U.S. patent application number 17/376627 was filed with the patent office on 2022-06-30 for antibodies against the ectodomain of erbb3 and uses thereof.
The applicant listed for this patent is Elevation Oncology, Inc.. Invention is credited to David BUCKLER, Michael J. FELDHAUS, Arumugam MURUGANANDAM, Ulrik B. NIELSEN, Birgit M. SCHOEBERL.
Application Number | 20220204642 17/376627 |
Document ID | / |
Family ID | |
Filed Date | 2022-06-30 |
United States Patent
Application |
20220204642 |
Kind Code |
A1 |
SCHOEBERL; Birgit M. ; et
al. |
June 30, 2022 |
ANTIBODIES AGAINST THE ECTODOMAIN OF ERBB3 AND USES THEREOF
Abstract
The present invention provides a novel class of antibodies and
antigen binding fragments thereof that bind the extracellular
domain of ErbB3 receptor and inhibit various ErbB3 functions. For
example, the antibodies and antigen binding fragments described
herein are capable of binding to the receptor designated ErbB3 and
inhibiting EGF-like ligand mediated phosphorylation of the
receptor. Such antibodies and antigen binding fragments thereof
have the useful characteristic of inhibiting the proliferation of
cancer cells expressing ErbB3.
Inventors: |
SCHOEBERL; Birgit M.;
(Cambridge, MA) ; NIELSEN; Ulrik B.; (Quincy,
MA) ; FELDHAUS; Michael J.; (Grantham, NH) ;
MURUGANANDAM; Arumugam; (Bangalore, IN) ; BUCKLER;
David; (Chester, NJ) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Elevation Oncology, Inc. |
New York |
NY |
US |
|
|
Appl. No.: |
17/376627 |
Filed: |
July 15, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16181054 |
Nov 5, 2018 |
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17376627 |
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15274989 |
Sep 23, 2016 |
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16181054 |
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14181334 |
Feb 14, 2014 |
9487588 |
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15274989 |
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12545279 |
Aug 21, 2009 |
8691225 |
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14181334 |
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12425874 |
Apr 17, 2009 |
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12545279 |
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12281925 |
Sep 5, 2008 |
7846440 |
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PCT/US2008/002119 |
Feb 15, 2008 |
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12425874 |
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60901904 |
Feb 16, 2007 |
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61009796 |
Jan 2, 2008 |
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International
Class: |
C07K 16/32 20060101
C07K016/32; A61K 39/395 20060101 A61K039/395; A61K 31/337 20060101
A61K031/337; A61K 31/517 20060101 A61K031/517; C07K 16/28 20060101
C07K016/28; A61K 9/00 20060101 A61K009/00 |
Claims
1. A composition comprising a first agent that is an anti-ErbB3
antibody and a second agent that is an anti-cancer agent other than
the first agent, wherein the anti-ErbB3 antibody comprises heavy
chain variable region CDR1, CDR2, and CDR3 amino acid sequences as
set forth in SEQ ID NOs: 7, 8, and 9, respectively, and light chain
variable region CDR1, CDR2, and CDR3 amino acid sequences as set
forth in SEQ ID NOs: 10, 11, and 12, respectively.
2. The composition of claim 1, wherein the anti-ErbB3 antibody
comprises heavy and light chain variable regions as set forth in
SEQ ID NOs: 1 and 2, respectively.
3. The composition of claim 1, wherein the second agent is selected
from the group consisting of erlotinib, paclitaxel, and
cisplatin.
4-6. (canceled)
7. A method of treating a cancer in a patient, the method
comprising co-administering to the patient, 1) a composition
comprising a first agent that is an anti-ErbB3 antibody and 2) a
second agent that is an anti-cancer agent other than the first
agent, wherein: (a). the antibody comprises heavy chain variable
region CDR1, CDR2, and CDR3 amino acid sequences as set forth in
SEQ ID NOs: 7, 8, and 9, respectively, and light chain variable
region CDR1, CDR2, and CDR3 amino acid sequences as set forth in
SEQ ID NOs: 10, 11, and 12, respectively, and (b). the anti-cancer
agent is selected from the group consisting of erlotinib,
paclitaxel, and cisplatin.
8. The method of claim 7, wherein co-administration of the first
agent and the second agent has an additive effect on suppressing
tumor growth, compared to administration of the first agent alone
or the second agent alone.
9. The method of claim 7, wherein co-administration of the first
agent and the second agent has a synergistic effect on suppressing
tumor growth, compared to administration of the first agent alone
or the second agent alone.
10. The method of claim 7, wherein the anti-cancer agent is
administered either simultaneously with or before or after
administration of the anti-ErbB3 antibody.
11. The method of claim 7, wherein the cancer is selected from the
group consisting of melanoma, breast cancer, ovarian cancer, renal
carcinoma, gastrointestinal/colon cancer, lung cancer, clear cell
sarcoma, and prostate cancer.
12. The method of claim 7, wherein the cancer comprises cells
comprising a KRAS mutation.
13. The method of claim 12, wherein the KRAS mutation is a G12S
KRAS mutation.
14. The method of claim 7, wherein the cancer comprises cells
comprising a PI3K (phosphatidylinositol 3-kinase) mutation.
15. An isolated monoclonal antibody, or antigen binding portion
thereof, which binds residues within an epitope of human ErbB3
comprising residues 92-104 and 129 of SEQ ID NO: 73.
16. A composition comprising the antibody, or antigen binding
portion thereof, of claim 15 in a pharmaceutically acceptable
carrier.
17. A method of treating a cancer in a subject comprising
administering to the subject the antibody, or antigen binding
portion thereof, of claim 15.
18. A method of treating a cancer in a subject comprising
administering to the subject the antibody, or antigen binding
portion thereof, wherein the anti-ErbB3 antibody comprises SEQ ID
NO:1, or an amino acid sequence at least 90% identical thereto, and
a light chain variable region comprising SEQ ID NO:2, or an amino
acid sequence at least 90% identical thereto, wherein the antibody
binds the ectodomain of human ErbB3, and wherein the antibody
comprises: (a) variable heavy chain residues Tyr32 or Phe32, Val33,
Trp57, Met102, Thr104, and Ile105 of SEQ ID NO: 1; and (b) variable
light chain residues Asp28, Tyr32 or Phe32, and Tyr93 or Phe93 of
SEQ ID NO: 2.
19. The antibody, or antigen binding portion thereof, of claim 15,
wherein the antibody is a human, humanized, bispecific, or chimeric
antibody.
20. The antibody, or antigen binding portion thereof, of claim 15,
wherein the antibody is selected from the group consisting of a
Fab, Fab'2, ScFv, SMIP, affibody, nanobody and a domain
antibody.
21. The antibody, or antigen binding portion thereof, of claim 15,
wherein the antibody is selected from the group consisting of IgG1,
IgG2, IgG3, IgG4, IgM, IgA1, IgA2, IgAsec, IgD and IgE isotype
antibodies.
22. The antibody, or antigen binding portion thereof, of claim 21,
wherein the antibody is IgG2 isotype and/or binds to ErbB3 with a
K.sub.D of better than 50 nM.
23. (canceled)
24. The antibody of claim 15 wherein the antibody, or antigen
binding portion thereof: (a) inhibits the migration of MCF-7 cells
induced by fetal bovine serum; (b) downregulates the ErbB3 receptor
on MALME-3M cells, as measured using FACS analysis; (c) inhibits
proliferation of ACHN cells; and/or (d) inhibits VEGF secretion by
heregulin-stimulated MCF-7 cells.
25-27. (canceled)
Description
CROSS-REFERENCE TO RELATED APPLICATION
[0001] This application is a continuation of U.S. Ser. No.
16/181,054, filed Nov. 5, 2018, which is a divisional of U.S. Ser.
No. 15/274,989, filed Sep. 23, 2016, which is a divisional of U.S.
Ser. No. 14/181,334, filed Feb. 14, 2014 (U.S. Pat. No. 9,487,588),
which is a continuation of U.S. Ser. No. 12/545,279, filed Aug. 21,
2009 (U.S. Pat. No. 8,691,225), which is a continuation-in-part of,
and claims priority to, U.S. Ser. No. 12/425,874, filed Apr. 17,
2009, which is a continuation-in-part of U.S. Ser. No. 12/281,925,
filed Sep. 5, 2008 (U.S. Pat. No. 7,846,440), which is a 371 U.S.
national stage application of International Application No.
PCT/US2008/002119, filed Feb. 15, 2008, which claims the benefit of
U.S. Provisional Patent Application Serial Nos. 61/009,796, filed
Jan. 2, 2008, and 60/901,904, filed Feb. 16, 2007, the contents of
each of which are hereby incorporated by reference.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Nov. 5, 2018, is named FNJ-001USCP2CNDV2CN_Sequence_Listing.txt
and is 51,811 bytes in size.
BACKGROUND OF THE INVENTION
[0003] The ErbB/HER subfamily of polypeptide growth factor
receptors include the epidermal growth factor (EGF) receptor
(EGFR/ErbB1/HER1), the neu oncogene product (ErbB2/HER2), and the
more recently identified ErbB3/HER3 and ErbB4/HER4 receptor
proteins (see, e.g., Hynes et. al. (1994) Biochim. Biophys. Acta
Rev. Cancer 1198, 165-184). Each of these receptors is predicted to
consist of an ectodomain (extracellular ligand-binding domain), a
membrane-spanning domain, a cytosolic, protein tyrosine kinase
(PTK) domain and a C-terminal phosphorylation domain (see, e.g.,
Kim et al., (1998) Biochem. J 334, 189-195). The ectodomains of the
ErbB receptors are further characterized as being divided into four
domains (I-IV). Domains I and III of the ErbB ectodomain are
involved in ligand binding (see, e.g., Hynes et. al. (2005) Nature
Rev. Cancer 5, 341-354). Ligands for these receptors include
heregulin (HRG) and betacellulin (BTC).
[0004] Experiments in vitro have indicated that the protein
tyrosine kinase activity of the ErbB3 receptor (ErbB3) protein is
attenuated significantly relative to that of other ErbB/HER family
members and this attenuation has been attributed, in part, to the
occurrence of non-conservative amino acid substitutions in the
predicted intracellular catalytic domain of ErbB3 (see, e.g., Guy
et al. (1994) Proc. Natl. Acad. Sci. USA. 91, 8132-8136; Sierke et
al. (1997) Biochem. J. 322, 757-763). However, the ErbB3 protein
has been shown to be phosphorylated in a variety of cellular
contexts. For example, ErbB3 is constitutively phosphorylated on
tyrosine residues in a subset of human breast cancer cell lines
overexpressing this protein (see, e.g., Kraus et al. (1993) Proc.
Natl. Acad. Sci. USA. 90, 2900-2904; and Kim et al. Supra; see,
also, Schaefer et al. (2006) Neoplasia 8(7):613-22 and Schaefer et
al. Cancer Res (2004) 64(10):3395-405).
