising sequence KSSQSLLNSGNQENYLA
(SEQ ID NO:1); (b) HVR-L2 comprising sequence GASTRES (SEQ ID
NO:2); (c) HVR-L3 comprising sequence QNDHSYPFT (SEQ ID NO:3); (d)
HVR-H1 comprising sequence SYWMH (SEQ ID NO:4); (e) HVR-H2
comprising sequence FINPSTGYTDYNQKFKD (SEQ ID NO:5); and (f) HVR-H3
comprising sequence RLKLLRYAMDY (SEQ ID NO:6).
[0022] In one embodiment, an antibody of the invention comprises a
light chain comprising at least one, at least two or all three of
HVR sequences selected from the group consisting of
KSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and
QNDHSYPFT (SEQ ID NO:3). In one embodiment, the antibody comprises
light chain HVR-L1 having amino acid sequence KSSQSLLNSGNQENYLA
(SEQ ID NO:1). In one embodiment, the antibody comprises light
chain HVR-L2 having amino acid sequence GASTRES (SEQ ID NO:2). In
one embodiment, the antibody comprises light chain HVR-L3 having
amino acid sequence QNDHSYPFT (SEQ ID NO:3). In one embodiment, an
antibody of the invention comprises a heavy chain comprising at
least one, at least two or all three of HVR sequences selected from
the group consisting of SYWMH (SEQ ID NO:4), FINPSTGYTDYNQKFKD (SEQ
ID NO:5), and RLKLLRYAMDY (SEQ ID NO:6). In one embodiment, the
antibody comprises heavy chain HVR-H1 having amino acid sequence
SYWMH (SEQ ID NO:4). In one embodiment, the antibody comprises
heavy chain HVR-H2 having amino acid sequence FINPSTGYTDYNQKFKD
(SEQ ID NO:5). In one embodiment, the antibody comprises heavy
chain HVR-H3 having amino acid sequence RLKLLRYAMDY (SEQ ID NO:6).
In one embodiment, an antibody of the invention comprises a heavy
chain comprising at least one, at least two or all three of HVR
sequences selected from the group consisting of SYWMH (SEQ ID
NO:4), FINPSTGYTDYNQKFKD (SEQ ID NO:5), and RLKLLRYAMDY (SEQ ID
NO:6) and a light chain comprising at least one, at least two or
all three of HVR sequences selected from the group consisting of
KSSQSLLNSGNQENYLA (SEQ ID NO:1), GASTRES (SEQ ID NO:2), and
QNDHSYPFT (SEQ ID NO:3).
[0023] In one embodiment, an antibody of the invention comprises a
light chain variable domain having the sequence:
TABLE-US-00001 (SEQ ID NO: 7)
DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPG
QPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC
QNDHSYPFTFGAGTKVEIKR.
[0024] In one embodiment, an antibody of the invention comprises a
heavy chain variable domain having the sequence:
TABLE-US-00002 (SEQ ID NO: 8)
QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEW
IGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYY
CTRRLKLLRYAMDYWGQGTTLTVSA.
[0025] In one embodiment, an antibody of the invention comprises a
light chain variable domain having the sequence:
TABLE-US-00003 (SEQ ID NO: 7)
DIVMTQSPSSLSVSAGEKVTMNCKSSQSLLNSGNQENYLAWYQQKPG
QPPKLLIYGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC
QNDHSYPFTFGAGTKVEIKR;
and comprises a heavy chain variable domain having the
sequence:
TABLE-US-00004 (SEQ ID NO: 8)
QVQLQQSGAELAKPGASVKMSCKASGYTFTSYWMHWVKQRPGQGLEW
IGFINPSTGYTDYNQKFKDKATLTVKSSNTAYMQLSRLTSEDSAVYY
CTRRLKLLRYAMDYWGQGTTLTVSA.
[0026] In one aspect, the invention provides an antibody that
competes with any of the above-mentioned antibodies for binding to
EphB2. In one aspect, the invention provides an antibody that binds
to the same epitope on EphB2 as any of the above-mentioned
antibodies.
[0027] As is known in the art, and as described in greater detail
hereinbelow, the amino acid position/boundary delineating a
hypervariable region of an antibody can vary, depending on the
context and the various definitions known in the art (as described
below). Some positions within a variable domain may be viewed as
hybrid hypervariable positions in that these positions can be
deemed to be within a hypervariable region under one set of
criteria while being deemed to be outside a hypervariable region
under a different set of criteria. One or more of these positions
can also be found in extended hypervariable regions (as further
defined below).
[0028] In some embodiments, the antibody is a monoclonal antibody.
In some embodiments, the antibody is a polyclonal antibody. In some
embodiments, the antibody is selected from the group consisting of
a chimeric antibody, an affinity matured antibody, a humanized
antibody, and a human antibody. In some embodiments, the antibody
is an antibody fragment. In some embodiments, the antibody is a
Fab, Fab', Fab'-SH, F(ab').sub.2, or scFv.
[0029] In one embodiment, the antibody is a chimeric antibody, for
example, an antibody comprising antigen binding sequences from a
non-human donor grafted to a heterologous non-human, human or
humanized sequence (e.g., framework and/or constant domain
sequences). In one embodiment, the non-human donor is a mouse. In
one embodiment, an antigen binding sequence is synthetic, e.g.
obtained by mutagenesis (e.g., phage display screening, etc.). In
one embodiment, a chimeric antibody of the invention has murine V
regions and human C region. In one embodiment, the murine light
chain V region is fused to a human kappa light chain. In one
embodiment, the murine heavy chain V region is fused to a human
IgG1 C region.
[0030] Humanized antibodies of the invention include those that
have amino acid substitutions in the FR and affinity maturation
variants with changes in the grafted CDRs. The substituted amino
acids in the CDR or FR are not limited to those present in the
donor or recipient antibody. In other embodiments, the antibodies
of the invention further comprise changes in amino acid residues in
the Fc region that lead to improved effector function including
enhanced CDC and/or ADCC function and B-cell killing. Other
antibodies of the invention include those having specific changes
that improve stability. Antibodies of the invention also include
fucose deficient variants having improved ADCC function in vivo. In
other embodiments, the antibodies of the invention comprise changes
in amino acid residues in the Fc region that lead to decreased
effector function, e.g. decreased CDC and/or ADCC function and/or
decreased B-cell killing. In some embodiments, the antibodies of
the invention are characterized by decreased binding (such as
absence of binding) to human complement factor C1q and/or human Fc
receptor on natural killer (NK) cells. In some embodiments, the
antibodies of the invention are characterized by decreased binding
(such as the absence of binding) to human Fc.gamma.RI,
Fc.gamma.RIIA, and/or Fc.gamma.RIIIA. In some embodiments, the
antibodies of the invention is of the IgG class (e.g., IgG1 or
IgG4) and comprises at least one mutation in E233, L234, L235,
G236, D265, D270, N297, E318, K320, K322, A327, A330, P331 and/or
P329 (numbering according to the EU index). In some embodiments,
the antibodies comprise the mutation L234A/L235A or
D265A/N297A.
[0031] In one aspect, the invention provides anti-EphB2
polypeptides comprising any of the antigen binding sequences
provided herein, wherein the anti-EphB2 polypeptides specifically
bind to EphB2.
[0032] In one aspect, the invention provides an immunoconjugate
(interchangeably termed "antibody drug conjugate" or "ADC")
comprising any of the anti-EphB2 antibodies disclosed herein
conjugated to an agent, such as a drug. EphB2 overexpression has
been observed in gastric cancer, small cell lung cancer,
neuroblastomas, melanoma, breast carcinoma, and hepatocellular
carcinoma and in all stages of colorectal tumorogenesis, indicating
that EphB2 is a suitable target for immunoconjugate therapy. EphB2
expression has been observed in colon adenomas, indicating that
EphB2 is a suitable target for disorders characterized by colon
adenomas.
[0033] In some embodiments, the drug in the immunoconjugate is a
chemotherapeutic agent, a growth inhibitory agent, a toxin (e.g.,
an enzymatically active toxin of bacterial, fungal, plant, or
animal origin, or fragments thereof), or a radioactive isotope
(i.e., a radioconjugate). In some embodiments, the drug is a
maytansinoid, an auristatin, a dolastatin, or a calicheamicin. In
some embodiments, the drug is DM1, DM3, DM4, MMAE, or MMAF.
[0034] In the immunoconjugates of the invention, an antibody (Ab)
is conjugated to one or more drug moieties (D), e.g. about 1 to
about 20 drug moieties per antibody, through a linker (L). In some
embodiments, the linker comprises linker components selected from
one or more of 6-maleimidocaproyl ("MC"), maleimidopropanoyl
("MP"), valine-citrulline ("val-cit"), alanine-phenylalanine
("ala-phe"), p-aminobenzyloxycarbonyl ("PAB"), N-Succinimidyl
4-(2-pyridylthio) entanoate ("SPP"), N-Succinimidyl
4-(N-maleimidomethyl)cyclohexane-1 carboxylate ("SMCC`), and/or
N-Succinimidyl (4-iodo-acetyl)aminobenzoate ("SIAB"). In some
embodiments, the linker comprises MC-val-cit-PAB.
[0035] In some embodiments, the immunoconjugate comprises SPP-DM1,
SMCC-DM1, BMPEO-DM1, MC-vc-PAB-MMAF, MC-vc-PAB-MMAE, MC-MMAF, or
MC-MMAE.
[0036] In one aspect, the invention provides an immunoconjugate
comprising an anti-EphB2 antibody that kills tumor cells. In some
embodiments, tumor cells are killed in vitro (in some embodiments,
with an IC50 of about 50 ng/ml, 40 ng/ml, 30 ng/ml, 20 ng/ml, 10
ng/ml, 5 ng/ml, 1 ng/ml, or less, such as 900 pg/ml, 800 pg/ml, 700
pg/ml, 600 pg/ml, 500 pg/ml, or less). In some embodiments, tumor
cells are killed in vivo. In some embodiments, administration of
the immunoconjugate reduces tumor growth (in some embodiments,
having about 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20% or 10%, or less
reduction in tumor growth compared to a control tumor) or reduces
time to tumor doubling.
[0037] The antibodies and immunoconjugates of the invention bind
(such as specifically bind) EphB2, and in some embodiments, may
modulate one or more aspects of EphB2-associated effects, including
but not limited to EphB2 activation, EphB2 downstream molecular
signaling, EphB2 ligand activation, EphB2 ligand downstream
molecular signaling, disruption of ligand (e.g., ephrin-B1,
ephrin-B2, and/or ephrin-B3) binding to EphB2, EphB2
phosphorylation and/or EphB2 multimerization, and/or EphB2 ligand
phosphorylation, and/or disruption of any biologically relevant
EphB2 and/or EphB2 ligand biological pathway, and/or treatment
and/or prevention of a tumor, cell proliferative disorder or a
cancer; and/or treatment or prevention of a disorder associated
with EphB2 expression and/or activity (such as increased EphB2
expression and/or activity). In some embodiments, the antibody or
immunoconjugate of the invention specifically binds to EphB2. In
some embodiments, the antibody or immunoconjugate specifically
binds to the EphB2 extracellular domain (ECD). In some embodiments,
the antibody or immunoconjugate specifically binds to a polypeptide
consisting of or consisting essentially of amino acids about 19 to
about 208 of human EphB2. In some embodiments, the antibody or
immunoconjugate specifically binds EphB2 with a KD of 70 pM or
stronger. In some embodiments, the antibody or immunoconjugate of
the invention reduces, inhibits, and/or blocks EphB2 activity in
vivo and/or in vitro. In some embodiments, the antibody or
immunoconjugate reduces, inhibits and/or blocks EphB2
autophosphorylation. In some embodiments, the antibody or
immunoconjugate competes for binding with EphB2-ligand (reduces
and/or blocks EphB2 ligand binding to EphB2). In some embodiments,
the antibody or immunoconjugate is internalized upon binding to
EphB2 expressed on a mammalian cell.
[0038] In one aspect, the invention provides use of an antibody or
immunoconjugate of the invention in the preparation of a medicament
for the therapeutic and/or prophylactic treatment of a disorder,
such as a cancer, a tumor, and/or a cell proliferative disorder. In
some embodiments, the disorder is characterized by colon
adenomas.
[0039] In one aspect, the invention provides compositions
comprising one or more antibodies or immunoconjugates of the
invention and a carrier. In one embodiment, the carrier is
pharmaceutically acceptable.
[0040] In one aspect, the invention provides nucleic acids encoding
an anti-EphB2 antibody of the invention.
[0041] In one aspect, the invention provides vectors comprising a
nucleic acid of the invention.
[0042] In one aspect, the invention provides compositions
comprising one or more nucleic acid of the invention and a carrier.
In one embodiment, the carrier is pharmaceutically acceptable.
[0043] In one aspect, the invention provides host cells comprising
a nucleic acid or a vector of the invention. A vector can be of any
type, for example a recombinant vector such as an expression
vector. Any of a variety of host cells can be used. In one
embodiment, a host cell is a prokaryotic cell, for example, E.
coli. In one embodiment, a host cell is a eukaryotic cell, for
example a mammalian cell such as Chinese Hamster Ovary (CHO)
cell.
[0044] In one aspect, the invention provides methods of making an
antibody or immunoconjugate of the invention. For example, the
invention provides methods of making an anti-EphB2 antibody (which,
as defined herein includes full length and fragments thereof) or
immunoconjugate, said method comprising expressing in a suitable
host cell a recombinant vector of the invention encoding said
antibody (or fragment thereof), and recovering said antibody. The
invention further provides methods of making an anti-EphB2
immunoconjugate, said method comprising expressing in a suitable
host cell a recombinant vector of the invention encoding an
anti-EphB2 antibody (or fragment thereof) or the invention,
recovering said anti-EphB2 antibody, and conjugating the anti-EphB2
antibody to a drug.
[0045] In one aspect, the invention provides an article of
manufacture comprising a container; and a composition contained
within the container, wherein the composition comprises one or more
anti-EphB2 antibodies or immunoconjugates of the invention. In one
embodiment, the composition comprises a nucleic acid of the
invention. In one embodiment, a composition comprising an antibody
or immunoconjugate further comprises a carrier, which in some
embodiments is pharmaceutically acceptable. In one embodiment, an
article of manufacture of the invention further comprises
instructions for administering the composition (for e.g., the
antibody) to a subject (such as instructions for any of the methods
described herein).
[0046] In one aspect, the invention provides a kit comprising a
first container comprising a composition comprising one or more
anti-EphB2 antibodies or immunoconjugates of the invention; and a
second container comprising a buffer. In one embodiment, the buffer
is pharmaceutically acceptable. In one embodiment, a composition
comprising an antibody or immunoconjugate further comprises a
carrier, which in some embodiments is pharmaceutically acceptable.
In one embodiment, a kit further comprises instructions for
administering the composition (for e.g., the antibody) to a
subject.
[0047] In one aspect, the invention provides use of an anti-EphB2
antibody or immunoconjugate (in some embodiments, an anti-EphB2
antibody or immunoconjugate of the invention) in the preparation of
a medicament for the therapeutic and/or prophylactic treatment of a
disorder, such as a cancer, a tumor, and/or a cell proliferative
disorder.
[0048] In one aspect, the invention provides use of a nucleic acid
of the invention in the preparation of a medicament for the
therapeutic and/or prophylactic treatment of a disorder, such as a
cancer, a tumor, and/or a cell proliferative disorder.
[0049] In one aspect, the invention provides use of an expression
vector of the invention in the preparation of a medicament for the
therapeutic and/or prophylactic treatment of a disorder, such as a
cancer, a tumor, and/or a cell proliferative disorder.
[0050] In one aspect, the invention provides use of a host cell of
the invention in the preparation of a medicament for the
therapeutic and/or prophylactic treatment of a disorder, such as a
cancer, a tumor, and/or a cell proliferative disorder.
[0051] In one aspect, the invention provides use of an article of
manufacture of the invention in the preparation of a medicament for
the therapeutic and/or prophylactic treatment of a disorder, such
as a cancer, a tumor, and/or a cell proliferative disorder.
[0052] In one aspect, the invention provides use of a kit of the
invention in the preparation of a medicament for the therapeutic
and/or prophylactic treatment of a disorder, such as a cancer, a
tumor, and/or a cell proliferative disorder.
[0053] The invention provides methods and compositions useful for
modulating disease states associated with expression and/or
activity of EphB2, such as increased expression and/or activity or
undesired expression and/or activity or decreased expression and/or
activity.
[0054] In one aspect, the invention provides methods for treating
or preventing a tumor, a cancer, and/or a cell proliferative
disorder associated with increased expression and/or activity of
EphB2, the methods comprising administering an effective amount of
an anti-EphB2 antibody or immunoconjugate (in some embodiments, an
anti-EphB2 antibody of the invention) to a subject in need of such
treatment.
[0055] In one aspect, the invention provides methods for killing a
cell (such as a cancer or tumor cell), the methods comprising
administering an effective amount of an anti-EphB2 antibody or
immunoconjugate (in some embodiments, an anti-EphB2 antibody of the
invention) to a subject in need of such treatment.
[0056] In one aspect, the invention provides methods for reducing,
inhibiting, blocking, or preventing growth of a tumor or cancer,
the methods comprising administering an effective amount of an
anti-EphB2 antibody or immunoconjugate (in some embodiments, an
anti-EphB2 antibody of the invention) to a subject in need of such
treatment.
[0057] In one aspect, the invention provides methods for treating
or preventing a neuropathy or neurodegenerative disease, or
repairing a damaged nerve cell, the methods comprising
administering an effective amount of an anti-EphB2 antibody or
immunoconjugate (in some embodiments, an anti-EphB2 antibody of the
invention) to a subject in need of such treatment.
[0058] In one aspect, the invention provides methods for promoting
the development, proliferation, maintenance or regeneration of
neurons, the methods comprising administering an effective amount
of an anti-EphB2 antibody or immunoconjugate (in some embodiments,
an anti-EphB2 antibody of the invention) to a subject in need of
such treatment.
[0059] In one aspect, the invention provides methods for inhibiting
angiogenesis, the methods comprising administering an effective
amount of an anti-EphB2 antibody or immunoconjugate (in some
embodiments, an anti-EphB2 antibody of the invention) to a subject
in need of such treatment. In some embodiments, the site of
angiogenesis is a tumor or cancer.
[0060] Methods of the invention can be used to affect any suitable
pathological state. Exemplary disorders are described herein, and
include a cancer selected from the group consisting of small cell
lung cancer, neuroblastomas, melanoma, breast carcinoma, gastric
cancer, colorectal cancer (CRC), and hepatocellular carcinoma; and
disorders characterized by colon adenomas.
[0061] In one embodiment, a cell that is targeted in a method of
the invention is a cancer cell. For example, a cancer cell can be
one selected from the group consisting of a breast cancer cell, a
colorectal cancer cell, a lung cancer cell, a papillary carcinoma
cell, a colon cancer cell, a pancreatic cancer cell, an ovarian
cancer cell, a cervical cancer cell, a central nervous system
cancer cell, an osteogenic sarcoma cell, a renal carcinoma cell, a
hepatocellular carcinoma cell, a bladder cancer cell, a gastric
carcinoma cell, a head and neck squamous carcinoma cell, a melanoma
cell, a leukemia cell, and a colon adenoma cell. In one embodiment,
a cell that is targeted in a method of the invention is a
hyperproliferative and/or hyperplastic cell. In one embodiment, a
cell that is targeted in a method of the invention is a dysplastic
cell. In yet another embodiment, a cell that is targeted in a
method of the invention is a metastatic cell. In some embodiments,
the cell that is targeted is a colon adenoma cell. In some
embodiments, the cell that is targeted expresses on the cell
membrane at least about 20,000; 30,000; 40,000; 50,000; 60,000;
70,000; 80,000; 90,000; 100,000; 150,000; 200,000; 250,000;
300,000; 350,000; 400,000; 450,000; 500,000; 550,000; 600,000;
650,000; 700,000; 750,000; 800,000; 850,000, or more EphB2
molecules.
[0062] Methods of the invention can further comprise additional
treatment steps. For example, in one embodiment, a method further
comprises a step wherein a targeted cell and/or tissue (for e.g., a
cancer cell) is exposed to radiation treatment or a
chemotherapeutic agent.
[0063] In another aspect, the invention provides methods for
detection of EphB2, the methods comprising detecting
EphB2-anti-EphB2 antibody complex in the sample. The term
"detection" as used herein includes qualitative and/or quantitative
detection (e.g., measuring levels) with or without reference to a
control.
[0064] In another aspect, the invention provides methods for
diagnosing a disorder associated with EphB2 expression and/or
activity, the methods comprising detecting EphB2-anti-EphB2
antibody complex in a biological sample from a patient having or
suspected of having the disorder. In some embodiments, the EphB2
expression is increased expression or abnormal expression. In some
embodiments, the disorder is a tumor, cancer, and/or a cell
proliferative disorder.
[0065] In another aspect, the invention provides any of the
anti-EphB2 antibodies described herein, wherein the anti-EphB2
antibody comprises a detectable label.
[0066] In another aspect, the invention provides a complex of any
of the anti-EphB2 antibodies described herein and EphB2. In some
embodiments, the complex is in vivo or in vitro. In some
embodiments, the complex comprises a cancer cell. In some
embodiments, the anti-EphB2 antibody is detectably labeled.
[0067] In another aspect, the invention provides a polypeptide
comprising, consisting of, or consisting essentially of amino acids
19-208 of EphB2 (FIG. 12).
BRIEF DESCRIPTION OF THE FIGURES
[0068] FIG. 1: depicts the amino acid sequences of monoclonal
antibody 2H9 heavy chain variable region. Amino acids are numbered
according to Kabat.
[0069] FIG. 2: depicts the amino acid sequence of monoclonal
antibody 2H9 light chain variable regions. Amino acids are numbered
according to Kabat.
[0070] FIG. 3: EphB2 mRNA is overexpressed in human cancer tissues
verses normal human tissues. A, oligonucleotide microarray analysis
was performed on RNA extracted from 38 human colorectal tumors and
7 specimens of normal human colonic mucosa. The average difference
represents signal intensity (scaled to 1500). B, real-time PCR was
performed on RNA extracted from 11 human colorectal cancer biopsy
specimens and the corresponding patient-matched normal colon tissue
specimens.
[0071] FIG. 4: EphB2 expression in cancer and normal human colon
tissues. A, in situ hybridization. EphB2 transcript is detected as
deposited silver grains in the dark-field images, and the
corresponding bright-field images were generated by staining the
sections with H&E. Top and bottom panels are from colon tumor
and normal colon tissues, respectively. B, EphB2 protein expression
was detected using immunohistochemistry. Frozen serial tissue
sections of a human adenocarcinoma were stained with anti-EphB2
monoclonal antibody 2H9 (right panel) or with control antibody
(left panel) and counterstained with hematoxylin.
[0072] FIG. 5: Monoclonal antibody (MAb) 2H9 antagonizes the
ephrin-EphB2 interaction. A, the SVT2-EphB2 cell line was incubated
with purified Fc-EphrinB2 fusion protein, and EphB2 protein was
recovered from cell lysates by immunoprecipitation (IP) through the
GD epitope tag fused to its NH2 terminus. Western blotting (WB) was
performed with anti-phosphotyrosine (PTyr; top panel), to detect
phosphotyrosine, and anti-GD (bottom panel), to detect total EphB2
protein. During ligand incubation, MAb 2H9 or control antibody
(EGVEGF MAb) was included in the culture medium. B, binding of
purified human Fc-EphrinB1 fusion protein to HT1080 cells
overexpressing EphB2 was assessed by flow cytometry using human
anti-Fc conjugated to FITC. Relative fluorescence intensity was
then measured in the presence of increasing concentrations of MAb
2H9. As controls, Fc-EphrinB1 was omitted in the presence or
absence of Mab 2H9 or secondary antibody.
[0073] FIG. 6: Internalization of anti-EphB2 monoclonal antibody
(Mab) 2H9. A, MAb 2H9 was incubated on ice with HT1080 cells
overexpressing EphB2. The cells either remained on ice or were
shifted to 37.degree. C. for 1 h before fixing and staining with
secondary antibody. B, Mab 2H9 was labeled with .sup.125I and
incubated with HT1080-EphB2 cells on ice. Cells remained on ice
(4.degree. C.) or were shifted to 37.degree. C. for 1 hour, and
then the percentage of internalized .sup.125I was determined by
scintillation counting.
[0074] FIG. 7: Immunoconjugate 2H9-MC-valine-citrulline
(vc)-PAB-monomethylauristatin E (MMAE) kills tumor cells in vitro.
The HT1080 cell line stably overexpressing EphB2 (HT1080-EphB2) or
a vector control HT1080 cell line (HT1080-GD) was treated with
increasing concentrations of naked (i.e. not conjugated) monoclonal
antibody 2H9, immunoconjugate 2H9-MC-vc-PAB-MMAE (abbreviated
"MMAE-vc-2H9" in this figure), or immunoconjugate
anti-interleukin-8-MC-vc-PAB-MMAE (abbreviated "MMAE-vc-anti-IL8"
in this figure), and cell viability was measured after 2 days. The
antibody concentration required to attain half-maximal killing is
indicated as IC50.
[0075] FIG. 8: Characterization of HT1080 cell lines and
immunoconjugate 2H9-MC-vc-PAB-MMAE. A, monoclonal antibody 2H9
binding assays were performed on the HT1080-EphB2 and HT1080-GD
cell lines. The estimated number of total binding sites and the
dissociation constants (Kd) were determined by Scatchard analysis.
B, flow cytometry was performed with MAb 2H9 on the HT1080-EphB2
and HT1080-GD cell lines. Relative fluorescence intensity is
presented in the histogram for MAb 2H9 and for secondary antibody
only (control). C, saturation binding was performed on the
HT1080-EphB2 and HT1080-GD cell lines with both naked Mab 2H9
(abbreviated "2H9" in this figure) and immunoconjugate
2H9-MC-vc-PAB-MMAE (abbreviated "2H9-vc-MMAE" in this figure).
Relative binding was determined using a horseradish
peroxidase-conjugated secondary antibody, and absorbance was read
at 450 nm.
[0076] FIG. 9: Immunoconjugates 2H9-SPP-Dm1, 2H9-SMCC-DM1,
2H9-MC-vc-PAB-MMAE, and 2H9-MC-vc-PAB-MMAF kill tumor cells in
vitro. A, the HT1080 cell line stably overexpressing EphB2
(HT1080-EphB2) was treated with increasing concentrations of
2H9-MC-vc-PAB-MMAE (abbreviated "vc-MMAE" in this figure),
2H9-SMCC-DM1 (abbreviated "SMCC-DM1" in this figure), 2H9-SPP-DM1
(abbreviated "Spp-DM1" in this figure), or
anti-interleukin-8-MC-vc-PAB-MMAE (abbreviated "IL8MMAE" in this
figure), and cell viability was measured after 2 days. B, the
HT1080 cell line stably overexpressing EphB2 (HT1080-EphB2) was
treated with increasing concentrations of 2H9-MC-vc-PAB-MMAE
(abbreviated "vc-MMAE" in this figure), 2H9-MC-vc-PAB-MMAF
(abbreviated "vc-MMAF" in this figure), 2H9-SMCC-DM1 (abbreviated
"SMCC-DM1" in this figure), or 2H9-SPP-DM1 (abbreviated "Spp-DM1"
in this figure), and cell viability was measured after 2 days.
[0077] FIG. 10: 2H9-MC-vc-PAB-MMAE specifically inhibits growth of
human tumors in vivo. A, nude mice were inoculated s.c. on one
flank with HT1080-GD cells and on the other with HT1080-EphB2, and
the resulting tumor xenografts were grown to an average size of 150
mm.sup.3 each. Ten animals in each group received vehicle control (
) or 3 mg/kg body weight of either immunoconjugate 2H9
MC-vc-PAB-MMAE (.box-solid.) (abbreviated "MMAE-vc-2H9" in this
figure) or immunoconjugate anti-interleukin 8 MC-vc-PAB-MMAE
(.tangle-solidup.)(abbreviated "MMAE-vc-anti-I1-8" in this figure)
once per week. B, the CXF1103 human colon tumor line was grown as a
xenograft in nude mice that underwent a treatment protocol
identical to that described for the HT1080 model. The control
antibody was anti-GD conjugated to MC-vc-PAB-MMAE (abbreviated
"MMAE-vc-GD" in this figure). Mean tumor volumes with SEs are
presented.
[0078] FIG. 11: depicts an amino acid sequence of the ligand
binding domain of EphB2 (SEQ ID NO:9).
DETAILED DESCRIPTION OF THE INVENTION
[0079] The invention herein provides anti-EphB2 antibodies, or
immunoconjugates comprising anti-EphB2 antibodies, that are useful
for, e.g., treatment or prevention of disease states associated
with expression and/or activity of EphB2, such as increased
expression and/or activity or undesired expression and/or activity.
In some embodiments, the antibodies or immunoconjugates of the
invention are used to treat a tumor, a cancer, and/or a cell
proliferative disorder.
[0080] In another aspect, the anti-EphB2 antibodies of the
invention find utility as reagents for detection and/or isolation
of EphB2, such as detention of EphB2 in various tissues and cell
type.
[0081] The invention further provides methods of making anti-EphB2
antibodies, and polynucleotides encoding anti-EphB2 antibodies.
General Techniques
[0082] The techniques and procedures described or referenced herein
are generally well understood and commonly employed using
conventional methodology by those skilled in the art, such as, for
example, the widely utilized methodologies described in Sambrook et
al., Molecular Cloning: A Laboratory Manual 3rd. edition (2001)
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
CURRENT PROTOCOLS 1N MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds.,
(2003)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.):
PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G.
R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A
LABORATORY MANUAL, and ANIMAL CELL CULTURE (R. I. Freshney, ed.
(1987)).
DEFINITIONS
[0083] An "isolated" antibody is one which has been identified and
separated and/or recovered from a component of its natural
environment. Contaminant components of its natural environment are
materials which would interfere with diagnostic or therapeutic uses
for the antibody, and may include enzymes, hormones, and other
proteinaceous or nonproteinaceous solutes. In preferred
embodiments, the antibody will be purified (1) to greater than 95%
by weight of antibody as determined by the Lowry method, and most
preferably more than 99% by weight, (2) to a degree sufficient to
obtain at least 15 residues of N-terminal or internal amino acid
sequence by use of a spinning cup sequenator, or (3) to homogeneity
by SDS-PAGE under reducing or nonreducing conditions using
Coomassie blue or, preferably, silver stain. Isolated antibody
includes the antibody in situ within recombinant cells since at
least one component of the antibody's natural environment will not
be present. Ordinarily, however, isolated antibody will be prepared
by at least one purification step.
[0084] An "isolated" nucleic acid molecule is a nucleic acid
molecule that is identified and separated from at least one
contaminant nucleic acid molecule with which it is ordinarily
associated in the natural source of the antibody nucleic acid. An
isolated nucleic acid molecule is other than in the form or setting
in which it is found in nature. Isolated nucleic acid molecules
therefore are distinguished from the nucleic acid molecule as it
exists in natural cells. However, an isolated nucleic acid molecule
includes a nucleic acid molecule contained in cells that ordinarily
express the antibody where, for example, the nucleic acid molecule
is in a chromosomal location different from that of natural
cells.
[0085] The term "variable domain residue numbering as in Kabat" or
"amino acid position numbering as in Kabat", and variations
thereof, refers to the numbering system used for heavy chain
variable domains or light chain variable domains of the compilation
of antibodies in Kabat et al., Sequences of Proteins of
Immunological Interest, 5th Ed. Public Health Service, National
Institutes of Health, Bethesda, Md. (1991). Using this numbering
system, the actual linear amino acid sequence may contain fewer or
additional amino acids corresponding to a shortening of, or
insertion into, a FR or CDR of the variable domain. For example, a
heavy chain variable domain may include a single amino acid insert
(residue 52a according to Kabat) after residue 52 of H2 and
inserted residues (e.g. residues 82a, 82b, and 82c, etc according
to Kabat) after heavy chain FR residue 82. The Kabat numbering of
residues may be determined for a given antibody by alignment at
regions of homology of the sequence of the antibody with a
"standard" Kabat numbered sequence.
[0086] The phrase "substantially similar," or "substantially the
same", as used herein, denotes a sufficiently high degree of
similarity between two numeric values (generally one associated
with an antibody of the invention and the other associated with a
reference/comparator antibody) such that one of skill in the art
would consider the difference between the two values to be of
little or no biological and/or statistical significance within the
context of the biological characteristic measured by said values
(e.g., Kd values). The difference between said two values is
preferably less than about 50%, preferably less than about 40%,
preferably less than about 30%, preferably less than about 20%,
preferably less than about 10% as a function of the value for the
reference/comparator antibody.
[0087] "Binding affinity" generally refers to the strength of the
sum total of noncovalent interactions between a single binding site
of a molecule (e.g., an antibody) and its binding partner (e.g., an
antigen). Unless indicated otherwise, as used herein, "binding
affinity" refers to intrinsic binding affinity which reflects a 1:1
interaction between members of a binding pair (e.g., antibody and
antigen). The affinity of a molecule X for its partner Y can
generally be represented by the dissociation constant (Kd).
Affinity can be measured by common methods known in the art,
including those described herein. Low-affinity antibodies generally
bind antigen slowly and tend to dissociate readily, whereas
high-affinity antibodies generally bind antigen faster and tend to
remain bound longer. A variety of methods of measuring binding
affinity are known in the art, any of which can be used for
purposes of the present invention. Specific illustrative
embodiments are described in the following.
[0088] In one embodiment, the "Kd" or "Kd value" according to this
invention is measured by a radiolabeled antigen binding assay (RIA)
performed with the Fab version of an antibody of interest and its
antigen as described by the following assay that measures solution
binding affinity of Fabs for antigen by equilibrating Fab with a
minimal concentration of (.sup.125I)-labeled antigen in the
presence of a titration series of unlabeled antigen, then capturing
bound antigen with an anti-Fab antibody-coated plate (Chen, et al.,
(1999) J. Mol. Biol 293:865-881). To establish conditions for the
assay, microtiter plates (Dynex) are coated overnight with 5 ug/ml
of a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium
carbonate (pH 9.6), and subsequently blocked with 2% (w/v) bovine
serum albumin in PBS for two to five hours at room temperature
(approximately 23.degree. C.). In a non-adsorbant plate (Nunc
#269620), 100 pM or 26 pM [.sup.125]-antigen are mixed with serial
dilutions of a Fab of interest (e.g., consistent with assessment of
an anti-VEGF antibody, Fab-12, in Presta et al., (1997) Cancer Res.
57:4593-4599). The Fab of interest is then incubated overnight;
however, the incubation may continue for a longer period (e.g., 65
hours) to insure that equilibrium is reached. Thereafter, the
mixtures are transferred to the capture plate for incubation at
room temperature (e.g., for one hour). The solution is then removed
and the plate washed eight times with 0.1% Tween-20 in PBS. When
the plates have dried, 150 ul/well of scintillant (MicroScint-20;
Packard) is added, and the plates are counted on a Topcount gamma
counter (Packard) for ten minutes. Concentrations of each Fab that
give less than or equal to 20% of maximal binding are chosen for
use in competitive binding assays. According to another embodiment
the Kd or Kd value is measured by using surface plasmon resonance
assays using a BIAcore.TM.-2000 or a BIAcore.TM.-3000 (BIAcore,
Inc., Piscataway, N.J.) at 25 C with immobilized antigen CM5 chips
at .about.10 response units (RU). Briefly, carboxymethylated
dextran biosensor chips (CM5, BIAcore Inc.) are activated with
N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC)
and N-hydroxysuccinimide (NHS) according to the supplier's
instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8,
into 5 ug/ml (.about.0.2 uM) before injection at a flow rate of 5
ul/minute to achieve approximately 10 response units (RU) of
coupled protein. Following the injection of antigen, 1M
ethanolamine is injected to block unreacted groups. For kinetics
measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM)
are injected in PBS with 0.05% Tween 20 (PBST) at 25.degree. C. at
a flow rate of approximately 25 ul/min. Association rates
(k.sub.on) and dissociation rates (k.sub.off) are calculated using
a simple one-to-one Langmuir binding model (BIAcore Evaluation
Software version 3.2) by simultaneous fitting the association and
dissociation sensorgram. The equilibrium dissociation constant (Kd)
is calculated as the ratio k.sub.off/k.sub.on. See, e.g., Chen, Y.,
et al., (1999) J. Mol. Biol 293:865-881. If the on-rate exceeds
10.sup.6 M.sup.-1 S.sup.-1 by the surface plasmon resonance assay
above, then the on-rate can be determined by using a fluorescent
quenching technique that measures the increase or decrease in
fluorescence emission intensity (excitation=295 nm; emission=340
nm, 16 nm band-pass) at 25.degree. C. of a 20 nM anti-antigen
antibody (Fab form) in PBS, pH 7.2, in the presence of increasing
concentrations of antigen as measured in a spectrometer, such as a
stop-flow equipped spectrophometer (Aviv Instruments) or a
8000-series SLM-Aminco spectrophotometer (ThermoSpectronic) with a
stir red cuvette.
[0089] An "on-rate" or "rate of association" or "association rate"
or "k.sub.on" according to this invention can also be determined
with the same surface plasmon resonance technique described above
using a BIAcore.TM.-2000 or a BIAcore.TM.-3000 (BIAcore, Inc.,
Piscataway, N.J.) at 25 C with immobilized antigen CM5 chips at
.about.10 response units (RU). Briefly, carboxymethylated dextran
biosensor chips (CM5, BIAcore Inc.) are activated with
N-ethyl-N'-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC)
and N-hydroxysuccinimide (NHS) according to the supplier's
instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8,
into 5 ug/ml (.about.0.2 uM) before injection at a flow rate of 5
ul/minute to achieve approximately 10 response units (RU) of
coupled protein. Following the injection of antigen, 1M
ethanolamine is injected to block unreacted groups. For kinetics
measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM)
are injected in PBS with 0.05% Tween 20 (PBST) at 25.degree. C. at
a flow rate of approximately 25 ul/min. Association rates
(k.sub.on) and dissociation rates (k.sub.off) are calculated using
a simple one-to-one Langmuir binding model (BIAcore Evaluation
Software version 3.2) by simultaneous fitting the association and
dissociation sensorgram. The equilibrium dissociation constant (Kd)
was calculated as the ratio k.sub.off/k.sub.on. See, e.g., Chen,
Y., et al., (1999) J. Mol. Biol 293:865-881. However, if the
on-rate exceeds 10.sup.6 M.sup.-1 S.sup.-1 by the surface plasmon
resonance assay above, then the on-rate is preferably determined by
using a fluorescent quenching technique that measures the increase
or decrease in fluorescence emission intensity (excitation=295 nm;
emission=340 nm, 16 nm band-pass) at 25.degree. C. of a 20 nM
anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of
increasing concentrations of antigen as measured in a a
spectrometer, such as a stop-flow equipped spectrophometer (Aviv
Instruments) or a 8000-series SLM-Aminco spectrophotometer
(ThermoSpectronic) with a stirred cuvette.
[0090] The term "vector," as used herein, is intended to refer to a
nucleic acid molecule capable of transporting another nucleic acid
to which it has been linked. One type of vector is a "plasmid",
which refers to a circular double stranded DNA loop into which
additional DNA segments may be ligated. Another type of vector is a
phage vector. Another type of vector is a viral vector, wherein
additional DNA segments may be ligated into the viral genome.
Certain vectors are capable of autonomous replication in a host
cell into which they are introduced (e.g., bacterial vectors having
a bacterial origin of replication and episomal mammalian vectors).
Other vectors (e.g., non-episomal mammalian vectors) can be
integrated into the genome of a host cell upon introduction into
the host cell, and thereby are replicated along with the host
genome. Moreover, certain vectors are capable of directing the
expression of genes to which they are operatively linked. Such
vectors are referred to herein as "recombinant expression vectors"
(or simply, "recombinant vectors"). In general, expression vectors
of utility in recombinant DNA techniques are often in the form of
plasmids. In the present specification, "plasmid" and "vector" may
be used interchangeably as the plasmid is the most commonly used
form of vector.
[0091] "Polynucleotide," or "nucleic acid," as used interchangeably
herein, refer to polymers of nucleotides of any length, and include
DNA and RNA. The nucleotides can be deoxyribonucleotides,
ribonucleotides, modified nucleotides or bases, and/or their
analogs, or any substrate that can be incorporated into a polymer
by DNA or RNA polymerase, or by a synthetic reaction. A
polynucleotide may comprise modified nucleotides, such as
methylated nucleotides and their analogs. If present, modification
to the nucleotide structure may be imparted before or after
assembly of the polymer. The sequence of nucleotides may be
interrupted by non-nucleotide components. A polynucleotide may be
further modified after synthesis, such as by conjugation with a
label. Other types of modifications include, for example, "caps",
substitution of one or more of the naturally occurring nucleotides
with an analog, internucleotide modifications such as, for example,
those with uncharged linkages (e.g., methyl phosphonates,
phosphotriesters, phosphoamidates, carbamates, etc.) and with
charged linkages (e.g., phosphorothioates, phosphorodithioates,
etc.), those containing pendant moieties, such as, for example,
proteins (e.g., nucleases, toxins, antibodies, signal peptides,
ply-L-lysine, etc.), those with intercalators (e.g., acridine,
psoralen, etc.), those containing chelators (e.g., metals,
radioactive metals, boron, oxidative metals, etc.), those
containing alkylators, those with modified linkages (e.g., alpha
anomeric nucleic acids, etc.), as well as unmodified forms of the
polynucleotide(s). Further, any of the hydroxyl groups ordinarily
present in the sugars may be replaced, for example, by phosphonate
groups, phosphate groups, protected by standard protecting groups,
or activated to prepare additional linkages to additional
nucleotides, or may be conjugated to solid or semi-solid supports.
The 5' and 3' terminal OH can be phosphorylated or substituted with
amines or organic capping group moieties of from 1 to 20 carbon
atoms. Other hydroxyls may also be derivatized to standard
protecting groups. Polynucleotides can also contain analogous forms
of ribose or deoxyribose sugars that are generally known in the
art, including, for example, 2'-O-methyl-, 2'-O-allyl, 2'-fluoro-
or 2'-azido-ribose, carbocyclic sugar analogs, alpha-anomeric
sugars, epimeric sugars such as arabinose, xyloses or lyxoses,
pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs
and a basic nucleoside analogs such as methyl riboside. One or more
phosphodiester linkages may be replaced by alternative linking
groups. These alternative linking groups include, but are not
limited to, embodiments wherein phosphate is replaced by
P(O)S("thioate"), P(S)S ("dithioate"), "(O)NR.sub.2 ("amidate"),
P(O)R, P(O)OR', CO or CH.sub.2 ("formacetal"), in which each R or
R' is independently H or substituted or unsubstituted alkyl (1-20
C) optionally containing an ether (--O--) linkage, aryl, alkenyl,
cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a
polynucleotide need be identical. The preceding description applies
to all polynucleotides referred to herein, including RNA and
DNA.
[0092] "Oligonucleotide," as used herein, generally refers to
short, generally single stranded, generally synthetic
polynucleotides that are generally, but not necessarily, less than
about 200 nucleotides in length. The terms "oligonucleotide" and
"polynucleotide" are not mutually exclusive. The description above
for polynucleotides is equally and fully applicable to
oligonucleotides.
[0093] The term "EphB2" (interchangeably termed "EphB2R"), as used
herein, refers, unless specifically or contextually indicated
otherwise, to any native or variant (whether native or synthetic)
EphB2 polypeptide. The term "native sequence" specifically
encompasses naturally occurring truncated or secreted forms (e.g.,
an extracellular domain sequence), naturally occurring variant
forms (e.g., alternatively spliced forms) and naturally-occurring
allelic variants. The term "wild type EphB2" generally refers to a
polypeptide comprising the amino acid sequence of a naturally
occurring EphB2 protein. The term "wild type EphB2 sequence"
generally refers to an amino acid sequence found in a naturally
occurring EphB2.
[0094] The terms "antibody" and "immunoglobulin" are used
interchangeably in the broadest sense and include monoclonal
antibodies (for e.g., full length or intact monoclonal antibodies),
polyclonal antibodies, multivalent antibodies, multispecific
antibodies (e.g., bispecific antibodies so long as they exhibit the
desired biological activity) and may also include certain antibody
fragments (as described in greater detail herein). An antibody can
be human, humanized and/or affinity matured.
[0095] The term "variable" refers to the fact that certain portions
of the variable domains differ extensively in sequence among
antibodies and are used in the binding and specificity of each
particular antibody for its particular antigen. However, the
variability is not evenly distributed throughout the variable
domains of antibodies. It is concentrated in three segments called
complementarity-determining regions (CDRs) or hypervariable regions
both in the light-chain and the heavy-chain variable domains. The
more highly conserved portions of variable domains are called the
framework (FR). The variable domains of native heavy and light
chains each comprise four FR regions, largely adopting a
.beta.-sheet configuration, connected by three CDRs, which form
loops connecting, and in some cases forming part of, the
.beta.-sheet structure. The CDRs in each chain are held together in
close proximity by the FR regions and, with the CDRs from the other
chain, contribute to the formation of the antigen-binding site of
antibodies (see Kabat et al., Sequences of Proteins of
Immunological Interest, Fifth Edition, National Institute of
Health, Bethesda, Md. (1991)). The constant domains are not
involved directly in binding an antibody to an antigen, but exhibit
various effector functions, such as participation of the antibody
in antibody-dependent cellular toxicity.
[0096] Papain digestion of antibodies produces two identical
antigen-binding fragments, called "Fab" fragments, each with a
single antigen-binding site, and a residual "Fc" fragment, whose
name reflects its ability to crystallize readily. Pepsin treatment
yields an F(ab').sub.2 fragment that has two antigen-combining
sites and is still capable of cross-linking antigen.
[0097] "Fv" is the minimum antibody fragment which contains a
complete antigen-recognition and -binding site. In a two-chain Fv
species, this region consists of a dimer of one heavy- and one
light-chain variable domain in tight, non-covalent association. In
a single-chain Fv species, one heavy- and one light-chain variable
domain can be covalently linked by a flexible peptide linker such
that the light and heavy chains can associate in a "dimeric"
structure analogous to that in a two-chain Fv species. It is in
this configuration that the three CDRs of each variable domain
interact to define an antigen-binding site on the surface of the
VH-VL dimer. Collectively, the six CDRs confer antigen-binding
specificity to the antibody. However, even a single variable domain
(or half of an Fv comprising only three CDRs specific for an
antigen) has the ability to recognize and bind antigen, although at
a lower affinity than the entire binding site.
[0098] The Fab fragment also contains the constant domain of the
light chain and the first constant domain (CH1) of the heavy chain.
Fab' fragments differ from Fab fragments by the addition of a few
residues at the carboxy terminus of the heavy chain CH1 domain
including one or more cysteines from the antibody hinge region.
Fab'-SH is the designation herein for Fab' in which the cysteine
residue(s) of the constant domains bear a free thiol group.
F(ab').sub.2 antibody fragments originally were produced as pairs
of Fab' fragments which have hinge cysteines between them. Other
chemical couplings of antibody fragments are also known.
[0099] The "light chains" of antibodies (immunoglobulins) from any
vertebrate species can be assigned to one of two clearly distinct
types, called kappa (.kappa.) and lambda (.lamda.), based on the
amino acid sequences of their constant domains.
[0100] Depending on the amino acid sequence of the constant domain
of their heavy chains, immunoglobulins can be assigned to different
classes. There are five major classes of immunoglobulins: IgA, IgD,
IgE, IgG, and IgM, and several of these can be further divided into
subclasses (isotypes), e.g., IgG.sub.1, IgG.sub.2, IgG.sub.3,
IgG.sub.4, IgA.sub.1, and IgA.sub.2. The heavy-chain constant
domains that correspond to the different classes of immunoglobulins
are called .alpha., .delta., .epsilon., .gamma., and .mu.,
respectively. The subunit structures and three-dimensional
configurations of different classes of immunoglobulins are well
known.
[0101] "Antibody fragments" comprise only a portion of an intact
antibody, wherein the portion preferably retains at least one,
preferably most or all, of the functions normally associated with
that portion when present in an intact antibody. In one embodiment,
an antibody fragment comprises an antigen binding site of the
intact antibody and thus retains the ability to bind antigen. In
another embodiment, an antibody fragment, for example one that
comprises the Fc region, retains at least one of the biological
functions normally associated with the Fc region when present in an
intact antibody, such as FcRn binding, antibody half life
modulation, ADCC function and complement binding. In one
embodiment, an antibody fragment is a monovalent antibody that has
an in vivo half life substantially similar to an intact antibody.
For e.g., such an antibody fragment may comprise on antigen binding
arm linked to an Fc sequence capable of conferring in vivo
stability to the fragment.
[0102] The term "monoclonal antibody" as used herein refers to an
antibody from a population of substantially homogeneous antibodies,
i.e., the individual antibodies comprising the population are
identical and/or bind the same epitope(s), except for possible
variants that may arise during production of the monoclonal
antibody, such variants generally being present in minor amounts.
Such monoclonal antibody typically includes an antibody comprising
a polypeptide sequence that binds a target, wherein the
target-binding polypeptide sequence was obtained by a process that
includes the selection of a single target binding polypeptide
sequence from a plurality of polypeptide sequences. For example,
the selection process can be the selection of a unique clone from a
plurality of clones, such as a pool of hybridoma clones, phage
clones or recombinant DNA clones. It should be understood that the
selected target binding sequence can be further altered, for
example, to improve affinity for the target, to humanize the target
binding sequence, to improve its production in cell culture, to
reduce its immunogenicity in vivo, to create a multispecific
antibody, etc., and that an antibody comprising the altered target
binding sequence is also a monoclonal antibody of this invention.
In contrast to polyclonal antibody preparations which typically
include different antibodies directed against different
determinants (epitopes), each monoclonal antibody of a monoclonal
antibody preparation is directed against a single determinant on an
antigen. In addition to their specificity, the monoclonal antibody
preparations are advantageous in that they are typically
uncontaminated by other immunoglobulins. The modifier "monoclonal"
indicates the character of the antibody as being obtained from a
substantially homogeneous population of antibodies, and is not to
be construed as requiring production of the antibody by any
particular method. For example, the monoclonal antibodies to be
used in accordance with the present invention may be made by a
variety of techniques, including, for example, the hybridoma method
(e.g., Kohler et al., Nature, 256:495 (1975); Harlow et al.,
Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory
Press, 2nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies
and T-Cell Hybridomas 563-681, (Elsevier, N.Y., 1981)), recombinant
DNA methods (see, e.g., U.S. Pat. No. 4,816,567), phage display
technologies (see, e.g., Clackson et al., Nature, 352:624-628
(1991); Marks et al., J. Mol. Biol., 222:581-597 (1991); Sidhu et
al., J. Mol. Biol. 338(2):299-310 (2004); Lee et al., J. Mol. Biol.
340(5):1073-1093 (2004); Fellouse, Proc. Nat. Acad. Sci. USA
101(34):12467-12472 (2004); and Lee et al. J. Immunol. Methods
284(1-2):119-132 (2004), and technologies for producing human or
human-like antibodies in animals that have parts or all of the
human immunoglobulin loci or genes encoding human immunoglobulin
sequences (see, e.g., WO 1998/24893; WO 1996/34096; WO 1996/33735;
WO 1991/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA,
90:2551 (1993); Jakobovits et al., Nature, 362:255-258 (1993);
Bruggemann et al., Year in Immuno., 7:33 (1993); U.S. Pat. Nos.
5,545,806; 5,569,825; 5,591,669 (all of GenPharm); 5,545,807; WO
1997/17852; U.S. Pat. Nos. 5,545,807; 5,545,806; 5,569,825;
5,625,126; 5,633,425; and 5,661,016; Marks et al., Bio/Technology,
10: 779-783 (1992); Lonberg et al., Nature, 368: 856-859 (1994);
Morrison, Nature, 368: 812-813 (1994); Fishwild et al., Nature
Biotechnology, 14: 845-851 (1996); Neuberger, Nature Biotechnology,
14: 826 (1996); and Lonberg and Huszar, Intern. Rev. Immunol., 13:
65-93 (1995).
[0103] "Humanized" forms of non-human (e.g., murine) antibodies are
chimeric antibodies that contain minimal sequence derived from
non-human immunoglobulin. For the most part, humanized antibodies
are human immunoglobulins (recipient antibody) in which residues
from a hypervariable region of the recipient are replaced by
residues from a hypervariable region of a non-human species (donor
antibody) such as mouse, rat, rabbit or nonhuman primate having the
desired specificity, affinity, and capacity. In some instances,
framework region (FR) residues of the human immunoglobulin are
replaced by corresponding non-human residues. Furthermore,
humanized antibodies may comprise residues that are not found in
the recipient antibody or in the donor antibody. These
modifications are made to further refine antibody performance. In
general, the humanized antibody will comprise substantially all of
at least one, and typically two, variable domains, in which all or
substantially all of the hypervariable loops 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
antibody optionally will also comprise at least a portion of an
immunoglobulin constant region (Fc), typically that of a human
immunoglobulin. For further details, see Jones et al., Nature
321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988);
and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the
following review articles and references cited therein: Vaswani and
Hamilton, Ann. Allergy, Asthma & Immunol. 1:105-115 (1998);
Harris, Biochem. Soc. Transactions 23:1035-1038 (1995); Hurle and
Gross, Curr. Op. Biotech. 5:428-433 (1994).
[0104] "Chimeric" antibodies (immunoglobulins) have a portion of
the heavy and/or light chain identical with or homologous to
corresponding sequences in antibodies derived from a particular
species or belonging to a particular antibody class or subclass,
while the remainder of the chain(s) is identical with or homologous
to corresponding sequences in antibodies derived from another
species or belonging to another antibody class or subclass, as well
as fragments of such antibodies, so long as they exhibit the
desired biological activity (U.S. Pat. No. 4,816,567; and Morrison
et al., Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)). Humanized
antibody as used herein is a subset of chimeric antibodies.
[0105] An "antigen" is a predetermined antigen to which an antibody
can selectively bind. The target antigen may be polypeptide,
carbohydrate, nucleic acid, lipid, hapten or other naturally
occurring or synthetic compound. Preferably, the target antigen is
a polypeptide.
[0106] The term "hypervariable region", "HVR", or "HV", when used
herein refers to the regions of an antibody variable domain which
are hypervariable in sequence and/or form structurally defined
loops. Generally, antibodies comprise six hypervariable regions;
three in the VH (H1, H2, H3), and three in the VL (L1, L2, L3). A
number of hypervariable region delineations are in use and are
encompassed herein. The Kabat Complementarity Determining Regions
(CDRs) are based on sequence variability and are the most commonly
used (Kabat et al., Sequences of Proteins of Immunological
Interest, 5th Ed. Public Health Service, National Institutes of
Health, Bethesda, Md. (1991)). Chothia refers instead to the
location of the structural loops (Chothia and Lesk J. Mol. Biol.
196:901-917 (1987)). The AbM hypervariable regions represent a
compromise between the Kabat CDRs and Chothia structural loops, and
are used by Oxford Molecular's AbM antibody modeling software. The
"contact" hypervariable regions are based on an analysis of the
available complex crystal structures. The residues from the Kabat,
Chothia and contact hypervariable regions are noted below.
TABLE-US-00005 Loop Kabat Chothia Contact L1 L24-L34 L24-L34
L30-L36 L2 L50-L56 L50-L56 L46-L55 L3 L89-L97 L89-L97 L89-L96 H1
H31-H35B H26-H32 H30-H35B (Kabat Numbering) H2 H50-H65 H52-H56
H47-H58 H3 H95-H102 H95-H102 H93-H101
[0107] Hypervariable regions may comprise "extended hypervariable
regions" as follows: 24-36 or 24-34 (L1), 46-56 or 50-56 (L2) and
89-97 or 89-96 (L3) in the VL and 26-35 (H1), 50-65 or 49-65 (H2)
and 93-102, 94-102 or 95-102 (H3) in the VH. The variable domain
residues are numbered according to Kabat et al., supra for each of
these definitions.
[0108] "Framework" or "FR" residues are those variable domain
residues other than the hypervariable region residues as herein
defined.
[0109] "Single-chain Fv" or "scFv" antibody fragments comprise the
VH and VL domains of antibody, wherein these domains are present in
a single polypeptide chain. Generally, the scFv polypeptide further
comprises a polypeptide linker between the VH and VL domains which
enables the scFv to form the desired structure for antigen binding.
For a review of scFv see Pluckthun, in The Pharmacology of
Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds.,
Springer-Verlag, New York, pp. 269-315 (1994).
[0110] The term "diabodies" refers to small antibody fragments with
two antigen-binding sites, which fragments comprise a heavy-chain
variable domain (VH) connected to a light-chain variable domain
(VL) in the same polypeptide chain (VH-VL). By using a linker that
is too short to allow pairing between the two domains on the same
chain, the domains are forced to pair with the complementary
domains of another chain and create two antigen-binding sites.
Diabodies are described more fully in, for example, EP 404,097; WO
93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA,
90:6444-6448 (1993).
[0111] A "human antibody" is one which possesses an amino acid
sequence which corresponds to that of an antibody produced by a
human and/or has been made using any of the techniques for making
human antibodies as disclosed herein. This definition of a human
antibody specifically excludes a humanized antibody comprising
non-human antigen-binding residues.
[0112] An "affinity matured" antibody is one with one or more
alterations in one or more CDRs thereof which result in an
improvement in the affinity of the antibody for antigen, compared
to a parent antibody which does not possess those alteration(s).
Preferred affinity matured antibodies will have nanomolar or even
picomolar affinities for the target antigen. Affinity matured
antibodies are produced by procedures known in the art. Marks et
al. Bio/Technology 10:779-783 (1992) describes affinity maturation
by VH and VL domain shuffling. Random mutagenesis of CDR and/or
framework residues is described by: Barbas et al. Proc Nat. Acad.
Sci, USA 91:3809-3813 (1994); Schier et al. Gene 169:147-155
(1995); Yelton et al. J. Immunol. 155:1994-2004 (1995); Jackson et
al., J. Immunol. 154(7):3310-9 (1995); and Hawkins et al, J. Mol.
Biol. 226:889-896 (1992).
[0113] Antibody "effector functions" refer to those biological
activities attributable to the Fc region (a native sequence Fc
region or amino acid sequence variant Fc region) of an antibody,
and vary with the antibody isotype. Examples of antibody effector
functions include: C1q binding and complement dependent
cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated
cytotoxicity (ADCC); phagocytosis; down regulation of cell surface
receptors (e.g. B cell receptor); and B cell activation.
[0114] Antibody-dependent cell-mediated cytotoxicity" or "ADCC"
refers to a form of cytotoxicity in which secreted Ig bound onto Fc
receptors (FcRs) present on certain cytotoxic cells (e.g. Natural
Killer (NK) cells, neutrophils, and macrophages) enable these
cytotoxic effector cells to bind specifically to an antigen-bearing
target cell and subsequently kill the target cell with cytotoxins.
The antibodies "arm" the cytotoxic cells and are absolutely
required for such killing. The primary cells for mediating ADCC, NK
cells, express Fc.gamma.RIII only, whereas monocytes express
Fc.gamma.RI, Fc.gamma.RII and Fc.gamma.RIII. FcR expression on
hematopoietic cells is summarized in Table 3 on page 464 of Ravetch
and Kinet, Annu. Rev. Immunol 9:457-92 (1991). To assess ADCC
activity of a molecule of interest, an in vitro ADCC assay, such as
that described in U.S. Pat. No. 5,500,362 or 5,821,337 or Presta
U.S. Pat. No. 6,737,056 may be performed. Useful effector cells for
such assays include peripheral blood mononuclear cells (PBMC) and
Natural Killer (NK) cells. Alternatively, or additionally, ADCC
activity of the molecule of interest may be assessed in vivo, e.g.,
in a animal model such as that disclosed in Clynes et al. PNAS
(USA) 95:652-656 (1998).
[0115] "Human effector cells" are leukocytes which express one or
more FcRs and perform effector functions. Preferably, the cells
express at least Fc.gamma.RIII and perform ADCC effector function.
Examples of human leukocytes which mediate ADCC include peripheral
blood mononuclear cells (PBMC), natural killer (NK) cells,
monocytes, cytotoxic T cells and neutrophils; with PBMCs and NK
cells being preferred. The effector cells may be isolated from a
native source, e.g. from blood.
[0116] "Fc receptor" or "FcR" describes a receptor that binds to
the Fc region of an antibody. The preferred FcR is a native
sequence human FcR. Moreover, a preferred FcR is one which binds an
IgG antibody (a gamma receptor) and includes receptors of the
Fc.gamma.RI, Fc.gamma.RII, and Fc.gamma.RIII subclasses, including
allelic variants and alternatively spliced forms of these
receptors. Fc.gamma.RII receptors include Fc.gamma.RIIA (an
"activating receptor") and Fc.gamma.RIIB (an "inhibiting
receptor"), which have similar amino acid sequences that differ
primarily in the cytoplasmic domains thereof. Activating receptor
Fc.gamma.RIIA contains an immunoreceptor tyrosine-based activation
motif (ITAM) in its cytoplasmic domain Inhibiting receptor
Fc.gamma.RIIB contains an immunoreceptor tyrosine-based inhibition
motif (ITIM) in its cytoplasmic domain. (see review M. in Daeron,
Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in
Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991); Capel et
al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab.
Clin. Med. 126:330-41 (1995). Other FcRs, including those to be
identified in the future, are encompassed by the term "FcR" herein.
The term also includes the neonatal receptor, FcRn, which is
responsible for the transfer of maternal IgGs to the fetus (Guyer
et al., J. Immunol. 117:587 (1976) and Kim et al., J. Immunol.
24:249 (1994)) and regulates homeostasis of immunoglobulins.
WO00/42072 (Presta) describes antibody variants with improved or
diminished binding to FcRs. The content of that patent publication
is specifically incorporated herein by reference. See, also,
Shields et al. J. Biol. Chem. 9(2): 6591-6604 (2001).
[0117] Methods of measuring binding to FcRn are known (see, e.g.,
Ghetie 1997, Hinton 2004). Binding to human FcRn in vivo and serum
half life of human FcRn high affinity binding polypeptides can be
assayed, e.g., in transgenic mice or transfected human cell lines
expressing human FcRn, or in primates administered with the Fc
variant polypeptides.
[0118] "Complement dependent cytotoxicity" or "CDC" refers to the
lysis of a target cell in the presence of complement. Activation of
the classical complement pathway is initiated by the binding of the
first component of the complement system (C1q) to antibodies (of
the appropriate subclass) which are bound to their cognate antigen.
To assess complement activation, a CDC assay, e.g. as described in
Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), may be
performed.
[0119] Polypeptide variants with altered Fc region amino acid
sequences and increased or decreased C1q binding capability are
described in U.S. Pat. No. 6,194,551B1 and WO99/51642. The contents
of those patent publications are specifically incorporated herein
by reference. See, also, Idusogie et al. J. Immunol. 164: 4178-4184
(2000).
[0120] A "disorder" or "disease" is any condition that would
benefit from treatment with a substance/molecule or method of the
invention. This includes chronic and acute disorders or diseases
including those pathological conditions which predispose the mammal
to the disorder in question. Non-limiting examples of disorders to
be treated herein include malignant and benign tumors; carcinoma,
blastoma, and sarcoma.
[0121] The terms "cell proliferative disorder" and "proliferative
disorder" refer to disorders that are associated with some degree
of abnormal cell proliferation. In one embodiment, the cell
proliferative disorder is cancer.
[0122] "Tumor", as used herein, refers to all neoplastic cell
growth and proliferation, whether malignant or benign, and all
pre-cancerous and cancerous cells and tissues. The terms "cancer",
"cancerous", "cell proliferative disorder", "proliferative
disorder" and "tumor" are not mutually exclusive as referred to
herein.
[0123] The terms "cancer" and "cancerous" refer to or describe the
physiological condition in mammals that is typically characterized
by unregulated cell growth/proliferation. Examples of cancer
include but are not limited to, carcinoma, lymphoma, blastoma,
sarcoma, and leukemia. More particular examples of such cancers
include squamous cell cancer, small-cell lung cancer, non-small
cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of
the lung, cancer of the peritoneum, hepatocellular cancer,
gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical
cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma,
breast cancer, colon cancer, colorectal cancer, endometrial or
uterine carcinoma, salivary gland carcinoma, kidney cancer, liver
cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic
carcinoma, gastric cancer, melanoma, and various types of head and
neck cancer. Dysregulation of angiogenesis can lead to many
disorders that can be treated by compositions and methods of the
invention. These disorders include both non-neoplastic and
neoplastic conditions. Neoplastics include but are not limited
those described above. Non-neoplastic disorders include but are not
limited to undesired or aberrant hypertrophy, arthritis, rheumatoid
arthritis (RA), psoriasis, psoriatic plaques, sarcoidosis,
atherosclerosis, atherosclerotic plaques, diabetic and other
proliferative retinopathies including retinopathy of prematurity,
retrolental fibroplasia, neovascular glaucoma, age-related macular
degeneration, diabetic macular edema, corneal neovascularization,
corneal graft neovascularization, corneal graft rejection,
retinal/choroidal neovascularization, neovascularization of the
angle (rubeosis), ocular neovascular disease, vascular restenosis,
arteriovenous malformations (AVM), meningioma, hemangioma,
angiofibroma, thyroid hyperplasias (including Grave's disease),
corneal and other tissue transplantation, chronic inflammation,
lung inflammation, acute lung injury/ARDS, sepsis, primary
pulmonary hypertension, malignant pulmonary effusions, cerebral
edema (e.g., associated with acute stroke/closed head
injury/trauma), synovial inflammation, pannus formation in RA,
myositis ossificans, hypertropic bone formation, osteoarthritis
(OA), refractory ascites, polycystic ovarian disease,
endometriosis, 3rd spacing of fluid diseases (pancreatitis,
compartment syndrome, burns, bowel disease), uterine fibroids,
premature labor, chronic inflammation such as IBD (Crohn's disease
and ulcerative colitis), renal allograft rejection, inflammatory
bowel disease, nephrotic syndrome, undesired or aberrant tissue
mass growth (non-cancer), hemophilic joints, hypertrophic scars,
inhibition of hair growth, Osler-Weber syndrome, pyogenic granuloma
retrolental fibroplasias, scleroderma, trachoma, vascular
adhesions, synovitis, dermatitis, preeclampsia, ascites,
pericardial effusion (such as that associated with pericarditis),
and pleural effusion.
[0124] The terms "neurodegenerative disease" and "neurodegenerative
disorder" are used in the broadest sense to include all disorders
the pathology of which involves neuronal degeneration and/or
dysfunction, including, without limitation, peripheral
neuropathies; motorneuron disorders, such as amylotrophic lateral
sclerosis (ALS, Lou Gehrig's disease), Bell's palsy, and various
conditions involving spinal muscular atrophy or paralysis; and
other human neurodegenerative diseases, such as Alzheimer's
disease, Parkinson's disease, epilepsy, multiple sclerosis,
Huntington's chorea, Down's Syndrome, nerve deafness, and Meniere's
disease.
[0125] "Peripheral neuropathy" is a neurodegenerative disorder that
affects the peripheral nerves, most often manifested as one or a
combination of motor, sensory, sensorimotor, or autonomic
dysfunction. Peripheral neuropathies may, for example, be
genetically acquired, can result from a systemic disease, or can be
induced by a toxic agent, such as a neurotoxic drug, e.g.
antineoplastic agent, or industrial or environmental pollutant.