[0005] Although, the role of ErbB3 in cancer has been explored
(see, e.g., Horst et al. (2005) 115, 519-527; Xue et al. (2006)
Cancer Res. 66, 1418-1426), ErbB3 remains largely unappreciated as
a target for clinical intervention. Current immunotherapies
primarily focus on inhibiting the action of ErbB2 and, in
particular, heterodimerization of ErbB2/ErbB3 complexes (see, e.g.,
Sliwkowski et al. (1994) J. Biol. Chem. 269(20):14661-14665
(1994)). Accordingly, it is an object of the present invention to
provide improved immunotherapies that effectively inhibit ErbB3
signaling, and can be used to treat and diagnose a variety of
cancers.
SUMMARY OF THE INVENTION
[0006] In certain of its aspects, the present invention provides a
novel class of antibodies (e.g., monoclonal antibodies) that bind
to the ErbB3 receptor and inhibit various ErbB3 functions. For
example, the antibodies described herein are capable of binding to
ErbB3 and inhibiting EGF-like ligand mediated phosphorylation of
the receptor. As described herein, EGF-like ligands include EGF,
TGF-.alpha., betacellulin, heparin-binding epidermal growth factor,
biregulin and amphiregulin, which bind to EGFR and induce
dimerization of EGFR with ErbB3. This dimerization, in turn, causes
phosphorylation of ErbB3, and activates signaling through the
receptor. Antibodies of the present invention are thus useful for
treating and diagnosing a variety of cancers associated with
ErbB3-mediated cellular signaling. Accordingly, in one embodiment,
the present invention provides antibodies (including antigen
binding portions thereof) which bind to ErbB3 and inhibit EGF-like
ligand mediated phosphorylation of ErbB3.
[0007] In another embodiment, the antibodies and fragments thereof
are further characterized by one or more of the following
properties: (i) inhibition of ErbB3 ligand-mediated signaling,
including signaling mediated by binding of ErbB3 ligands, such as
heregulin, epiregulin, epigen and biregulin, to ErbB3; (ii)
inhibition of proliferation of cells expressing ErbB3; (iii) the
ability to decrease levels of ErbB3 on cell surfaces (e.g., by
inducing internalization of ErbB3); (iv) inhibition of secretion of
VEGF (vascular endothelial growth factor) by cells expressing
ErbB3; (v) inhibition of the migration of cells expressing ErbB3;
(vi) inhibition of spheroid growth of cells expressing ErbB3; and
(vii) binding to an epitope located on ectodomain (extracellular
domain) Domain I, which corresponds to amino acid residues 1 to
about 190 of mature ErbB3 (SEQ ID NO: 73), for example, an epitope
involving or spanning any portion of residues 1-183 of SEQ ID NO:
73, more preferably involving or spanning residues 93-104 or 92-129
of SEQ ID NO: 73, even more preferably involving residues 92, 93,
99, 101, 102, 104 and 129 of SEQ ID NO: 73 or residues 93, 101,
102, and 104 of SEQ ID NO: 73.
[0008] Preferred antibodies and antigen binding portions thereof
disclosed herein exhibit a K.sub.D of 50 nM or less, as measured by
a surface plasmon resonance assay or a cell binding assay
[0009] In further embodiments, particular antibodies and antigen
binding portions thereof of the present invention include a heavy
chain variable region (V.sub.H) comprising an amino acid sequence
which is at least 80% (e.g., 85%, 90%, 95%, 96%, 97%, 98% or 99%)
identical to the heavy chain variable region amino acid sequence
set forth in SEQ ID NO:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:35,
or SEQ ID NO: 37. Other particular antibodies and antigen binding
portions thereof of the invention include a light chain variable
region (V.sub.L) comprising an amino acid sequence which is at
least 80% (e.g., 85%, 90%, 95%, 96%, 97%, 98% or 99%) identical to
the light chain variable region amino acid sequence set forth in
SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:36, or SEQ ID
NO:38. The antibodies may also include both of the aforementioned
heavy chain and light chain variable regions.
[0010] The variable heavy and light chain regions of the antibodies
or antigen binding portions thereof typically include one or more
complementarity determining regions (CDRs). These include one or
more CDR1, CDR2, and CDR3 regions. Accordingly, other particular
antibodies and antigen binding portions thereof of the present
disclosure include one or more CDR sequences selected from a heavy
chain variable region CDR1 comprising SEQ ID NO:7; a heavy chain
variable region CDR2 comprising SEQ ID NO:8; a heavy chain variable
region CDR3 comprising SEQ ID NO:9; a light chain variable region
CDR1 comprising SEQ ID NO:10; a light chain variable region CDR2
comprising SEQ ID NO:11; a light chain variable region CDR3
comprising SEQ ID NO:12; and combinations thereof.
[0011] Still other particular antibodies and antigen binding
portions thereof of the present disclosure include one or more CDR
sequences selected from a heavy chain variable region CDR1
comprising SEQ ID NO:13; a heavy chain variable region CDR2
comprising SEQ ID NO:14; a heavy chain variable region CDR3
comprising SEQ ID NO:15; a light chain variable region CDR1
comprising SEQ ID NO:16; a light chain variable region CDR2
comprising SEQ ID NO:17; a light chain variable region CDR3
comprising SEQ ID NO:18; and combinations thereof.
[0012] Still other particular antibodies and antigen binding
portions thereof of the present disclosure include; or one or more
CDR sequences selected from a heavy chain variable region CDR1
comprising SEQ ID NO:19; a heavy chain variable region CDR2
comprising SEQ ID NO:20; a heavy chain variable region CDR3
comprising SEQ ID NO:21; a light chain variable region CDR1
comprising SEQ ID NO:22; a light chain variable region CDR2
comprising SEQ ID NO:23; a light chain variable region CDR3
comprising SEQ ID NO:24; and combinations thereof.
[0013] Still other particular antibodies and antigen binding
portions thereof of the present disclosure include; or one or more
CDR sequences selected from a heavy chain variable region CDR1
comprising SEQ ID NO:39; a heavy chain variable region CDR2
comprising SEQ ID NO:40; a heavy chain variable region CDR3
comprising SEQ ID NO:41; a light chain variable region CDR1
comprising SEQ ID NO:42; a light chain variable region CDR2
comprising SEQ ID NO:43; a light chain variable region CDR3
comprising SEQ ID NO:44; and combinations thereof.
[0014] Still other particular antibodies and antigen binding
portions thereof of the present disclosure include; or one or more
CDR sequences selected from a heavy chain variable region CDR1
comprising SEQ ID NO:45; a heavy chain variable region CDR2
comprising SEQ ID NO:46; a heavy chain variable region CDR3
comprising SEQ ID NO:47; a light chain variable region CDR1
comprising SEQ ID NO:48; a light chain variable region CDR2
comprising SEQ ID NO:49; a light chain variable region CDR3
comprising SEQ ID NO:50; and combinations thereof.
[0015] The antibodies and antigen binding portions thereof may also
comprise one or more CDRs which are at least 80% (e.g., 85%, 90%,
95%, 96%, 97%, 98% or 99%) identical to any of the aforementioned
CDRs, or combinations of CDRs.
[0016] In one embodiment, the antibodies and antibody portions
thereof are fully human (i.e., contains human CDR and framework
sequences). Particular human antibodies of the present disclosure
include those having a heavy chain variable region that is from a
human VH3 germ line gene, and/or a light chain variable region from
human VL2 germ line gene.
[0017] Also encompassed by the present invention are antibodies and
antigen binding portions thereof that bind to the same or
overlapping epitopes bound by any of the antibodies or portions
thereof described herein (e.g., an epitope located on Domain I of
the ectodomain of ErbB3), such as an epitope involving or spanning
any of residues 1-183 of the amino acid sequence of mature ErbB3
(SEQ ID NO: 73), more preferably involving or spanning residues
93-104 or 92-129 of SEQ ID NO: 73, even more preferably involving
residues 92, 93, 99, 101, 102, 104 and 129 of SEQ ID NO: 73 or
residues 93, 101, 102, and 104 of SEQ ID NO: 73. Antibodies which
have the same epitope binding activity as the antibodies described
herein, e.g., antibodies having the same sequence as Ab #6 or
binding epitopes involving residues 93-104 of SEQ ID NO: 73, are
also encompassed by the present invention.
[0018] Also encompassed by the present invention are antibodies and
antigen binding portions thereof that bind to the ectodomain of
human ErbB3 and comprise:
[0019] a heavy chain variable region comprising CDR1, CDR2, and
CDR3 sequences; and a light chain variable region comprising CDR1,
CDR2, and CDR3 sequences, wherein:
[0020] the heavy chain variable region CDR1, CDR2 and CDR3
sequences comprise consensus heavy chain CDR1, CDR2 and CDR3
sequences shown in SEQ ID NOs: 60 or 75 (CDR1), 61 (CDR2) and 62
(CDR3), respectively, and
[0021] the light chain variable region CDR1, CDR2 and CDR3
sequences comprise consensus light chain CDR1, CDR2 and CDR3
sequences shown in SEQ ID NOs: 66 or 77 (CDR1), 67 (CDR2) and 68 or
79 (CDR3), respectively.
[0022] In a preferred embodiment, the isolated antibody, or antigen
binding portion thereof, binds to an epitope within Domain I of the
ectodomain of human ErbB3 comprising residues 92-129 or 93-104 of
SEQ ID NO: 73. Even more preferably, the isolated antibody, or
antigen binding portion thereof, binds to an epitope within Domain
I of the ectodomain of human ErbB3 comprising residues 92-129 or
93-104 of SEQ ID NO: 73 and inhibits proliferation of a cancer cell
expressing ErbB3. Preferably, the cancer cell is a MALME-3M
melanoma cell, an AdrR (ADRr) ovarian adenocarcinoma cell or an
ACHN renal carcinoma cell and the proliferation is reduced by at
least 10% relative to a control (i.e., matched untreated
cells).
[0023] In another embodiment of the isolated antibody, or antigen
binding portion thereof, that binds to Domain I of the ectodomain
of human ErbB3, when any one of amino acid residues of Domain I of
the ectodomain of human ErbB3 selected from residue 93
(asparagine), residue 99 (phenylalanine), residue 101 (methionine),
residue 102 (leucine) and residue 104 (tyrosine) of SEQ ID NO: 73
is replaced by an alanine, or residue 92 (tyrosine) or 129
(tyrosine) of SEQ ID NO: 73 is replaced by phenylalanine, to
generate a mutant ErbB3 with a single amino acid substitution,
there is a substantial reduction in binding of the antibody or
antigen binding portion thereof to the mutant ErbB3 (or fragment
thereof) as compared to binding of the antibody or antigen binding
portion thereof to human ErbB3 comprising the unaltered amino acid
sequence of SEQ ID NO: 73 (or a corresponding fragment thereof).
Preferably, the substantial reduction in binding is at least a
ten-fold change in K.sub.D value of binding.
[0024] Also encompassed by the present invention are antibodies and
antigen binding portions thereof that bind to the Domain I of the
ectodomain of human ErbB3 and comprise:
[0025] a heavy chain variable region comprising CDR1, CDR2, and
CDR3 sequences; and a light chain variable region comprising CDR1,
CDR2, and CDR3 sequences, wherein:
[0026] the heavy chain variable region paratope comprises CDR1,
CDR2 and CDR3 sequences shown in SEQ ID NOs: 63 or 76 (CDR1), 64
(CDR2) and 65 (CDR3), respectively, and
[0027] the light chain variable region paratope comprises CDR1,
CDR2 and CDR3 sequences shown in SEQ ID NOs: 69 or 78 (CDR1), 70
(CDR2) and 71 or 80 (CDR3), respectively.