"Peripheral sensory neuropathy" is characterized by the
degeneration of peripheral sensory neurons, which may be
idiopathic, may occur, for example, as a consequence of diabetes
(diabetic neuropathy), cytostatic drug therapy in cancer (e.g.
treatment with chemotherapeutic agents such as vincristine,
cisplatin, methotrexate, 3'-azido-3'-deoxythymidine, or taxanes,
e.g. paclitaxel [TAXOL.RTM., Bristol-Myers Squibb Oncology,
Princeton, N.J.] and doxetaxel [TAXOTERE.RTM., Rhone-Poulenc Rorer,
Antony, France]), alcoholism, acquired immunodeficiency syndrom
(AIDS), or genetic predisposition. Genetically acquired peripheral
neuropathies include, for example, Refsum's disease, Krabbe's
disease, Metachromatic leukodystrophy, Fabry's disease,
Dejerine-Sottas syndrome, Abetalipoproteinemia, and
Charcot-Marie-Tooth (CMT) Disease (also known as Proneal Muscular
Atrophy or Hereditary Motor Sensory Neuropathy (HMSN)). Most types
of peripheral neuropathy develop slowly, over the course of several
months or years. In clinical practice such neuropathies are called
chronic. Sometimes a peripheral neuropathy develops rapidly, over
the course of a few days, and is referred to as acute. Peripheral
neuropathy usually affects sensory and motor nerves together so as
to cause a mixed sensory and motor neuropathy, but pure sensory and
pure motor neuropathy are also known.
[0126] As used herein, "treatment" refers to clinical intervention
in an attempt to alter the natural course of the individual or cell
being treated, and can be performed either for prophylaxis or
during the course of clinical pathology. Desirable effects of
treatment include preventing occurrence or recurrence of disease,
alleviation of symptoms, diminishment of any direct or indirect
pathological consequences of the disease, preventing metastasis,
decreasing the rate of disease progression, amelioration or
palliation of the disease state, and remission or improved
prognosis. In some embodiments, antibodies of the invention are
used to delay development of a disease or disorder.
[0127] An "individual" is a vertebrate, preferably a mammal, more
preferably a human. Mammals include, but are not limited to, farm
animals (such as cows), sport animals, pets (such as cats, dogs and
horses), primates, mice and rats.
[0128] "Mammal" for purposes of treatment refers to any animal
classified as a mammal, including humans, domestic and farm
animals, and zoo, sports, or pet animals, such as dogs, horses,
cats, cows, etc. Preferably, the mammal is human.
[0129] An "effective amount" refers to an amount effective, at
dosages and for periods of time necessary, to achieve the desired
therapeutic or prophylactic result.
[0130] A "therapeutically effective amount" of a substance/molecule
of the invention, agonist or antagonist may vary according to
factors such as the disease state, age, sex, and weight of the
individual, and the ability of the substance/molecule, agonist or
antagonist to elicit a desired response in the individual. A
therapeutically effective amount is also one in which any toxic or
detrimental effects of the substance/molecule, agonist or
antagonist are outweighed by the therapeutically beneficial
effects. A "prophylactically effective amount" refers to an amount
effective, at dosages and for periods of time necessary, to achieve
the desired prophylactic result. Typically but not necessarily,
since a prophylactic dose is used in subjects prior to or at an
earlier stage of disease, the prophylactically effective amount
will be less than the therapeutically effective amount.
[0131] The term "cytotoxic agent" as used herein refers to a
substance that inhibits or prevents the function of cells and/or
causes destruction of cells. The term is intended to include
radioactive isotopes (e.g., At.sup.211, I.sup.131, I.sup.125,
Y.sup.90, Re.sup.186, Re.sup.188, Sm.sup.153, Bi.sup.212, P.sup.32
and radioactive isotopes of Lu), chemotherapeutic agents e.g.
methotrexate, adriamicin, vinca alkaloids (vincristine,
vinblastine, etoposide), doxorubicin, melphalan, mitomycin C,
chlorambucil, daunorubicin or other intercalating agents, enzymes
and fragments thereof such as nucleolytic enzymes, antibiotics, and
toxins such as small molecule toxins or enzymatically active toxins
of bacterial, fungal, plant or animal origin, including fragments
and/or variants thereof, and the various antitumor or anticancer
agents disclosed below. Other cytotoxic agents are described below.
A tumoricidal agent causes destruction of tumor cells.
[0132] A "chemotherapeutic agent" is a chemical compound useful in
the treatment of cancer. Examples of chemotherapeutic agents
include alkylating agents such as thiotepa and CYTOXAN.RTM.
cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan
and piposulfan; aziridines such as benzodopa, carboquone,
meturedopa, and uredopa; ethylenimines and methylamelamines
including altretamine, triethylenemelamine,
trietylenephosphoramide, triethiylenethiophosphoramide and
trimethylolomelamine; acetogenins (especially bullatacin and
bullatacinone); delta-9-tetrahydrocannabinol (dronabinol,
MARINOL.RTM.); beta-lapachone; lapachol; colchicines; betulinic
acid; a camptothecin (including the synthetic analogue topotecan
(HYCAMTIN.RTM.), CPT-11 (irinotecan, CAMPTOSAR.RTM.),
acetylcamptothecin, scopolectin, and 9-aminocamptothecin);
bryostatin; callystatin; CC-1065 (including its adozelesin,
carzelesin and bizelesin synthetic analogues); podophyllotoxin;
podophyllinic acid; teniposide; cryptophycins (particularly
cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin
(including the synthetic analogues, KW-2189 and CB1-TM1);
eleutherobin; pancratistatin; a sarcodictyin; spongistatin;
nitrogen mustards such as chlorambucil, chlornaphazine,
cholophosphamide, estramustine, ifosfamide, mechlorethamine,
mechlorethamine oxide hydrochloride, melphalan, novembichin,
phenesterine, prednimustine, trofosfamide, uracil mustard;
nitrosureas such as carmustine, chlorozotocin, fotemustine,
lomustine, nimustine, and ranimnustine; antibiotics such as the
enediyne antibiotics (e.g., calicheamicin, especially calicheamicin
gamma1nd calicheamicin omegaI1 (see, e.g., Agnew, Chem. Intl. Ed.
Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; an
esperamicin; as well as neocarzinostatin chromophore and related
chromoprotein enediyne antiobiotic chromophores), aclacinomysins,
actinomycin, authramycin, azaserine, bleomycins, cactinomycin,
carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin,
daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine,
ADRIAMYCIN.RTM. doxorubicin (including morpholino-doxorubicin,
cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and
deoxydoxorubicin), epirubicin, esorubicin, idarubicin,
marcellomycin, mitomycins such as mitomycin C, mycophenolic acid,
nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin,
quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin,
ubenimex, zinostatin, zorubicin; anti-metabolites such as
methotrexate and 5-fluorouracil (5-FU); folic acid analogues such
as denopterin, methotrexate, pteropterin, trimetrexate; purine
analogs such as fludarabine, 6-mercaptopurine, thiamiprine,
thioguanine; pyrimidine analogs such as ancitabine, azacitidine,
6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine,
enocitabine, floxuridine; androgens such as calusterone,
dromostanolone propionate, epitiostanol, mepitiostane,
testolactone; anti-adrenals such as aminoglutethimide, mitotane,
trilostane; folic acid replenisher such as frolinic acid;
aceglatone; aldophosphamide glycoside; aminolevulinic acid;
eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate;
defofamine; demecolcine; diaziquone; elformithine; elliptinium
acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea;
lentinan; lonidainine; maytansinoids such as maytansine and
ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine;
pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide;
procarbazine; PSK.RTM. polysaccharide complex (JHS Natural
Products, Eugene, Oreg.); razoxane; rhizoxin; sizofuran;
spirogermanium; tenuazonic acid; triaziquone;
2,2',2''-trichlorotriethylamine; trichothecenes (especially T-2
toxin, verracurin A, roridin A and anguidine); urethan; vindesine
(ELDISINE.RTM., FILDESIN.RTM.); dacarbazine; mannomustine;
mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside
("Ara-C"); thiotepa; taxoids, e.g., TAXOL.RTM. paclitaxel
(Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE.TM.
Cremophor-free, albumin-engineered nanoparticle formulation of
paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.),
and TAXOTERE.RTM. doxetaxel (Rhone-Poulenc Rorer, Antony, France);
chloranbucil; gemcitabine (GEMZAR.RTM.); 6-thioguanine;
mercaptopurine; methotrexate; platinum analogs such as cisplatin
and carboplatin; vinblastine (VELBAN.RTM.); platinum; etoposide
(VP-16); ifosfamide; mitoxantrone; vincristine (ONCOVIN.RTM.);
oxaliplatin; leucovovin; vinorelbine (NAVELBINE.RTM.); novantrone;
edatrexate; daunomycin; aminopterin; ibandronate; topoisomerase
inhibitor RFS 2000; difluoromefihylornithine (DMFO); retinoids such
as retinoic acid; capecitabine (XELODA.RTM.); pharmaceutically
acceptable salts, acids or derivatives of any of the above; as well
as combinations of two or more of the above such as CHOP, an
abbreviation for a combined therapy of cyclophosphamide,
doxorubicin, vincristine, and prednisolone, and FOLFOX, an
abbreviation for a treatment regimen with oxaliplatin
(ELOXATIN.TM.) combined with 5-FU and leucovovin.
[0133] Also included in this definition are anti-hormonal agents
that act to regulate, reduce, block, or inhibit the effects of
hormones that can promote the growth of cancer, and are often in
the form of systemic, or whole-body treatment. They may be hormones
themselves. Examples include anti-estrogens and selective estrogen
receptor modulators (SERMs), including, for example, tamoxifen
(including NOLVADEX.RTM. tamoxifen), EVISTA.RTM. raloxifene,
droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LY 117018,
onapristone, and FARESTON.RTM. toremifene; anti-progesterones;
estrogen receptor down-regulators (ERDs); agents that function to
suppress or shut down the ovaries, for example, leutinizing
hormone-releasing hormone (LHRH) agonists such as LUPRON.RTM. and
ELIGARD.RTM. leuprolide acetate, goserelin acetate, buserelin
acetate and tripterelin; other anti-androgens such as flutamide,
nilutamide and bicalutamide; and aromatase inhibitors that inhibit
the enzyme aromatase, which regulates estrogen production in the
adrenal glands, such as, for example, 4(5)-imidazoles,
aminoglutethimide, MEGASE.RTM. megestrol acetate, AROMASIN.RTM.
exemestane, formestanie, fadrozole, RIVISOR.RTM. vorozole,
FEMARA.RTM. letrozole, and ARIMIDEX.RTM. anastrozole. In addition,
such definition of chemotherapeutic agents includes bisphosphonates
such as clodronate (for example, BONEFOS.RTM. or OSTAC.RTM.),
DIDROCAL.RTM. etidronate, NE-58095, ZOMETA.RTM. zoledronic
acid/zoledronate, FOSAMAX.RTM. alendronate, AREDIA.RTM.
pamidronate, SKELID.RTM. tiludronate, or ACTONEL.RTM. risedronate;
as well as troxacitabine (a 1,3-dioxolane nucleoside cytosine
analog); antisense oligonucleotides, particularly those that
inhibit expression of genes in signaling pathways implicated in
abherant cell proliferation, such as, for example, PKC-alpha, Raf,
H-Ras, and epidermal growth factor receptor (EGF-R); vaccines such
as THERATOPE.RTM. vaccine and gene therapy vaccines, for example,
ALLOVECTIN.RTM. vaccine, LEUVECTIN.RTM. vaccine, and VAXID.RTM.
vaccine; LURTOTECAN.RTM. topoisomerase 1 inhibitor; ABARELIX.RTM.
rmRH; lapatinib ditosylate (an ErbB-2 and EGFR dual tyrosine kinase
small-molecule inhibitor also known as GW572016); and
pharmaceutically acceptable salts, acids or derivatives of any of
the above.
[0134] A "growth inhibitory agent" when used herein refers to a
compound or composition which inhibits growth of a cell (such as a
cell expressing EphB2) either in vitro or in vivo. Thus, the growth
inhibitory agent may be one which significantly reduces the
percentage of cells (such as a cell expressing EphB2) in S phase.
Examples of growth inhibitory agents include agents that block cell
cycle progression (at a place other than S phase), such as agents
that induce G1 arrest and M-phase arrest. Classical M-phase
blockers include the vincas (vincristine and vinblastine), taxanes,
and topoisomerase II inhibitors such as doxorubicin, epirubicin,
daunorubicin, etoposide, and bleomycin. Those agents that arrest G1
also spill over into S-phase arrest, for example, DNA alkylating
agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine,
cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further
information can be found in The Molecular Basis of Cancer,
Mendelsohn and Israel, eds., Chapter 1, entitled "Cell cycle
regulation, oncogenes, and antineoplastic drugs" by Murakami et al.
(WB Saunders: Philadelphia, 1995), especially p. 13. The taxanes
(paclitaxel and docetaxel) are anticancer drugs both derived from
the yew tree. Docetaxel (TAXOTERE.RTM., Rhone-Poulenc Rorer),
derived from the European yew, is a semisynthetic analogue of
paclitaxel (TAXOL.RTM., Bristol-Myers Squibb). Paclitaxel and
docetaxel promote the assembly of microtubules from tubulin dimers
and stabilize microtubules by preventing depolymerization, which
results in the inhibition of mitosis in cells.
[0135] "Doxorubicin" is an anthracycline antibiotic. The full
chemical name of doxorubicin is
(8S-cis)-10-[(3-amino-2,3,6-trideoxy-.alpha.-L-lyxo-hexapyranosyl)oxy]-7,-
8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-napht-
hacenedione.
Compositions of the Invention and Methods of Making Same
[0136] This invention encompasses compositions, including
pharmaceutical compositions, comprising an anti-EphB2 antibody; and
polynucleotides comprising sequences encoding an anti-EphB2
antibody. As used herein, compositions comprise one or more
antibodies that bind to EphB2, and/or one or more polynucleotides
comprising sequences encoding one or more antibodies that bind to
EphB2. These compositions may further comprise suitable carriers,
such as pharmaceutically acceptable excipients including buffers,
which are well known in the art.
[0137] The invention also encompasses isolated antibody and
polynucleotide embodiments. The invention also encompasses
substantially pure antibody and polynucleotide embodiments.
[0138] The anti-EphB2 antibodies of the invention are preferably
monoclonal. Also encompassed within the scope of the invention are
Fab, Fab', Fab'-SH and F(ab').sub.2 fragments of the anti-EphB2
antibodies provided herein. These antibody fragments can be created
by traditional means, such as enzymatic digestion, or may be
generated by recombinant techniques. Such antibody fragments may be
chimeric or humanized. These fragments are useful for the
diagnostic and therapeutic purposes set forth below.
[0139] Monoclonal antibodies are obtained from a population of
substantially homogeneous antibodies, i.e., the individual
antibodies comprising the population are identical except for
possible naturally occurring mutations that may be present in minor
amounts. Thus, the modifier "monoclonal" indicates the character of
the antibody as not being a mixture of discrete antibodies.
[0140] The anti-EphB2 monoclonal antibodies of the invention can be
made using the hybridoma method first described by Kohler et al.,
Nature, 256:495 (1975), or may be made by recombinant DNA methods
(e.g., U.S. Pat. No. 4,816,567).
[0141] In the hybridoma method, a mouse or other appropriate host
animal, such as a hamster, is immunized to elicit lymphocytes that
produce or are capable of producing antibodies that will
specifically bind to the protein used for immunization. Antibodies
to EphB2 generally are raised in animals by multiple subcutaneous
(sc) or intraperitoneal (ip) injections of EphB2 and an adjuvant.
EphB2 may be prepared using methods well-known in the art, some of
which are further described herein. For example, recombinant
production of EphB2 is described below. In one embodiment, animals
are immunized with a derivative of EphB2 that contains the
extracellular domain (ECD) of EphB2 fused to the Fc portion of an
immunoglobulin heavy chain. In a preferred embodiment, animals are
immunized with an EphB2-IgG1 fusion protein. Animals ordinarily are
immunized against immunogenic conjugates or derivatives of EphB2
with monophosphoryl lipid A (MPL)/trehalose dicrynomycolate (TDM)
(Ribi Immunochem. Research, Inc., Hamilton, Mont.) and the solution
is injected intradermally at multiple sites. Two weeks later the
animals are boosted. 7 to 14 days later animals are bled and the
serum is assayed for anti-EphB2 titer. Animals are boosted until
titer plateaus.
[0142] Alternatively, lymphocytes may be immunized in vitro.
Lymphocytes then are fused with myeloma cells using a suitable
fusing agent, such as polyethylene glycol, to form a hybridoma cell
(Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103
(Academic Press, 1986)).
[0143] The hybridoma cells thus prepared are seeded and grown in a
suitable culture medium that preferably contains one or more
substances that inhibit the growth or survival of the unfused,
parental myeloma cells. For example, if the parental myeloma cells
lack the enzyme hypoxanthine guanine phosphoribosyl transferase
(HGPRT or HPRT), the culture medium for the hybridomas typically
will include hypoxanthine, aminopterin, and thymidine (HAT medium),
which substances prevent the growth of HGPRT-deficient cells.
[0144] Preferred myeloma cells are those that fuse efficiently,
support stable high-level production of antibody by the selected
antibody-producing cells, and are sensitive to a medium such as HAT
medium. Among these, preferred myeloma cell lines are murine
myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse
tumors available from the Salk Institute Cell Distribution Center,
San Diego, Calif. USA, and SP-2 or X63-Ag8-653 cells available from
the American Type Culture Collection, Rockville, Md. USA. Human
myeloma and mouse-human heteromyeloma cell lines also have been
described for the production of human monoclonal antibodies
(Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal
Antibody Production Techniques and Applications, pp. 51-63 (Marcel
Dekker, Inc., New York, 1987)).
[0145] Culture medium in which hybridoma cells are growing is
assayed for production of monoclonal antibodies directed against
EphB2. Preferably, the binding specificity of monoclonal antibodies
produced by hybridoma cells is determined by immunoprecipitation or
by an in vitro binding assay, such as radioimmunoassay (RIA) or
enzyme-linked immunoadsorbent assay (ELISA).
[0146] The binding affinity of the monoclonal antibody can, for
example, be determined by the Scatchard analysis of Munson et al.,
Anal. Biochem., 107:220 (1980).
[0147] After hybridoma cells are identified that produce antibodies
of the desired specificity, affinity, and/or activity, the clones
may be subcloned by limiting dilution procedures and grown by
standard methods (Goding, Monoclonal Antibodies: Principles and
Practice, pp. 59-103 (Academic Press, 1986)). Suitable culture
media for this purpose include, for example, D-MEM or RPMI-1640
medium. In addition, the hybridoma cells may be grown in vivo as
ascites tumors in an animal.
[0148] The monoclonal antibodies secreted by the subclones are
suitably separated from the culture medium, ascites fluid, or serum
by conventional immunoglobulin purification procedures such as, for
example, protein A-Sepharose, hydroxylapatite chromatography, gel
electrophoresis, dialysis, or affinity chromatography.
[0149] The anti-EphB2 antibodies of the invention can be made by
using combinatorial libraries to screen for synthetic antibody
clones with the desired activity or activities. In principle,
synthetic antibody clones are selected by screening phage libraries
containing phage that display various fragments of antibody
variable region (Fv) fused to phage coat protein. Such phage
libraries are panned by affinity chromatography against the desired
antigen. Clones expressing Fv fragments capable of binding to the
desired antigen are adsorbed to the antigen and thus separated from
the non-binding clones in the library. The binding clones are then
eluted from the antigen, and can be further enriched by additional
cycles of antigen adsorption/elution. Any of the anti-EphB2
antibodies of the invention can be obtained by designing a suitable
antigen screening procedure to select for the phage clone of
interest followed by construction of a full length anti-EphB2
antibody clone using the Fv sequences from the phage clone of
interest and suitable constant region (Fc) sequences described in
Kabat et al., Sequences of Proteins of Immunological Interest,
Fifth Edition, NIH Publication 91-3242, Bethesda Md. (1991), vols.
1-3.
[0150] The antigen-binding domain of an antibody is formed from two
variable (V) regions of about 110 amino acids, one each from the
light (VL) and heavy (VH) chains, that both present three
hypervariable loops or complementarity-determining regions (CDRs).
Variable domains can be displayed functionally on phage, either as
single-chain Fv (scFv) fragments, in which VH and VL are covalently
linked through a short, flexible peptide, or as Fab fragments, in
which they are each fused to a constant domain and interact
non-covalently, as described in Winter et al., Ann. Rev. Immunol.,
12: 433-455 (1994). As used herein, scFv encoding phage clones and
Fab encoding phage clones are collectively referred to as "Fv phage
clones" or "Fv clones".
[0151] Repertoires of VH and VL genes can be separately cloned by
polymerase chain reaction (PCR) and recombined randomly in phage
libraries, which can then be searched for antigen-binding clones as
described in Winter et al., Ann. Rev. Immunol., 12: 433-455 (1994).
Libraries from immunized sources provide high-affinity antibodies
to the immunogen without the requirement of constructing
hybridomas. Alternatively, the naive repertoire can be cloned to
provide a single source of human antibodies to a wide range of
non-self and also self antigens without any immunization as
described by Griffiths et al., EMBO J, 12: 725-734 (1993). Finally,
naive libraries can also be made synthetically by cloning the
unrearranged V-gene segments from stem cells, and using PCR primers
containing random sequence to encode the highly variable CDR3
regions and to accomplish rearrangement in vitro as described by
Hoogenboom and Winter, J. Mol. Biol., 227: 381-388 (1992).
[0152] Filamentous phage is used to display antibody fragments by
fusion to the minor coat protein pIII. The antibody fragments can
be displayed as single chain Fv fragments, in which VH and VL
domains are connected on the same polypeptide chain by a flexible
polypeptide spacer, e.g. as described by Marks et al., J. Mol.
Biol., 222: 581-597 (1991), or as Fab fragments, in which one chain
is fused to pIII and the other is secreted into the bacterial host
cell periplasm where assembly of a Fab-coat protein structure which
becomes displayed on the phage surface by displacing some of the
wild type coat proteins, e.g. as described in Hoogenboom et al.,
Nucl. Acids Res., 19: 4133-4137 (1991).
[0153] In general, nucleic acids encoding antibody gene fragments
are obtained from immune cells harvested from humans or animals. If
a library biased in favor of anti-EphB2 clones is desired, the
subject is immunized with EphB2 to generate an antibody response,
and spleen cells and/or circulating B cells other peripheral blood
lymphocytes (PBLs) are recovered for library construction. In a
preferred embodiment, a human antibody gene fragment library biased
in favor of anti-human EphB2 clones is obtained by generating an
anti-human EphB2 antibody response in transgenic mice carrying a
functional human immunoglobulin gene array (and lacking a
functional endogenous antibody production system) such that EphB2
immunization gives rise to B cells producing human antibodies
against EphB2. The generation of human antibody-producing
transgenic mice is described below.
[0154] Additional enrichment for anti-EphB2 reactive cell
populations can be obtained by using a suitable screening procedure
to isolate B cells expressing EphB2-specific membrane bound
antibody, e.g., by cell separation with EphB2 affinity
chromatography or adsorption of cells to fluorochrome-labeled EphB2
followed by flow-activated cell sorting (FACS).
[0155] Alternatively, the use of spleen cells and/or B cells or
other PBLs from an unimmunized donor provides a better
representation of the possible antibody repertoire, and also
permits the construction of an antibody library using any animal
(human or non-human) species in which EphB2 is not antigenic. For
libraries incorporating in vitro antibody gene construction, stem
cells are harvested from the subject to provide nucleic acids
encoding unrearranged antibody gene segments. The immune cells of
interest can be obtained from a variety of animal species, such as
human, mouse, rat, lagomorpha, luprine, canine, feline, porcine,
bovine, equine, and avian species, etc.
[0156] Nucleic acid encoding antibody variable gene segments
(including VH and VL segments) are recovered from the cells of
interest and amplified. In the case of rearranged VH and VL gene
libraries, the desired DNA can be obtained by isolating genomic DNA
or mRNA from lymphocytes followed by polymerase chain reaction
(PCR) with primers matching the 5' and 3' ends of rearranged VH and
VL genes as described in Orlandi et al., Proc. Natl. Acad. Sci.
(USA), 86: 3833-3837 (1989), thereby making diverse V gene
repertoires for expression. The V genes can be amplified from cDNA
and genomic DNA, with back primers at the 5' end of the exon
encoding the mature V-domain and forward primers based within the
J-segment as described in Orlandi et al. (1989) and in Ward et al.,
Nature, 341: 544-546 (1989). However, for amplifying from cDNA,
back primers can also be based in the leader exon as described in
Jones et al., Biotechnol., 9: 88-89 (1991), and forward primers
within the constant region as described in Sastry et al., Proc.
Natl. Acad. Sci. (USA), 86: 5728-5732 (1989). To maximize
complementarity, degeneracy can be incorporated in the primers as
described in Orlandi et al. (1989) or Sastry et al. (1989).
Preferably, the library diversity is maximized by using PCR primers
targeted to each V-gene family in order to amplify all available VH
and VL arrangements present in the immune cell nucleic acid sample,
e.g. as described in the method of Marks et al., J. Mol. Biol.,
222: 581-597 (1991) or as described in the method of Orum et al.,
Nucleic Acids Res., 21: 4491-4498 (1993). For cloning of the
amplified DNA into expression vectors, rare restriction sites can
be introduced within the PCR primer as a tag at one end as
described in Orlandi et al. (1989), or by further PCR amplification
with a tagged primer as described in Clackson et al., Nature, 352:
624-628 (1991).
[0157] Repertoires of synthetically rearranged V genes can be
derived in vitro from V gene segments. Most of the human VH-gene
segments have been cloned and sequenced (reported in Tomlinson et
al., J. Mol. Biol., 227: 776-798 (1992)), and mapped (reported in
Matsuda et al., Nature Genet., 3: 88-94 (1993); these cloned
segments (including all the major conformations of the H1 and H2
loop) can be used to generate diverse VH gene repertoires with PCR
primers encoding H3 loops of diverse sequence and length as
described in Hoogenboom and Winter, J. Mol. Biol., 227: 381-388
(1992). VH repertoires can also be made with all the sequence
diversity focused in a long H3 loop of a single length as described
in Barbas et al., Proc. Natl. Acad. Sci. USA, 89: 4457-4461 (1992).
Human V.kappa. and V.lamda. segments have been cloned and sequenced
(reported in Williams and Winter, Eur. J. Immunol., 23: 1456-1461
(1993)) and can be used to make synthetic light chain repertoires.
Synthetic V gene repertoires, based on a range of VH and VL folds,
and L3 and H3 lengths, will encode antibodies of considerable
structural diversity. Following amplification of V-gene encoding
DNAs, germline V-gene segments can be rearranged in vitro according
to the methods of Hoogenboom and Winter, J. Mol. Biol., 227:
381-388 (1992).
[0158] Repertoires of antibody fragments can be constructed by
combining VH and VL gene repertoires together in several ways. Each
repertoire can be created in different vectors, and the vectors
recombined in vitro, e.g., as described in Hogrefe et al., Gene,
128: 119-126 (1993), or in vivo by combinatorial infection, e.g.,
the loxP system described in Waterhouse et al., Nucl. Acids Res.,
21: 2265-2266 (1993). The in vivo recombination approach exploits
the two-chain nature of Fab fragments to overcome the limit on
library size imposed by E. coli transformation efficiency. Naive VH
and VL repertoires are cloned separately, one into a phagemid and
the other into a phage vector. The two libraries are then combined
by phage infection of phagemid-containing bacteria so that each
cell contains a different combination and the library size is
limited only by the number of cells present (about 10.sup.12
clones). Both vectors contain in vivo recombination signals so that
the VH and VL genes are recombined onto a single replicon and are
co-packaged into phage virions. These huge libraries provide large
numbers of diverse antibodies of good affinity (e.g.,
K.sub.d.sup.-1 of about 10.sup.-8 M).
[0159] Alternatively, the repertoires may be cloned sequentially
into the same vector, e.g. as described in Barbas et al., Proc.
Natl. Acad. Sci. USA, 88: 7978-7982 (1991), or assembled together
by PCR and then cloned, e.g. as described in Clackson et al.,
Nature, 352: 624-628 (1991). PCR assembly can also be used to join
VH and VL DNAs with DNA encoding a flexible peptide spacer to form
single chain Fv (scFv) repertoires. In yet another technique, "in
cell PCR assembly" is used to combine VH and VL genes within
lymphocytes by PCR and then clone repertoires of linked genes as
described in Embleton et al., Nucl. Acids Res., 20: 3831-3837
(1992).
[0160] The antibodies produced by naive libraries (either natural
or synthetic) can be of moderate affinity (K.sub.d.sup.-1 of about
10.sup.6 to 10.sup.7 M.sup.-1), but affinity maturation can also be
mimicked in vitro by constructing and reselecting from secondary
libraries as described in Winter et al. (1994), supra. For example,
mutation can be introduced at random in vitro by using error-prone
polymerase (reported in Leung et al., Technique, 1: 11-15 (1989))
in the method of Hawkins et al., J. Mol. Biol., 226: 889-896 (1992)
or in the method of Gram et al., Proc. Natl. Acad. Sci. USA, 89:
3576-3580 (1992). Additionally, affinity maturation can be
performed by randomly mutating one or more CDRs, e.g. using PCR
with primers carrying random sequence spanning the CDR of interest,
in selected individual Fv clones and screening for higher affinity
clones. WO 9607754 (published 14 Mar. 1996) described a method for
inducing mutagenesis in a complementarity determining region of an
immunoglobulin light chain to create a library of light chain
genes. Another effective approach is to recombine the VH or VL
domains selected by phage display with repertoires of naturally
occurring V domain variants obtained from unimmunized donors and
screen for higher affinity in several rounds of chain reshuffling
as described in Marks et al., Biotechnol., 10: 779-783 (1992). This
technique allows the production of antibodies and antibody
fragments with affinities in the 10.sup.-9 M range.
[0161] Nucleic acid sequence encoding the EphB2 can be designed
using the amino acid sequence of the desired region of EphB2, e.g.
the extracellular domain spanning amino acids 19 to 542 of the
amino acid sequence shown in GenBank Accession Nos.
NM.sub.--017449, or NM.sub.--004442, or FIG. 101 of WO03/000113,
and/or the polypeptide comprising amino acids about 19 to about 208
of the amino acid sequence shown in GenBank Accession Nos.
NM.sub.--017449, or NM.sub.--004442, or FIG. 101 of WO03/000113.
Alternatively, the cDNA sequence (or fragments thereof) of GenBank
Accession Nos. NM.sub.--017449, or NM.sub.--004442, or shown in
FIG. 23 of WO03/000113 may be used. Additional EphB2 sequences are
further disclosed in, e.g., Annu Rev. Neurosci. 21:309-345 (1998),
Int. Rev. Cytol. 196:177-244 (2000)); WO2003042661; WO200053216;
WO2004065576; WO2004020583; WO2003004529 (Page 128-132); and
WO200053216. DNAs encoding EphB2 can be prepared by a variety of
methods known in the art. These methods include, but are not
limited to, chemical synthesis by any of the methods described in
Engels et al., Agnew. Chem. Int. Ed. Engl., 28: 716-734 (1989),
such as the triester, phosphite, phosphoramidite and H-phosphonate
methods. In one embodiment, codons preferred by the expression host
cell are used in the design of the EphB2 encoding DNA.
Alternatively, DNA encoding the EphB2 can be isolated from a
genomic or cDNA library.
[0162] Following construction of the DNA molecule encoding the
EphB2, the DNA molecule is operably linked to an expression control
sequence in an expression vector, such as a plasmid, wherein the
control sequence is recognized by a host cell transformed with the
vector. In general, plasmid vectors contain replication and control
sequences which are derived from species compatible with the host
cell. The vector ordinarily carries a replication site, as well as
sequences which encode proteins that are capable of providing
phenotypic selection in transformed cells. Suitable vectors for
expression in prokaryotic and eukaryotic host cells are known in
the art and some are further described herein. Eukaryotic
organisms, such as yeasts, or cells derived from multicellular
organisms, such as mammals, may be used.
[0163] Optionally, the DNA encoding the EphB2 is operably linked to
a secretory leader sequence resulting in secretion of the
expression product by the host cell into the culture medium.
Examples of secretory leader sequences include stII, ecotin, lamB,
herpes GD, 1 pp, alkaline phosphatase, invertase, and alpha factor.
Also suitable for use herein is the 36 amino acid leader sequence
of protein A (Abrahmsen et al., EMBO J., 4: 3901 (1985)).
[0164] Host cells are transfected and preferably transformed with
the above-described expression or cloning vectors of this invention
and cultured in conventional nutrient media modified as appropriate
for inducing promoters, selecting transformants, or amplifying the
genes encoding the desired sequences.
[0165] Transfection refers to the taking up of an expression vector
by a host cell whether or not any coding sequences are in fact
expressed. Numerous methods of transfection are known to the
ordinarily skilled artisan, for example, CaPO.sub.4 precipitation
and electroporation. Successful transfection is generally
recognized when any indication of the operation of this vector
occurs within the host cell. Methods for transfection are well
known in the art, and some are further described herein.
[0166] Transformation means introducing DNA into an organism so
that the DNA is replicable, either as an extrachromosomal element
or by chromosomal integrant. Depending on the host cell used,
transformation is done using standard techniques appropriate to
such cells. Methods for transformation are well known in the art,
and some are further described herein.
[0167] Prokaryotic host cells used to produce the EphB2 can be
cultured as described generally in Sambrook et al., supra.
[0168] The mammalian host cells used to produce the EphB2 can be
cultured in a variety of media, which is well known in the art and
some of which is described herein.
[0169] The host cells referred to in this disclosure encompass
cells in in vitro culture as well as cells that are within a host
animal.
[0170] Purification of EphB2 may be accomplished using
art-recognized methods, some of which are described herein.
[0171] The purified EphB2 can be attached to a suitable matrix such
as agarose beads, acrylamide beads, glass beads, cellulose, various
acrylic copolymers, hydroxyl methacrylate gels, polyacrylic and
polymethacrylic copolymers, nylon, neutral and ionic carriers, and
the like, for use in the affinity chromatographic separation of
phage display clones. Attachment of the EphB2 protein to the matrix
can be accomplished by the methods described in Methods in
Enzymology, vol. 44 (1976). A commonly employed technique for
attaching protein ligands to polysaccharide matrices, e.g. agarose,
dextran or cellulose, involves activation of the carrier with
cyanogen halides and subsequent coupling of the peptide ligand's
primary aliphatic or aromatic amines to the activated matrix.
[0172] Alternatively, EphB2 can be used to coat the wells of
adsorption plates, expressed on host cells affixed to adsorption
plates or used in cell sorting, or conjugated to biotin for capture
with streptavidin-coated beads, or used in any other art-known
method for panning phage display libraries.
[0173] The phage library samples are contacted with immobilized
EphB2 under conditions suitable for binding of at least a portion
of the phage particles with the adsorbent. Normally, the
conditions, including pH, ionic strength, temperature and the like
are selected to mimic physiological conditions. The phages bound to
the solid phase are washed and then eluted by acid, e.g. as
described in Barbas et al., Proc. Natl. Acad. Sci. USA, 88:
7978-7982 (1991), or by alkali, e.g. as described in Marks et al.,
J. Mol. Biol., 222: 581-597 (1991), or by EphB2 antigen
competition, e.g. in a procedure similar to the antigen competition
method of Clackson et al., Nature, 352: 624-628 (1991). Phages can
be enriched 20-1.000-fold in a single round of selection. Moreover,
the enriched phages can be grown in bacterial culture and subjected
to further rounds of selection.
[0174] The efficiency of selection depends on many factors,
including the kinetics of dissociation during washing, and whether
multiple antibody fragments on a single phage can simultaneously
engage with antigen. Antibodies with fast dissociation kinetics
(and weak binding affinities) can be retained by use of short
washes, multivalent phage display and high coating density of
antigen in solid phase. The high density not only stabilizes the
phage through multivalent interactions, but favors rebinding of
phage that has dissociated. The selection of antibodies with slow
dissociation kinetics (and good binding affinities) can be promoted
by use of long washes and monovalent phage display as described in
Bass et al., Proteins, 8: 309-314 (1990) and in WO 92/09690, and a
low coating density of antigen as described in Marks et al.,
Biotechnol., 10: 779-783 (1992).
[0175] It is possible to select between phage antibodies of
different affinities, even with affinities that differ slightly,
for EphB2. However, random mutation of a selected antibody (e.g. as
performed in some of the affinity maturation techniques described
above) is likely to give rise to many mutants, most binding to
antigen, and a few with higher affinity. With limiting EphB2, rare
high affinity phage could be competed out. To retain all the higher
affinity mutants, phages can be incubated with excess biotinylated
EphB2, but with the biotinylated EphB2 at a concentration of lower
molarity than the target molar affinity constant for EphB2. The
high affinity-binding phages can then be captured by
streptavidin-coated paramagnetic beads. Such "equilibrium capture"
allows the antibodies to be selected according to their affinities
of binding, with sensitivity that permits isolation of mutant
clones with as little as two-fold higher affinity from a great
excess of phages with lower affinity. Conditions used in washing
phages bound to a solid phase can also be manipulated to
discriminate on the basis of dissociation kinetics.
[0176] Anti-EphB2 clones may be activity selected. In one
embodiment, the invention provides anti-EphB2 antibodies that block
the binding between an EphB2 ligand (such as ephrin-B1, ephrin-B2
and/or ephrin-B3) and EphB2, but do not block the binding between
an EphB2 ligand and a second protein (such as EphB1, EphB3, EphB4,
EphB5 and/or EphB6). Fv clones corresponding to such anti-EphB2
antibodies can be selected by (1) isolating anti-EphB2 clones from
a phage library as described in Section B(I)(2) above, and
optionally amplifying the isolated population of phage clones by
growing up the population in a suitable bacterial host; (2)
selecting EphB2 and a second protein against which blocking and
non-blocking activity, respectively, is desired; (3) adsorbing the
anti-EphB2 phage clones to immobilized EphB2; (4) using an excess
of the second protein to elute any undesired clones that recognize
EphB2-binding determinants which overlap or are shared with the
binding determinants of the second protein; and (5) eluting the
clones which remain adsorbed following step (4). Optionally, clones
with the desired blocking/non-blocking properties can be further
enriched by repeating the selection procedures described herein one
or more times.
[0177] DNA encoding the hybridoma-derived monoclonal antibodies or
phage display Fv clones of the invention is readily isolated and
sequenced using conventional procedures (e.g. by using
oligonucleotide primers designed to specifically amplify the heavy
and light chain coding regions of interest from hybridoma or phage
DNA template). Once isolated, the DNA can be placed into expression
vectors, which are then transfected into host cells such as E. coli
cells, simian COS cells, Chinese hamster ovary (CHO) cells, or
myeloma cells that do not otherwise produce immunoglobulin protein,
to obtain the synthesis of the desired monoclonal antibodies in the
recombinant host cells. Review articles on recombinant expression
in bacteria of antibody-encoding DNA include Skerra et al., Curr.
Opinion in Immunol., 5: 256 (1993) and Pluckthun, Immunol. Revs,
130: 151 (1992).
[0178] DNA encoding the Fv clones of the invention can be combined
with known DNA sequences encoding heavy chain and/or light chain
constant regions (e.g. the appropriate DNA sequences can be
obtained from Kabat et al., supra) to form clones encoding full or
partial length heavy and/or light chains. It will be appreciated
that constant regions of any isotype can be used for this purpose,
including IgG, IgM, IgA, IgD, and IgE constant regions, and that
such constant regions can be obtained from any human or animal
species. A Fv clone derived from the variable domain DNA of one
animal (such as human) species and then fused to constant region
DNA of another animal species to form coding sequence(s) for
"hybrid", full length heavy chain and/or light chain is included in
the definition of "chimeric" and "hybrid" antibody as used herein.
In a preferred embodiment, a Fv clone derived from human variable
DNA is fused to human constant region DNA to form coding
sequence(s) for all human, full or partial length heavy and/or
light chains. DNA encoding anti-EphB2 antibody derived from a
hybridoma of the invention can also be modified, for example, by
substituting the coding sequence for human heavy- and light-chain
constant domains in place of homologous murine sequences derived
from the hybridoma clone (e.g. as in the method of Morrison et al.,
Proc. Natl. Acad. Sci. USA, 81: 6851-6855 (1984)). DNA encoding a
hybridoma or Fv clone-derived antibody or fragment can be further
modified by covalently joining to the immunoglobulin coding
sequence all or part of the coding sequence for a
non-immunoglobulin polypeptide. In this manner, "chimeric" or
"hybrid" antibodies are prepared that have the binding specificity
of the Fv clone or hybridoma clone-derived antibodies of the
invention.
Antibody Fragments
[0179] The present invention encompasses antibody fragments. In
certain circumstances there are advantages of using antibody
fragments, rather than whole antibodies. The smaller size of the
fragments allows for rapid clearance, and may lead to improved
access to solid tumors.
[0180] Various techniques have been developed for the production of
antibody fragments. Traditionally, these fragments were derived via
proteolytic digestion of intact antibodies (see, e.g., Morimoto et
al., Journal of Biochemical and Biophysical Methods 24:107-117
(1992); and Brennan et al., Science, 229:81 (1985)). However, these
fragments can now be produced directly by recombinant host cells.
Fab, Fv and ScFv antibody fragments can all be expressed in and
secreted from E. coli, thus allowing the facile production of large
amounts of these fragments. Antibody fragments can be isolated from
the antibody phage libraries discussed above. Alternatively,
Fab'-SH fragments can be directly recovered from E. coli and
chemically coupled to form F(ab').sub.2 fragments (Carter et al.,
Bio/Technology 10:163-167 (1992)). According to another approach,
F(ab').sub.2 fragments can be isolated directly from recombinant
host cell culture. Fab and F(ab').sub.2 fragment with increased in
vivo half-life comprising a salvage receptor binding epitope
residues are described in U.S. Pat. No. 5,869,046. Other techniques
for the production of antibody fragments will be apparent to the
skilled practitioner. In other embodiments, the antibody of choice
is a single chain Fv fragment (scFv). See WO 93/16185; U.S. Pat.
Nos. 5,571,894; and 5,587,458. Fv and sFv are the only species with
intact combining sites that are devoid of constant regions; thus,
they are suitable for reduced nonspecific binding during in vivo
use. sFv fusion proteins may be constructed to yield fusion of an
effector protein at either the amino or the carboxy terminus of an
sFv. See Antibody Engineering, ed. Borrebaeck, supra. The antibody
fragment may also be a "linear antibody", e.g., as described in
U.S. Pat. No. 5,641,870 for example. Such linear antibody fragments
may be monospecific or bispecific.
Humanized Antibodies
[0181] The present invention encompasses humanized antibodies.
Various methods for humanizing non-human antibodies are known in
the art. For example, a humanized antibody can have one or more
amino acid residues introduced into it from a source which is
non-human. These non-human amino acid residues are often referred
to as "import" residues, which are typically taken from an "import"
variable domain. Humanization can be essentially performed
following the method of Winter and co-workers (Jones et al. (1986)
Nature 321:522-525; Riechmann et al. (1988) Nature 332:323-327;
Verhoeyen et al. (1988) Science 239:1534-1536), by substituting
hypervariable region sequences for the corresponding sequences of a
human antibody. Accordingly, such "humanized" antibodies are
chimeric antibodies (U.S. Pat. No. 4,816,567) wherein substantially
less than an intact human variable domain has been substituted by
the corresponding sequence from a non-human species. In practice,
humanized antibodies are typically human antibodies in which some
hypervariable region residues and possibly some FR residues are
substituted by residues from analogous sites in rodent
antibodies.
[0182] The choice of human variable domains, both light and heavy,
to be used in making the humanized antibodies is very important to
reduce antigenicity. According to the so-called "best-fit" method,
the sequence of the variable domain of a rodent antibody is
screened against the entire library of known human variable-domain
sequences. The human sequence which is closest to that of the
rodent is then accepted as the human framework for the humanized
antibody (Sims et al. (1993) J. Immunol. 151:2296; Chothia et al.
(1987) J. Mol. Biol. 196:901. Another method uses a particular
framework derived from the consensus sequence of all human
antibodies of a particular subgroup of light or heavy chains. The
same framework may be used for several different humanized
antibodies (Carter et al. (1992) Proc. Natl. Acad. Sci. USA,
89:4285; Presta et al. (1993) J. Immunol., 151:2623.
[0183] It is further important that antibodies be humanized with
retention of high affinity for the antigen and other favorable
biological properties. To achieve this goal, according to one
method, humanized antibodies are prepared by a process of analysis
of the parental sequences and various conceptual humanized products
using three-dimensional models of the parental and humanized
sequences. Three-dimensional immunoglobulin models are commonly
available and are familiar to those skilled in the art. Computer
programs are available which illustrate and display probable
three-dimensional conformational structures of selected candidate
immunoglobulin sequences. Inspection of these displays permits
analysis of the likely role of the residues in the functioning of
the candidate immunoglobulin sequence, i.e., the analysis of
residues that influence the ability of the candidate immunoglobulin
to bind its antigen. In this way, FR residues can be selected and
combined from the recipient and import sequences so that the
desired antibody characteristic, such as increased affinity for the
target antigen(s), is achieved. In general, the hypervariable
region residues are directly and most substantially involved in
influencing antigen binding.
Human Antibodies
[0184] Human anti-EphB2 antibodies of the invention can be
constructed by combining Fv clone variable domain sequence(s)
selected from human-derived phage display libraries with known
human constant domain sequences(s) as described above.
Alternatively, human monoclonal anti-EphB2 antibodies of the
invention can be made by the hybridoma method. Human myeloma and
mouse-human heteromyeloma cell lines for the production of human
monoclonal antibodies have been described, for example, by Kozbor
J. Immunol., 133: 3001 (1984); Brodeur et al., Monoclonal Antibody
Production Techniques and Applications, pp. 51-63 (Marcel Dekker,
Inc., New York, 1987); and Boerner et al., J. Immunol., 147: 86
(1991).
[0185] It is now possible to produce transgenic animals (e.g. mice)
that are capable, upon immunization, of producing a full repertoire
of human antibodies in the absence of endogenous immunoglobulin
production. For example, it has been described that the homozygous
deletion of the antibody heavy-chain joining region (JH) gene in
chimeric and germ-line mutant mice results in complete inhibition
of endogenous antibody production. Transfer of the human germ-line
immunoglobulin gene array in such germ-line mutant mice will result
in the production of human antibodies upon antigen challenge. See,
e.g., Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90: 2551
(1993); Jakobovits et al., Nature, 362: 255 (1993); Bruggermann et
al., Year in Immunol., 7: 33 (1993).
[0186] Gene shuffling can also be used to derive human antibodies
from non-human, e.g. rodent, antibodies, where the human antibody
has similar affinities and specificities to the starting non-human
antibody. According to this method, which is also called "epitope
imprinting", either the heavy or light chain variable region of a
non-human antibody fragment obtained by phage display techniques as
described above is replaced with a repertoire of human V domain
genes, creating a population of non-human chain/human chain scFv or
Fab chimeras. Selection with antigen results in isolation of a
non-human chain/human chain chimeric scFv or Fab wherein the human
chain restores the antigen binding site destroyed upon removal of
the corresponding non-human chain in the primary phage display
clone, i.e. the epitope governs (imprints) the choice of the human
chain partner. When the process is repeated in order to replace the
remaining non-human chain, a human antibody is obtained (see PCT WO
93/06213 published Apr. 1, 1993). Unlike traditional humanization
of non-human antibodies by CDR grafting, this technique provides
completely human antibodies, which have no FR or CDR residues of
non-human origin.
Bispecific Antibodies
[0187] Bispecific antibodies are monoclonal, preferably human or
humanized, antibodies that have binding specificities for at least
two different antigens. In the present case, one of the binding
specificities is for EphB2 and the other is for any other antigen.
Exemplary bispecific antibodies may bind to two different epitopes
of the EphB2 protein. Bispecific antibodies may also be used to
localize cytotoxic agents to cells which express EphB2. These
antibodies possess an EphB2-binding arm and an arm which binds the
cytotoxic agent (e.g. saporin, anti-interferon-.alpha., vinca
alkaloid, ricin A chain, methotrexate or radioactive isotope
hapten). Bispecific antibodies can be prepared as full length
antibodies or antibody fragments (e.g. F(ab').sub.2 bispecific
antibodies).
[0188] Methods for making bispecific antibodies are known in the
art. Traditionally, the recombinant production of bispecific
antibodies is based on the co-expression of two immunoglobulin
heavy chain-light chain pairs, where the two heavy chains have
different specificities (Milstein and Cuello, Nature, 305: 537
(1983)). Because of the random assortment of immunoglobulin heavy
and light chains, these hybridomas (quadromas) produce a potential
mixture of 10 different antibody molecules, of which only one has
the correct bispecific structure. The purification of the correct
molecule, which is usually done by affinity chromatography steps,
is rather cumbersome, and the product yields are low. Similar
procedures are disclosed in WO 93/08829 published May 13, 1993, and
in Traunecker et al., EMBO J., 10: 3655 (1991).
[0189] According to a different and more preferred approach,
antibody variable domains with the desired binding specificities
(antibody-antigen combining sites) are fused to immunoglobulin
constant domain sequences. The fusion preferably is with an
immunoglobulin heavy chain constant domain, comprising at least
part of the hinge, CH2, and CH3 regions. It is preferred to have
the first heavy-chain constant region (CH1), containing the site
necessary for light chain binding, present in at least one of the
fusions. DNAs encoding the immunoglobulin heavy chain fusions and,
if desired, the immunoglobulin light chain, are inserted into
separate expression vectors, and are co-transfected into a suitable
host organism. This provides for great flexibility in adjusting the
mutual proportions of the three polypeptide fragments in
embodiments when unequal ratios of the three polypeptide chains
used in the construction provide the optimum yields. It is,
however, possible to insert the coding sequences for two or all
three polypeptide chains in one expression vector when the
expression of at least two polypeptide chains in equal ratios
results in high yields or when the ratios are of no particular
significance.
[0190] In a preferred embodiment of this approach, the bispecific
antibodies are composed of a hybrid immunoglobulin heavy chain with
a first binding specificity in one arm, and a hybrid immunoglobulin
heavy chain-light chain pair (providing a second binding
specificity) in the other arm. It was found that this asymmetric
structure facilitates the separation of the desired bispecific
compound from unwanted immunoglobulin chain combinations, as the
presence of an immunoglobulin light chain in only one half of the
bispecific molecule provides for a facile way of separation. This
approach is disclosed in WO 94/04690. For further details of
generating bispecific antibodies see, for example, Suresh et al.,
Methods in Enzymology, 121:210 (1986).
[0191] According to another approach, the interface between a pair
of antibody molecules can be engineered to maximize the percentage
of heterodimers which are recovered from recombinant cell culture.
The preferred interface comprises at least a part of the C.sub.H3
domain of an antibody constant domain. In this method, one or more
small amino acid side chains from the interface of the first
antibody molecule are replaced with larger side chains (e.g.
tyrosine or tryptophan). Compensatory "cavities" of identical or
similar size to the large side chain(s) are created on the
interface of the second antibody molecule by replacing large amino
acid side chains with smaller ones (e.g. alanine or threonine).
This provides a mechanism for increasing the yield of the
heterodimer over other unwanted end-products such as
homodimers.
[0192] Bispecific antibodies include cross-linked or
"heteroconjugate" antibodies. For example, one of the antibodies in
the heteroconjugate can be coupled to avidin, the other to biotin.
Such antibodies have, for example, been proposed to target immune
system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for
treatment of HIV infection (WO 91/00360, WO 92/00373, and EP
03089). Heteroconjugate antibodies may be made using any convenient
cross-linking methods. Suitable cross-linking agents are well known
in the art, and are disclosed in U.S. Pat. No. 4,676,980, along
with a number of cross-linking techniques.
[0193] Techniques for generating bispecific antibodies from
antibody fragments have also been described in the literature. For
example, bispecific antibodies can be prepared using chemical
linkage. Brennan et al., Science, 229: 81 (1985) describe a
procedure wherein intact antibodies are proteolytically cleaved to
generate F(ab').sub.2 fragments. These fragments are reduced in the
presence of the dithiol complexing agent sodium arsenite to
stabilize vicinal dithiols and prevent intermolecular disulfide
formation. The Fab' fragments generated are then converted to
thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB
derivatives is then reconverted to the Fab'-thiol by reduction with
mercaptoethylamine and is mixed with an equimolar amount of the
other Fab'-TNB derivative to form the bispecific antibody. The
bispecific antibodies produced can be used as agents for the
selective immobilization of enzymes.
[0194] Recent progress has facilitated the direct recovery of
Fab'-SH fragments from E. coli, which can be chemically coupled to
form bispecific antibodies. Shalaby et al., J. Exp. Med., 175:
217-225 (1992) describe the production of a fully humanized
bispecific antibody F(ab').sub.2 molecule. Each Fab' fragment was
separately secreted from E. coli and subjected to directed chemical
coupling in vitro to form the bispecific antibody. The bispecific
antibody thus formed was able to bind to cells overexpressing the
HER2 receptor and normal human T cells, as well as trigger the
lytic activity of human cytotoxic lymphocytes against human breast
tumor targets.
[0195] Various techniques for making and isolating bispecific
antibody fragments directly from recombinant cell culture have also
been described. For example, bispecific antibodies have been
produced using leucine zippers. Kostelny et al., J. Immunol.,
148(5):1547-1553 (1992). The leucine zipper peptides from the Fos
and Jun proteins were linked to the Fab' portions of two different
antibodies by gene fusion. The antibody homodimers were reduced at
the hinge region to form monomers and then re-oxidized to form the
antibody heterodimers. This method can also be utilized for the
production of antibody homodimers. The "diabody" technology
described by Hollinger et al., Proc. Natl. Acad. Sci. USA,
90:6444-6448 (1993) has provided an alternative mechanism for
making bispecific antibody fragments. The fragments comprise a
heavy-chain variable domain (VH) connected to a light-chain
variable domain (VL) by a linker which is too short to allow
pairing between the two domains on the same chain. Accordingly, the
VH and VL domains of one fragment are forced to pair with the
complementary VL and VH domains of another fragment, thereby
forming two antigen-binding sites. Another strategy for making
bispecific antibody fragments by the use of single-chain Fv (sFv)
dimers has also been reported. See Gruber et al., J. Immunol.,
152:5368 (1994).
[0196] Antibodies with more than two valencies are contemplated.
For example, trispecific antibodies can be prepared. Tutt et al. J.
Immunol. 147: 60 (1991).
Multivalent Antibodies
[0197] A multivalent antibody may be internalized (and/or
catabolized) faster than a bivalent antibody by a cell expressing
an antigen to which the antibodies bind. The antibodies of the
present invention can be multivalent antibodies (which are other
than of the IgM class) with three or more antigen binding sites
(e.g. tetravalent antibodies), which can be readily produced by
recombinant expression of nucleic acid encoding the polypeptide
chains of the antibody. The multivalent antibody can comprise a
dimerization domain and three or more antigen binding sites. The
preferred dimerization domain comprises (or consists of) an Fc
region or a hinge region. In this scenario, the antibody will
comprise an Fc region and three or more antigen binding sites
amino-terminal to the Fe region. The preferred multivalent antibody
herein comprises (or consists of) three to about eight, but
preferably four, antigen binding sites. The multivalent antibody
comprises at least one polypeptide chain (and preferably two
polypeptide chains), wherein the polypeptide chain(s) comprise two
or more variable domains. For instance, the polypeptide chain(s)
may comprise VD1-(X1)n-VD2-(X2)n-Fc, wherein VD1 is a first
variable domain, VD2 is a second variable domain, Fc is one
polypeptide chain of an Fc region, X1 and X2 represent an amino
acid or polypeptide, and n is 0 or 1. For instance, the polypeptide
chain(s) may comprise: VH-CH1-flexible linker-VH-CH1-Fc region
chain; or VH-CH1-VH-CH1-Fc region chain. The multivalent antibody
herein preferably further comprises at least two (and preferably
four) light chain variable domain polypeptides. The multivalent
antibody herein may, for instance, comprise from about two to about
eight light chain variable domain polypeptides. The light chain
variable domain polypeptides contemplated here comprise a light
chain variable domain and, optionally, further comprise a CL
domain.
Antibody Variants
[0198] In some embodiments, amino acid sequence modification(s) of
the antibodies described herein are contemplated. For example, it
may be desirable to improve the binding affinity and/or other
biological properties of the antibody. Amino acid sequence variants
of the antibody are prepared by introducing appropriate nucleotide
changes into the antibody nucleic acid, or by peptide synthesis.
Such modifications include, for example, deletions from, and/or
insertions into and/or substitutions of, residues within the amino
acid sequences of the antibody. Any combination of deletion,
insertion, and substitution is made to arrive at the final
construct, provided that the final construct possesses the desired
characteristics. The amino acid alterations may be introduced in
the subject antibody amino acid sequence at the time that sequence
is made.
[0199] A useful method for identification of certain residues or
regions of the antibody that are preferred locations for
mutagenesis is called "alanine scanning mutagenesis" as described
by Cunningham and Wells (1989) Science, 244:1081-1085. Here, a
residue or group of target residues are identified (e.g., charged
residues such as arg, asp, his, lys, and glu) and replaced by a
neutral or negatively charged amino acid (most preferably alanine
or polyalanine) to affect the interaction of the amino acids with
antigen. Those amino acid locations demonstrating functional
sensitivity to the substitutions then are refined by introducing
further or other variants at, or for, the sites of substitution.
Thus, while the site for introducing an amino acid sequence
variation is predetermined, the nature of the mutation per se need
not be predetermined. For example, to analyze the performance of a
mutation at a given site, ala scanning or random mutagenesis is
conducted at the target codon or region and the expressed
immunoglobulins are screened for the desired activity.
[0200] Amino acid sequence insertions include amino- and/or
carboxyl-terminal fusions ranging in length from one residue to
polypeptides containing a hundred or more residues, as well as
intrasequence insertions of single or multiple amino acid residues.
Examples of terminal insertions include an antibody with an
N-terminal methionyl residue or the antibody fused to a cytotoxic
polypeptide. Other insertional variants of the antibody molecule
include the fusion to the N- or C-terminus of the antibody to an
enzyme (e.g. for ADEPT) or a polypeptide which increases the serum
half-life of the antibody.
[0201] Glycosylation of polypeptides is typically either N-linked
or O-linked. N-linked refers to the attachment of the carbohydrate
moiety to the side chain of an asparagine residue. The tripeptide
sequences asparagine-X-serine and asparagine-X-threonine, where X
is any amino acid except proline, are the recognition sequences for
enzymatic attachment of the carbohydrate moiety to the asparagine
side chain. Thus, the presence of either of these tripeptide
sequences in a polypeptide creates a potential glycosylation site.
O-linked glycosylation refers to the attachment of one of the
sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino
acid, most commonly serine or threonine, although 5-hydroxyproline
or 5-hydroxylysine may also be used.
[0202] Addition of glycosylation sites to the antibody is
conveniently accomplished by altering the amino acid sequence such
that it contains one or more of the above-described tripeptide
sequences (for N-linked glycosylation sites). The alteration may
also be made by the addition of, or substitution by, one or more
serine or threonine residues to the sequence of the original
antibody (for O-linked glycosylation sites).
[0203] Where the antibody comprises an Fc region, the carbohydrate
attached thereto may be altered. For example, antibodies with a
mature carbohydrate structure that lacks fucose attached to an Fc
region of the antibody are described in US Pat Appl No US
2003/0157108 (Presta, L.). See also US 2004/0093621 (Kyowa Hakko
Kogyo Co., Ltd). Antibodies with a bisecting N-acetylglucosamine
(GlcNAc) in the carbohydrate attached to an Fc region of the
antibody are referenced in WO 2003/011878, Jean-Mairet et al. and
U.S. Pat. No. 6,602,684, Umana et al. Antibodies with at least one
galactose residue in the oligosaccharide attached to an Fc region
of the antibody are reported in WO 1997/30087, Patel et al. See,
also, WO 1998/58964 (Raju, S.) and WO 1999/22764 (Raju, S.)
concerning antibodies with altered carbohydrate attached to the Fc
region thereof. See also US 2005/0123546 (Umana et al.) on
antigen-binding molecules with modified glycosylation.
[0204] The preferred glycosylation variant herein comprises an Fc
region, wherein a carbohydrate structure attached to the Fc region
lacks fucose. Such variants have improved ADCC function.
Optionally, the Fc region further comprises one or more amino acid
substitutions therein which further improve ADCC, for example,
substitutions at positions 298, 333, and/or 334 of the Fc region
(Eu numbering of residues). Examples of publications related to
"defucosylated" or "fucose-deficient" antibodies include: US
2003/0157108; WO 2000/61739; WO 2001/29246; US 2003/0115614; US
2002/0164328; US 2004/0093621; US 2004/0132140; US 2004/0110704; US
2004/0110282; US 2004/0109865; WO 2003/085119; WO 2003/084570; WO
2005/035586; WO 2005/035778; WO2005/053742; Okazaki et al. J. Mol.
Biol. 336:1239-1249 (2004); Yamane-Ohnuki et al. Biotech. Bioeng.
87: 614 (2004). Examples of cell lines producing defucosylated
antibodies include Lec13 CHO cells deficient in protein
fucosylation (Ripka et al. Arch. Biochem. Biophys. 249:533-545
(1986); US Pat Appl No US 2003/0157108 A1, Presta, L; and WO
2004/056312 A1, Adams et al., especially at Example 11), and
knockout cell lines, such as alpha-1,6-fucosyltransferase gene,
FUT8, knockout CHO cells (Yamane-Ohnuki et al. Biotech. Bioeng. 87:
614 (2004)).
[0205] Another type of variant is an amino acid substitution
variant. These variants have at least one amino acid residue in the
antibody molecule replaced by a different residue. The sites of
greatest interest for substitutional mutagenesis include the
hypervariable regions, but FR alterations are also contemplated.
Conservative substitutions are shown in Table 1 under the heading
of "preferred substitutions". If such substitutions result in a
change in biological activity, then more substantial changes,
denominated "exemplary substitutions" in Table 1, or as further
described below in reference to amino acid classes, may be
introduced and the products screened.
TABLE-US-00006 TABLE 1 Original Exemplary Preferred Residue
Substitutions Substitutions Ala (A) Val; Leu; Ile Val Arg (R) Lys;
Gln; Asn Lys Asn (N) Gln; His; Asp, Lys; Arg Gln Asp (D) Glu; Asn
Glu Cys (C) Ser; Ala Ser Gln (Q) Asn; Glu Asn Glu (E) Asp; Gln Asp
Gly (G) Ala Ala His (H) Asn; Gln; Lys; Arg Arg Ile (I) Leu; Val;
Met; Ala; Leu Phe; Norleucine Leu (L) Norleucine; Ile; Val; Ile
Met; Ala; Phe Lys (K) Arg; Gln; Asn Arg Met (M) Leu; Phe; Ile Leu
Phe (F) Trp; Leu; Val; Ile; Ala; Tyr Tyr Pro (P) Ala Ala Ser (S)
Thr Thr Thr (T) Val; Ser Ser Trp (W) Tyr; Phe Tyr Tyr (Y) Trp; Phe;
Thr; Ser Phe Val (V) Ile; Leu; Met; Phe; Leu Ala; Norleucine
[0206] Substantial modifications in the biological properties of
the antibody are accomplished by selecting substitutions that
differ significantly in their effect on maintaining (a) the
structure of the polypeptide backbone in the area of the
substitution, for example, as a sheet or helical conformation, (b)
the charge or hydrophobicity of the molecule at the target site, or
(c) the bulk of the side chain. Naturally occurring residues are
divided into groups based on common side-chain properties: [0207]
(1) hydrophobic: norleucine, met, ala, val, leu, ile; [0208] (2)
neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; [0209] (3) acidic:
asp, glu; [0210] (4) basic: his, lys, arg; [0211] (5) residues that
influence chain orientation: gly, pro; and [0212] (6) aromatic:
trp, tyr, phe.
[0213] Non-conservative substitutions will entail exchanging a
member of one of these classes for another class.
[0214] One type of substitutional variant involves substituting one
or more hypervariable region residues of a parent antibody (e.g. a
humanized or human antibody). Generally, the resulting variant(s)
selected for further development will have improved biological
properties relative to the parent antibody from which they are
generated. A convenient way for generating such substitutional
variants involves affinity maturation using phage display. Briefly,
several hypervariable region sites (e.g. 6-7 sites) are mutated to
generate all possible amino acid substitutions at each site. The
antibodies thus generated are displayed from filamentous phage
particles as fusions to the gene III product of M13 packaged within
each particle. The phage-displayed variants are then screened for
their biological activity (e.g. binding affinity) as herein
disclosed. In order to identify candidate hypervariable region
sites for modification, alanine scanning mutagenesis can be
performed to identify hypervariable region residues contributing
significantly to antigen binding. Alternatively, or additionally,
it may be beneficial to analyze a crystal structure of the
antigen-antibody complex to identify contact points between the
antibody and antigen. Such contact residues and neighboring
residues are candidates for substitution according to the
techniques elaborated herein. Once such variants are generated, the
panel of variants is subjected to screening as described herein and
antibodies with superior properties in one or more relevant assays
may be selected for further development.
[0215] Nucleic acid molecules encoding amino acid sequence variants
of the antibody are prepared by a variety of methods known in the
art. These methods include, but are not limited to, isolation from
a natural source (in the case of naturally occurring amino acid
sequence variants) or preparation by oligonucleotide-mediated (or
site-directed) mutagenesis, PCR mutagenesis, and cassette
mutagenesis of an earlier prepared variant or a non-variant version
of the antibody.
[0216] It may be desirable to introduce one or more amino acid
modifications in an Fc region of the immunoglobulin polypeptides of
the invention, thereby generating a Fc region variant. The Fc
region variant may comprise a human Fc region sequence (e.g., a
human IgG1, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid
modification (e.g. a substitution) at one or more amino acid
positions including that of a hinge cysteine.
[0217] In accordance with this description and the teachings of the
art, it is contemplated that in some embodiments, an antibody used
in methods of the invention may comprise one or more alterations as
compared to the wild type counterpart antibody, e.g. in the Fc
region. These antibodies would nonetheless retain substantially the
same characteristics required for therapeutic utility as compared
to their wild type counterpart. For example, it is thought that
certain alterations can be made in the Fc region that would result
in altered (i.e., either improved or diminished) C1q binding and/or
Complement Dependent Cytotoxicity (CDC), e.g., as described in
WO99/51642. See also Duncan & Winter Nature 322:738-40 (1988);
U.S. Pat. No. 5,648,260; U.S. Pat. No. 5,624,821; and WO94/29351
concerning other examples of Fc region variants. WO00/42072
(Presta) and WO 2004/056312 (Lowman) describe antibody variants
with improved or diminished binding to FcRs. The content of these
patent publications are specifically incorporated herein by
reference. See, also, Shields et al. J. Biol. Chem. 9(2): 6591-6604
(2001). Antibodies with increased half lives and improved binding
to the neonatal Fc receptor (FcRn), which is responsible for the
transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol.
117:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)), are
described in US2005/0014934A1 (Hinton et al.). These antibodies
comprise an Fc region with one or more substitutions therein which
improve binding of the Fc region to FcRn. Polypeptide variants with
altered Fc region amino acid sequences and increased or decreased
C1q binding capability are described in U.S. Pat. No. 6,194,551B1,
WO99/51642. The contents of those patent publications are
specifically incorporated herein by reference. See, also, Idusogie
et al. J. Immunol. 164: 4178-4184 (2000).
Antibody Derivatives
[0218] The antibodies of the present invention can be further
modified to contain additional nonproteinaceous moieties that are
known in the art and readily available. Preferably, the moieties
suitable for derivatization of the antibody are water soluble
polymers. Non-limiting examples of water soluble polymers include,
but are not limited to, polyethylene glycol (PEG), copolymers of
ethylene glycol/propylene glycol, carboxymethylcellulose, dextran,
polyvinyl alcohol, polyvinyl pyrrolidone, poly-1,3-dioxolane,
poly-1,3,6-trioxane, ethylene/maleic anhydride copolymer,
polyaminoacids (either homopolymers or random copolymers), and
dextran or poly(n-vinyl pyrrolidone)polyethylene glycol,
propropylene glycol homopolymers, prolypropylene oxide/ethylene
oxide co-polymers, polyoxyethylated polyols (e.g., glycerol),
polyvinyl alcohol, and mixtures thereof. Polyethylene glycol
propionaldehyde may have advantages in manufacturing due to its
stability in water. The polymer may be of any molecular weight, and
may be branched or unbranched. The number of polymers attached to
the antibody may vary, and if more than one polymers are attached,
they can be the same or different molecules. In general, the number
and/or type of polymers used for derivatization can be determined
based on considerations including, but not limited to, the
particular properties or functions of the antibody to be improved,
whether the antibody derivative will be used in a therapy under
defined conditions, etc. Screening for Antibodies with Desired
Properties
[0219] The antibodies of the present invention can be characterized
for their physical/chemical properties and biological functions by
various assays known in the art. In some embodiments, antibodies
are characterized for any one or more of reduction or blocking of
EphB2 activation, reduction or blocking of EphB2 downstream
molecular signaling, reduction or blocking of EphB2 ligand
activation, reduction or blocking or EphB2 ligand downstream
molecular signaling, disruption or blocking of ligand (e.g.,
ephrin-B1, ephrin-B2, and/or ephrin-B3) binding to EphB2, EphB2
phosphorylation and/or EphB2 multimerization, and/or EphB2 ligand
phosphorylation, and/or treatment and/or prevention of a tumor,
cell proliferative disorder or a cancer; and/or treatment or
prevention of a disorder associated with EphB2 expression and/or
activity (such as increased EphB2 expression and/or activity).
[0220] The purified antibodies can be further characterized by a
series of assays including, but not limited to, N-terminal
sequencing, amino acid analysis, non-denaturing size exclusion high
pressure liquid chromatography (HPLC), mass spectrometry, ion
exchange chromatography and papain digestion.
[0221] In certain embodiments of the invention, the antibodies
produced herein are analyzed for their biological activity. In some
embodiments, the antibodies of the present invention are tested for
their antigen binding activity. The antigen binding assays that are
known in the art and can be used herein include without limitation
any direct or competitive binding assays using techniques such as
western blots, radioimmunoassays, ELISA (enzyme linked
immunosorbent assay), "sandwich" immunoassays, immunoprecipitation
assays, fluorescent immunoassays, and protein A immunoassays.
Illustrative antigen binding assay are provided below in the
Examples section.
[0222] In another embodiment, the invention provides the anti-EphB2
monoclonal antibody produced by hybridoma cell line 2H9.11.14 (ATCC
Deposit No. PTA-6606) (interchangeably termed "2H9" or "Mab 2H9"
herein).
[0223] In still another embodiment, the invention provides
anti-EphB2 monoclonal antibodies that compete with 2H9 antibody for
binding to EphB2. Such competitor antibodies include antibodies
that recognize an EphB2 epitope that is the same as or overlaps
with the EphB2 epitope recognized by antibody 2H9. Such competitor
antibodies can be obtained by screening anti-EphB2 hybridoma
supernatants for binding to immobilized EphB2 in competition with
labeled 2H9 antibody. A hybridoma supernatant containing competitor
antibody will reduce the amount of bound, labeled antibody detected
in the subject competition binding mixture as compared to the
amount of bound, labeled antibody detected in a control binding
mixture containing irrelevant (or no) antibody. Any of the
competition binding assays described herein are suitable for use in
the foregoing procedure.
[0224] In another aspect, the invention provides an anti-EphB2
monoclonal antibody that comprises one or more (such as 2, 3, 4, 5,
and/or 6) HVRs of the 2H9 antibody. An anti-EphB2 monoclonal
antibody that comprises one or more HVR(s) of 2H9 can be
constructed by grafting one or more HVR(s) of 2H9 onto a template
antibody sequence, e.g. a human antibody sequence which is closest
to the corresponding murine sequence of the parental antibody, or a
consensus sequence of all human antibodies in the particular
subgroup of the parental antibody light or heavy chain, and
expressing the resulting chimeric light and/or heavy chain variable
region sequence(s), with or without accompanying constant region
sequence(s), in recombinant host cells as described herein.
[0225] Anti-EphB2 antibodies of the invention possessing the unique
properties described herein can be obtained by screening anti-EphB2
hybridoma clones for the desired properties by any convenient
method. For example, if an anti-EphB2 monoclonal antibody that
blocks or does not block the binding of EphB2 ligands to EphB2 is
desired, the candidate antibody can be tested in a binding
competition assay, such as a competitive binding ELISA, wherein
plate wells are coated with EphB2, and a solution of antibody in an
excess of the Eph ligand of interest is layered onto the coated
plates, and bound antibody is detected enzymatically, e.g.
contacting the bound antibody with HRP-conjugated anti-Ig antibody
or biotinylated anti-Ig antibody and developing the HRP color
reaction., e.g. by developing plates with streptavidin-HRP and/or
hydrogen peroxide and detecting the HRP color reaction by
spectrophotometry at 490 nm with an ELISA plate reader.
[0226] If an anti-EphB2 antibody that inhibits EphB2 activation is
desired, the candidate antibody can be tested in an EphB2
phosphorylation assay. Such assays are known in the art and one
such assay is described and exemplified in the Examples section. If
an antibody that interferes with antibody internalization is
desired, the candidate assay can be tested in a cell
internalization assay. Such assays are known in the art and one
such assay is described and exemplified in the Examples
section.
[0227] If an anti-EphB2 antibody or immunoconjugate that kills
cells or inhibits cell growth is desired, the candidate antibody or
immunoconjugate can be tested in in vitro and/or in vivo assays
that measure cell killing and/or inhibition of cell growth. Such
assays are known in the art and are further described and
exemplified herein.
[0228] In one embodiment, the present invention contemplates an
altered antibody that possesses some but not all effector
functions, which make it a desired candidate for many applications
in which the half life of the antibody in vivo is important yet
certain effector functions (such as complement and ADCC) are
unnecessary or deleterious. In certain embodiments, the Fc
activities of the produced immunoglobulin are measured to ensure
that only the desired properties are maintained. In vitro and/or in
vivo cytotoxicity assays can be conducted to confirm the
reduction/depletion of CDC and/or ADCC activities. For example, Fc
receptor (FcR) binding assays can be conducted to ensure that the
antibody lacks Fc.gamma.R binding (hence likely lacking ADCC
activity), but retains FcRn binding ability. The primary cells for
mediating ADCC, NK cells, express Fc.gamma.RIII only, whereas
monocytes express Fc.gamma.RI, Fc.gamma.RII and Fc.gamma.RIII. FcR
expression on hematopoietic cells is summarized in Table 3 on page
464 of Ravetch and Kinet, Annu Rev. Immunol 9:457-92 (1991). An
example of an in vitro assay to assess ADCC activity of a molecule
of interest is described in U.S. Pat. No. 5,500,362 or 5,821,337.
Useful effector cells for such assays include peripheral blood
mononuclear cells (PBMC) and Natural Killer (NK) cells.
Alternatively, or additionally, ADCC activity of the molecule of
interest may be assessed in vivo, e.g., in a animal model such as
that disclosed in Clynes et al. PNAS (USA) 95:652-656 (1998). C1q
binding assays may also be carried out to confirm that the antibody
is unable to bind C1q and hence lacks CDC activity. To assess
complement activation, a CDC assay, e.g. as described in
Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), may be
performed. FcRn binding and in vivo clearance/half life
determinations can also be performed using methods known in the
art, e.g. those described in the Examples section.
Vectors, Host Cells and Recombinant Methods
[0229] For recombinant production of an antibody of the invention,
the nucleic acid encoding it is isolated and inserted into a
replicable vector for further cloning (amplification of the DNA) or
for expression. DNA encoding the antibody is readily isolated and
sequenced using conventional procedures (e.g., by using
oligonucleotide probes that are capable of binding specifically to
genes encoding the heavy and light chains of the antibody). Many
vectors are available. The choice of vector depends in part on the
host cell to be used. Generally, preferred host cells are of either
prokaryotic or eukaryotic (generally mammalian) origin. It will be
appreciated that constant regions of any isotype can be used for
this purpose, including IgG, IgM, IgA, IgD, and IgE constant
regions, and that such constant regions can be obtained from any
human or animal species.
[0230] a. Generating Antibodies Using Prokaryotic Host Cells:
[0231] i. Vector Construction
[0232] Polynucleotide sequences encoding polypeptide components of
the antibody of the invention can be obtained using standard
recombinant techniques. Desired polynucleotide sequences may be
isolated and sequenced from antibody producing cells such as
hybridoma cells. Alternatively, polynucleotides can be synthesized
using nucleotide synthesizer or PCR techniques. Once obtained,
sequences encoding the polypeptides are inserted into a recombinant
vector capable of replicating and expressing heterologous
polynucleotides in prokaryotic hosts. Many vectors that are
available and known in the art can be used for the purpose of the
present invention. Selection of an appropriate vector will depend
mainly on the size of the nucleic acids to be inserted into the
vector and the particular host cell to be transformed with the
vector. Each vector contains various components, depending on its
function (amplification or expression of heterologous
polynucleotide, or both) and its compatibility with the particular
host cell in which it resides. The vector components generally
include, but are not limited to: an origin of replication, a
selection marker gene, a promoter, a ribosome binding site (RBS), a
signal sequence, the heterologous nucleic acid insert and a
transcription termination sequence.
[0233] In general, plasmid vectors containing replicon and control
sequences which are derived from species compatible with the host
cell are used in connection with these hosts. The vector ordinarily
carries a replication site, as well as marking sequences which are
capable of providing phenotypic selection in transformed cells. For
example, E. coli is typically transformed using pBR322, a plasmid
derived from an E. coli species. pBR322 contains genes encoding
ampicillin (Amp) and tetracycline (Tet) resistance and thus
provides easy means for identifying transformed cells. pBR322, its
derivatives, or other microbial plasmids or bacteriophage may also
contain, or be modified to contain, promoters which can be used by
the microbial organism for expression of endogenous proteins.
Examples of pBR322 derivatives used for expression of particular
antibodies are described in detail in Carter et al., U.S. Pat. No.
5,648,237.
[0234] In addition, phage vectors containing replicon and control
sequences that are compatible with the host microorganism can be
used as transforming vectors in connection with these hosts. For
example, bacteriophage such as .lamda.GEM.TM.-11 may be utilized in
making a recombinant vector which can be used to transform
susceptible host cells such as E. coli LE392.
[0235] The expression vector of the invention may comprise two or
more promoter-cistron pairs, encoding each of the polypeptide
components. A promoter is an untranslated regulatory sequence
located upstream (5') to a cistron that modulates its expression.
Prokaryotic promoters typically fall into two classes, inducible
and constitutive. Inducible promoter is a promoter that initiates
increased levels of transcription of the cistron under its control
in response to changes in the culture condition, e.g. the presence
or absence of a nutrient or a change in temperature.
[0236] A large number of promoters recognized by a variety of
potential host cells are well known. The selected promoter can be
operably linked to cistron DNA encoding the light or heavy chain by
removing the promoter from the source DNA via restriction enzyme
digestion and inserting the isolated promoter sequence into the
vector of the invention. Both the native promoter sequence and many
heterologous promoters may be used to direct amplification and/or
expression of the target genes. In some embodiments, heterologous
promoters are utilized, as they generally permit greater
transcription and higher yields of expressed target gene as
compared to the native target polypeptide promoter.
[0237] Promoters suitable for use with prokaryotic hosts include
the PhoA promoter, the .beta.-galactamase and lactose promoter
systems, a tryptophan (trp) promoter system and hybrid promoters
such as the tac or the trc promoter. However, other promoters that
are functional in bacteria (such as other known bacterial or phage
promoters) are suitable as well. Their nucleotide sequences have
been published, thereby enabling a skilled worker operably to
ligate them to cistrons encoding the target light and heavy chains
(Siebenlist et al. (1980) Cell 20: 269) using linkers or adaptors
to supply any required restriction sites.
[0238] In one aspect of the invention, each cistron within the
recombinant vector comprises a secretion signal sequence component
that directs translocation of the expressed polypeptides across a
membrane. In general, the signal sequence may be a component of the
vector, or it may be a part of the target polypeptide DNA that is
inserted into the vector. The signal sequence selected for the
purpose of this invention should be one that is recognized and
processed (i.e. cleaved by a signal peptidase) by the host cell.
For prokaryotic host cells that do not recognize and process the
signal sequences native to the heterologous polypeptides, the
signal sequence is substituted by a prokaryotic signal sequence
selected, for example, from the group consisting of the alkaline
phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II
(STII) leaders, LamB, PhoE, PelB, OmpA and MBP. In one embodiment
of the invention, the signal sequences used in both cistrons of the
expression system are STII signal sequences or variants
thereof.
[0239] In another aspect, the production of the immunoglobulins
according to the invention can occur in the cytoplasm of the host
cell, and therefore does not require the presence of secretion
signal sequences within each cistron. In that regard,
immunoglobulin light and heavy chains are expressed, folded and
assembled to form functional immunoglobulins within the cytoplasm.
Certain host strains (e.g., the E. coli trxB-strains) provide
cytoplasm conditions that are favorable for disulfide bond
formation, thereby permitting proper folding and assembly of
expressed protein subunits (Proba and Pluckthun Gene, 159:203
(1995)).
[0240] Prokaryotic host cells suitable for expressing antibodies of
the invention include Archaebacteria and Eubacteria, such as
Gram-negative or Gram-positive organisms. Examples of useful
bacteria include Escherichia (e.g., E. coli), Bacilli (e.g., B.
subtilis), Enterobacteria, Pseudomonas species (e.g., P.
aeruginosa), Salmonella typhimurium, Serratia marcescans,
Klebsiella, Proteus, Shigella, Rhizobia, Vitreoscilla, or
Paracoccus. In one embodiment, gram-negative cells are used. In one
embodiment, E. coli cells are used as hosts for the invention.
Examples of E. coli strains include strain W3110 (Bachmann,
Cellular and Molecular Biology, vol. 2 (Washington, D.C.: American
Society for Microbiology, 1987), pp. 1190-1219; ATCC Deposit No.
27,325) and derivatives thereof, including strain 33D3 having
genotype W3110 .DELTA.fhuA (.DELTA.tonA) ptr3 lac Iq lacL8
.DELTA.ompT.DELTA.(nmpc-fepE) degP41 kanR (U.S. Pat. No.
5,639,635). Other strains and derivatives thereof, such as E. coli
294 (ATCC 31,446), E. coli B, E. coli.lamda. 1776 (ATCC 31,537) and
E. coli RV308(ATCC 31,608) are also suitable. These examples are
illustrative rather than limiting. Methods for constructing
derivatives of any of the above-mentioned bacteria having defined
genotypes are known in the art and described in, for example, Bass
et al., Proteins, 8:309-314 (1990). It is generally necessary to
select the appropriate bacteria taking into consideration
replicability of the replicon in the cells of a bacterium. For
example, E. coli, Serratia, or Salmonella species can be suitably
used as the host when well known plasmids such as pBR322, pBR325,
pACYC177, or pKN410 are used to supply the replicon. Typically the
host cell should secrete minimal amounts of proteolytic enzymes,
and additional protease inhibitors may desirably be incorporated in
the cell culture.
[0241] ii. Antibody Production
[0242] Host cells are transformed with the above-described
expression vectors and cultured in conventional nutrient media
modified as appropriate for inducing promoters, selecting
transformants, or amplifying the genes encoding the desired
sequences.
[0243] Transformation means introducing DNA into the prokaryotic
host so that the DNA is replicable, either as an extrachromosomal
element or by chromosomal integrant. Depending on the host cell
used, transformation is done using standard techniques appropriate
to such cells. The calcium treatment employing calcium chloride is
generally used for bacterial cells that contain substantial
cell-wall barriers. Another method for transformation employs
polyethylene glycol/DMSO. Yet another technique used is
electroporation.
[0244] Prokaryotic cells used to produce the polypeptides of the
invention are grown in media known in the art and suitable for
culture of the selected host cells. Examples of suitable media
include luria broth (LB) plus necessary nutrient supplements. In
some embodiments, the media also contains a selection agent, chosen
based on the construction of the expression vector, to selectively
permit growth of prokaryotic cells containing the expression
vector. For example, ampicillin is added to media for growth of
cells expressing ampicillin resistant gene.
[0245] Any necessary supplements besides carbon, nitrogen, and
inorganic phosphate sources may also be included at appropriate
concentrations introduced alone or as a mixture with another
supplement or medium such as a complex nitrogen source. Optionally
the culture medium may contain one or more reducing agents selected
from the group consisting of glutathione, cysteine, cystamine,
thioglycollate, dithioerythritol and dithiothreitol.
[0246] The prokaryotic host cells are cultured at suitable
temperatures. For E. coli growth, for example, the preferred
temperature ranges from about 20.degree. C. to about 39.degree. C.,
more preferably from about 25.degree. C. to about 37.degree. C.,
even more preferably at about 30.degree. C. The pH of the medium
may be any pH ranging from about 5 to about 9, depending mainly on
the host organism. For E. coli, the pH is preferably from about 6.8
to about 7.4, and more preferably about 7.0.
[0247] If an inducible promoter is used in the expression vector of
the invention, protein expression is induced under conditions
suitable for the activation of the promoter. In one aspect of the
invention, PhoA promoters are used for controlling transcription of
the polypeptides. Accordingly, the transformed host cells are
cultured in a phosphate-limiting medium for induction. Preferably,
the phosphate-limiting medium is the C.R.A.P medium (see, e.g.,
Simmons et al., J. Immunol. Methods (2002), 263:133-147). A variety
of other inducers may be used, according to the vector construct
employed, as is known in the art.
[0248] In one embodiment, the expressed polypeptides of the present
invention are secreted into and recovered from the periplasm of the
host cells. Protein recovery typically involves disrupting the
microorganism, generally by such means as osmotic shock, sonication
or lysis. Once cells are disrupted, cell debris or whole cells may
be removed by centrifugation or filtration. The proteins may be
further purified, for example, by affinity resin chromatography.
Alternatively, proteins can be transported into the culture media
and isolated therein. Cells may be removed from the culture and the
culture supernatant being filtered and concentrated for further
purification of the proteins produced. The expressed polypeptides
can be further isolated and identified using commonly known methods
such as polyacrylamide gel electrophoresis (PAGE) and Western blot
assay.
[0249] In one aspect of the invention, antibody production is
conducted in large quantity by a fermentation process. Various
large-scale fed-batch fermentation procedures are available for
production of recombinant proteins. Large-scale fermentations have
at least 1000 liters of capacity, preferably about 1,000 to 100,000
liters of capacity. These fermentors use agitator impellers to
distribute oxygen and nutrients, especially glucose (the preferred
carbon/energy source). Small scale fermentation refers generally to
fermentation in a fermentor that is no more than approximately 100
liters in volumetric capacity, and can range from about 1 liter to
about 100 liters.
[0250] In a fermentation process, induction of protein expression
is typically initiated after the cells have been grown under
suitable conditions to a desired density, e.g., an OD550 of about
180-220, at which stage the cells are in the early stationary
phase. A variety of inducers may be used, according to the vector
construct employed, as is known in the art and described above.
Cells may be grown for shorter periods prior to induction. Cells
are usually induced for about 12-50 hours, although longer or
shorter induction time may be used.
[0251] To improve the production yield and quality of the
polypeptides of the invention, various fermentation conditions can
be modified. For example, to improve the proper assembly and
folding of the secreted antibody polypeptides, additional vectors
overexpressing chaperone proteins, such as Dsb proteins (DsbA,
DsbB, DsbC, DsbD and or DsbG) or FkpA (a peptidylprolyl
cis,trans-isomerase with chaperone activity) can be used to
co-transform the host prokaryotic cells. The chaperone proteins
have been demonstrated to facilitate the proper folding and
solubility of heterologous proteins produced in bacterial host
cells. Chen et al. (1999) J Bio Chem 274:19601-19605; Georgiou et
al., U.S. Pat. No. 6,083,715; Georgiou et al., U.S. Pat. No.
6,027,888; Bothmann and Pluckthun (2000) J. Biol. Chem.
275:17100-17105; Ramm and Pluckthun (2000) J. Biol. Chem.
275:17106-17113; Arie et al. (2001) Mol. Microbiol. 39:199-210.
[0252] To minimize proteolysis of expressed heterologous proteins
(especially those that are proteolytically sensitive), certain host
strains deficient for proteolytic enzymes can be used for the
present invention. For example, host cell strains may be modified
to effect genetic mutation(s) in the genes encoding known bacterial
proteases such as Protease III, OmpT, DegP, Tsp, Protease I,
Protease Mi, Protease V, Protease VI and combinations thereof. Some
E. coli protease-deficient strains are available and described in,
for example, Joly et al. (1998), supra; Georgiou et al., U.S. Pat.
No. 5,264,365; Georgiou et al., U.S. Pat. No. 5,508,192; Hara et
al., Microbial Drug Resistance, 2:63-72 (1996).
[0253] In one embodiment, E. coli strains deficient for proteolytic
enzymes and transformed with plasmids overexpressing one or more
chaperone proteins are used as host cells in the expression system
of the invention.
[0254] iii. Antibody Purification
[0255] Standard protein purification methods known in the art can
be employed. The following procedures are exemplary of suitable
purification procedures: fractionation on immunoaffinity or
ion-exchange columns, ethanol precipitation, reverse phase HPLC,
chromatography on silica or on a cation-exchange resin such as
DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation,
and gel filtration using, for example, Sephadex G-75.
[0256] In one aspect, Protein A immobilized on a solid phase is
used for immunoaffinity purification of the full length antibody
products of the invention. Protein A is a 41kD cell wall protein
from Staphylococcus aureas which binds with a high affinity to the
Fc region of antibodies. Lindmark et al (1983) J. Immunol. Meth.
62:1-13. The solid phase to which Protein A is immobilized is
preferably a column comprising a glass or silica surface, more
preferably a controlled pore glass column or a silicic acid column.
In some applications, the column has been coated with a reagent,
such as glycerol, in an attempt to prevent nonspecific adherence of
contaminants.
[0257] As the first step of purification, the preparation derived
from the cell culture as described above is applied onto the
Protein A immobilized solid phase to allow specific binding of the
antibody of interest to Protein A. The solid phase is then washed
to remove contaminants non-specifically bound to the solid phase.
Finally the antibody of interest is recovered from the solid phase
by elution.
[0258] b. Generating Antibodies Using Eukaryotic Host Cells:
[0259] The vector components generally include, but are not limited
to, one or more of the following: a signal sequence, an origin of
replication, one or more marker genes, an enhancer element, a
promoter, and a transcription termination sequence.
[0260] (i) Signal Sequence Component
[0261] A vector for use in a eukaryotic host cell may also contain
a signal sequence or other polypeptide having a specific cleavage
site at the N-terminus of the mature protein or polypeptide of
interest. The heterologous signal sequence selected preferably is
one that is recognized and processed (i.e., cleaved by a signal
peptidase) by the host cell. In mammalian cell expression,
mammalian signal sequences as well as viral secretory leaders, for
example, the herpes simplex gD signal, are available.
[0262] The DNA for such precursor region is ligated in reading
frame to DNA encoding the antibody.
[0263] (ii) Origin of Replication
[0264] Generally, an origin of replication component is not needed
for mammalian expression vectors. For example, the SV40 origin may
typically be used only because it contains the early promoter.
[0265] (iii) Selection Gene Component
[0266] Expression and cloning vectors may contain a selection gene,
also termed a selectable marker. Typical selection genes encode
proteins that (a) confer resistance to antibiotics or other toxins,
e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b)
complement auxotrophic deficiencies, where relevant, or (c) supply
critical nutrients not available from complex media.
[0267] One example of a selection scheme utilizes a drug to arrest
growth of a host cell. Those cells that are successfully
transformed with a heterologous gene produce a protein conferring
drug resistance and thus survive the selection regimen. Examples of
such dominant selection use the drugs neomycin, mycophenolic acid
and hygromycin.
[0268] Another example of suitable selectable markers for mammalian
cells are those that enable the identification of cells competent
to take up the antibody nucleic acid, such as DHFR, thymidine
kinase, metallothionein-I and -II, preferably primate
metallothionein genes, adenosine deaminase, ornithine
decarboxylase, etc.
[0269] For example, cells transformed with the DHFR selection gene
are first identified by culturing all of the transformants in a
culture medium that contains methotrexate (Mtx), a competitive
antagonist of DHFR. An appropriate host cell when wild-type DHFR is
employed is the Chinese hamster ovary (CHO) cell line deficient in
DHFR activity (e.g., ATCC CRL-9096).
[0270] Alternatively, host cells (particularly wild-type hosts that
contain endogenous DHFR) transformed or co-transformed with DNA
sequences encoding an antibody, wild-type DHFR protein, and another
selectable marker such as aminoglycoside 3'-phosphotransferase
(APH) can be selected by cell growth in medium containing a
selection agent for the selectable marker such as an
aminoglycosidic antibiotic, e.g., kanamycin, neomycin, or G418. See
U.S. Pat. No. 4,965,199.
[0271] (iv) Promoter Component
[0272] Expression and cloning vectors usually contain a promoter
that is recognized by the host organism and is operably linked to
the antibody polypeptide nucleic acid. Promoter sequences are known
for eukaryotes. Virtually all eukaryotic genes have an AT-rich
region located approximately 25 to 30 bases upstream from the site
where transcription is initiated. Another sequence found 70 to 80
bases upstream from the start of transcription of many genes is a
CNCAAT region where N may be any nucleotide. At the 3' end of most
eukaryotic genes is an AATAAA sequence that may be the signal for
addition of the poly A tail to the 3' end of the coding sequence.
All of these sequences are suitably inserted into eukaryotic
expression vectors.
[0273] Antibody polypeptide transcription from vectors in mammalian
host cells is controlled, for example, by promoters obtained from
the genomes of viruses such as polyoma virus, fowlpox virus,
adenovirus (such as Adenovirus 2), bovine papilloma virus, avian
sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and
Simian Virus 40 (SV40), from heterologous mammalian promoters,
e.g., the actin promoter or an immunoglobulin promoter, from
heat-shock promoters, provided such promoters are compatible with
the host cell systems.
[0274] The early and late promoters of the SV40 virus are
conveniently obtained as an SV40 restriction fragment that also
contains the SV40 viral origin of replication. The immediate early
promoter of the human cytomegalovirus is conveniently obtained as a
HindIII E restriction fragment. A system for expressing DNA in
mammalian hosts using the bovine papilloma virus as a vector is
disclosed in U.S. Pat. No. 4,419,446. A modification of this system
is described in U.S. Pat. No. 4,601,978. Alternatively, the Rous
Sarcoma Virus long terminal repeat can be used as the promoter.
[0275] (v) Enhancer Element Component
[0276] Transcription of DNA encoding the antibody polypeptide of
this invention by higher eukaryotes is often increased by inserting
an enhancer sequence into the vector. Many enhancer sequences are
now known from mammalian genes (globin, elastase, albumin,
a-fetoprotein, and insulin). Typically, however, one will use an
enhancer from a eukaryotic cell virus. Examples include the SV40
enhancer on the late side of the replication origin (bp 100-270),
the cytomegalovirus early promoter enhancer, the polyoma enhancer
on the late side of the replication origin, and adenovirus
enhancers. See also Yaniv, Nature 297:17-18 (1982) on enhancing
elements for activation of eukaryotic promoters. The enhancer may
be spliced into the vector at a position 5' or 3' to the antibody
polypeptide-encoding sequence, but is preferably located at a site
5' from the promoter.
[0277] (vi) Transcription Termination Component
[0278] Expression vectors used in eukaryotic host cells will
typically also contain sequences necessary for the termination of
transcription and for stabilizing the mRNA. Such sequences are
commonly available from the 5' and, occasionally 3', untranslated
regions of eukaryotic or viral DNAs or cDNAs. These regions contain
nucleotide segments transcribed as polyadenylated fragments in the
untranslated portion of the mRNA encoding an antibody. One useful
transcription termination component is the bovine growth hormone
polyadenylation region. See WO94/11026 and the expression vector
disclosed therein.
[0279] (vii) Selection and Transformation of Host Cells
[0280] Suitable host cells for cloning or expressing the DNA in the
vectors herein include higher eukaryote cells described herein,
including vertebrate host cells. Propagation of vertebrate cells in
culture (tissue culture) has become a routine procedure. Examples
of useful mammalian host cell lines are monkey kidney CV1 line
transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney
line (293 or 293 cells subcloned for growth in suspension culture,
Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney
cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR(CHO,
Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse
sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980));
monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney
cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells
(HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34);
buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells
(W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse
mammary tumor (MMT 060562, ATCC CCL51); TR1 cells (Mather et al.,
Annals N.Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells;
and a human hepatoma line (Hep G2).
[0281] Host cells are transformed with the above-described
expression or cloning vectors for antibody production and cultured
in conventional nutrient media modified as appropriate for inducing
promoters, selecting transformants, or amplifying the genes
encoding the desired sequences.
[0282] (viii) Culturing the Host Cells
[0283] The host cells used to produce an antibody of this invention
may be cultured in a variety of media. Commercially available media
such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM),
(Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium
((DMEM), Sigma) are suitable for culturing the host cells. In
addition, any of the media described in Ham et al., Meth. Enz.
58:44 (1979), Barnes et al., Anal. Biochem. 102:255 (1980), U.S.
Pat. Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469;
WO 90/03430; WO 87/00195; or U.S. Pat. Re. 30,985 may be used as
culture media for the host cells. Any of these media may be
supplemented as necessary with hormones and/or other growth factors
(such as insulin, transferrin, or epidermal growth factor), salts
(such as sodium chloride, calcium, magnesium, and phosphate),
buffers (such as HEPES), nucleotides (such as adenosine and
thymidine), antibiotics (such as GENTAMYCIN.TM. drug), trace
elements (defined as inorganic compounds usually present at final
concentrations in the micromolar range), and glucose or an
equivalent energy source. Any other necessary supplements may also
be included at appropriate concentrations that would be known to
those skilled in the art. The culture conditions, such as
temperature, pH, and the like, are those previously used with the
host cell selected for expression, and will be apparent to the
ordinarily skilled artisan.
[0284] (ix) Purification of Antibody
[0285] When using recombinant techniques, the antibody can be
produced intracellularly, or directly secreted into the medium. If
the antibody is produced intracellularly, as a first step, the
particulate debris, either host cells or lysed fragments, are
removed, for example, by centrifugation or ultrafiltration. Where
the antibody is secreted into the medium, supernatants from such
expression systems are generally first concentrated using a
commercially available protein concentration filter, for example,
an Amicon or Millipore Pellicon ultrafiltration unit. A protease
inhibitor such as PMSF may be included in any of the foregoing
steps to inhibit proteolysis and antibiotics may be included to
prevent the growth of adventitious contaminants.
[0286] The antibody composition prepared from the cells can be
purified using, for example, hydroxylapatite chromatography, gel
electrophoresis, dialysis, and affinity chromatography, with
affinity chromatography being the preferred purification technique.
The suitability of protein A as an affinity ligand depends on the
species and isotype of any immunoglobulin Fc domain that is present
in the antibody. Protein A can be used to purify antibodies that
are based on human .gamma.1, .gamma.2, or .gamma.4 heavy chains
(Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G is
recommended for all mouse isotypes and for human .gamma.3 (Guss et
al., EMBO J. 5:15671575 (1986)). The matrix to which the affinity
ligand is attached is most often agarose, but other matrices are
available. Mechanically stable matrices such as controlled pore
glass or poly(styrenedivinyl)benzene allow for faster flow rates
and shorter processing times than can be achieved with agarose.
Where the antibody comprises a CH3 domain, the Bakerbond
ABX.TM.resin (J. T. Baker, Phillipsburg, N.J.) is useful for
purification. Other techniques for protein purification such as
fractionation on an ion-exchange column, ethanol precipitation,
Reverse Phase HPLC, chromatography on silica, chromatography on
heparin SEPHAROSE.TM. chromatography on an anion or cation exchange
resin (such as a polyaspartic acid column), chromatofocusing,
SDS-PAGE, and ammonium sulfate precipitation are also available
depending on the antibody to be recovered.
[0287] Following any preliminary purification step(s), the mixture
comprising the antibody of interest and contaminants may be
subjected to low pH hydrophobic interaction chromatography using an
elution buffer at a pH between about 2.5-4.5, preferably performed
at low salt concentrations (e.g., from about 0-0.25M salt).
Immunoconjugates
[0288] The invention also provides immunoconjugates
(interchangeably termed "antibody-drug conjugates" or "ADC"),
comprising any of the anti-EphB2 antibodies described herein
conjugated to a cytotoxic agent such as a chemotherapeutic agent, a
drug, a growth inhibitory agent, a toxin (e.g., an enzymatically
active toxin of bacterial, fungal, plant, or animal origin, or
fragments thereof), or a radioactive isotope (i.e., a
radioconjugate).