[0028] Also encompassed by the present invention are antibodies and
antigen binding portions thereof, that bind specifically to Domain
I of the ectodomain of human ErbB3, wherein the antibody or antigen
binding portion thereof comprises: [0029] a heavy chain variable
region CDR1 comprising SEQ ID NO:7 or conservative amino acid
substitutions thereof; [0030] a heavy chain variable region CDR2
comprising SEQ ID NO:8 or conservative amino acid substitutions
thereof; [0031] a heavy chain variable region CDR3 comprising SEQ
ID NO:9 or conservative amino acid substitutions thereof; [0032] a
light chain variable region CDR1 comprising SEQ ID NO:10 or
conservative amino acid substitutions thereof; [0033] a light chain
variable region CDR2 comprising SEQ ID NO:11 or conservative amino
acid substitutions thereof; and
[0034] a light chain variable region CDR3 comprising SEQ ID NO:12
or conservative amino acid substitutions thereof,
[0035] wherein the binding of the antibody or antigen binding
portion thereof to ErbB3 exhibits a K.sub.D of 50 nM or better as
measured by a surface plasmon resonance assay or a cell binding
assay.
[0036] Antibodies of the present invention include all known forms
of antibodies and other protein scaffolds with antibody-like
properties. For example, the antibody can be a human antibody, a
humanized antibody, a bispecific antibody, a chimeric antibody or a
protein scaffold with antibody-like properties, such as fibronectin
or ankyrin repeats. The antibody also can be a Fab, Fab'2, ScFv,
SMIP, affibody, nanobody, or a domain antibody. The antibody also
can have any of the following isotypes: IgG1, IgG2, IgG3, IgG4,
IgM, IgA1, IgA2, IgAsec, IgD, and IgE.
[0037] In yet another embodiment, the present invention further
provides compositions comprising combinations of antibodies or
antigen binding portions described herein, formulated with an
acceptable carrier and/or adjuvant. In a particular embodiment, the
composition comprises two or more antibodies that bind different
epitopes on ErbB3 or antibodies described herein combined with
anti-cancer antibodies which do not bind ErbB3.
[0038] In still another embodiment, the present invention provides
isolated nucleic acids encoding the antibodies and antigen binding
portions thereof described herein. In particular embodiments, the
nucleic acid encodes a heavy chain variable region comprising a
nucleotide sequence which is at least 80% (e.g., 85%, 90%, 95%,
96%, 97%, 98% or 99%) identical to, or which hybridizes under high
stringency conditions to, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29,
SEQ ID NO:35, or SEQ ID NO:37; or a light chain variable region
comprising a nucleotide sequence which is at least 80% (e.g., 85%,
90%, 95%, 96%, 97%, 98% or 99%) identical to, or which hybridizes
under high stringency conditions to, SEQ ID NO:26, SEQ ID NO:28,
SEQ ID NO:30, SEQ ID NO:36, or SEQ ID NO:38; or combinations of
such heavy and light variable regions.
[0039] The present invention further provides transgenic non-human
mammals, hybridomas, and transgenic plants that express and/or
produce the antibodies and antigen binding portions described
herein.
[0040] Also provided by the invention are kits comprising one or
more isolated antibodies or antigen binding portions thereof
described herein and, optionally, instructions for use in treating
or diagnosing a disease associated with ErbB3 dependent signaling,
such as cancers.
[0041] Antibodies and antigen binding portions thereof disclosed
herein can be used in a broad variety of therapeutic and diagnostic
applications, particularly oncological applications. Accordingly,
in another aspect, the present invention provides method for
inhibiting EGF-like ligand mediated phosphorylation of ErbB3 in a
subject by administering one or more antibodies or antigen binding
portions thereof described herein in an amount sufficient to
inhibit EGF-like mediated phosphorylation of ErbB3. The invention
further provides methods for treating a variety of cancers in a
subject, including, but not limited to, melanoma, breast cancer,
ovarian cancer, renal carcinoma, gastrointestinal/colon cancer,
lung cancer, clear cell sarcoma, and prostate cancer, by
administering one or more antibodies or antigen binding portions
thereof described herein in an amount sufficient to treat the
cancer. In one embodiment, the cancer comprises cells comprising a
KRAS mutation. Exemplary KRAS mutations are in either or both of
codon 12 and codon 13 of the human KRAS gene. Mutations in codon 12
or codon 13, each of which normally codes for a glycine (including
any of those changing the wild-type glycine 12 or glycine 13 to
serine, arginine, cysteine, aspartate, or valine) are activating
KRAS mutations that promote oncogenesis, as are mutations in codons
15, 20, 61 and 146 of the human KRAS gene. In another embodiment,
the cancer comprises cells comprising a PI3K (phosphatidylinositol
3-kinase) mutation. Exemplary PI3K mutations are activating
mutations in the human PIK3CA gene in either or both of exon 9 or
exon 20. The antibodies or antigen binding portions thereof can be
administered alone or in combination with other therapeutic agents,
such as anti-cancer agents, e.g., other antibodies,
chemotherapeutic agents and/or radiation.
[0042] In one embodiment, an antibody or antigen binding portion
thereof is administered in combination with a second agent, which
second agent is selected from the group consisting of a protein
synthesis inhibitor, a somatostatin analogue, an immunotherapeutic
agent, and an enzyme inhibitor. In other embodiments, the second
agent is selected from: a small molecule targeting IGF1R, a small
molecule targeting EGFR, a small molecule targeting ErbB2, a small
molecule targeting cMET, an antimetabolite, an alkylating agent, a
topoisomerase inhibitor, a microtubule targeting agent, a kinase
inhibitor, a hormonal therapy, a glucocorticoid, an aromatase
inhibitor, an mTOR inhibitor, a chemotherapeutic agent, a protein
kinase B inhibitor, a phosphatidylinositol 3-kinase inhibitor, a
cyclin dependent kinase inhibitor, and an MEK inhibitor. Exemplary
antibodies for use as second agents in combination therapy include
anti-Her2 antibodies, e.g., trastuzumab and anti-EGFR antibodies,
e.g., panitumumab or cetuximab. Certain preferred anti-cancer
agents for use as second agents in combination therapy include
erlotinib, lapatinib, paclitaxel and cisplatin.
[0043] In yet other embodiments, the present invention provides
methods for diagnosing and prognosing diseases (e.g., cancers)
associated with ErbB3. In one embodiment, this is achieved by
contacting antibodies or antigen binding portions of the present
disclosure (e.g., ex vivo or in vivo) with cells from the subject,
and measuring the level of binding to ErbB3 on the cells, wherein
abnormally high levels of binding to ErbB3 indicate that the
subject has a cancer associated with ErbB3.
[0044] Other features and advantages of the invention will be
apparent from the following detailed description, and from the
claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0045] FIGS. 1A and 1B are bar graphs depicting the binding of
various anti-ErbB3 antibody candidates to ErbB3 expressed on
MALME-3M melanoma cells using a goat anti-human Alexa 647 secondary
antibody (GAHu-Alexa 674). In these experiments the antibodies
indicated as "Ab #" are used in the form of Fab fragments and
"GAHu-Alexa 674" indicates the fluorescent dye-conjugated secondary
antibody used alone as a control, while "unstained" indicates a
control in the absence of the secondary antibody.
[0046] FIGS. 2A-2D are graphs depicting binding of antibodies to
ErbB3 set forth as K.sub.D values of various anti-ErbB3 antibody
candidates. FIGS. 2A and 2B are graphs depicting the K.sub.D value
of Ab #6 and Ab #3, respectively, as measured using surface plasmon
resonance (SPR) technology and the formula K.sub.D=k.sub.d/k.sub.a.
FIGS. 2C and 2D are graphs depicting the K.sub.D values of Ab #6
and Ab #3, respectively, as measured using a cell binding assay
using MALME-3M melanoma cells and the formula
Y=Bmax*X/K.sub.D+X.
[0047] FIG. 3 is a graph depicting the binding specificity of an
anti-ErbB3 antibody (Ab #6) to ErbB3 using ELISA. EGFR
extracellular domain, bovine serum albumin (BSA) and TGF.alpha.
were used as controls.
[0048] FIG. 4 is a graph depicting the ability of an anti-ErbB3
antibody (Ab #6) to decrease total ErbB3 levels in MALME-3M
melanoma cells in vitro, as measured using ELISA.
[0049] FIGS. 5A and 5B are graphs depicting the ability of an
anti-ErbB3 antibody (Ab #6) to downregulate ErbB3 receptors on
MALME-3M cells, measured using FACS analysis, as described in
Example 5 below. FIG. 5A shows the results using an IgG1 isotype of
the antibody. FIG. 5B shows the results using an IgG2 isotype of
the antibody.
[0050] FIGS. 6A-6D are graphs depicting the timecourse of
antibody-mediated ErbB3 downregulation (Ab #6), as measured using
FACS analysis.
[0051] FIG. 7 shows the results of a pharmacodynamic study. The a
bar graph depicts 24 hrs post-injection results of indicated
anti-ErbB3 antibodies on total ErbB3 levels in MALME3M melanoma
cells in xenografts in vivo. As can be seen, the data demonstrate
the ability of Ab #6 to downregulate ErbB3.
[0052] FIG. 8 is a bar graph depicting the ability of an anti-ErbB3
antibody (Ab #6) to downregulate ErbB3 in AdrR xenografts in vivo.
Total ErbB3 levels in AdrR xenografts are shown.
[0053] FIG. 9 is a graph depicting the ability of an anti-ErbB3
antibody (Ab #6) to inhibit proliferation of MALME-3M cells in a
CellTiter-Glo.RTM. assay.
[0054] FIG. 10 is a graph depicting the ability of an anti-ErbB3
antibody (Ab #6) to inhibit cell proliferation of AdrR cells.
[0055] FIG. 11 is a graph depicting the ability of an anti-ErbB3
antibody (Ab #6) to inhibit proliferation of ACHN cells.
[0056] FIG. 12 is a bar graph depicting the ability of an
anti-ErbB3 antibody (Ab #6) to inhibit ErbB3 phosphorylation in
AdrR xenografts in vivo.
[0057] FIGS. 13A-13C are graphs depicting the ability of an
anti-ErbB3 antibody (Ab #6) to inhibit betacellulin, heregulin, and
TGF.alpha.-mediated phosphorylation of ErbB3 in AdrR cells.
[0058] FIGS. 14A-14B are graphs depicting the ability of an
anti-ErbB3 antibody (Ab #6 IgG2 isotype) to inhibit ErbB3
phosphorylation in ovarian tumor cell lines OVCAR 5 and OVCAR
8.
[0059] FIGS. 15A-15C are graphs depicting the ability of
betacellulin (BTC) to bind ErbB1 as shown by a lack of binding to
ErbB1 negative MALME-3M cells (FIG. 15A); binding to ErbB1 positive
AdrR cells at concentrations of 10 nM (FIG. 15B) and 200 nM (FIG.