[0289] The use of antibody-drug conjugates for the local delivery
of cytotoxic or cytostatic agents, i.e. drugs to kill or inhibit
tumor cells in the treatment of cancer (Syrigos and Epenetos (1999)
Anticancer Research 19:605-614; Niculescu-Duvaz and Springer (1997)
Adv. Drg Del. Rev. 26:151-172; U.S. Pat. No. 4,975,278) allows
targeted delivery of the drug moiety to tumors, and intracellular
accumulation therein, where systemic administration of these
unconjugated drug agents may result in unacceptable levels of
toxicity to normal cells as well as the tumor cells sought to be
eliminated (Baldwin et al., (1986) Lancet pp. (Mar. 15,
1986):603-05; Thorpe, (1985) "Antibody Carriers Of Cytotoxic Agents
In Cancer Therapy: A Review," in Monoclonal Antibodies '84:
Biological And Clinical Applications, A. Pinchera et al. (ed.s),
pp. 475-506). Maximal efficacy with minimal toxicity is sought
thereby. Both polyclonal antibodies and monoclonal antibodies have
been reported as useful in these strategies (Rowland et al., (1986)
Cancer Immunol. Immunother., 21:183-87). Drugs used in these
methods include daunomycin, doxorubicin, methotrexate, and
vindesine (Rowland et al., (1986) supra). Toxins used in
antibody-toxin conjugates include bacterial toxins such as
diphtheria toxin, plant toxins such as ricin, small molecule toxins
such as geldanamycin (Mandler et al (2000) Jour. of the Nat. Cancer
Inst. 92(19):1573-1581; Mandler et al (2000) Bioorganic & Med.
Chem. Letters 10:1025-1028; Mandler et al (2002) Bioconjugate Chem.
13:786-791), maytansinoids (EP 1391213; Liu et al., (1996) Proc.
Natl. Acad. Sci. USA 93:8618-8623), and calicheamicin (Lode et al
(1998) Cancer Res. 58:2928; Hinman et al (1993) Cancer Res.
53:3336-3342). The toxins may effect their cytotoxic and cytostatic
effects by mechanisms including tubulin binding, DNA binding, or
topoisomerase inhibition. Some cytotoxic drugs tend to be inactive
or less active when conjugated to large antibodies or protein
receptor ligands.
[0290] ZEVALIN.RTM. (ibritumomab tiuxetan, Biogen/Idec) is an
antibody-radioisotope conjugate composed of a murine IgG1 kappa
monoclonal antibody directed against the CD20 antigen found on the
surface of normal and malignant B lymphocytes and .sup.111In or
.sup.90Y radioisotope bound by a thiourea linker-chelator (Wiseman
et al (2000) Eur. Jour. Nucl. Med. 27(7):766-77; Wiseman et al
(2002) Blood 99(12):4336-42; Witzig et al (2002) J. Clin. Oncol.
20(10):2453-63; Witzig et al (2002) J. Clin. Oncol.
20(15):3262-69). Although ZEVALIN has activity against B-cell
non-Hodgkin's Lymphoma (NHL), administration results in severe and
prolonged cytopenias in most patients. MYLOTARG.TM. (gemtuzumab
ozogamicin, Wyeth Pharmaceuticals), an antibody drug conjugate
composed of a hu CD33 antibody linked to calicheamicin, was
approved in 2000 for the treatment of acute myeloid leukemia by
injection (Drugs of the Future (2000) 25(7):686; U.S. Pat. Nos.
4,970,198; 5,079,233; 5,585,089; 5,606,040; 5,693,762; 5,739,116;
5,767,285; 5,773,001). Cantuzumab mertansine (Immunogen, Inc.), an
antibody drug conjugate composed of the huC242 antibody linked via
the disulfide linker SPP to the maytansinoid drug moiety, DM1, is
advancing into Phase II trials for the treatment of cancers that
express CanAg, such as colon, pancreatic, gastric, and others.
MLN-2704 (Millennium Pharm., BZL Biologics, Immunogen Inc.), an
antibody drug conjugate composed of the anti-prostate specific
membrane antigen (PSMA) monoclonal antibody linked to the
maytansinoid drug moiety, DM1, is under development for the
potential treatment of prostate tumors. The auristatin peptides,
auristatin E (AE) and monomethylauristatin (MMAE), synthetic
analogs of dolastatin, were conjugated to chimeric monoclonal
antibodies cBR96 (specific to Lewis Y on carcinomas) and cAC10
(specific to CD30 on hematological malignancies) (Doronina et al
(2003) Nature Biotechnology 21(7):778-784) and are under
therapeutic development. Chemotherapeutic agents useful in the
generation of immunoconjugates are described herein (above).
Enzymatically active toxins and fragments thereof that can be used
include diphtheria A chain, nonbinding active fragments of
diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa),
ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin,
Aleurites fordii proteins, dianthin proteins, Phytolaca americana
proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor,
curcin, crotin, sapaonaria officinalis inhibitor, gelonin,
mitogellin, restrictocin, phenomycin, enomycin, and the
tricothecenes. See, e.g., WO 93/21232 published Oct. 28, 1993. A
variety of radionuclides are available for the production of
radioconjugated antibodies. Examples include .sup.212Bi, 131I,
.sup.131In, .sup.90Y, and .sup.186Re. Conjugates of the antibody
and cytotoxic agent are made using a variety of bifunctional
protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol)
propionate (SPDP), iminothiolane (IT), bifunctional derivatives of
imidoesters (such as dimethyl adipimidate HCl), active esters (such
as disuccinimidyl suberate), aldehydes (such as glutaraldehyde),
bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine),
bis-diazonium derivatives (such as
bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as
toluene 2,6-diisocyanate), and bis-active fluorine compounds (such
as 1,5-difluoro-2,4-dinitrobenzene). For example, a ricin
immunotoxin can be prepared as described in Vitetta et al.,
Science, 238: 1098 (1987). Carbon-14-labeled
1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid
(MX-DTPA) is an exemplary chelating agent for conjugation of
radionucleotide to the antibody. See WO94/11026.
[0291] Conjugates of an antibody and one or more small molecule
toxins, such as a calicheamicin, maytansinoids, dolastatins,
aurostatins, a trichothecene, and CC1065, and the derivatives of
these toxins that have toxin activity, are also contemplated
herein.
[0292] i. Maytansine and Maytansinoids
[0293] In some embodiments, the immunoconjugate comprises an
antibody (full length or fragments) of the invention conjugated to
one or more maytansinoid molecules.
[0294] Maytansinoids are mitototic inhibitors which act by
inhibiting tubulin polymerization. Maytansine was first isolated
from the east African shrub Maytenus serrata (U.S. Pat. No.
3,896,111). Subsequently, it was discovered that certain microbes
also produce maytansinoids, such as maytansinol and C-3 maytansinol
esters (U.S. Pat. No. 4,151,042). Synthetic maytansinol and
derivatives and analogues thereof are disclosed, for example, in
U.S. Pat. Nos. 4,137,230; 4,248,870; 4,256,746; 4,260,608;
4,265,814; 4,294,757; 4,307,016; 4,308,268; 4,308,269; 4,309,428;
4,313,946; 4,315,929; 4,317,821; 4,322,348; 4,331,598; 4,361,650;
4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371,533.
[0295] Maytansinoid drug moieties are attractive drug moieties in
antibody drug conjugates because they are: (i) relatively
accessible to prepare by fermentation or chemical modification,
derivatization of fermentation products, (ii) amenable to
derivatization with functional groups suitable for conjugation
through the non-disulfide linkers to antibodies, (iii) stable in
plasma, and (iv) effective against a variety of tumor cell
lines.
[0296] Exemplary embodiments of maytansinoid drug moieties include:
DM1; DM3; and DM4, having the structures:
##STR00001##
[0297] wherein the wavy line indicates the covalent attachment of
the sulfur atom of the drug to a linker (L) of an antibody drug
conjugate.
[0298] Other exemplary maytansinoid antibody drug conjugates have
the following structures and abbreviations, (wherein Ab is antibody
and p is 1 to about 8):
##STR00002##
[0299] Exemplary antibody drug conjugates where DM1 is linked
through a BMPEO linker to a thiol group of the antibody have the
structure and abbreviation:
##STR00003##
[0300] wherein Ab is antibody; n is 0, 1, or 2; and p is 1, 2, 3,
or 4.
[0301] Immunoconjugates containing maytansinoids, methods of making
same, and their therapeutic use are disclosed, for example, in U.S.
Pat. Nos. 5,208,020, 5,416,064 and European Patent EP 0 425 235 B1,
the disclosures of which are hereby expressly incorporated by
reference. Liu et al., Proc. Natl. Acad. Sci. USA 93:8618-8623
(1996) described immunoconjugates comprising a maytansinoid
designated DM1 linked to the monoclonal antibody C242 directed
against human colorectal cancer. The conjugate was found to be
highly cytotoxic towards cultured colon cancer cells, and showed
antitumor activity in an in vivo tumor growth assay. Chari et al.,
Cancer Research 52:127-131 (1992) describe immunoconjugates in
which a maytansinoid was conjugated via a disulfide linker to the
murine antibody A7 binding to an antigen on human colon cancer cell
lines, or to another murine monoclonal antibody TA.1 that binds the
HER-2/neu oncogene. The cytotoxicity of the TA.1-maytansinoid
conjugate was tested in vitro on the human breast cancer cell line
SK-BR-3, which expresses 3.times.10.sup.5 HER-2 surface antigens
per cell. The drug conjugate achieved a degree of cytotoxicity
similar to the free maytansinoid drug, which could be increased by
increasing the number of maytansinoid molecules per antibody
molecule. The A7-maytansinoid conjugate showed low systemic
cytotoxicity in mice.
[0302] Antibody-maytansinoid conjugates are prepared by chemically
linking an antibody to a maytansinoid molecule without
significantly diminishing the biological activity of either the
antibody or the maytansinoid molecule. See, e.g., U.S. Pat. No.
5,208,020 (the disclosure of which is hereby expressly incorporated
by reference). An average of 3-4 maytansinoid molecules conjugated
per antibody molecule has shown efficacy in enhancing cytotoxicity
of target cells without negatively affecting the function or
solubility of the antibody, although even one molecule of
toxin/antibody would be expected to enhance cytotoxicity over the
use of naked antibody. Maytansinoids are well known in the art and
can be synthesized by known techniques or isolated from natural
sources. Suitable maytansinoids are disclosed, for example, in U.S.
Pat. No. 5,208,020 and in the other patents and nonpatent
publications referred to hereinabove. Preferred maytansinoids are
maytansinol and maytansinol analogues modified in the aromatic ring
or at other positions of the maytansinol molecule, such as various
maytansinol esters.
[0303] There are many linking groups known in the art for making
antibody-maytansinoid conjugates, including, for example, those
disclosed in U.S. Pat. No. 5,208,020 or EP Patent 0 425 235 B1,
Chari et al., Cancer Research 52:127-131 (1992), and U.S. patent
application Ser. No. 10/960,602, filed Oct. 8, 2004, the
disclosures of which are hereby expressly incorporated by
reference. Antibody-maytansinoid conjugates comprising the linker
component SMCC may be prepared as disclosed in U.S. patent
application Ser. No. 10/960,602, filed Oct. 8, 2004. The linking
groups include disulfide groups, thioether groups, acid labile
groups, photolabile groups, peptidase labile groups, or esterase
labile groups, as disclosed in the above-identified patents,
disulfide and thioether groups being preferred. Additional linking
groups are described and exemplified herein.
[0304] Conjugates of the antibody and maytansinoid may be made
using a variety of bifunctional protein coupling agents such as
N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP),
succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCl), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutaraldehyde), bis-azido compounds
(such as bis (p-azidobenzoyl)hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as toluene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene).
Particularly preferred coupling agents include
N-succinimidyl-3-(2-pyridyldithio)propionate (SPDP) (Carlsson et
al., Biochem. J. 173:723-737 (1978)) and
N-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for a
disulfide linkage.
[0305] The linker may be attached to the maytansinoid molecule at
various positions, depending on the type of the link. For example,
an ester linkage may be formed by reaction with a hydroxyl group
using conventional coupling techniques. The reaction may occur at
the C-3 position having a hydroxyl group, the C-14 position
modified with hydroxymethyl, the C-15 position modified with a
hydroxyl group, and the C-20 position having a hydroxyl group. In a
preferred embodiment, the linkage is formed at the C-3 position of
maytansinol or a maytansinol analogue.
[0306] ii. Auristatins and Dolastatins
[0307] In some embodiments, the immunoconjugate comprises an
antibody of the invention conjugated to dolastatins or dolostatin
peptidic analogs and derivatives, the auristatins (U.S. Pat. Nos.
5,635,483; 5,780,588). Dolastatins and auristatins have been shown
to interfere with microtubule dynamics, GTP hydrolysis, and nuclear
and cellular division (Woyke et al (2001) Antimicrob. Agents and
Chemother. 45(12):3580-3584) and have anticancer (U.S. Pat. No.
5,663,149) and antifungal activity (Pettit et al (1998) Antimicrob.
Agents Chemother. 42:2961-2965). The dolastatin or auristatin drug
moiety may be attached to the antibody through the N (amino)
terminus or the C (carboxyl) terminus of the peptidic drug moiety
(WO 02/088172).
[0308] Exemplary auristatin embodiments include the N-terminus
linked monomethylauristatin drug moieties DE and DF, disclosed in
"Monomethylvaline Compounds Capable of Conjugation to Ligands",
U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, the disclosure of
which is expressly incorporated by reference in its entirety.
[0309] An exemplary auristatin embodiment is MMAE (wherein the wavy
line indicates the covalent attachment to a linker (L) of an
antibody drug conjugate).
##STR00004##
[0310] Another exemplary auristatin embodiment is MMAF (wherein the
wavy line indicates the covalent attachment to a linker (L) of an
antibody drug conjugate):
##STR00005##
[0311] Additional exemplary embodiments comprising MMAE or MMAF and
various linker components (described further herein) have the
following structures and abbreviations (wherein Ab means antibody
and p is 1 to about 8):
##STR00006##
[0312] Typically, peptide-based drug moieties can be prepared by
forming a peptide bond between two or more amino acids and/or
peptide fragments. Such peptide bonds can be prepared, for example,
according to the liquid phase synthesis method (see E. Schroder and
K. Lubke, "The Peptides", volume 1, pp 76-136, 1965, Academic
Press) that is well known in the field of peptide chemistry. The
auristatin/dolastatin drug moieties may be prepared according to
the methods of: U.S. Pat. No. 5,635,483; U.S. Pat. No. 5,780,588;
Pettit et al (1989) J. Am. Chem. Soc. 111:5463-5465; Pettit et al
(1998) Anti-Cancer Drug Design 13:243-277; Pettit, G. R., et al.
Synthesis, 1996, 719-725; and Pettit et al (1996) J. Chem. Soc.
Perkin Trans. 1 5:859-863. See also Doronina (2003) Nat Biotechnol
21(7):778-784; "Monomethylvaline Compounds Capable of Conjugation
to Ligands", U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, hereby
incorporated by reference in its entirety (disclosing, e.g.,
linkers and methods of preparing monomethylvaline compounds such as
MMAE and MMAF conjugated to linkers).
[0313] iii. Calicheamicin
[0314] In other embodiments, the immunoconjugate comprises an
antibody of the invention conjugated to one or more calicheamicin
molecules. The calicheamicin family of antibiotics are capable of
producing double-stranded DNA breaks at sub-picomolar
concentrations. For the preparation of conjugates of the
calicheamicin family, see U.S. Pat. Nos. 5,712,374, 5,714,586,
5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, 5,877,296
(all to American Cyanamid Company). Structural analogues of
calicheamicin which may be used include, but are not limited to,
.gamma..sub.1.sup.I, .alpha..sub.2.sup.I, .alpha..sub.3.sup.I,
N-acetyl-.gamma..sub.1.sup.I, PSAG and .theta..sup.I.sub.1 (Hinman
et al., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer
Research 58:2925-2928 (1998) and the aforementioned U.S. patents to
American Cyanamid). Another anti-tumor drug that the antibody can
be conjugated is QFA which is an antifolate. Both calicheamicin and
QFA have intracellular sites of action and do not readily cross the
plasma membrane. Therefore, cellular uptake of these agents through
antibody mediated internalization greatly enhances their cytotoxic
effects.
[0315] iv. Other Cytotoxic Agents
[0316] Other antitumor agents that can be conjugated to the
antibodies of the invention include BCNU, streptozoicin,
vincristine and 5-fluorouracil, the family of agents known
collectively LL-E33288 complex described in U.S. Pat. Nos.
5,053,394, 5,770,710, as well as esperamicins (U.S. Pat. No.
5,877,296).
[0317] Enzymatically active toxins and fragments thereof which can
be used include diphtheria A chain, nonbinding active fragments of
diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa),
ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin,
Aleurites fordii proteins, dianthin proteins, Phytolaca americana
proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor,
curcin, crotin, sapaonaria officinalis inhibitor, gelonin,
mitogellin, restrictocin, phenomycin, enomycin and the
tricothecenes. See, for example, WO 93/21232 published Oct. 28,
1993.
[0318] The present invention further contemplates an
immunoconjugate formed between an antibody and a compound with
nucleolytic activity (e.g., a ribonuclease or a DNA endonuclease
such as a deoxyribonuclease; DNase).
[0319] For selective destruction of the tumor, the antibody may
comprise a highly radioactive atom. A variety of radioactive
isotopes are available for the production of radioconjugated
antibodies. Examples include At.sup.211, I.sup.131, I.sup.125,
Y.sup.90, Re.sup.186, Re.sup.188, Sm.sup.153, Bi.sup.212, P.sup.32,
Pb.sup.212 and radioactive isotopes of Lu. When the conjugate is
used for detection, it may comprise a radioactive atom for
scintigraphic studies, for example tc.sup.99m or I.sup.123, or a
spin label for nuclear magnetic resonance (NMR) imaging (also known
as magnetic resonance imaging, mri), such as iodine-123 again,
iodine-131, indium-111, fluorine-19, carbon-13, nitrogen-15,
oxygen-17, gadolinium, manganese or iron.
[0320] The radio- or other labels may be incorporated in the
conjugate in known ways. For example, the peptide may be
biosynthesized or may be synthesized by chemical amino acid
synthesis using suitable amino acid precursors involving, for
example, fluorine-19 in place of hydrogen. Labels such as
tc.sup.99m or I.sup.123, Re.sup.186, Re.sup.188 and In.sup.111 can
be attached via a cysteine residue in the peptide. Yttrium-90 can
be attached via a lysine residue. The IODOGEN method (Fraker et al
(1978) Biochem. Biophys. Res. Commun. 80: 49-57 can be used to
incorporate iodine-123. "Monoclonal Antibodies in
Immunoscintigraphy" (Chatal, CRC Press 1989) describes other
methods in detail.
[0321] Conjugates of the antibody and cytotoxic agent may be made
using a variety of bifunctional protein coupling agents such as
N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP),
succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC),
iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCl), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutaraldehyde), bis-azido compounds
(such as bis (p-azidobenzoyl)hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as toluene 2,6-diisocyanate), and bis-active
fluorine compounds (such as 1,5-difluoro-2,4-dinitrobenzene). For
example, a ricin immunotoxin can be prepared as described in
Vitetta et al., Science 238:1098 (1987). Carbon-14-labeled
1-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid
(MX-DTPA) is an exemplary chelating agent for conjugation of
radionucleotide to the antibody. See WO94/11026. The linker may be
a "cleavable linker" facilitating release of the cytotoxic drug in
the cell. For example, an acid-labile linker, peptidase-sensitive
linker, photolabile linker, dimethyl linker or disulfide-containing
linker (Chari et al., Cancer Research 52:127-131 (1992); U.S. Pat.
No. 5,208,020) may be used.
[0322] The compounds of the invention expressly contemplate, but
are not limited to, ADC prepared with cross-linker reagents: BMPS,
EMCS, GMBS, HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB,
SMPH, sulfo-EMCS, sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB,
sulfo-SMCC, and sulfo-SMPB, and SVSB
(succinimidyl-(4-vinylsulfone)benzoate) which are commercially
available (e.g., from Pierce Biotechnology, Inc., Rockford, Ill.,
U.S.A). See pages 467-498, 2003-2004 Applications Handbook and
Catalog.
[0323] v. Preparation of Antibody Drug Conjugates
[0324] In the antibody drug conjugates (ADC) of the invention, an
antibody (Ab) is conjugated to one or more drug moieties (D), e.g.
about 1 to about 20 drug moieties per antibody, through a linker
(L). The ADC of Formula I may be prepared by several routes,
employing organic chemistry reactions, conditions, and reagents
known to those skilled in the art, including: (1) reaction of a
nucleophilic group of an antibody with a bivalent linker reagent,
to form Ab-L, via a covalent bond, followed by reaction with a drug
moiety D; and (2) reaction of a nucleophilic group of a drug moiety
with a bivalent linker reagent, to form D-L, via a covalent bond,
followed by reaction with the nucleophilic group of an antibody.
Additional methods for preparing ADC are described herein.
Ab-(L-D).sub.p I
[0325] The linker may be composed of one or more linker components.
Exemplary linker components include 6-maleimidocaproyl ("MC"),
maleimidopropanoyl ("MP"), valine-citrulline ("val-cit"),
alanine-phenylalanine ("ala-phe"), p-aminobenzyloxycarbonyl
("PAB"), N-Succinimidyl 4-(2-pyridylthio)pentanoate ("SPP"),
N-Succinimidyl 4-(N-maleimidomethyl)cyclohexane-1 carboxylate
("SMCC`), and N-Succinimidyl (4-iodo-acetyl)aminobenzoate
("SIAB''). Additional linker components are known in the art and
some are described herein. See also "Monomethylvaline Compounds
Capable of Conjugation to Ligands", U.S. Ser. No. 10/983,340, filed
Nov. 5, 2004, the contents of which are hereby incorporated by
reference in its entirety.
[0326] In some embodiments, the linker may comprise amino acid
residues. Exemplary amino acid linker components include a
dipeptide, a tripeptide, a tetrapeptide or a pentapeptide.
Exemplary dipeptides include: valine-citrulline (vc or val-cit),
alanine-phenylalanine (af or ala-phe). Exemplary tripeptides
include: glycine-valine-citrulline (gly-val-cit) and
glycine-glycine-glycine (gly-gly-gly). Amino acid residues which
comprise an amino acid linker component include those occurring
naturally, as well as minor amino acids and non-naturally occurring
amino acid analogs, such as citrulline. Amino acid linker
components can be designed and optimized in their selectivity for
enzymatic cleavage by a particular enzymes, for example, a
tumor-associated protease, cathepsin B, C and D, or a plasmin
protease.
[0327] Exemplary linker component structures are shown below
(wherein the wavy line indicates sites of covalent attachment to
other components of the ADC):
##STR00007##
[0328] Additional exemplary linker components and abbreviations
include (wherein the antibody (Ab) and linker are depicted, and p
is 1 to about 8):
##STR00008##
[0329] Nucleophilic groups on antibodies include, but are not
limited to: (i) N-terminal amine groups, (ii) side chain amine
groups, e.g. lysine, (iii) side chain thiol groups, e.g. cysteine,
and (iv) sugar hydroxyl or amino groups where the antibody is
glycosylated. Amine, thiol, and hydroxyl groups are nucleophilic
and capable of reacting to form covalent bonds with electrophilic
groups on linker moieties and linker reagents including: (i) active
esters such as NHS esters, HOBt esters, haloformates, and acid
halides; (ii) alkyl and benzyl halides such as haloacetamides;
(iii) aldehydes, ketones, carboxyl, and maleimide groups. Certain
antibodies have reducible interchain disulfides, i.e. cysteine
bridges. Antibodies may be made reactive for conjugation with
linker reagents by treatment with a reducing agent such as DTT
(dithiothreitol). Each cysteine bridge will thus form,
theoretically, two reactive thiol nucleophiles. Additional
nucleophilic groups can be introduced into antibodies through the
reaction of lysines with 2-iminothiolane (Traut's reagent)
resulting in conversion of an amine into a thiol. Reactive thiol
groups may be introduced into the antibody (or fragment thereof) by
introducing one, two, three, four, or more cysteine residues (e.g.,
preparing mutant antibodies comprising one or more non-native
cysteine amino acid residues).
[0330] Antibody drug conjugates of the invention may also be
produced by modification of the antibody to introduce electrophilic
moieties, which can react with nucleophilic substituents on the
linker reagent or drug. The sugars of glycosylated antibodies may
be oxidized, e.g. with periodate oxidizing reagents, to form
aldehyde or ketone groups which may react with the amine group of
linker reagents or drug moieties. The resulting imine Schiff base
groups may form a stable linkage, or may be reduced, e.g. by
borohydride reagents to form stable amine linkages. In one
embodiment, reaction of the carbohydrate portion of a glycosylated
antibody with either glactose oxidase or sodium meta-periodate may
yield carbonyl (aldehyde and ketone) groups in the protein that can
react with appropriate groups on the drug (Hermanson, Bioconjugate
Techniques). In another embodiment, proteins containing N-terminal
serine or threonine residues can react with sodium meta-periodate,
resulting in production of an aldehyde in place of the first amino
acid (Geoghegan & Stroh, (1992) Bioconjugate Chem. 3:138-146;
U.S. Pat. No. 5,362,852). Such aldehyde can be reacted with a drug
moiety or linker nucleophile.
[0331] Likewise, nucleophilic groups on a drug moiety include, but
are not limited to: amine, thiol, hydroxyl, hydrazide, oxime,
hydrazine, thiosemicarbazone, hydrazine carboxylate, and
arylhydrazide groups capable of reacting to form covalent bonds
with electrophilic groups on linker moieties and linker reagents
including: (i) active esters such as NHS esters, HOBt esters,
haloformates, and acid halides; (ii) alkyl and benzyl halides such
as haloacetamides; (iii) aldehydes, ketones, carboxyl, and
maleimide groups.
[0332] Alternatively, a fusion protein comprising the antibody and
cytotoxic agent may be made, e.g., by recombinant techniques or
peptide synthesis. The length of DNA may comprise respective
regions encoding the two portions of the conjugate either adjacent
one another or separated by a region encoding a linker peptide
which does not destroy the desired properties of the conjugate.
[0333] In yet another embodiment, the antibody may be conjugated to
a "receptor" (such streptavidin) for utilization in tumor
pre-targeting wherein the antibody-receptor conjugate is
administered to the patient, followed by removal of unbound
conjugate from the circulation using a clearing agent and then
administration of a "ligand" (e.g., avidin) which is conjugated to
a cytotoxic agent (e.g., a radionucleotide).
[0334] Antibody (Ab)-MC-MMAE may be prepared by conjugation of any
of the antibodies provided herein with MC-MMAE as follows.
Antibody, dissolved in 500 mM sodium borate and 500 mM sodium
chloride at pH 8.0 is treated with an excess of 100 mM
dithiothreitol (DTT). After incubation at 37.degree. C. for about
30 minutes, the buffer is exchanged by elution over Sephadex G25
resin and eluted with PBS with 1 mM DTPA. The thiol/Ab value is
checked by determining the reduced antibody concentration from the
absorbance at 280 nm of the solution and the thiol concentration by
reaction with DTNB (Aldrich, Milwaukee, Wis.) and determination of
the absorbance at 412 nm. The reduced antibody dissolved in PBS is
chilled on ice. The drug linker reagent,
maleimidocaproyl-monomethyl auristatin E (MMAE), i.e. MC-MMAE,
dissolved in DMSO, is diluted in acetonitrile and water at known
concentration, and added to the chilled reduced antibody 2H9 in
PBS. After about one hour, an excess of maleimide is added to
quench the reaction and cap any unreacted antibody thiol groups.
The reaction mixture is concentrated by centrifugal ultrafiltration
and 2H9-MC-MMAE is purified and desalted by elution through G25
resin in PBS, filtered through 0.2 .mu.m filters under sterile
conditions, and frozen for storage.
[0335] Antibody-MC-MMAF may be prepared by conjugation of any of
the antibodies provided herein with MC-MMAF following the protocol
provided for preparation of Ab-MC-MMAE.
[0336] Antibody-MC-val-cit-PAB-MMAE may be prepared by conjugation
of any of the antibodies provided herein with MC-val-cit-PAB-MMAE
following the protocol provided for preparation of Ab-MC-MMAE.
[0337] Antibody-MC-val-cit-PAB-MMAF may be prepared by conjugation
of any of the antibodies provided herein with MC-val-cit-PAB-MMAF
following the protocol provided for preparation of Ab-MC-MMAE.
[0338] Antibody-SMCC-DM1 may be prepared by conjugation of any of
the antibodies provided herein with SMCC-DM1 as follows. Purified
antibody is derivatized with (Succinimidyl
4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC, Pierce
Biotechnology, Inc) to introduce the SMCC linker. Specifically,
antibody is treated at 20 mg/mL in 50 mM potassium phosphate/50 mM
sodium chloride/2 mM EDTA, pH 6.5 with 7.5 molar equivalents of
SMCC (20 mM in DMSO, 6.7 mg/mL). After stirring for 2 hours under
argon at ambient temperature, the reaction mixture is filtered
through a Sephadex G25 column equilibrated with 50 mM potassium
phosphate/50 mM sodium chloride/2 mM EDTA, pH 6.5. Antibody
containing fractions are pooled and assayed.
[0339] Antibody-SMCC prepared thus is diluted with 50 mM potassium
phosphate/50 mM sodium chloride/2 mM EDTA, pH 6.5, to a final
concentration of about 10 mg/ml, and reacted with a 10 mM solution
of DM1 in dimethylacetamide. The reaction is stirred at ambient
temperature under argon 16.5 hours. The conjugation reaction
mixture is filtered through a Sephadex G25 gel filtration column
(1.5.times.4.9 cm) with 1.times.PBS at pH 6.5. The DM1 drug to
antibody ratio (p) may be about 2 to 5, as measured by the
absorbance at 252 nm and at 280 nm.
[0340] Ab-SPP-DM1 may be prepared by conjugation of any of the
antibodies provided herein with SPP-DM1 as follows. Purified
antibody is derivatized with
N-succinimidyl-4-(2-pyridylthio)pentanoate to introduce
dithiopyridyl groups. Antibody (376.0 mg, 8 mg/mL) in 44.7 mL of 50
mM potassium phosphate buffer (pH 6.5) containing NaCl (50 mM) and
EDTA (1 mM) is treated with SPP (5.3 molar equivalents in 2.3 mL
ethanol). After incubation for 90 minutes under argon at ambient
temperature, the reaction mixture is gel filtered through a
Sephadex G25 column equilibrated with 35 mM sodium citrate, 154 mM
NaCl, 2 mM EDTA. Antibody containing fractions were pooled and
assayed. The degree of modification of the antibody is determined
as described above.
[0341] Antibody-SPP-Py (about 10 .mu.moles of releasable
2-thiopyridine groups) is diluted with the above 35 mM sodium
citrate buffer, pH 6.5, to a final concentration of about 2.5
mg/mL. DM1 (1.7 equivalents, 17 .mu.moles) in 3.0 mM
dimethylacetamide (DMA, 3% v/v in the final reaction mixture) is
then added to the antibody solution. The reaction proceeds at
ambient temperature under argon for about 20 hours. The reaction is
loaded on a Sephacryl S300 gel filtration column (5.0 cm.times.90.0
cm, 1.77 L) equilibrated with 35 mM sodium citrate, 154 mM NaCl, pH
6.5. The flow rate may be about 5.0 mL/min and 65 fractions (20.0
mL each) are collected. The number of DM1 drug molecules linked per
antibody molecule (p') is determined by measuring the absorbance at
252 nm and 280 nm, and may be about 2 to 4 DM1 drug moieties per
antibody.
[0342] Antibody-BMPEO-DM1 may be prepared by conjugation of any of
the antibodies provided herein with BMPEO-DM1 as follows. The
antibody is modified by the bis-maleimido reagent BM(PEO).sub.4
(Pierce Chemical), leaving an unreacted maleimido group on the
surface of the antibody. This may be accomplished by dissolving
BM(PEO).sub.4 in a 50% ethanol/water mixture to a concentration of
10 mM and adding a tenfold molar excess to a solution containing
antibody in phosphate buffered saline at a concentration of
approximately 1.6 mg/ml (10 micromolar) and allowing it to react
for 1 hour to form antibody-linker intermediate, antibody-BMPEO.
Excess BM(PEO).sub.4 is removed by gel filtration (HiTrap column,
Pharmacia) in 30 mM citrate, pH 6 with 150 mM NaCl buffer. An
approximate 10 fold molar excess DM1 is dissolved in dimethyl
acetamide (DMA) and added to the antibody-BMPEO intermediate.
Dimethyl formamide (DMF) may also be employed to dissolve the drug
moiety reagent. The reaction mixture is allowed to react overnight
before gel filtration or dialysis into PBS to remove unreacted DM1.
Gel filtration on 5200 columns in PBS is used to remove high
molecular weight aggregates and furnish purified
antibody-BMPEO-DM1.
Pharmaceutical Formulations
[0343] Therapeutic formulations comprising an antibody of the
invention are prepared for storage by mixing the antibody having
the desired degree of purity with optional physiologically
acceptable carriers, excipients or stabilizers (Remington: The
Science and Practice of Pharmacy 20th edition (2000)), in the form
of aqueous solutions, lyophilized or other dried formulations.