15C), respectively, and the inhibition of such binding by
cetuximab.
[0060] FIGS. 16A-16D are graphs depicting the ability of an
anti-ErbB3 antibody (Ab #6, IgG2 isotype) to inhibit
heregulin-mediated signaling in MALME-3M cells (FIGS. 16A and 16B)
and OVCAR8 cells (16C and 16D). FIG. 16A depicts the ability of the
Ab #6 to inhibit heregulin-mediated phosphorylation of ErbB3 in
MALME-3M cells (IC.sub.50=1.5 e-8). FIG. 16B depicts the ability of
Ab #6 to inhibit phosphorylation of AKT in MALME-3M cells
(IC.sub.50=1.1e-8). FIG. 16C depicts the ability of the Ab #6 to
inhibit heregulin-mediated phosphorylation of ErbB3 in OVCAR8 cells
(IC.sub.50=2.4 e-8). FIG. 16B depicts the ability of Ab #6 to
inhibit phosphorylation of AKT in OVCAR8 cells (IC.sub.50=6.7
e-8).
[0061] FIGS. 17A-D are graphs depicting the ability of an
anti-ErbB3 antibody (Ab #6) to inhibit: (FIG. 17A) ovarian (AdrR
cells), (FIG. 17B) prostate (Du145 cells), (FIG. 17C) ovarian
(OVCAR8 cells), and (FIG. 17D) pancreatic (Colo-357 cells) tumor
growth via xenograft studies.
[0062] FIGS. 18A and 18B are graphs depicting the ability of Ab #6
(FIG. 18A) and Fab for Ab #3 (FIG. 18B) to inhibit heregulin
binding to ErbB3 on MALME-3M cells, as measured using FACS
analysis.
[0063] FIG. 19A depicts the binding of epiregulin to AdrR cells,
and FIG. 19B depicts the ability of Ab #6, but not ERBITUX
(cetuximab) to inhibit epiregulin binding to AdrR cells.
[0064] FIG. 20 is a graph depicting the ability of heparin binding
epidermal growth factor (HB-EGF) to bind to AdrR cells.
[0065] FIGS. 21A-21C show the amino acid sequences of the variable
heavy and light chain regions of antibodies: Ab #6, Ab #3, Ab #14,
Ab #17, and Ab #19.
[0066] FIGS. 22A-22B show the nucleotide sequences of the variable
heavy and light chain regions of antibodies: Ab #6, Ab #3, and Ab
#14.
[0067] FIG. 23 shows the amino acid sequences of the variable light
chain regions of antibodies: Ab #6, Ab #17, and Ab #19, which have
been reverted to the corresponding germline amino acid sequence.
Amino acid residue changes accomplishing this reversion (compare
FIG. 21) are underlined.
[0068] FIGS. 24A and B are graphs showing the ability of Ab #6 to
inhibit VEGF secretion by tumor cells (see Example 11). FIG. 24C
shows the correlation between inhibition of VEGF secretion and
inhibition of pErbB3 in cancer cells by Ab #6.
[0069] FIG. 25 is a graph showing the effect of Ab #6 on cell
migration (see Example 12). Control 0 uM=RPMI medium alone, Control
8 uM=RPMI medium+8 uM Ab #6, FBS 0 mM=RPMI medium+10% FBS, FBS 8
uM=RPMI medium+10% FBS+8 uM Ab #6.
[0070] FIGS. 26A-C are graphs showing (FIG. 26A) inhibition of
spheroid growth in AdrR cells, (FIG. 26B) inhibition of HRG-induced
spheroid growth in AdrR, and (FIG. 26C) inhibition of HRG-induced
spheroid growth in Du145 cells.
[0071] FIGS. 27A and B are graphs showing the effect of Ab #6 on
HRG (FIG. 27A) and BTC (FIG. 27B) binding to AdrR cells.
[0072] FIG. 28 is a graph showing the effect of Ab #6 on HGF
(hepatocyte growth factor) induced ErbB3 phosphorylation in AdrR
cells. The IC.sub.50 for HGF was determined to be 2.439e-10.
[0073] FIGS. 29A and B show the effect of Ab #6 on phosphorylation
of (FIG. 29A) pErbB1 and pErbB3 and (FIG. 29B) HRG induced ErbB2/3
complex formation.
[0074] FIG. 30 is a graph showing the effect of Ab #6 alone,
erlotinib alone or Ab #6 plus erlotinib on the growth of ACHN
xenograft tumors in nude mice. The data show that after 27 days the
combination a dose of 300 ug of Ab #6 (a suboptimal dose when
administered alone) plus erlotinib synergistically inhibits tumor
growth to a statistically significant extent.
[0075] FIG. 31 is a graph showing the effect of Ab #6 alone, taxol
alone or Ab #6 plus taxol on the growth of DU145 xenograft tumors
in nude mice. The data show that after 27 days the combination of a
dose of 300 ug of Ab #6 (a suboptimal dose when administered alone)
plus taxol inhibits tumor growth to a greater extent than does
treatment with either drug alone to a statistically significant
extent.
[0076] FIG. 32A is a graph showing the effect of Ab #6 treatment
alone on the growth of multicellular tumor spheroids of KRAS mutant
A549 lung cancer cells. Cells were treated with 0, 0.001, 0.01, 0.1
or 1 .mu.M Ab #6 for seven days. The "-4" on the x axis corresponds
to the "0" dose. The results show the Ab #6 dose response effect on
KRAS mutant tumor spheroid growth.
[0077] FIG. 32B is a set of photographs of representative A549
spheroids, either untreated or treated with 1 .mu.M Ab #6, on day 1
and day 7 of treatment.
[0078] FIG. 32C is a graph showing the effect of Ab #6 treatment
alone on the growth of KRAS mutant A549 subcutaneous xenograft
tumors in nude mice. Dosing of Ab #6 (600 .mu.g every three days)
was stopped on day 22.
[0079] FIG. 33A is a graph showing the effect of Ab #6 treatment
alone, erlotinib treatment alone or combined treatment with Ab #6
and erlotinib on the growth of KRAS mutant A549 subcutaneous
xenograft tumors in nude mice.
[0080] FIG. 33B is a graph showing the effect of Ab #6 treatment
alone, taxol treatment alone or combined treatment with Ab #6 and
taxol on the growth of KRAS mutant A549 subcutaneous xenograft
tumors in nude mice.
[0081] FIGS. 34A-34E shows the results of a FACS analysis for the
binding of Ab #6 and a control anti-ErbB3 antibody (SGP1) to CHO
cells expressing either wild-type ErbB3 (FIG. 34A) or CHO cells
expressing ErbB3 having one of the following point mutations: D93A
(FIG. 34B), M101A (FIG. 34C), L102A (FIG. 34D) or Y104A (FIG.
34E).
[0082] FIG. 35A is a graph showing the effect of Ab #6 treatment
alone on the growth of PI3K mutant SKOV3 xenograft tumors in
mice.
[0083] FIG. 35B is a graph showing the showing the effect of Ab #6
treatment alone, or in combination with cisplatin (CDDP), on the
growth of PI3K mutant SKOV3 xenograft tumors in mice.
[0084] FIG. 36 presents data from paratope mapping experiments.
Shown are the effects of single amino acid mutations (for identity
of indicated mutations see example 20, Table 2) on the binding of
Ab #6 mutants to ErbB3 as compared to the binding of the same
mutants of Ab #6 to protein A. The diagonal bisecting the graph
indicates a 1:1 correspondence of the effect on ErbB3 and protein A
binding. The additional, parallel lines were located created by
moving the diagonal down the y axis by 0.33 and 0.66 for convenient
grouping of the mutations into three categories (large, small and
no effect on binding). The graph shows the effect on binding of the
mutation normalized to the wild type Ab #6. Values on the Y axis
are ratios of binding of wild type Ab #6 to binding of Ab #6
mutants to ErbB3. A ratio of <1 means that the mutant has loss
of binding to ErbB3 compared to wild type Ab #6, while a ratio of
>1 means that the mutant exhibits stronger binding to ErbB3 than
wild type Ab #6.
[0085] FIGS. 37A and 37B are schematic diagrams of the Ab #6 wild
type heavy chain variable region (V.sub.H) CDR1, CDR2 and CDR3
sequences (SEQ ID NOs: 7, 8 and 9, respectively), the consensus
V.sub.H CDR1, CDR2 and CDR3 sequences (SEQ ID NOs: 60, 61 and 62,
respectively, for FIG. 37A and SEQ ID NOs: 75, 61 and 62,
respectively, for FIG. 37B), the V.sub.H CDR1, CDR2 and CDR3
paratope sequences (SEQ ID NOs: 63, 64 and 65, respectively, for
FIG. 37A and SEQ ID NOs: 76, 64, 65, respectively, for FIG. 37B),
the Ab #6 wild type light chain variable region (V.sub.L) CDR1,
CDR2 and CDR3 sequences (SEQ ID NOs: 10, 11 and 12, respectively),
the consensus V.sub.L CDR1, CDR2 and CDR3 sequences (SEQ ID NOs:
66, 67 and 68, respectively, for FIG. 37A and SEQ ID NOs: 77, 67
and 79, respectively, for FIG. 37B) and the V.sub.L CDR1, CDR2 and
CDR3 paratope sequences (SEQ ID NOs: 69, 70 and 71, respectively,
for FIG. 37A and SEQ ID NOs: 78, 70 and 80, respectively, for FIG.
37B). In these figures, the standard single letter amino acid
abbreviations are used and the separation of single letters
indicating amino acids by dashes indicates sequential residues in
the sequence, while any group of two or more adjacent single
letters indicating amino acids separated by one or more slashes
indicates that any of the grouped adjacent amino acids so separated
may be substituted for any of the others at that position in the
sequence. For example, the notation
"(Xaa).sub.7-W-T/A/G/S-L-(Xaa).sub.7" indicates a sequence running
from amino to carboxy terminus as follows: seven unspecified amino
acids followed by tryptophan, followed by (threonine or alanine or
glycine or serine), followed by leucine, followed by seven
unspecified amino acids. "Unspecified amino acid" is used here to
indicate that any amino acid may appear independently at each
position designated Xaa, even where several such positions appear
together. The repetition of Xaa or of any group designated as
Xaa.sub.#--e.g., "(Xaa).sub.7"--does not indicate any
correspondence between the designated group of unspecified amino
acids at one position in these sequences and designated group of
unspecified amino acids at any other position. Thus the repetition
of (Xaa).sub.7 at the beginning and end of the sequence
"(Xaa).sub.7-W-T/A/G/S-L-(Xaa).sub.7" does not indicate any
correspondence between the sequence of each (Xaa).sub.7 other than
that each contains seven unspecified amino acids.
[0086] FIGS. 38A-D show the effects of Ab #6 (decreasing
concentrations along the X axis, as indicated) on ligand-induced
ErbB3 phosphorylation (pErbB3 levels; increasing concentrations
along the Y axis as indicated) in AdrR cells. In FIG. 38A, the
ligand is HRG, in FIG. 38B, the ligand is BTC, in FIG. 38C, the
ligand is HGF, and in FIG. 38D, the ligand is EGF.
[0087] FIG. 39 is a FACS profile demonstrating that Ab #6 binds to
Domain I of the ectodomain of ErbB3.
DETAILED DESCRIPTION OF THE INVENTION
[0088] In order that the present invention may be more readily
understood, certain terms are first defined. Additional definitions
are set forth throughout the detailed description.
I. Definitions
[0089] The terms "ErbB3," "HER3," "ErbB3 receptor," and "HER3
receptor," as used interchangeably herein, refer to human ErbB3
protein, as described in U.S. Pat. No. 5,480,968 and Plowman et
al., Proc. Natl. Acad. Sci. USA, 87:4905-4909 (1990); see, also,
Kani et al., Biochemistry 44:15842-857 (2005), Cho and Leahy,
Science 297:1330-1333 (2002)). The full-length, mature human ErbB3
protein sequence (without leader sequence) is shown in SEQ ID NO:
73. This sequence corresponds to the sequence shown in FIG. 4 and
SEQ ID NO: 4 of U.S. Pat. No. 5,480,968, minus the 19 amino acid
leader sequence that is cleaved from the mature protein.
[0090] The term "EGF-like ligand," as used herein, refers to
ligands of epidermal growth factor receptor (EGFR), including
epidermal growth factor (EGF) and closely related proteins, such as
transforming growth factor-.alpha. (TGF.alpha.), betacellulin
(BTC), heparin-binding epidermal growth factor (HB-EGF), biregulin
(BIR) and amphiregulin (AR), which bind to EGFR on the surface of
cells and stimulate the receptor's intrinsic protein-tyrosine
kinase activity. Typically, EGF-like ligands induce formation of
EGFR and ErbB3 protein complex (see e.g., Kim et al., (1998)
Biochem J., 334:189-195), which results in phosphorylation of
tyrosine residues in the complex.
[0091] Preferred antibodies and antigen binding portions thereof
disclosed herein inhibit EGF-like ligand mediated phosphorylation
of ErbB3 and, in certain embodiments, exhibit one or more of the
following additional properties: (i) inhibition of one or more of
heregulin, epiregulin, epigen and biregulin-mediated signaling
through ErbB3; (ii) inhibition of proliferation of cells expressing
ErbB3; (iii) the ability to decrease levels of ErbB3 on cell
surfaces; (iv) inhibition of VEGF secretion of cells expressing
ErbB3; (v) inhibition of the migration of cells expressing ErbB3;
(vi) inhibition of spheroid growth of cells expressing ErbB3;
and/or (vii) specific binding to an epitope located on Domain I of
the ectodomain of ErbB3, e.g., an epitope which involves or spans
residues 1-183 of the amino acid sequence of mature ErbB3 (SEQ ID
NO: 73, more preferably involving or spanning or containing or
comprising or including residues 92-129 or 93-104 or of SEQ ID NO:
73, even more preferably involving or containing or comprising or
including residues 92, 93, 101, 102 and 104 and 129, or residues
93, 101, 102 and 104, of SEQ ID NO: 73. One such antibody, Ab #6,
is currently undergoing phase I clinical trails as MM-121.
[0092] The term "inhibition" as used herein, refers to any
statistically significant decrease in biological activity,
including full blocking of the activity. For example, "inhibition"
can refer to a decrease of about 10%, 20%, 30%, 40%, 50%, 60%, 70%,
80%, 90%, or 100% in biological activity.
[0093] Accordingly, the phrase "inhibition of EGF-like ligand
mediated phosphorylation of ErbB3," as used herein, refers to the
ability of an antibody or antigen binding portion to statistically
significantly decrease the phosphorylation of ErbB3 induced by an
EGF-like ligand, relative to the phosphorylation in an untreated
(control) cell. The cell which expresses ErbB3 can be a naturally
occurring cell or cell line or can be recombinantly produced by
introducing nucleic acid encoding ErbB3 into a host cell. In one
embodiment, the antibody or antigen binding portion thereof
inhibits EGF-like ligand mediated phosphorylation of ErbB3 by at
least 10%, or at least 20%, or at least 30%, or at least 40%, or at
least 50%, or at least 60%, or at least 70%, or at least 80%, or at
least 90%, or about 100%, as determined, for example, by Western
blotting followed by probing with an anti-phosphotyrosine antibody
as described in Kim et al., (1998) Biochem J., 334:189-195 and the
Examples infra.
[0094] The phrase "inhibition of heregulin, epiregulin, epigen or
biregulin-mediated signaling through ErbB3," as used herein, refers
to the ability of an antibody or an antigen-binding portion thereof
to statistically significantly decrease signaling mediated by an
ErbB3 ligand (e.g., heregulin, epiregullin, epigen and biregulin)
through ErbB3, relative to the signaling in the absence of the
antibody (control). ErbB3-ligands are also referred to herein as
"heregulin-like ligands." This means that, in the presence of the
antibody or antigen binding portion thereof, a signal mediated in a
cell expressing ErbB3 by one or more of heregulin, epiregulin,
epigen and biregulin, relative to a control (no antibody), is
statistically significantly decreased. An ErbB3-ligand mediated
signal can be measured by assaying for the level or activity of an
ErbB3 substrate, and/or a protein which is present in a cellular
cascade involving ErbB3. In one embodiment, the antibody or antigen
binding portion thereof decreases the level or activity of an ErbB3
substrate and/or that of a protein in a cellular cascade involving
ErbB3, by at least 10%, or at least 20%, or at least 30%, or at
least 40%, or at least 50%, or at least 60%, or at least 70%, or at
least 80%, or at least 90%, or about 100% relative to the level or
activity in the absence of such antibody or antigen binding portion
thereof (control). Such ErbB3-ligand mediated signaling can be
measured using art recognized techniques which measure the level or
activity of a substrate of ErbB3 (e.g., SHC or PI3K) or a protein
in a cellular cascade involving ErbB3 (e.g., the AKT pathway--AKT
refers to a set of serine/threonine kinases also referred to as
protein kinases B or PKB) using kinase assays for such proteins
(see, e.g., Horst et al. supra, Sudo et al. (2000) Methods Enzymol,
322:388-92; and Morgan et al. (1990) Eur. J. Biochem.,
191:761-767).
[0095] In a particular embodiment, the antibody or antigen binding
portion thereof inhibits ErbB3-ligand (e.g., heregulin, epiregulin,
epigen or biregulin) mediated signaling through ErbB3 by inhibiting
the binding of the ErbB3-ligand (e.g., one or more of heregulin,
epiregulin, epigen or biregulin) to ErbB3. Some ligands (e.g.,
biregulin, an artificial chimeric ligand: Barbacci, et al., J Biol
Chem 1995 270(16) 9585-9) function both as EGF-like ligands (i.e.,
bind to EGFR/ErbB1) as well as ErbB3-like ligands (i.e., bind to
ErbB3).
[0096] The phrase "inhibition of heregulin, epiregulin, epigen or
biregulin binding to ErbB3," as used herein, refers to the ability
of an antibody or an antigen-binding portion thereof to
statistically significantly decrease the binding of an ErbB3 ligand
(e.g., one or more of heregulin, epiregulin, epigen or biregulin)
to ErbB3, relative to the binding in the absence of the antibody
(control). This means that, in the presence of the antibody or
antigen binding portion thereof, the amount of the ErbB3-ligand
(e.g., heregulin, epiregulin, epigen or biregulin) which binds to
ErbB3 relative to a control (no antibody), is statistically
significantly decreased. The amount of an ErbB3 ligand which binds
ErbB3 may be decreased in the presence of an antibody or antigen
binding portion thereof of the present disclosure by at least 10%,
or at least 20%, or at least 30%, or at least 40%, or at least 50%,
or at least 60%, or at least 70%, or at least 80%, or at least 90%,
or 100% relative to the amount in the absence of the antibody or
antigen binding portion thereof (control). A decrease in
ErbB3-ligand binding can be measured using art recognized
techniques which measure the level of binding of labeled
ErbB3-ligand (e.g., radiolabeled heregulin, epiregulin, epigen or
biregulin) to cells expressing ErbB3 in the presence or absence
(control) of the antibody or antigen binding portion thereof.
[0097] The phrase "inhibition of proliferation of a cell expressing
ErbB3," as used herein, refers to the ability of an antibody or an
antigen-binding portion thereof to statistically significantly
decrease proliferation of a cell expressing ErbB3 relative to the
proliferation in the absence of the antibody. In one embodiment,
the proliferation of a cell expressing ErbB3 (e.g., a cancer cell)
may be decreased by at least 10%, or at least 20%, or at least 30%,
or at least 40%, or at least 50%, or at least 60%, or at least 70%,
or at least 80%, or at least 90%, or 100% when the cells are
contacted with an antibody or antigen binding portion thereof of
the present disclosure, relative to the proliferation measured in
the absence of the antibody or antigen binding portion thereof
(control). Cellular proliferation can be assayed using art
recognized techniques which measure rate of cell division, the
fraction of cells within a cell population undergoing cell
division, and/or rate of cell loss from a cell population due to
terminal differentiation or cell death (e.g., using a
CellTiter-Glo.RTM. assay or thymidine incorporation).
[0098] The phrase "the ability to decrease levels of ErbB3 on cell
surfaces," as used herein, refers to the ability of an antibody or
antigen binding portion thereof to statistically significantly
reduce the amount of ErbB3 found on the surface of a cell which has
been exposed to the antibody relative to an untreated (control)
cell. For example, a decrease in levels of ErbB3 on cell surfaces
may result from increased internalization of ErbB3 (or increased
ErbB3 endocytosis). In one embodiment, the antibody or antigen
binding portion thereof decreases cell surface expression of ErbB3
by at least 10%, or at least 20%, or at least 30%, or at least 40%,
or at least 50%, or at least 60%, or at least 70%, or at least 80%,
or at least 90%, or 100% and/or increases internalization of the
ErbB3 receptor by at least 10%, or at least 20%, or at least 30%,
or at least 40%, or at least 50%, or at least 60%, or at least 70%,
or at least 80%, or at least 90%, or 100% relative to the cell
surface expression or internalization in the absence of the
antibody or antigen binding portion thereof (control). The levels
of ErbB3 on surfaces of cells and/or internalization of the ErbB3
receptor in the absence and the presence of an antibody or
antigen-binding portion thereof can be readily measured using art
recognized techniques, such as those described in Horst et al.,
supra and in the examples herein.
[0099] The phrase "inhibition of VEGF secretion of cells expressing
ErbB3," as used herein, refers to the ability of an antibody or an
antigen-binding portion thereof to statistically significantly
decrease VEGF secretion of a cell expressing ErbB3 relative to the
VEGF secretion in the absence of the antibody. In one embodiment,
the VEGF secretion of a cell expressing ErbB3 (e.g., a cancer cell)
may be decreased by at least 10%, or at least 20%, or at least 30%,
or at least 40%, or at least 50%, or at least 60%, or at least 70%,
or at least 80%, or at least 90%, or 100% when the cells are
contacted with an antibody or antigen binding portion thereof of
the present disclosure, relative to the VEGF secretion measured in
the absence of the antibody or antigen binding portion thereof
(control). VEGF secretion can be assayed using art recognized
techniques, such as those described herein.