Acceptable carriers, excipients, or stabilizers are nontoxic to
recipients at the dosages and concentrations employed, and include
buffers such as phosphate, citrate, histidine and other organic
acids; antioxidants including ascorbic acid and methionine;
preservatives (such as octadecyldimethylbenzyl ammonium chloride;
hexamethonium chloride; benzalkonium chloride, benzethonium
chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as
methyl or propyl paraben; catechol; resorcinol; cyclohexanol;
3-pentanol; and m-cresol); low molecular weight (less than about 10
residues) polypeptides; proteins, such as serum albumin, gelatin,
or immunoglobulins; hydrophilic polymers such as
polyvinylpyrrolidone; amino acids such as glycine, glutamine,
asparagine, histidine, arginine, or lysine; monosaccharides,
disaccharides, and other carbohydrates including glucose, mannose,
or dextrins; chelating agents such as EDTA; sugars such as sucrose,
mannitol, trehalose or sorbitol; salt-forming counter-ions such as
sodium; metal complexes (e.g., Zn-protein complexes); and/or
non-ionic surfactants such as TWEEN.TM., PLURONICS.TM. or
polyethylene glycol (PEG).
[0344] The formulation herein may also contain more than one active
compound as necessary for the particular indication being treated,
preferably those with complementary activities that do not
adversely affect each other. Such molecules are suitably present in
combination in amounts that are effective for the purpose
intended.
[0345] The active ingredients may also be entrapped in microcapsule
prepared, for example, by coacervation techniques or by interfacial
polymerization, for example, hydroxymethylcellulose or
gelatin-microcapsule and poly-(methylmethacylate) microcapsule,
respectively, in colloidal drug delivery systems (for example,
liposomes, albumin microspheres, microemulsions, nano-particles and
nanocapsules) or in macroemulsions. Such techniques are disclosed
in Remington: The Science and Practice of Pharmacy 20th edition
(2000).
[0346] The formulations to be used for in vivo administration must
be sterile. This is readily accomplished by filtration through
sterile filtration membranes.
[0347] Sustained-release preparations may be prepared. Suitable
examples of sustained-release preparations include semipermeable
matrices of solid hydrophobic polymers containing the
immunoglobulin of the invention, which matrices are in the form of
shaped articles, e.g., films, or microcapsule. Examples of
sustained-release matrices include polyesters, hydrogels (for
example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)),
polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic
acid and .gamma. ethyl-L-glutamate, non-degradable ethylene-vinyl
acetate, degradable lactic acid-glycolic acid copolymers such as
the LUPRON DEPOT.TM. (injectable microspheres composed of lactic
acid-glycolic acid copolymer and leuprolide acetate), and
poly-D-(-)-3-hydroxybutyric acid. While polymers such as
ethylene-vinyl acetate and lactic acid-glycolic acid enable release
of molecules for over 100 days, certain hydrogels release proteins
for shorter time periods. When encapsulated immunoglobulins remain
in the body for a long time, they may denature or aggregate as a
result of exposure to moisture at 37.degree. C., resulting in a
loss of biological activity and possible changes in immunogenicity.
Rational strategies can be devised for stabilization depending on
the mechanism involved. For example, if the aggregation mechanism
is discovered to be intermolecular S--S bond formation through
thio-disulfide interchange, stabilization may be achieved by
modifying sulfhydryl residues, lyophilizing from acidic solutions,
controlling moisture content, using appropriate additives, and
developing specific polymer matrix compositions.
Uses
[0348] An antibody of the present invention may be used in, for
example, in vitro, ex vivo and in vivo therapeutic methods.
[0349] In one aspect, the invention provides methods for treating
or preventing a tumor, a cancer, and/or a cell proliferative
disorder associated with increased expression and/or activity of
EphB2, the methods comprising administering an effective amount of
an anti-EphB2 antibody or immunoconjugate to a subject in need of
such treatment.
[0350] In one aspect, the invention provides methods for killing a
tumor cell, the methods comprising administering an effective
amount of an anti-EphB2 antibody or immunoconjugate (in some
embodiments, an anti-EphB2 antibody or immunoconjugate of the
invention) to a subject in need of such treatment.
[0351] In one aspect, the invention provides methods for reducing,
inhibiting, or preventing growth of a tumor or cancer, the methods
comprising administering an effective amount of an anti-EphB2
antibody or immunoconjugate to a subject in need of such
treatment.
[0352] Moreover, at least some of the antibodies of the invention
can bind antigen from other species. Accordingly, the antibodies of
the invention can be used to bind specific antigen activity, e.g.,
in a cell culture containing the antigen, in human subjects or in
other mammalian subjects having the antigen with which an antibody
of the invention cross-reacts (e.g. chimpanzee, baboon, marmoset,
cynomolgus and rhesus, pig or mouse). In one embodiment, the
antibody of the invention can be used for inhibiting antigen
activities by contacting the antibody with the antigen such that
antigen activity is inhibited. Preferably, the antigen is a human
protein molecule.
[0353] In one embodiment, an antibody of the invention can be used
in a method for binding an antigen in a subject suffering from a
disorder associated with increased antigen expression and/or
activity, comprising administering to the subject an antibody of
the invention such that the antigen in the subject is bound.
Preferably, the antigen is a human protein molecule and the subject
is a human subject. Alternatively, the subject can be a mammal
expressing the antigen with which an antibody of the invention
binds. Still further the subject can be a mammal into which the
antigen has been introduced (e.g., by administration of the antigen
or by expression of an antigen transgene). An antibody of the
invention can be administered to a human subject for therapeutic
purposes. Moreover, an antibody of the invention can be
administered to a non-human mammal expressing an antigen with which
the immunoglobulin cross-reacts (e.g., a primate, pig or mouse) for
veterinary purposes or as an animal model of human disease.
Regarding the latter, such animal models may be useful for
evaluating the therapeutic efficacy of antibodies of the invention
(e.g., testing of dosages and time courses of administration).
[0354] The antibodies of the invention can be used to treat,
inhibit, delay progression of, prevent/delay recurrence of,
ameliorate, or prevent diseases, disorders or conditions associated
with expression and/or activity of one or more antigen
molecules.
[0355] Exemplary disorders include carcinoma, lymphoma, blastoma,
sarcoma, and leukemia or lymphoid malignancies. More particular
examples of such cancers include squamous cell cancer (e.g.,
epithelial squamous cell cancer), lung cancer including small-cell
lung cancer, non-small cell lung cancer, adenocarcinoma of the lung
and squamous carcinoma of the lung, cancer of the peritoneum,
hepatocellular cancer, gastric or stomach cancer including
gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical
cancer, ovarian cancer, liver cancer, bladder cancer, cancer of the
urinary tract, hepatoma, breast cancer, colon cancer, rectal
cancer, colorectal cancer, endometrial or uterine carcinoma,
salivary gland carcinoma, kidney or renal cancer, prostate cancer,
vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma,
penile carcinoma, melanoma, multiple myeloma and B-cell lymphoma,
brain, as well as head and neck cancer, and associated metastases.
In some embodiments, the cancer is selected from the group
consisting of small cell lung cancer, neuroblastomas, melanoma,
breast carcinoma, gastric cancer, colorectal cancer (CRC), and
hepatocellular carcinoma. In some embodiments, the cancer is
colorectal cancer.
[0356] The antibodies of the invention are also useful in the
treatment (including prevention) of disorders the pathology of
which involves cellular degeneration or dysfunction, such as
treatment of various (chronic) neurodegenerative disorders and
acute nerve cell injuries. Such neurodegenerative disorders
include, without limitation, peripheral neuropathies; motorneuron
disorders, such as amylotrophic lateral sclerosis (ALS, Lou
Gehrig's disease), Bell's palsy, and various conditions involving
spinal muscular atrophy or paralysis; and other human
neurodegenerative diseases, such as Alzheimer's disease,
Parkinson's disease, epilepsy, multiple sclerosis, Huntington's
chorea, Down's Syndrome, nerve deafness, and Meniere's disease, and
acute nerve cell injuries, for example due to trauma or spinal cord
injury.
[0357] The antibodies of the invention are also useful for
inhibiting angiogenesis. In some embodiments, the site of
angiogenesis is a tumor or cancer.
[0358] In some embodiments, the disorder is characterized by colon
adenoma(s). The methods of the invention are particularly suitable
for disorders characterized by a plurality of colon adenomas (such
as more than 10, 20, 30, 40, 50, 100, 200, 300, 400, 500, 600, 700,
800, 900, 1000, or more colon adenomas), including at least the
following: autosomal dominant familial adenomatous polyposis (FAP)
disorder caused by mutation in the APC gene (Tomlinson et al., J
Med Genet. 1996; 33:268-73); Peutz-Jegher's syndrome (PJS),
Juvenile Polyposis Syndrome (JPS), Attenuated FAP caused by
mutations in the MYH gene (Sieber et al. N Eng J Med 348:791-9
(2003)), Hereditary Mixed Polyposis syndrome (HMPS), Cowden
disease, and Bannayan-Ruvalcaba-Riley syndrome.
[0359] EphB2 has been implicated in motoaxon guidance and neural
crest cell migration in the developing embryo. Accordingly, the
antibodies of the invention are also useful for modulating axon
guidance, neuronal development, and/or neural crest migration in
vitro or in vivo.
[0360] In certain embodiments, an immunoconjugate comprising an
antibody conjugated with one or more cytotoxic agent(s) is
administered to the patient. In some embodiments, the
immunoconjugate and/or antigen to which it is bound is/are
internalized by the cell, resulting in increased therapeutic
efficacy of the immunoconjugate in killing the target cell to which
it binds. In one embodiment, the cytotoxic agent targets or
interferes with nucleic acid in the target cell. In one embodiment,
the cytotoxic agent targets or interferes with microtubule
polymerization. Examples of such cytotoxic agents include any of
the chemotherapeutic agents noted herein (such as a maytansinoid,
auristatin, dolastatin, or a calicheamicin), a radioactive isotope,
or a ribonuclease or a DNA endonuclease.
[0361] Antibodies and immunoconjugates of the invention can be used
either alone or in combination with other compositions in a
therapy. For instance, an antibody of the invention may be
co-administered with another antibody, chemotherapeutic agent(s)
(including cocktails of chemotherapeutic agents), other cytotoxic
agent(s), anti-angiogenic agent(s), cytokines, and/or growth
inhibitory agent(s). Where an antibody of the invention inhibits
tumor growth, it may be particularly desirable to combine it with
one or more other therapeutic agent(s) which also inhibits tumor
growth. For instance, anti-VEGF antibodies blocking VEGF activities
may be combined with anti-ErbB antibodies (e.g. HERCEPTIN.RTM.
anti-HER2 antibody) in a treatment of metastatic breast cancer.
Alternatively, or additionally, the patient may receive combined
radiation therapy (e.g. external beam irradiation or therapy with a
radioactive labeled agent, such as an antibody). Such combined
therapies noted above include combined administration (where the
two or more agents are included in the same or separate
formulations), and separate administration, in which case,
administration of the antibody of the invention can occur prior to,
and/or following, administration of the adjunct therapy or
therapies.
[0362] The antibody of the invention (and adjunct therapeutic
agent) is/are administered by any suitable means, including
parenteral, subcutaneous, intraperitoneal, intrapulmonary, and
intranasal, and, if desired for local treatment, intralesional
administration. Parenteral infusions include intramuscular,
intravenous, intraarterial, intraperitoneal, or subcutaneous
administration. In addition, the antibody is suitably administered
by pulse infusion, particularly with declining doses of the
antibody. Dosing can be by any suitable route, e.g. by injections,
such as intravenous or subcutaneous injections, depending in part
on whether the administration is brief or chronic.
[0363] The antibody composition of the invention will be
formulated, dosed, and administered in a fashion consistent with
good medical practice. Factors for consideration in this context
include the particular disorder being treated, the particular
mammal being treated, the clinical condition of the individual
patient, the cause of the disorder, the site of delivery of the
agent, the method of administration, the scheduling of
administration, and other factors known to medical practitioners.
The antibody need not be, but is optionally formulated with one or
more agents currently used to prevent or treat the disorder in
question. The effective amount of such other agents depends on the
amount of antibodies of the invention present in the formulation,
the type of disorder or treatment, and other factors discussed
above. These are generally used in the same dosages and with
administration routes as used hereinbefore or about from 1 to 99%
of the heretofore employed dosages.
[0364] For the prevention or treatment of disease, the appropriate
dosage of an antibody of the invention (when used alone or in
combination with other agents such as chemotherapeutic agents) will
depend on the type of disease to be treated, the type of antibody,
the severity and course of the disease, whether the antibody is
administered for preventive or therapeutic purposes, previous
therapy, the patient's clinical history and response to the
antibody, and the discretion of the attending physician. The
antibody is suitably administered to the patient at one time or
over a series of treatments. Depending on the type and severity of
the disease, about 1 .mu.g/kg to 15 mg/kg (e.g. 0.1 mg/kg-10 mg/kg)
of antibody is an initial candidate dosage for administration to
the patient, whether, for example, by one or more separate
administrations, or by continuous infusion. One typical daily
dosage might range from about 1 .mu.g/kg to 100 mg/kg or more,
depending on the factors mentioned above. For repeated
administrations over several days or longer, depending on the
condition, the treatment is sustained until a desired suppression
of disease symptoms occurs. One exemplary dosage of the antibody
would be in the range from about 0.05 mg/kg to about 10 mg/kg.
Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 4.0 mg/kg or
10 mg/kg (or any combination thereof) may be administered to the
patient. Such doses may be administered intermittently, e.g. every
week or every three weeks (e.g. such that the patient receives from
about two to about twenty, e.g. about six doses of the antibody).
An initial higher loading dose, followed by one or more lower doses
may be administered. An exemplary dosing regimen comprises
administering an initial loading dose of about 4 mg/kg, followed by
a weekly maintenance dose of about 2 mg/kg of the antibody.
However, other dosage regimens may be useful. The progress of this
therapy is easily monitored by conventional techniques and
assays.
[0365] The anti-EphB2 antibodies of the invention are useful in
assays detecting EphB2 expression (such as diagnostic or prognostic
assays) in specific cells or tissues wherein the antibodies are
labeled as described below and/or are immobilized on an insoluble
matrix.
[0366] In another aspect, the invention provides methods for
detection of EphB2, the methods comprising detecting
EphB2-anti-EphB2 antibody complex in the sample. The term
"detection" as used herein includes qualitative and/or quantitative
detection (measuring levels) with or without reference to a
control.
[0367] In another aspect, the invention provides methods for
diagnosing a disorder associated with EphB2 expression and/or
activity, the methods comprising detecting EphB2-anti-EphB2
antibody complex in a biological sample from a patient having or
suspected of having the disorder. In some embodiments, the EphB2
expression is increased expression or abnormal (undesired)
expression. In some embodiments, the disorder is a tumor, cancer,
and/or a cell proliferative disorder.
[0368] In another aspect, the invention provides methods for
evaluation (prognostic evaluation) of a patient having or suspected
of having cancer, the method comprising: (a) obtaining a biological
sample from the patient; (b) detecting EphB2 expression in the
biological sample; (c) comparing EphB2 expression in the biological
sample with expression of EphB2 in a control sample (control
reference value); and (d) predicting cancer prognosis of the
patient based on the comparison in (a), wherein increased EphB2
expression in the patient biological sample relative to the control
sample is prognostic for cancer in the patient. Increased EphB2
expression is prognostic for cancer. See Jubb et al, U.S. patent
application Ser. No. ______., filed Jan. 6, 2005. Thus, determining
cancer prognosis can provide for convenient, efficient, and
potentially cost-effective means to obtain data and information
useful in assessing future course of the disorder, including
selection of appropriate therapies for treating patients.
[0369] In another aspect, the invention provides any of the
anti-EphB2 antibodies described herein, wherein the anti-EphB2
antibody comprises a detectable label.
[0370] In another aspect, the invention provides a complex of any
of the anti-EphB2 antibodies described herein and EphB2. In some
embodiments, the complex is in vivo or in vitro. In some
embodiments, the complex comprises a cancer cell. In some
embodiments, the anti-EphB2 antibody is detectably labeled.
[0371] Anti-EphB2 antibodies can be used for the detection of EphB2
in any one of a number of well known detection assay methods. For
example, a biological sample may be assayed for EphB2 by obtaining
the sample from a desired source, admixing the sample with
anti-EphB2 antibody to allow the antibody to form antibody/EphB2
complex with any EphB2 present in the mixture, and detecting any
antibody/EphB2 complex present in the mixture. The biological
sample may be prepared for assay by methods known in the art which
are suitable for the particular sample. The methods of admixing the
sample with antibodies and the methods of detecting antibody/EphB2
complex are chosen according to the type of assay used. Such assays
include immunohistochemistry, competitive and sandwich assays, and
steric inhibition assays.
[0372] Analytical methods for EphB2 all use one or more of the
following reagents: labeled EphB2 analogue, immobilized EphB2
analogue, labeled anti-EphB2 antibody, immobilized anti-EphB2
antibody and steric conjugates. The labeled reagents also are known
as "tracers."
[0373] The label used is any detectable functionality that does not
interfere with the binding of EphB2 and anti-EphB2 antibody.
Numerous labels are known for use in immunoassay, examples
including moieties that may be detected directly, such as
fluorochrome, chemiluminescent, and radioactive labels, as well as
moieties, such as enzymes, that must be reacted or derivatized to
be detected. Examples of such labels include: The label used is any
detectable functionality that does not interfere with the binding
of EphB2 and anti-EphB2 antibody. Numerous labels are known for use
in immunoassay, examples including moieties that may be detected
directly, such as fluorochrome, chemiluminescent, and radioactive
labels, as well as moieties, such as enzymes, that must be reacted
or derivatized to be detected. Examples of such labels include the
radioisotopes .sup.32P, .sup.14C, .sup.125I, .sup.3H, and
.sup.131I, fluorophores such as rare earth chelates or fluorescein
and its derivatives, rhodamine and its derivatives, dansyl,
umbelliferone, luceriferases, e.g., firefly luciferase and
bacterial luciferase (U.S. Pat. No. 4,737,456), luciferin,
2,3-dihydrophthalazinediones, horseradish peroxidase (HRP),
alkaline phosphatase, .beta.-galactosidase, glucoamylase, lysozyme,
saccharide oxidases, e.g., glucose oxidase, galactose oxidase, and
glucose-6-phosphate dehydrogenase, heterocyclic oxidases such as
uricase and xanthine oxidase, coupled with an enzyme that employs
hydrogen peroxide to oxidize a dye precursor such as HRP,
lactoperoxidase, or microperoxidase, biotin/avidin, spin labels,
bacteriophage labels, stable free radicals, and the like.
[0374] Conventional methods are available to bind these labels
covalently to proteins or polypeptides. For instance, coupling
agents such as dialdehydes, carbodiimides, dimaleimides,
bis-imidates, bis-diazotized benzidine, and the like may be used to
tag the antibodies with the above-described fluorescent,
chemiluminescent, and enzyme labels. See, for example, U.S. Pat.
Nos. 3,940,475 (fluorimetry) and 3,645,090 (enzymes); Hunter et
al., Nature, 144: 945 (1962); David et al., Biochemistry, 13:
1014-1021 (1974); Pain et al., J. Immunol. Methods, 40: 219-230
(1981); and Nygren, J. Histochem. and Cytochem., 30: 407-412
(1982). Preferred labels herein are enzymes such as horseradish
peroxidase and alkaline phosphatase. The conjugation of such label,
including the enzymes, to the antibody is a standard manipulative
procedure for one of ordinary skill in immunoassay techniques. See,
for example, O'Sullivan et al., "Methods for the Preparation of
Enzyme-antibody Conjugates for Use in Enzyme Immunoassay," in
Methods in Enzymology, ed. J. J. Langone and H. Van Vunakis, Vol.
73 (Academic Press, New York, N.Y., 1981), pp. 147-166.
[0375] Immobilization of reagents is required for certain assay
methods. Immobilization entails separating the anti-EphB2 antibody
from any EphB2 that remains free in solution. This conventionally
is accomplished by either insolubilizing the anti-EphB2 antibody or
EphB2 analogue before the assay procedure, as by adsorption to a
water-insoluble matrix or surface (Bennich et al., U.S. Pat. No.
3,720,760), by covalent coupling (for example, using glutaraldehyde
cross-linking), or by insolubilizing the anti-EphB2 antibody or
EphB2 analogue afterward, e.g., by immunoprecipitation.
[0376] The expression of proteins in a sample may be examined using
immunohistochemistry and staining protocols. Immunohistochemical
staining of tissue sections has been shown to be a reliable method
of assessing or detecting presence of proteins in a sample.
Immunohistochemistry ("IHC") techniques utilize an antibody to
probe and visualize cellular antigens in situ, generally by
chromogenic or fluorescent methods. For sample preparation, a
tissue or cell sample from a mammal (typically a human patient) may
be used. Examples of samples include, but are not limited to,
cancer cells such as colon, breast, prostate, ovary, lung, stomach,
pancreas, lymphoma, and leukemia cancer cells. The sample can be
obtained by a variety of procedures known in the art including, but
not limited to surgical excision, aspiration or biopsy. The tissue
may be fresh or frozen. In one embodiment, the sample is fixed and
embedded in paraffin or the like. The tissue sample may be fixed
(i.e. preserved) by conventional methodology. One of ordinary skill
in the art will appreciate that the choice of a fixative is
determined by the purpose for which the sample is to be
histologically stained or otherwise analyzed. One of ordinary skill
in the art will also appreciate that the length of fixation depends
upon the size of the tissue sample and the fixative used.
[0377] IHC may be performed in combination with additional
techniques such as morphological staining and/or fluorescence
in-situ hybridization. Two general methods of IHC are available;
direct and indirect assays. According to the first assay, binding
of antibody to the target antigen (e.g., EphB2) is determined
directly. This direct assay uses a labeled reagent, such as a
fluorescent tag or an enzyme-labeled primary antibody, which can be
visualized without further antibody interaction. In a typical
indirect assay, unconjugated primary antibody binds to the antigen
and then a labeled secondary antibody binds to the primary
antibody. Where the secondary antibody is conjugated to an
enzymatic label, a chromogenic or fluorogenic substrate is added to
provide visualization of the antigen. Signal amplification occurs
because several secondary antibodies may react with different
epitopes on the primary antibody.
[0378] The primary and/or secondary antibody used for
immunohistochemistry typically will be labeled with a detectable
moiety. Numerous labels are available which can be generally
grouped into the following categories:
[0379] Aside from the sample preparation procedures discussed
above, further treatment of the tissue section prior to, during or
following IHC may be desired, For example, epitope retrieval
methods, such as heating the tissue sample in citrate buffer may be
carried out (see, e.g., Leong et al. Appl. Immunohistochem.
4(3):201 (1996)).
[0380] Following an optional blocking step, the tissue section is
exposed to primary antibody for a sufficient period of time and
under suitable conditions such that the primary antibody binds to
the target protein antigen in the tissue sample. Appropriate
conditions for achieving this can be determined by routine
experimentation. The extent of binding of antibody to the sample is
determined by using any one of the detectable labels discussed
above. Preferably, the label is an enzymatic label (e.g. HRPO)
which catalyzes a chemical alteration of the chromogenic substrate
such as 3,3'-diaminobenzidine chromogen. Preferably the enzymatic
label is conjugated to antibody which binds specifically to the
primary antibody (e.g. the primary antibody is rabbit polyclonal
antibody and secondary antibody is goat anti-rabbit antibody).
[0381] Specimens thus prepared may be mounted and coverslipped.
Slide evaluation is then determined, e.g. using a microscope, and
staining intensity criteria, routinely used in the art, may be
employed. Staining intensity criteria may be evaluated as
follows:
TABLE-US-00007 TABLE 2 Staining Pattern Score No staining is
observed in cells. 0 Faint/barely perceptible staining is detected
in more than 10% 1+ of the cells. Weak to moderate staining is
observed in more than 10% of 2+ the cells. Moderate to strong
staining is observed in more than 10% of 3+ the cells.
[0382] Typically, a staining pattern score of about 2+ or higher in
an IHC assay is diagnostic and/or prognostic. In some embodiments,
a staining pattern score of about 1+ or higher is diagnostic and/or
prognostic. In other embodiments, a staining pattern score of about
3 of higher is diagnostic and/or prognostic. It is understood that
when cells and/or tissue from a tumor or colon adenoma are examined
using IHC, staining is generally determined or assessed in tumor
cell and/or tissue (as opposed to stromal or surrounding tissue
that may be present in the sample).
[0383] Other assay methods, known as competitive or sandwich
assays, are well established and widely used in the commercial
diagnostics industry.
[0384] Competitive assays rely on the ability of a tracer EphB2
analogue to compete with the test sample EphB2 for a limited number
of anti-EphB2 antibody antigen-binding sites. The anti-EphB2
antibody generally is insolubilized before or after the competition
and then the tracer and EphB2 bound to the anti-EphB2 antibody are
separated from the unbound tracer and EphB2. This separation is
accomplished by decanting (where the binding partner was
preinsolubilized) or by centrifuging (where the binding partner was
precipitated after the competitive reaction). The amount of test
sample EphB2 is inversely proportional to the amount of bound
tracer as measured by the amount of marker substance. Dose-response
curves with known amounts of EphB2 are prepared and compared with
the test results to quantitatively determine the amount of EphB2
present in the test sample. These assays are called ELISA systems
when enzymes are used as the detectable markers.
[0385] Another species of competitive assay, called a "homogeneous"
assay, does not require a phase separation. Here, a conjugate of an
enzyme with the EphB2 is prepared and used such that when
anti-EphB2 antibody binds to the EphB2 the presence of the
anti-EphB2 antibody modifies the enzyme activity. In this case, the
EphB2 or its immunologically active fragments are conjugated with a
bifunctional organic bridge to an enzyme such as peroxidase.
Conjugates are selected for use with anti-EphB2 antibody so that
binding of the anti-EphB2 antibody inhibits or potentiates the
enzyme activity of the label. This method per se is widely
practiced under the name of EMIT.
[0386] Steric conjugates are used in steric hindrance methods for
homogeneous assay. These conjugates are synthesized by covalently
linking a low-molecular-weight hapten to a small EphB2 fragment so
that antibody to hapten is substantially unable to bind the
conjugate at the same time as anti-EphB2 antibody. Under this assay
procedure the EphB2 present in the test sample will bind anti-EphB2
antibody, thereby allowing anti-hapten to bind the conjugate,
resulting in a change in the character of the conjugate hapten,
e.g., a change in fluorescence when the hapten is a
fluorophore.
[0387] Sandwich assays particularly are useful for the
determination of EphB2 or anti-EphB2 antibodies. In sequential
sandwich assays an immobilized anti-EphB2 antibody is used to
adsorb test sample EphB2, the test sample is removed as by washing,
the bound EphB2 is used to adsorb a second, labeled anti-EphB2
antibody and bound material is then separated from residual tracer.
The amount of bound tracer is directly proportional to test sample
EphB2. In "simultaneous" sandwich assays the test sample is not
separated before adding the labeled anti-EphB2. A sequential
sandwich assay using an anti-EphB2 monoclonal antibody as one
antibody and a polyclonal anti-EphB2 antibody as the other is
useful in testing samples for EphB2.
[0388] The foregoing are merely exemplary detection assays for
EphB2. Other methods now or hereafter developed that use anti-EphB2
antibody for the determination of EphB2 are included within the
scope hereof, including the bioassays described herein.
Articles of Manufacture
[0389] In another aspect of the invention, an article of
manufacture containing materials useful for the treatment,
prevention and/or diagnosis of the disorders described above is
provided. The article of manufacture comprises a container and a
label or package insert on or associated with the container.
Suitable containers include, for example, bottles, vials, syringes,
etc. The containers may be formed from a variety of materials such
as glass or plastic. The container holds a composition which is by
itself or when combined with another composition(s) effective for
treating, preventing and/or diagnosing the condition and may have a
sterile access port (for example the container may be an
intravenous solution bag or a vial having a stopper pierceable by a
hypodermic injection needle). At least one active agent in the
composition is an antibody of the invention. The label or package
insert indicates that the composition is used for treating the
condition of choice, such as cancer. Moreover, the article of
manufacture may comprise (a) a first container with a composition
contained therein, wherein the composition comprises an antibody of
the invention; and (b) a second container with a composition
contained therein, wherein the composition comprises a further
cytotoxic agent. The article of manufacture in this embodiment of
the invention may further comprise a package insert indicating that
the first and second antibody compositions can be used to treat a
particular condition, e.g. cancer. Alternatively, or additionally,
the article of manufacture may further comprise a second (or third)
container comprising a pharmaceutically-acceptable buffer, such as
bacteriostatic water for injection (BWFI), phosphate-buffered
saline, Ringer's solution and dextrose solution. It may further
include other materials desirable from a commercial and user
standpoint, including other buffers, diluents, filters, needles,
and syringes.
[0390] The following are examples of the methods and compositions
of the invention. It is understood that various other embodiments
may be practiced, given the general description provided above.
EXAMPLES
[0391] The following materials and methods were used in the
Examples.
Antibodies and Recombinant Proteins.
[0392] Monoclonal anti-phosphotyrosine conjugated with horseradish
peroxidase was obtained from Santa Cruz Biotechnology (Santa Cruz,
Calif.). Antibodies to phospho-epidermal growth factor (EGF), EGF,
phospho-p44/42 MAP kinase, and p44/42 MAP kinase were purchased
from Cell Signaling Technology (Beverly, Mass.). Antibody to the GD
epitope and the fusion proteins ephrin-B1-Fc and ephrin-B2-Fc were
produced at Genentech (South San Francisco, Calif.).
Cell Lines and Plasmids.
[0393] The human colon adenocarcinoma cell lines SW480, SW620, and
Colo 205 and the fibrosarcoma cell line HT1080 were obtained from
the American Type Culture Collection (Manassas, Va.). The
HT1080-EphB2 and HT1080-GD cell lines were generated by
cotransfection with a SV40-driven vector encoding an NH2-terminal
GD epitope-tagged form of EphB2 or empty vector, respectively, and
with a cytomegalovirus promoter-driven puromycin vector. Cells were
selected in 1 .mu.g/ml puromycin. The SVT2-EphB2 cell line was
established in the same fashion, except that mouse 3T3 cells were
cotransfected with a cytomegalovirus promotor driving Neo, and
cells were selected in Geneticin (Life Technologies, Inc.) at 400
.mu.g/ml. Cells were grown in high-glucose DMEM supplemented with
10% fetal bovine serum, 2 mM glutamine, and penicillin-streptomycin
(100 units/ml).
[0394] EphB2 ligand binding domain construct (ss.EphB2LBD.gD.GPI)
was prepared by cloning a polynucleotide encoding amino acids 19 to
208 of human EphB2 into a vector encoding a COOH-terminal GPI
linker and an NH2-terminal GD epitope tag (ss.his.gD.GPI). This
vector was transiently transfected into 293 cells. Cells were grown
in F12 DMEM Mix (50:50) media with 10% FBS. The transfected cells
were subjected to further analysis 48 hours following
transfection.
RNA Expression Analysis.
[0395] For the analysis of tumor and normal colon tissue specimens
(FIG. 3A), approximately 10 .mu.g of total RNA from each human
tumor or normal colon tissue sample served as starting material for
the preparation of probes required for oligonucleotide array
analysis on the Affymetrix GeneChip. Probes were prepared according
to the manufacturer's recommendations. After hybridization, the
arrays were washed and stained with streptavidin-phycoerythrin and
then scanned with the Gene Array scanner (Agilent Technologies).
Default parameters provided in the Affymetrix data analysis
software package were applied in determining the signal
intensities, referred to as average differences. Sample
normalization was done using global scaling as stated in the
Affymetrix Expression Analysis Technical Manual, and a target
intensity of 1500 was used to determine average difference
expression values. For the analysis of EphB2 mRNA expression in
multiple human tumor and normal biopsy samples, the Affymetrix data
were obtained from Gene Logic, Inc. (Gaithersburg, Md.). In the
analysis shown, there are a total of 4841 samples (1808 normal
samples; 1545 cancer samples; and 1488 non-cancer diseased
samples). Gene Logic data were also normalized using global
scaling, but in this instance, the target intensity was 100. The
Affymetrix data for EphB2 mRNA expression was generated from the
U95 probe set ID 41678 at. Real-time PCR (TaqMan; Perkin-Elmer,
Applied Biosystems) for EphB2 mRNA was performed using
gene-specific primers (5'-CGA-GCC-ACG-TTA-CAT-CA-3' (SEQ ID NO:10)
and 5'-TCA-GTA-ACG-CCG-TTC-ACA-GC-3' (SEQ ID NO:11)) and probe
(5'-CCC-ACA-CCC-AGT-ACA-CCT-TCG-AGA-TCC-3' (SEQ ID NO:12)). For in
situ hybridization, a 458-bp .sup.33P-labeled antisense riboprobe
was generated from an EphB2 PCR product using a primer with
oligonucleotide sequence 5'-TCTGTCCATCTGTCCCGTCCT-3' (SEQ ID NO:13)
and a sense control riboprobe with the primer
5'-GCCCTCCTGGTGCTCTATCC-3' (SEQ ID NO:14).
Monoclonal Anti-EphB2 Antibodies.
[0396] BALB/c mice (Charles River Laboratories, Wilmington, Del.)
were immunized with baculovirus-derived His8-tagged EphB2 receptor
diluted in Ribi adjuvant (Corixia, Hamilton, Mont.) twice a week,
via footpad, five doses. B cells from lymph nodes were harvested
from five mice demonstrating high serum titers and were fused with
mouse myeloma cells (X63.Ag8.653; American Type Culture
Collection). After 10-14 days, the supernatants were screened for
antibody production by direct ELISA and by flow cytometry on
HT1080-GD and HT1080-EphBR cells. Positives were subcloned twice to
achieve monoclonality. For large-scale production of purified
antibody, hybridoma cells were injected i.p. into pristine-primed
BALB/c mice. The ascites fluids were pooled and purified by protein
A affinity chromatography (Pharmacia Fast Protein Liquid
Chromatography; Pharmacia, Uppsala, Sweden).