[0100] The phrase "inhibition of the migration of cells expressing
ErbB3," as used herein, refers to the ability of an antibody or an
antigen-binding portion thereof to statistically significantly
decrease the migration of a cell expressing ErbB3 relative to the
migration of the cell in the absence of the antibody. In one
embodiment, the migration of a cell expressing ErbB3 (e.g., a
cancer cell) may be decreased by at least 10%, or at least 20%, or
at least 30%, or at least 40%, or at least 50%, or at least 60%, or
at least 70%, or at least 80%, or at least 90%, or 100% when the
cells are contacted with an antibody or antigen binding portion
thereof of the present disclosure, relative to cell migration
measured in the absence of the antibody or antigen binding portion
thereof (control). Cell migration can be assayed using art
recognized techniques, such as those described herein.
[0101] The phrase "inhibition of spheroid growth of cells
expressing ErbB3," as used herein, refers to the ability of an
antibody or an antigen-binding portion thereof to statistically
significantly decrease the migration of a cell expressing ErbB3
relative to the migration of the cell in the absence of the
antibody. In one embodiment, the migration of a cell expressing
ErbB3 (e.g., a cancer cell) may be decreased by at least 10%, or at
least 20%, or at least 30%, or at least 40%, or at least 50%, or at
least 60%, or at least 70%, or at least 80%, or at least 90%, or
100% when the cells are contacted with an antibody or antigen
binding portion thereof of the present disclosure, relative to cell
migration measured in the absence of the antibody or antigen
binding portion thereof (control). Cell migration can be assayed
using art recognized techniques, such as those described
herein.
[0102] The term "antibody" or "immunoglobulin," as used
interchangeably herein, includes whole antibodies and any antigen
binding fragment (i.e., "antigen-binding portion") or single chains
thereof. A typical antibody comprises at least two heavy (H) chains
and two light (L) chains inter-connected by disulfide bonds. Each
heavy chain is comprised of a heavy chain variable region
(abbreviated herein as V.sub.H) and a heavy chain constant region.
The heavy chain constant region is comprised of three domains, CH1,
CH2 and CH3. Each light chain is comprised of a light chain
variable region (abbreviated herein as V.sub.L) and a light chain
constant region. The light chain constant region is comprised of
one domain, CL. The V.sub.H and V.sub.L regions can be further
subdivided into regions of hypervariability, termed complementarity
determining regions (CDR), interspersed with regions that are more
conserved, termed framework regions (FR). Each V.sub.H and V.sub.L
is composed of three CDRs and four FRs, arranged from
amino-terminus to carboxy-terminus in the following order: FR1,
CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy
and light chains contain a binding domain that interacts with an
antigen. The constant regions of the antibodies may mediate the
binding of the immunoglobulin to host tissues or factors, including
various cells of the immune system (e.g., effector cells) and the
first component (Clq) of the classical complement system. Exemplary
antibodies of the present disclosure include antibodies #1, 3, 6
and 14, and antigen-binding portions thereof.
[0103] The term "antigen-binding portion" of an antibody (or simply
"antibody portion"), as used herein, refers to one or more
fragments of an antibody that retain the ability to specifically
bind to an antigen (e.g., ErbB3). It has been shown that the
antigen-binding function of an antibody can be performed by
fragments of a full-length antibody. Examples of binding fragments
encompassed within the term "antigen-binding portion" of an
antibody include (i) a Fab fragment, a monovalent fragment
consisting of the V.sub.L, V.sub.H, CL and CH1 domains; (ii) a
F(ab').sub.2 fragment, a bivalent fragment comprising two Fab
fragments linked by a disulfide bridge at the hinge region; (iii) a
Fd fragment consisting of the V.sub.H and CH1 domains; (iv) a Fv
fragment consisting of the V.sub.L and V.sub.H domains of a single
arm of an antibody, (v) a dAb including VH and VL domains; (vi) a
dAb fragment (Ward et al. (1989) Nature 341, 544-546), which
consists of a V.sub.H domain; (vii) a dAb which consists of a VH or
a VL domain; and (viii) an isolated complementarity determining
region (CDR) or (ix) a combination of two or more isolated CDRs
which may optionally be joined by a synthetic linker. Furthermore,
although the two domains of the Fv fragment, V.sub.L and V.sub.H,
are coded for by separate genes, they can be joined, using
recombinant methods, by a synthetic linker that enables them to be
made as a single protein chain in which the V.sub.L and V.sub.H
regions pair to form monovalent molecules (known as single chain Fv
(scFv); see e.g., Bird et al. (1988) Science 242, 423-426; and
Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85, 5879-5883).
Such single chain antibodies are also intended to be encompassed
within the term "antigen-binding portion" of an antibody. These
antibody fragments are obtained using conventional techniques known
to those with skill in the art, and the fragments are screened for
utility in the same manner as are intact antibodies.
Antigen-binding portions can be produced by recombinant DNA
techniques, or by enzymatic or chemical cleavage of intact
immunoglobulins.
[0104] The term "monoclonal antibody" as used herein refers to an
antibody obtained from or prepared as 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.
Monoclonal antibodies are highly specific, being directed against a
single antigenic site. Furthermore, in contrast to conventional
(polyclonal) antibody preparations which typically include
different antibodies directed against different determinants
(epitopes), each monoclonal antibody is typically directed against
a single determinant on the antigen. Monoclonal antibodies can be
prepared using any art recognized technique and those described
herein such as, for example, a hybridoma method, as described by
Kohler et al. (1975) Nature, 256:495, a transgenic animal, as
described by, for example, (see e.g., Lonberg, et al. (1994) Nature
368(6474): 856-859), recombinant DNA methods (see, e.g., U.S. Pat.
No. 4,816,567), or using phage antibody libraries using the
techniques described in, for example, Clackson et al., Nature,
352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597
(1991). Monoclonal antibodies include chimeric antibodies, human
antibodies and humanized antibodies and may occur naturally or be
recombinantly produced.
[0105] The term "recombinant antibody," refers to antibodies that
are prepared, expressed, created or isolated by recombinant means,
such as (a) antibodies isolated from an animal (e.g., a mouse) that
is transgenic or transchromosomal for immunoglobulin genes (e.g.,
human immunoglobulin genes) or a hybridoma prepared therefrom, (b)
antibodies isolated from a host cell transformed to express the
antibody, e.g., from a transfectoma, (c) antibodies isolated from a
recombinant, combinatorial antibody library (e.g., containing human
antibody sequences) using phage display, and (d) antibodies
prepared, expressed, created or isolated by any other means that
involve splicing of immunoglobulin gene sequences (e.g., human
immunoglobulin genes) to other DNA sequences. Such recombinant
antibodies may have variable and constant regions derived from
human germline immunoglobulin sequences. In certain embodiments,
however, such recombinant human antibodies can be subjected to in
vitro mutagenesis and thus the amino acid sequences of the V.sub.H
and V.sub.L regions of the recombinant antibodies are sequences
that, while derived from and related to human germline V.sub.H and
V.sub.L sequences, may not naturally exist within the human
antibody germline repertoire in vivo.
[0106] The term "chimeric immunoglobulin" or "chimeric antibody"
refers to an immunoglobulin or antibody whose variable regions
derive from a first species and whose constant regions derive from
a second species. Chimeric immunoglobulins or antibodies can be
constructed, for example by genetic engineering, from
immunoglobulin gene segments belonging to different species.
[0107] The term "human antibody," as used herein, is intended to
include antibodies having variable regions in which both the
framework and CDR regions are derived from human germline
immunoglobulin sequences as described, for example, by Kabat et al.
(See Kabat, et al. (1991) Sequences of proteins of Immunological
Interest, Fifth Edition, U.S. Department of Health and Human
Services, NIH Publication No. 91-3242). Furthermore, if the
antibody contains a constant region, the constant region also is
derived from human germline immunoglobulin sequences. The human
antibodies may include amino acid residues not encoded by human
germline immunoglobulin sequences (e.g., mutations introduced by
random or site-specific mutagenesis in vitro or by somatic mutation
in vivo). However, the term "human antibody", as used herein, is
not intended to include antibodies in which CDR sequences derived
from the germline of another mammalian species, such as a mouse,
have been grafted onto human framework sequences.
[0108] The human antibody can have at least one ore more amino
acids replaced with an amino acid residue, e.g., an activity
enhancing amino acid residue which is not encoded by the human
germline immunoglobulin sequence. Typically, the human antibody can
have up to twenty positions replaced with amino acid residues which
are not part of the human germline immunoglobulin sequence. In a
particular embodiment, these replacements are within the CDR
regions as described in detail below.
[0109] The term "humanized immunoglobulin" or "humanized antibody"
refers to an immunoglobulin or antibody that includes at least one
humanized immunoglobulin or antibody chain (i.e., at least one
humanized light or heavy chain). The term "humanized immunoglobulin
chain" or "humanized antibody chain" (i.e., a "humanized
immunoglobulin light chain" or "humanized immunoglobulin heavy
chain") refers to an immunoglobulin or antibody chain (i.e., a
light or heavy chain, respectively) having a variable region that
includes a variable framework region substantially from a human
immunoglobulin or antibody and complementarity determining regions
(CDRs) (e.g., at least one CDR, preferably two CDRs, more
preferably three CDRs) substantially from a non-human
immunoglobulin or antibody, and further includes constant regions
(e.g., at least one constant region or portion thereof, in the case
of a light chain, and preferably three constant regions in the case
of a heavy chain). The term "humanized variable region" (e.g.,
"humanized light chain variable region" or "humanized heavy chain
variable region") refers to a variable region that includes a
variable framework region substantially from a human immunoglobulin
or antibody and complementarity determining regions (CDRs)
substantially from a non-human immunoglobulin or antibody.
[0110] A "bispecific" or "bifunctional" antibody is an artificial
hybrid antibody having two different heavy/light chain pairs and
two different binding sites. Bispecific antibodies can be produced
by a variety of methods including fusion of hybridomas or linking
of Fab' fragments. See, e.g., Songsivilai & Lachmann, (1990)
Clin. Exp. Immunol. 79, 315-321; Kostelny et al. (1992) J. Immunol.
148, 1547-1553. In a particular embodiment, a bispecific antibody
according to the present invention includes binding sites for both
ErbB3 and IGF1-R (i.e., insulin-like growth factor 1-receptor). In
another embodiment, a bispecific antibody according to the present
invention includes binding sites for both ErbB3 and C-MET. In other
embodiments, a bispecific antibody includes a binding site for
ErbB3 and a binding site for ErbB2, ERbB3, ErbB4, EGFR, Lewis Y,
MUC-1, EpCAM, CA125, prostate specific membrane antigen,
PDGFR-.alpha., PDGFR-.beta., C-KIT, or any of the FGF
receptors.
[0111] As used herein, a "heterologous antibody" is defined in
relation to the transgenic non-human organism or plant producing
such an antibody.