Determination of 2H9Fv Sequences
[0397] Total RNA was extracted from hybridoma cells producing the
mouse anti human EphB2 monoclonal antibody 2H9, using RNeasy Mini
Kit (Qiagen, Germany). The variable light (VL) and variable heavy
(VH) domains were amplified using RT-PCR with the following
degenerate primers:
TABLE-US-00008 Light chain (LC) forward: (SEQ ID NO: 15)
5'-GATCGATATCGTGATGACMCAGTCTCCATC-3' Light chain reverse: (SEQ ID
NO: 16) 5'-TTTDAKYTCCAGCTTGGTACC-3' Heavy chain (HC) forward: (SEQ
ID NO: 17) 5'-GATCCGTACGCTCAGGTYCARCTSCAGCAGTCTGG-3' Heavy chain
reverse: (SEQ ID NO: 17)
5'-ACAGTGGGCCCTTGGTGGAGGCTGMRGAGACDGTGASHRDRGT-3'
[0398] The forward primers were specific for the N-terminal amino
acid sequence of the VL and VH region. Respectively, the LC and HC
reverse primers were designed to anneal to a region in the constant
light (CL) and constant heavy domain 1 (CH1), which is highly
conserved across species. Amplified VL was cloned into a pRK
mammalian cell expression vector (Shields et al. J Biol Chem (2000)
276:659-604). Amplified VH was inserted to a pRK mammalian cell
expression vector. The polynucleotide sequence of the inserts was
determined using routine sequencing methods.
Analysis of EphB2 Activation
[0399] The analysis of EphB2 activation by soluble Ephrin-Fc ligand
was performed by stimulating the SVT2-EphB2 cell line with purified
Fc-EphrinB2 (5 .mu.g/ml, 15 min) and detecting EphB2
autophosphorylation using the following protocol. Cells were lysed
in radioimmunoprecipitation assay buffer (50 mM Tris, 150 mM NaCl,
1% deoxycholate, 1% NP40, 2 mM sodium vanadate, 1 mM
phenylmethylsulfonyl fluoride, and complete proteinase inhibitor
mixture (Roche Molecular Biochemicals)). Ten .mu.g of anti-GD MAb
were added to the lysates, followed by protein G-agarose (Life
Technologies, Inc.), and incubated overnight at 4.degree. C. The
immunoprecipitates were recovered, washed with lysis buffer, and
subjected to SDS-PAGE and immunoblotting. Blots were incubated with
1 .mu.g/ml anti-phosphotyrosine mouse MAb conjugated with
horseradish peroxidase (Santa Cruz Biotechnology) or anti-GD mouse
MAb. Goat antimouse horseradish peroxidase was used as a secondary
antibody, and the blots were washed and developed using the
Enhanced Chemiluminescence system (Pierce). Analysis of MAP kinase
activation was carried out using the HT1080-EphB2 cell line. Cells
were serum starved for 12 h and either left untreated or stimulated
with EGF 100 ng/ml in the absence or presence of 5 .mu.g human
Fc-EphrinB2/ml. Cell lysates were equalized for protein
concentration, subjected to SDS-PAGE, and immunoblotted with
anti-phospho-EGF receptor or phospho-MAP kinase antibody.
Flow Cytometry
[0400] For flow cytometry, cells were grown to 90% confluence and
removed from plates using Cell Dissociation Buffer (Invitrogen).
Cells were washed and resuspended in fluorescence-activated
cell-sorting buffer (PBS with 1% BSA) and incubated for 45 min with
anti-EphB2 MAb 2H9 or anti-GD antibody (Genentech) followed by
30-min incubation with antimouse secondary antibody conjugated to
phycoerythrin. Analysis was performed on FACSscan.
Binding Affinity, ELISA, and Isotype Testing
[0401] Binding affinity of Mab 2H9 was determined by surface
plasmon resonance using Pharmacia BIAcore.RTM. 3000 (BIAcore AB,
Uppsala, Sweden) at room temperature (see, e.g., Morton et al.
(1998) Methods in Enzymology, 295, 268-294). Anti-EphB2 antibodies
were immobilized to the sensor chip (CM5) through primary amine
groups. The carboxymethylated sensor chip surface matrix was
activated by injecting 20 .mu.l of a mixture of 0.025 M
N-hydroxysuccinimide and 0.1 M N-ethyl-N'(dimethylaminopropyl)
carbodiimide at 5 .mu.l/min. 5-10 .mu.l of 10 .mu.g/ml solution of
anti-EphB2 antibodies in 10 mM sodium acetate, pH 4.5, were
injected at 5 .mu.l/min. After coupling, unoccupied sites on the
chip were blocked by injecting 20 .mu.l of 1M ethanolamine, pH 8.5.
The running buffer was PBS containing 0.05% polysorbate 20. For
kinetic measurements, two-fold serial dilutions of polyhis-tagged
EphB2 in running buffer were injected over the flow cells for 3
minutes at a flow rate of 30 .mu.l/min and the bound polyhis tagged
EphB2 was allow to dissociate for 20 minutes. The binding surface
was regenerated by injecting 20 .mu.l of 10 mM glycine.HCl (pH
1.5). Flow cell one, which was activated but did not have antibody
immobilized, was used as a reference cell. There was no significant
non-specific binding of polyhis tagged EphB2 to flow cell one. For
calculate apparent binding affinity, data were analyzed using a 1:1
binding model using global fitting. The association and
dissociation rate constants were fitted simultaneously
(BIAevaluation software).
[0402] Mab 2H9 was determined to bind human and mouse EphB2
polypeptide using ELISA according to the following protocol.
Microtiter plates (Nunc, Roskilde, Sweden), were coated with 100
.mu.l/well of baculovirus-derived His8-tagged EphB2 receptor at 1
.mu.g/ml in 0.05 M carbonate buffer, pH 9.6, overnight at 4.degree.
C. Plates were washed with PBS/0.05% T20 and blocked with PBS
bovine serum albumin (BSA)/T20. Hybridoma supernatants were added
(100 .mu.l/well), incubated for 1 h at room temperature with
agitation. Following the wash step, bound antibodies was detected
with goat anti-mouse IgG (Fc specific) peroxidase conjugate (Sigma,
St. Louis, Mo.; diluted 1:10 K in PBS/BSA/T20 buffer; incubated for
1 h at RT). The plates were developed with TMB substrate solution
(KPL/Kirkegaard & Perry Laboratories, Galthersburg, Md.) and
reaction was stopped with TMB 1-component stop solution (KPL).
Plates were read at absorbance of 450 nm, with reference at 630 nm
using an automated plate reader.
[0403] Reactivity of Mab 2H9 with related Eph receptor EphB3 was
tested as follows. 293 cells expressing EphB3 were generated by
transient transfection with a vector containing EphB3 ECD
sequences, an NH2-terminal GD tag and a COOH-terminal GPI linker.
After 48 hours, Mab 2H9 was incubated with the cells, then,
following washing, the cell were subjected to FACS analysis as
described above. Mab 2H9 showed very low cross-binding with
EphB3.
[0404] Mab 2H9 was determined to be isotype IgG1, as determined
using standard methods.
Antibody Binding and Internalization, Immunohistochemistry.
[0405] Purified MAb 2H9 was iodinated using the lactoperoxidase
method, and the radiolabeled antibody was purified from free
.sup.125I--Na by gel filtration chromatography using a Pharmacia
PD-10 column. Assessment of internalization was carried out
essentially as described previously (Gladhaug I. P. et al., J.
Biol. Chem., 263: 12199-12203, 1988). Cells were incubated with
iodinated antibody on ice and then shifted to 37.degree. C. for 4
h, followed by an acid/salt/urea incubation at 4.degree. C. to
dissociate surface-bound ligand. Total surface-bound and
internalized antibody was determined by scintillation counting.
Internalization of EphB2 was also assessed by immunofluorescence
staining of cells.
[0406] Immunohistochemical staining of human colon tumor sections
with anti-EphB2 antibody was performed on frozen tissue sections.
Sections containing malignant epithelial cells of a colorectal
adenocarcinoma were incubated with primary antibody 2H9 at a
concentration of 5 .mu.g/ml, followed a biotinylated horse
antimouse IgG affinity-purified antiserum. As control, an adjacent
section was incubated with an irrelevant primary antibody and
counterstained with hematoxylin.
[0407] Slides containing HT1080-EphB2 cells were incubated with 1
.mu.g/ml 2H9 antibody for 30 min on ice and then shifted to
37.degree. C. in a CO2 incubator for 1 h. The slides were washed in
PBS, fixed in 3% paraformaldehyde, and incubated with
rhodamine-conjugated antimouse IgG antibody (Jackson Immunoresearch
Laboratories) at a 1:200 dilution for 20 min at room temperature.
The number of cell surface MAb 2H9 binding sites was estimated by
incubating cells for 4 h on ice with a fixed concentration of
.sup.125I-labeled MAb 2H9 combined with increasing concentrations
of unlabeled MAb 2H9, essentially as described previously (Holmes
W. et al., Science, 256: 1205-1210, 1992).
Determination of EphB2 Ligand Binding Domain and Mapping of 2H9
Binding Determinant
[0408] To determine EphB2's ligand binding domain, 48 hours
following transient transfection, 1 .mu.l EphB2 ligand
(ephrinB1-IgG at 91 ng/.mu.l) was added to ss.EphB2LBD.gD.GPI-293
cells, and cells were kept on ice for 20 minutes. Following two
washes, cells were incubated with FITC-conjugated Fc specific
anti-human IgG antibody (Sigma catalog no. F9512) on ice for 30
minutes. Following two more washed, cells were subjected to FACS
analysis as described above. The results demonstrated that EphB2
ligand EphrinB1 bound EphB2 amino acids 19-208, thus defining EphB2
amino acids 19-208 as containing the EphB2 ligand binding domain.
No binding was observed using cells that expressed a control
vector.
[0409] To determine reactivity of Mab 2H9 with amino acid numbers
19-208 of EphB2, Mab 2H9 (1 .mu.g/ml) or anti-GD antibody (4
.mu.g/ml) were incubated with ss.EphB2LBD.gD.GPI-293 cells, then,
following washing, cells were subjected to FACS analysis as
described above. The results demonstrated that GD protein and EphB2
ligand binding domain protein was detected by these antibodies.
These results indicated that Mab 2H9 bound the EphB2 ligand binding
domain. No 2H9 or anti-GD antibody binding was observed using cells
that expressed a control vector.
Preparation of Anti EphB2 Mab 2H9 Immunoconjugates
[0410] The conjugation of the anti-EphB2 antibody 2H9 and control
anti-interleukin (IL)-8 antibody with MC-vc-PAB-MMAE and the
conjugation of 2H9 with MC-vc-PAB-MMAF were performed as described
elsewhere (Doronina S. O. et al. Nat. Biotechnol., 21: 778-784,
2003; U.S. Ser. No. 10/983,340, filed Nov. 5, 2004). The
conjugation of 2H9 with MC-MMAE and MC-MMAF was performed as
described in U.S. Ser. No. 10/983,340, filed Nov. 5, 2004,
following the protocol provided in Doronina, supra. The conjugation
of 2H9 with SMCC-DM1 and SPP-DM1 was performed as described in U.S.
Ser. No. 10/960,602, filed Oct. 8, 2004.
In Vitro Tumor Cell Killing Assays.
[0411] The HT1080-EphB2 cell line or the vector control cell line
were added to each well of 96-well microtiter plates at
1.5.times.103 cells/well, 100 .mu.l/well, and incubated overnight
at 37.degree. C. in a humidified atmosphere of 5% CO2. Cells were
exposed to various concentrations of MAb 2H9-MC-vc-PAB-MMAE or Mab
anti-IL-8-MC-vc-PAB-MMAE based on 1:3 serial dilutions. After
incubation for 48 h, Cell Titer-Glo reagent (Promega, Madison,
Wis.) was added to the wells at 100 .mu.l/well, and after a 10-min
incubation at room temperature, the luminescent signal was
recorded.
[0412] In a separate experiment, HT1080-EphB2 cells were exposed to
various concentrations of 2H9-SPP-Dml, 2H9-SMCC-DM1,
2H9-MC-vc-PAB-MMAE, 2H9-MC-vc-PAB-MMAF or
anti-interleukin-8-MC-vc-PAB-MMAE, essentially as described above,
and cell viability was measured after 2 days as described
above.
In Vivo Tumor Growth Assays.
[0413] Female nude mice (Charles River Laboratories, Hollister,
Calif.) were maintained in accordance with the guide for the care
and use of laboratory animals. HT1080-EphB2 and HT1080-GD cells
were harvested, resuspended in PBS, and injected s.c. into the
right and left flanks (1.times.106 cells/flank), respectively, of
6-8-week-old mice. When tumors reached approximately 100 mm.sup.3,
animals were dosed i.p. with 0.2 ml of native EphB2 MAb or
2H9-MC-vc-PAB-MMAE or Mab anti-IL-8-MC-vc-PAB-MMAE once a week i.v.
at a final dose of 3 mg/kg body weight. The tumor volumes were
determined by measuring the length (l) and width (w) and
calculating the volume (V=1w2/2) as described previously.
[0414] Assays with the CXF1103 tumor line were performed by
Oncotest Gmbh (Feiburg, Germany). See U.S. Pat. No. 6,271,342.
Affymetrix oligonucleotide array analysis was performed on tumors
from the Oncotest collection, which demonstrated expression of
EphB2 mRNA in CXF1103. This was confirmed by real-time PCR and
immunohistochemistry. CXF1103 is a human colon tumor established by
serial passage in nude mice. Groups of 10 nude mice of NMRI
background received s.c. tumor implants to obtain 30 mice bearing
tumors of similar sizes for randomization. Tumors were grown to an
average size of 100-200 mg, whereupon treatment with vehicle
control, control antibody conjugate anti-GD-MC-vc-PAB-MMAE, or
anti-EphB2 antibody conjugate 2H9-MC-vc-PAB-MMAE was initiated by
i.v. injection. Antibody conjugates were administered at 3 mg/kg
body weight at 7-day intervals for 3 weeks.
Results
Example 1
Analysis of EphB2 mRNA and Protein Expression in Cancer and Normal
Human Tissues
[0415] EphB2 mRNA and protein are overexpressed in cancer tissues.
Oligonucleotide-based microarray expression analysis was performed
on 38 human colorectal tumors and 7 normal colon biopsy samples.
Data mining revealed that EphB2 was overexpressed by 2-6-fold in
the majority of the tumors relative to the average expression level
of the normal samples (FIG. 3A). To confirm the overexpression in
colon cancers, real-time PCR (TaqMan) was performed on 11
additional human colorectal tumors, each referenced to a
patient-matched normal colon sample. These data were highly
consistent with the microarray data (FIG. 3B). On mining of a
larger database, containing microarray data from over 4800 human
biopsy samples, it was noted that EphB2 mRNA was preferentially
expressed in intestinal tissue, with increased expression in
colorectal, soft tissue cancers (such as fibrosarcoma and other
sarcomas), and gastric cancers relative to numerous other
tissues.
[0416] EphB2 mRNA expression was also examined by in situ
hybridization on tissue microarrays. By this method, the only
normal human tissues in which EphB2 protein expression was detected
were the colon and small intestine. In situ hybridization was also
carried out on a gastrointestinal tissue microarray containing
samples from a variety of cancers. Here, EphB2 mRNA expression was
seen in 12 of 18 primary colonic adenocarcinomas, 6 of 8 metastatic
adenocarcinomas to the liver, 2 of 9 primary gastric carcinomas,
and 1 of 4 esophageal carcinomas. No expression was observed in
four of four pancreatic adenocarcinomas. Examples of expression in
normal colonic mucosa and colorectal cancer by in situ
hybridization are shown FIG. 4A.
[0417] Mab 2H9 reacted strongly with tissue sections obtained from
human colon adenocarcinomas (FIG. 4B). EphB2 protein expression has
been demonstrated at all stages of colorectal tumorigenesis,
including all normal crypts, and overexpression in 77% of adenomas,
82% of primary cancers, and 64% of metastases. See co-pending
co-owned U.S. Patent Application No. 60/642,164, filed Jan. 6,
2005.
Example 2
Preparation and Characterization of Anti-EphB2 Monoclonal Antibody
2H9
[0418] Antibodies to the extracellular sequence of EphB2 were
prepared as described above, and several hybridomas were cloned
that expressed MAbs reactive with the purified EphB2 immunogen and
with the full-length EphB2 by flow cytometry
(fluorescence-activated cell sorting) of cells expressing EphB2.
MAbs from positive hybridomas were purified and compared for
reactivity against colorectal cancer cell lines that endogenously
express EphB2 and against cell lines engineered to overexpress the
receptor (HT-1080EphB2 and SVT2EphB2). A MAb designated 2H9
performed well in these assays.
[0419] Elisa analysis demonstrated that Mab 2H9 bound human and
mouse EphB2. Isotype analysis revealed that Mab 2H9 possessed an
IgG1 isotype. Mab 2H9 binding affinity was also determined by
BiaCore analysis. Mab 2H9 bound human EphB2 with K.sub.a (1/Ms) of
8.28E+04, K.sub.d (1/s) of 1.03E-05, and K.sub.d (nM) of 0.12. Mab
2H9 showed very low cross-reactivity with related Eph receptor,
EphB3, in a FACS-based analysis.
Example 3
Mab 2H9 Inhibits EphB2 Activation by Competitively Inhibiting EphB2
Ligand Binding
[0420] The tyrosine kinase activity of EphB2 can be activated on
binding of the receptor with ephrinB ligands (Davis S. et al.
Science, 266: 816-819, 1994). This was observed when the murine 3T3
cell line expressing human EphB2 was incubated with a purified
Fc-ephrinB2 fusion protein (FIG. 5A). MAb 2H9 was tested in this
assay. The tyrosine autophosphorylation of EphB2 by Fc-ephrinB2 was
inhibited when the cells were preincubated with MAb 2H9, whereas a
control antibody had no effect (FIG. 5A). The mechanism by which
MAb 2H9 inhibits EphB2 activation was investigated and found to
involve competitive inhibition of ligand binding. This was
determined by performing flow cytometry on cells incubated with the
Fc-ephrinB1 ligand after their incubation with or without MAb 2H9.
In this experiment, a positive fluorescence-activated cell-sorting
signal results from the specific binding of FITC-conjugated
antihuman Fc antibody to the bound Fc-ephrinB1 ligand. Increasing
amounts of MAb 2H9 resulted in a corresponding decrease in
Fc-ephrinB1 ligand binding (FIG. 5B). The loss of binding was not
due to antibody-mediated receptor uptake because all incubations
were performed on ice, where receptor internalization is minimal.
Thus, MAb 2H9 inhibited the binding of ephrin ligands to the EphB2
receptor.
[0421] To determine whether MAb 2H9 was able to affect the
mitogenic or tumorigenic potential of cancer cells, growth effects
of Mab 2H9 on various cell lines in vitro was determined. However,
MAb 2H9 did not exhibit any specific effect on the growth of
various cell lines in vitro that express the receptor (cell lines
HT-1080-EphB2 and PC3-EphB2). An inhibition of cell growth might
not be expected, however, because Eph receptors are not considered
to be mitogenic and have even been reported to interfere with
mitogenic signaling as assessed by the activity of the MAP kinase
pathway (Kim et al., FASEB J., 16: 1126-1128, 2002; Elowe et al.,
Mol. Cell. Biol., 21: 7429-7441, 2001). To assess this in a
tumorigenic cell line strongly responsive to EGF, stable clones of
the fibrosarcoma cell line HT1080 overexpressing EphB2
(HT1080-EphB2) were generated. The HT1080 cell line produced
ephrinB1 transcript. EphrinB2 did not inhibit activation of the MAP
kinase pathway by EGF in these cells but rather appeared to enhance
it slightly.
Example 4
Mab 2H9 is Internalized After Binding EphB2
[0422] Internalization of MAb 2H9 after EphB2 binding was
investigated. HT1080-EphB2 cells were incubated with MAb 2H9 on ice
for 30 minutes and then shifted to 37.degree. C. for 1 hour before
fixation and staining with secondary antibody. Compared with cells
kept on ice for the course of the experiment, the cells shifted to
37.degree. C. contained significant amounts of internalized
antibody (FIG. 6A). MAb 2H9 uptake was examined by incubating cells
with .sup.125I-radiolabeled antibody at 4.degree. C. The amount of
.sup.125I-labeled MAb 2H9 that was internalized after cells were
shifted to 37.degree. C. for 1 hour was approximately double that
of cells maintained at 4.degree. C. (FIG. 6B). MAb 2H9 was readily
internalized on binding to EphB2. Thus, Mab 2H9 is suitable for
immunoconjugate therapy approaches wherein the uptake or
internalization of the antigen-antibody complex results in
preferential release of drug inside of the cancer cells.
Example 5
Mab 2H9 Binds to the EphB2 Ligand Binding Domain
[0423] The EphB2 ligand binding domain was defined by incubating
ss.EphB2LBD.gD.GPI-293 cells with EphrinB1-IgG, then subjecting the
cells to FACS analysis. The results demonstrated that an EphB2
ligand, EphrinB1, bound EphB2 amino acids 19-208, thus defining
EphB2 amino acids 19-208 (FIG. 11) as containing the EphB2 ligand
binding domain. No binding was observed using cells that expressed
a control vector.
[0424] Mab 2H9 binding to the EphB2 ligand binding domain was
investigated by incubating Mab 2H9 or anti-GD antibody with
ss.EphB2LBD.gD.GPI-293 cells, then subjecting the cells to FACS
analysis. The result demonstrated that GD protein and EphB2 ligand
binding domain was detected by these antibodies, indicating that
Mab 2H9 bound the EphB2 ligand binding domain. No 2H9 or anti-GD
antibody binding was observed using cells that expressed a control
vector.
Example 6
Mab 2H9 Immunoconjugate Effectively Kills Tumor Cells In Vitro
[0425] MAb 2H9 was covalently coupled to the drug MMAE through the
linker MC-vc-PAB that is susceptible to cleavage by cathepsin B
(Weiner L. M. Semin. Oncol., 26: 43-51, 1999). On cleavage by
cathepsin B, active MMAE is released, disrupting the dynamics of
tubulin polymerization in the cell. The 2H9-MC-vc-PAB antibody drug
conjugate (immunoconjugate) was tested in vitro by treating the
HT1080 cancer cells with increasing concentrations of antibody.
Both the vector control HT1080 cell line (HT1080-GD) and the clonal
derivative overexpressing EphB2 (HT1080-EphB2) were killed by
2H9-MC-vc-PAB-MMAE at significantly lower concentrations relative
to control antibody conjugate anti-IL-8-MC-vc-PAB (FIG. 7). No
effect was seen with underivatized MAb 2H9 up to a concentration of
10 mg/ml. The antibody concentration required for half-maximal cell
killing (IC50) was 0.006 .mu.g/ml for cancer cells
HT1080-EphB2.
[0426] To relate cell killing to receptor copy number, quantitative
binding assays were performed using MAb 2H9 on the HT1080-GD and
HT1080-EphB2 cell lines. By Scatchard analysis, approximately
71,000 and 308,000 copies/cell for these two lines, respectively,
were estimated (FIG. 8A). For both cell lines, the apparent
dissociation constant for MAb 2H9 was approximately 4 nM. The
difference in EphB2 copy number was also evident from the relative
fluorescence intensity observed when flow cytometry was performed
with MAb 2H9 on the two cell lines (FIG. 8B). Also, the conjugation
of MAb 2H9 with MC-vc-PAB-MMAE did not appreciably affect its
binding properties to the HT1080 cells. The relative difference in
receptor copy number on the two HT1080 cell lines was again evident
from the binding of 2H9-MC-vc-PAB-MMAE (FIG. 8C). These results
indicated that target copy number is an important factor in
determining the efficacy of a drug-conjugated antibody. In the case
of EphB2, a moderate difference in copy number resulted in a much
greater difference in the IC50 values determined in vitro.
[0427] In a separate experiment, HT1080-EphB2 cells were exposed to
various concentrations of 2H9-SPP-Dml, 2H9-SMCC-DM1,
2H9-MC-vc-PAB-MMAE, 2H9-MC-vc-PAB-MMAF or
anti-interleukin-8-MC-vc-PAB-MMAE essentially as described above,
and cell viability was measured after 2 days as described above.
HT1080-EphB2 cells were killed by 2H9-MC-vc-PAB-MMAE, 2H9-SMCC-DM1
and 2H9-SPP-DM1 at significantly lower concentrations relative to
control antibody conjugate anti-IL-8-MC-vc-PAB-MMAE (FIG. 9A).
Ht1080-EphB2 cells were killed by 2H9-MC-vc-PAB,
2H9-MC-vc-PAB-MMAF, 2H9-SPP-DM1 and 2H9-SMCC-DM1 (FIG. 9B).
Example 7
Mab 2H9 Antibody Drug Conjugate Effectively Kills Tumor Cells In
Vivo
[0428] 2H9-MC-vc-PAB-MMAE was tested for in vivo efficacy by
administration to nude mice bearing human tumor xenografts. Tumors
were established by inoculating mice on one flank with the
HT1080-GD cells and on the opposite flank with HT1080-EphB2 cells.
Tumors were grown to a size of 100-200 mm.sup.3 before i.v.
administration of 2H9-MC-vc-PAB-MMAE once per week at a dose of 3
mg/kg. Additional animals were treated with vehicle control or with
control antibody anti-IL-8-MC-vc-PAB-MMAE at 3 mg/kg. In this
experiment, the HT1080-EphB2 cell line grew more rapidly than the
HT1080-GD vector control cell line under control conditions. It is
not believed that this is due to overexpression of EphB2 because
previous testing of HT1080-EphB2 clones did not reveal a
reproducible effect on tumor growth rate. Nevertheless, both types
of tumors responded well to treatment with 2H9-MC-vc-PAB-MMAE
relative to vehicle control and control antibody conjugate
anti-IL-8-MC-vc-PAB-MMAE (FIG. 10A). Control animal groups were
terminated between day 7 and 14 due to the aggressive growth of
their tumors. Animals treated with 2H9-MC-vc-PAB-MMAE were
maintained out to 4 weeks, when treatment was discontinued. By
contrast, naked Mab 2H9 antibody was tested in a by growing the
HT1080-EphB2 cell line as a tumor xenograft in nude mice that were
then given MAb 2H9 at a dose of 10 mg/kg body weight twice per
week. However, treatment with naked MAb 2H9 did not result in any
significant effect on the rate of tumor growth in this assay.
[0429] As an additional test of in vivo efficacy, a human colon
tumor established by serial passage in nude mice was implanted
s.c., and growth was measured during a treatment course identical
to that described for the HT1080 model above. Significant growth
retardation was again observed with 2H9-MC-vc-PAB-MMAE, relative to
vehicle control or control antibody anti-GD-MC-vc-PAB-MMAE (FIG.
10B). Overall, these results demonstrated specificity and efficacy
of 2H9-MC-vc-PAB-MMAE in in vivo tumor growth models.
[0430] The following hybridoma has been deposited with the American
Type Culture Collection, PO Box 1549, Manassas, Va., 20108, USA
(ATCC):
TABLE-US-00009 Cell Lines ATCC Accession No. Deposit Date Hybridoma
2H9.11.14 PTA-6606 Feb. 24, 2005
[0431] These deposits were made under the provisions of the
Budapest Treaty on the International Recognition of the Deposit of
Microorganisms for the Purpose of Patent Procedure and the
Regulations thereunder (Budapest Treaty). This assures maintenance
of a viable deposit for 30 years from the date of deposit. These
cell lines will be made available by ATCC under the terms of the
Budapest Treaty, and subject to an agreement between Genentech,
Inc. and ATCC, which assures permanent and unrestricted
availability of the cell lines to the public upon issuance of the
pertinent U.S. patent or upon laying open to the public of any U.S.
or foreign patent application, whichever comes first, and assures
availability of the cell lines to one determined by the U.S.
Commissioner of Patents and Trademarks to be entitled thereto
according to 35 USC .sctn.122 and the Commissioner's rules pursuant
thereto (including 37 CFR .sctn.1.14 with particular reference to
8860G 638).
[0432] The assignee of the present application has agreed that if
the deposited cell lines should be lost or destroyed when
cultivated under suitable conditions, they will be promptly
replaced on notification with a specimen of the same cell line.
Availability of the deposited cell lines is not to be construed as
a license to practice the invention in contravention of the rights
granted under the authority of any government in accordance with
its patent laws.
[0433] Although the foregoing invention has been described in some
detail by way of illustration and example for purposes of clarity
of understanding, the descriptions and examples should not be
construed as limiting the scope of the invention.
Sequence CWU 1
1
18117PRTMus musculus 1Lys Ser Ser Gln Ser Leu Leu Asn Ser Gly Asn
Gln Glu Asn Tyr1 5 10 15Leu Ala27PRTMus musculus 2Gly Ala Ser Thr
Arg Glu Ser1 539PRTMus musculus 3Gln Asn Asp His Ser Tyr Pro Phe
Thr1 545PRTMus musculus 4Ser Tyr Trp Met His1 5517PRTMus musculus
5Phe Ile Asn Pro Ser Thr Gly Tyr Thr Asp Tyr Asn Gln Lys Phe1 5 10
15Lys Asp611PRTMus musculus 6Arg Leu Lys Leu Leu Arg Tyr Ala Met
Asp Tyr1 5 107114PRTMus musculus 7Asp Ile Val Met Thr Gln Ser Pro
Ser Ser Leu Ser Val Ser Ala1 5 10 15Gly Glu Lys Val Thr Met Asn Cys
Lys Ser Ser Gln Ser Leu Leu 20 25 30Asn Ser Gly Asn Gln Glu Asn Tyr
Leu Ala Trp Tyr Gln Gln Lys 35 40 45Pro Gly Gln Pro Pro Lys Leu Leu
Ile Tyr Gly Ala Ser Thr Arg 50 55 60Glu Ser Gly Val Pro Asp Arg Phe
Thr Gly Ser Gly Ser Gly Thr65 70 75Asp Phe Thr Leu Thr Ile Ser Ser
Val Gln Ala Glu Asp Leu Ala 80 85 90Val Tyr Tyr Cys Gln Asn Asp His
Ser Tyr Pro Phe Thr Phe Gly 95 100 105Ala Gly Thr Lys Val Glu Ile
Lys Arg 1108119PRTMus musculus 8Gln Val Gln Leu Gln Gln Ser Gly Ala
Glu Leu Ala Lys Pro Gly1 5 10 15Ala Ser Val Lys Met Ser Cys Lys Ala
Ser Gly Tyr Thr Phe Thr 20 25 30Ser Tyr Trp Met His Trp Val Lys Gln
Arg Pro Gly Gln Gly Leu 35 40 45Glu Trp Ile Gly Phe Ile Asn Pro Ser
Thr Gly Tyr Thr Asp Tyr 50 55 60Asn Gln Lys Phe Lys Asp Lys Ala Thr
Leu Thr Val Lys Ser Ser65 70 75Asn Thr Ala Tyr Met Gln Leu Ser Arg
Leu Thr Ser Glu Asp Ser 80 85 90Ala Val Tyr Tyr Cys Thr Arg Arg Leu
Lys Leu Leu Arg Tyr Ala 95 100 105Met Asp Tyr Trp Gly Gln Gly Thr
Thr Leu Thr Val Ser Ala 110 1159184PRTHomo sapiens 9Val Glu Glu Thr
Leu Met Asp Ser Thr Thr Ala Thr Ala Glu Leu1 5 10 15Gly Trp Met Val
His Pro Pro Ser Gly Trp Glu Glu Val Ser Gly 20 25 30Tyr Asp Glu Asn
Met Asn Thr Ile Arg Thr Tyr Gln Val Cys Asn 35 40 45Val Phe Glu Ser
Ser Gln Asn Asn Trp Leu Arg Thr Lys Phe Ile 50 55 60Arg Arg Arg Gly
Ala His Arg Ile His Val Glu Met Lys Phe Ser 65 70 75Val Arg Asp Cys
Ser Ser Ile Pro Ser Val Pro Gly Ser Cys Lys 80 85 90Glu Thr Phe Asn
Leu Tyr Tyr Tyr Glu Ala Asp Phe Asp Ser Ala 95 100 105Thr Lys Thr
Phe Pro Asn Trp Met Glu Asn Pro Trp Val Lys Val 110 115 120Asp Thr
Ile Ala Ala Asp Glu Ser Phe Ser Gln Val Asp Leu Gly 125 130 135Gly
Arg Val Met Lys Ile Asn Thr Glu Val Arg Ser Phe Gly Pro 140 145
150Val Ser Arg Ser Gly Phe Tyr Leu Ala Phe Gln Asp Tyr Gly Gly 155
160 165Cys Met Ser Leu Ile Ala Val Arg Val Phe Tyr Arg Lys Cys Pro
170 175 180Arg Ile Ile Gln1017DNAArtificial sequenceEphB2-specific
primer 1 10cgagccacgt tacatca 171120DNAArtificial
sequenceEphB2-specific primer2 11tcagtaacgc cgttcacagc
201227DNAArtificial sequenceEphB2-specific probe 12cccacaccca
gtacaccttc gagatcc 271321DNAArtificial sequenceEphB2 riboprobe
primer 1 13tctgtccatc tgtcccgtcc t 211420DNAArtificial
sequenceEphB2 riboprobe primer 1 14gccctcctgg tgctctatcc
201530DNAArtificial sequenceLC forward primer 15gatcgatatc
gtgatgacmc agtctccatc 301621DNAArtificial sequenceLC reverse primer
16tttdakytcc agcttggtac c 211735DNAArtificial sequenceHC forward
primer 17gatccgtacg ctcaggtyca rctscagcag tctgg 351843DNAArtificial
sequenceHC reverse primer 18acagtgggcc cttggtggag gctgmrgaga
cdgtgashrd rgt 43
* * * * *