[0112] An "isolated antibody," as used herein, is intended to refer
to an antibody which is substantially free of other antibodies
having different antigenic specificities (e.g., an isolated
antibody that specifically binds to ErbB3 is substantially free of
antibodies that specifically bind antigens other than ErbB3). In
addition, an isolated antibody is typically substantially free of
other cellular material and/or proteins. In one embodiment of the
invention, a combination of "isolated" antibodies having different
ErbB3 binding specificities are combined in a well defined
composition.
[0113] As used herein, "isotype" refers to the antibody class
(e.g., IgM or IgG1) that is encoded by heavy chain constant region
genes. In one embodiment, an antibody or antigen binding portion
thereof is of an isotype selected from an IgG1, an IgG2, an IgG3,
an IgG4, an IgM, an IgA1, an IgA2, an IgAsec, an IgD, or an IgE
antibody isotype. In some embodiments, an antibody is of the IgG1
isotype. In other embodiments, an antibody is of the IgG2
isotype.
[0114] As used herein, "isotype switching" refers to the phenomenon
by which the class, or isotype, of an antibody changes from one Ig
class to one of the other Ig classes.
[0115] As used herein, "nonswitched isotype" refers to the isotypic
class of heavy chain that is produced when no isotype switching has
taken place; the CH gene encoding the nonswitched isotype is
typically the first CH gene immediately downstream from the
functionally rearranged VDJ gene. Isotype switching has been
classified as classical or non-classical isotype switching.
Classical isotype switching occurs by recombination events which
involve at least one switch sequence regions in a gene encoding an
antibody. Non-classical isotype switching may occur by, for
example, homologous recombination between human .sigma..sub..mu.
and human .SIGMA..sub..mu. (.delta.-associated deletion).
Alternative non-classical switching mechanisms, such as
intertransgene and/or interchromosomal recombination, among others,
may occur and effectuate isotype switching.
[0116] As used herein, the term "switch sequence" refers to those
DNA sequences responsible for switch recombination. A "switch
donor" sequence, typically a .mu. switch region, will be 5' (i.e.,
upstream) of the construct region to be deleted during the switch
recombination. The "switch acceptor" region will be between the
construct region to be deleted and the replacement constant region
(e.g., .gamma., .epsilon., etc.). As there is no specific site
where recombination always occurs, the final gene sequence will
typically not be predictable from the construct.
[0117] An "antigen" is an entity (e.g., a proteinaceous entity or
peptide) to which an antibody or antigen-binding portion thereof
binds. In various embodiments disclosed herein, the antigen is
ErbB3 or a ErbB3-like molecule. In a particular embodiment
according to the invention, the antigen is human ErbB3.
[0118] The term "epitope" or "antigenic determinant" refers to a
site on an antigen to which an immunoglobulin or antibody
specifically binds. Epitopes can be formed both from contiguous
amino acids or noncontiguous amino acids juxtaposed by tertiary
folding of a protein. Epitopes formed from contiguous amino acids
are typically retained on exposure to denaturing solvents, whereas
epitopes formed by tertiary folding are typically lost on treatment
with denaturing solvents. An epitope typically includes at least 3,
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or 15 amino acids in a unique
spatial conformation. Methods of determining spatial conformation
of epitopes include techniques in the art and those described
herein, for example, x-ray crystallography and 2-dimensional
nuclear magnetic resonance. See, e.g., Epitope Mapping Protocols in
Methods in Molecular Biology, Vol. 66, G. E. Morris, Ed.
(1996).
[0119] Also encompassed by the present invention are antibodies
that bind the same or an overlapping epitope as the antibodies for
which amino acid sequences are disclosed herein, i.e., antibodies
that compete for binding to ErbB3, or bind epitopes which overlap
with epitopes bound by the antibodies described herein, i.e., an
epitope located on ectodomain of ErbB3, preferably on Domain I of
the ectodomain of ErbB3. Antibodies that recognize the same epitope
can be identified using routine techniques such as an immunoassay,
for example, by showing the ability of one antibody to block the
binding of another antibody to a target antigen, i.e., a
competitive binding assay. Competitive binding is determined in an
assay in which the immunoglobulin under test inhibits specific
binding of a reference antibody to a common antigen, such as ErbB3.
Numerous types of competitive binding assays are known, for
example: solid phase direct or indirect radioimmunoassay (RIA),
solid phase direct or indirect enzyme immunoassay (EIA), sandwich
competition assay (see Stahli et al., (1983) Methods in Enzymology
9:242); solid phase direct biotin-avidin EIA (see Kirkland et al.,
(1986) J. Immunol. 137:3614); solid phase direct labeled assay,
solid phase direct labeled sandwich assay (see Harlow and Lane,
(1988) Antibodies: A Laboratory Manual, Cold Spring Harbor Press);
solid phase direct label RIA using I-125 label (see Morel et al.,
(1988) Mol. Immunol. 25(1):7); solid phase direct biotin-avidin EIA
(Cheung et al., (1990) Virology 176:546); and direct labeled RIA.
(Moldenhauer et al., (1990) Scand. J. Immunol. 32:77). Typically,
such an assay involves the use of purified antigen (e.g., ErbB3)
bound to a solid surface or cells bearing either of these, an
unlabeled test immunoglobulin and a labeled reference
immunoglobulin. Competitive inhibition is measured by determining
the amount of label bound to the solid surface or cells in the
presence of the test immunoglobulin. Usually the test
immunoglobulin is present in excess. Usually, when a competing
antibody is present in excess, it will inhibit specific binding of
a reference antibody to a common antigen by at least 50-55%,
55-60%, 60-65%, 65-70% 70-75% or more.
[0120] The term "paratope" refers to the parts, or amino acid
residues, of an antibody that appear to be directly involved in
recognizing and contacting the epitope on an antigen to which the
antibody specifically binds. Paratopes typically comprise some but
not all amino acid residues within the complementarity determining
regions (CDRs) of the heavy and light chains. A paratope may
involve amino acid residues in all of the V.sub.H and V.sub.L CDRs
or only some of the CDRs (e.g., certain CDRs may not be involved in
binding antigen). The paratope for a particular antigen can be
defined, for example, by scanning mutagenesis (e.g., alanine
scanning mutagenesis) of amino acid residues within the antibody,
particularly the CDRs, that are thought to be surface exposed
(e.g., as determined by crystallographic modeling) and possibly
involved in antigen binding. Evaluation of the binding of the
mutants to the antigen then can determine whether the mutated amino
acid position is involved in antigen binding and thus forms part of
the paratope of the antibody. Methods for determining an antibody
paratope are described in further detail in Example 20. In a
preferred embodiment, an anti-ErbB3 antibody comprises a heavy
chain paratope comprising CDR1, CDR2 and CDR3 sequences as shown in
SEQ ID NOs: 63 or 76 (CDR1), 64 (CDR2) and 65 (CDR3), respectively.
In another preferred embodiment, an anti-ErbB3 antibody comprises a
light chain paratope comprising CDR1, CDR2 and CDR3 sequences as
shown in SEQ ID NOs: 69 or 78 (CDR1), 70 (CDR2) and 71 or 80
(CDR3), respectively. In another embodiment, the anti-ErbB3
antibody comprises a heavy chain paratope comprising CDR1, CDR2 and
CDR3 sequences as shown in SEQ ID NOs: 63, 64 and 65, respectively,
and a light chain paratope comprising CDR1, CDR2 and CDR3 sequences
as shown in SEQ ID NOs: 69, 70 and 71, respectively. In another
embodiment, the anti-ErbB3 antibody comprises a heavy chain
paratope comprising CDR1, CDR2 and CDR3 sequences as shown in SEQ
ID NOs: 76, 64 and 65, respectively, and a light chain paratope
comprising CDR1, CDR2 and CDR3 sequences as shown in SEQ ID NOs:
78, 70 and 80, respectively.
[0121] The term "consensus sequence", as used herein with respect
to complementarity determining regions (CDRs), refers to a
composite or genericized sequence for a CDR that has been defined
based on information as to which amino acid residues within the CDR
are amenable to modification without detriment to antigen binding.
Thus, in a "consensus sequence" for a CDR, certain amino acid
positions are occupied by one of multiple possible amino acid
residues at that position. For example, within a CDR, if antigen
binding has been found to be unaffected by the presence of either a
tyrosine or a phenylalanine at a particular position, then that
particular position within the consensus sequence can be either
tyrosine or phenylalanine (T/F). Consensus sequences for CDRs can
be defined, for example, by scanning mutagenesis (e.g., alanine
scanning mutagenesis) of amino acid residues within the antibody
CDRs, followed by evaluation of the binding of the mutants to the
antigen to determine whether the mutated amino acid position
affects antigen binding. Methods for determining antibody CDR
consensus sequences are described in further detail in Example 20.
In a preferred embodiment, an anti-ErbB3 antibody comprises a heavy
chain variable region comprising consensus heavy chain CDR1, CDR2
and CDR3 sequences shown in SEQ ID NOs: 60 or 75 (CDR1), 61 (CDR2)
and 62 (CDR3), respectively. In another preferred embodiment, an
anti-ErbB3 antibody comprises a light chain variable region
comprising consensus light chain CDR1, CDR2 and CDR3 sequences
shown in SEQ ID NOs: 66 or 77 (CDR1), 67 (CDR2) and 68 or 79
(CDR3), respectively. In another embodiment, the anti-ErbB3
antibody comprises a heavy chain variable region comprising
consensus heavy chain CDR1, CDR2 and CDR3 sequences shown in SEQ ID
NOs: 60, 61 and 62, respectively, and a light chain variable region
comprising consensus light chain CDR1, CDR2 and CDR3 sequences
shown in SEQ ID NOs: 66, 67 and 68, respectively. In another
embodiment, the anti-ErbB3 antibody comprises a heavy chain
variable region comprising consensus heavy chain CDR1, CDR2 and
CDR3 sequences shown in SEQ ID NOs: 75, 61 and 62, respectively,
and a light chain variable region comprising consensus light chain
CDR1, CDR2 and CDR3 sequences shown in SEQ ID NOs: 77, 67 and 79,
respectively.
[0122] As used herein, the terms "specific binding," "specifically
binds," "selective binding," and "selectively binds," mean that an
antibody or antigen-binding portion thereof, exhibits appreciable
affinity for a particular antigen or epitope and, generally, does
not exhibit significant cross-reactivity with other antigens and
epitopes. "Appreciable" or preferred binding includes binding with
an affinity of at least 10.sup.6, 10.sup.7, 10.sup.8, 10.sup.9
M.sup.-1, or 10.sup.10 M.sup.-1. Affinities greater than
10.sup.7M.sup.-1, preferably greater than 10.sup.8 M.sup.-1 are
more preferred. Values intermediate of those set forth herein are
also intended to be within the scope of the present invention and a
preferred binding affinity can be indicated as a range of
affinities, for example, 10.sup.6 to 10.sup.10 M.sup.-1, preferably
10.sup.7 to 10.sup.10 M.sup.-1, more preferably 10.sup.8 to
10.sup.10 M.sup.-1. An antibody that "does not exhibit significant
cross-reactivity" is one that will not appreciably bind to an
undesirable entity (e.g., an undesirable proteinaceous entity). For
example, in one embodiment, an antibody or antigen-binding portion
thereof that specifically binds to ErbB3 will appreciably bind that
ErbB3 molecule but will not significantly react with other ErbB
molecules and non-ErbB proteins or peptides. Specific or selective
binding can be determined according to any art-recognized means for
determining such binding, including, for example, according to
Scatchard analysis and/or competitive binding assays.
[0123] The term "K.sub.D," as used herein, is intended to refer to
the dissociation equilibrium constant of a particular
antibody-antigen interaction or the affinity of an antibody for an
antigen, preferably as measured using a surface plasmon resonance
assay (e.g., as determined in a BIACORE 3000 instrument (GE
Healthcare) using recombinant ErbB3 as the analyte and the antibody
as the ligand) or a cell binding assay. Both such assays are
detailed in Example 3, below. In one embodiment, the antibody or
antigen binding portion thereof according to the present invention
binds an antigen (e.g., ErbB3) with an affinity (K.sub.D) of 50 nM
or better (i.e., or less) (e.g., 40 nM or 30 nM or 20 nM or 10 nM
or less). In a particular embodiment, an antibody or antigen
binding portion thereof according to the present invention binds
ErbB3 with an affinity (K.sub.D) of 8 nM or better (e.g., 7 nM, 6
nM, 5 nM, 4 nM, 2 nM, 1.5 nM, 1.4 nM, 1.3 nM, 1 nM or less. In
other embodiments, an antibody or antigen binding portion thereof
binds an antigen (e.g., ErbB3) with an affinity (K.sub.D) of
approximately less than 10' M, such as approximately less than
10.sup.-8 M, 10.sup.-9 M or 10.sup.-10 M or even lower, and binds
to the predetermined antigen with an affinity that is at least
two-fold greater than its affinity for binding to a non-specific
antigen (e.g., BSA, casein) other than the predetermined antigen or
a closely-related antigen.
[0124] The term "K.sub.off," as used herein, is intended to refer
to the off rate constant for the dissociation of an antibody from
the antibody/antigen complex.
[0125] The term "EC50," as used herein, refers to the concentration
of an antibody or an antigen-binding portion thereof, which induces
a response, either in an in vitro or an in vivo assay, which is 50%
of the maximal response, i.e., halfway between the maximal response
and the baseline.
[0126] As used herein, "glycosylation pattern" is defined as the
pattern of carbohydrate units that are covalently attached to a
protein, more specifically to an immunoglobulin protein.
[0127] The term "naturally-occurring" as used herein as applied to
an object refers to the fact that an object can be found in nature.
For example, a polypeptide or polynucleotide sequence that is
present in an organism (including viruses) that can be isolated
from a source in nature and which has not been intentionally
modified by man in the laboratory is naturally-occurring.
[0128] The term "rearranged" as used herein refers to a
configuration of a heavy chain or light chain immunoglobulin locus
wherein a V segment is positioned immediately adjacent to a D-J or
J segment in a conformation encoding essentially a complete V.sub.H
or V.sub.L domain, respectively. A rearranged immunoglobulin gene
locus can be identified by comparison to germline DNA; a rearranged
locus will have at least one recombined heptamer/nonamer homology
element.
[0129] The term "unrearranged" or "germline configuration" as used
herein in reference to a V segment refers to the configuration
wherein the V segment is not recombined so as to be immediately
adjacent to a D or J segment.
[0130] The term "nucleic acid molecule," as used herein, is
intended to include DNA molecules and RNA molecules. A nucleic acid
molecule may be single-stranded or double-stranded, but preferably
is double-stranded DNA.
[0131] The term "isolated nucleic acid molecule," as used herein in
reference to nucleic acids encoding antibodies or antibody portions
(e.g., V.sub.H, V.sub.L, CDR3) that bind to ErbB3, is intended to
refer to a nucleic acid molecule in which the nucleotide sequences
encoding the antibody or antibody portion are free of other
nucleotide sequences encoding antibodies that bind antigens other
than ErbB3, which other sequences may naturally flank the nucleic
acid in human genomic DNA.
[0132] The term "modifying," or "modification," as used herein, is
intended to refer to changing one or more amino acids in the
antibodies or antigen-binding portions thereof.
[0133] The change can be produced by adding, substituting or
deleting an amino acid at one or more positions. The change can be
produced using known techniques, such as PCR mutagenesis. For
example, in some embodiments, an antibody or an antigen-binding
portion thereof identified using the methods of the present
disclosure can be modified, to thereby modify the binding affinity
of the antibody or antigen-binding portion thereof to ErbB3.
[0134] The present invention also encompasses "conservative amino
acid substitutions" in the sequences of the antibodies or fragments
thereof of the invention, i.e., nucleotide and amino acid sequence
modifications which do not abrogate the binding of the antibody
encoded by the nucleotide sequence or containing the amino acid
sequence, to the antigen, i.e., ErbB3. Conservative amino acid
substitutions include the substitution of an amino acid in one
class by an amino acid of the same class, where a class is defined
by common physicochemical amino acid side chain properties and high
substitution frequencies in homologous proteins found in nature, as
determined, for example, by a standard Dayhoff frequency exchange
matrix or BLOSUM matrix. Six general classes of amino acid side
chains have been categorized and include: Class I (Cys); Class II
(Ser, Thr, Pro, Ala, Gly); Class III (Asn, Asp, Gln, Glu); Class IV
(His, Arg, Lys); Class V (Ile, Leu, Val, Met); and Class VI (Phe,
Tyr, Trp). For example, substitution of an Asp for another class
III residue such as Asn, Gln, or Glu, is a conservative
substitution. Thus, a predicted nonessential amino acid residue in
an anti-ErbB3 antibody is preferably replaced with another amino
acid residue from the same class. Methods of identifying nucleotide
and amino acid conservative substitutions which do not eliminate
antigen binding are well-known in the art (see, e.g., Brummell et
al., Biochem. 32:1180-1187 (1993); Kobayashi et al. Protein Eng.
12(10):879-884 (1999); and Burks et al. Proc. Natl. Acad. Sci. USA
94:412-417 (1997)).
[0135] The term "non-conservative amino acid substitution" refers
to the substitution of an amino acid in one class with an amino
acid from another class; for example, substitution of an Ala, a
class II residue, with a class III residue such as Asp, Asn, Glu,
or Gln.
[0136] Alternatively, in another embodiment, mutations
(conservative or non-conservative) can be introduced randomly along
all or part of an anti-ErbB3 antibody coding sequence, such as by
saturation mutagenesis, and the resulting modified anti-ErbB3
antibodies can be screened for binding activity.
[0137] A "consensus sequence" is a sequence formed from the most
frequently occurring amino acids (or nucleotides) in a family of
related sequences (See e.g., Winnaker, From Genes to Clones
(Verlagsgesellschaft, Weinheim, Germany 1987). In a family of
proteins, each position in the consensus sequence is occupied by
the amino acid occurring most frequently at that position in the
family. If two amino acids occur equally frequently, either can be
included in the consensus sequence. A "consensus framework" of an
immunoglobulin refers to a framework region in the consensus
immunoglobulin sequence.
[0138] Similarly, the consensus sequence for the CDRs of can be
derived by optimal alignment of the CDR amino acid sequences of
ErbB3 antibodies for which CDR amino acid sequences are disclosed
herein.
[0139] For nucleic acids, the term "substantial homology" indicates
that two nucleic acids, or designated sequences thereof, when
optimally aligned and compared, are identical, with appropriate
nucleotide insertions or deletions, in at least about 80% of the
nucleotides, usually at least about 90% to 95%, and more preferably
at least about 98% to 99.5% of the nucleotides. Alternatively,
substantial homology exists when the segments will hybridize under
selective hybridization conditions, to the complement of the
strand.
[0140] The percent identity between two sequences is a function of
the number of identical positions shared by the sequences (i.e., %
homology=# of identical positions/total # of positions.times.100),
taking into account the number of gaps, and the length of each gap,
which need to be introduced for optimal alignment of the two
sequences. The comparison of sequences and determination of percent
identity between two sequences can be accomplished using a
mathematical algorithm, as described in the non-limiting examples
below.
[0141] The percent identity between two nucleotide sequences can be
determined using the GAP program in the GCG software, using a
NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and
a length weight of 1, 2, 3, 4, 5, or 6. The percent identity
between two nucleotide or amino acid sequences can also be
determined using the algorithm of E. Meyers and W. Miller (CABIOS,
4:11-17 (1989)) which has been incorporated into the ALIGN program
(version 2.0), using a PAM120 weight residue table, a gap length
penalty of 12 and a gap penalty of 4. In addition, the percent
identity between two amino acid sequences can be determined using
the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970))
algorithm which has been incorporated into the GAP program in the
GCG software package, using either a Blossum 62 matrix or a PAM250
matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length
weight of 1, 2, 3, 4, 5, or 6.
[0142] The nucleic acid and protein sequences of the present
disclosure can further be used as a "query sequence" to perform a
search against public databases to, for example, identify related
sequences. Such searches can be performed using the NBLAST and)
(BLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol.
Biol. 215:403-10. BLAST nucleotide searches can be performed with
the NBLAST program, score=100, wordlength=12 to obtain nucleotide
sequences homologous to the nucleic acid molecules of the
invention. BLAST protein searches can be performed with the) (BLAST
program, score=50, wordlength=3 to obtain amino acid sequences
homologous to the protein molecules of the invention. To obtain
gapped alignments for comparison purposes, Gapped BLAST can be
utilized as described in Altschul et al., (1997) Nucleic Acids Res.
25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs,
the default parameters of the respective programs (e.g., XBLAST and
NBLAST) can be used.
[0143] The nucleic acids may be present in whole cells, in a cell
lysate, or in a partially purified or substantially pure form. A
nucleic acid is "isolated" or "rendered substantially pure" when
purified away from other cellular components or other contaminants,
e.g., other cellular nucleic acids or proteins, by standard
techniques, including alkaline/SDS treatment, CsCl banding, column
chromatography, agarose gel electrophoresis and others well known
in the art. See, F. Ausubel, et al., ed. Current Protocols in
Molecular Biology, Greene Publishing and Wiley Interscience, New
York (1987).
[0144] The nucleic acid compositions of the present disclosure,
while often in a native sequence (except for modified restriction
sites and the like), from either cDNA, genomic or mixtures thereof
may be mutated, in accordance with standard techniques to provide
gene sequences. For coding sequences, these mutations, may affect
amino acid sequence as desired. In particular, DNA sequences
substantially homologous to or derived from native V, D, J,
constant, switches and other such sequences described herein are
contemplated (where "derived" indicates that a sequence is
identical or modified from another sequence).
[0145] The term "operably linked" refers to a nucleic acid sequence
placed into a functional relationship with another nucleic acid
sequence. For example, DNA for a presequence or secretory leader is
operably linked to DNA for a polypeptide if it is expressed as a
preprotein that participates in the secretion of the polypeptide; a
promoter or enhancer is operably linked to a coding sequence if it
affects the transcription of the sequence; or a ribosome binding
site is operably linked to a coding sequence if it is positioned so
as to facilitate translation. Generally, "operably linked" means
that the DNA sequences being linked are contiguous, and, in the
case of a secretory leader, contiguous and in reading phase.
However, enhancers do not have to be contiguous. Linking is
accomplished by ligation at convenient restriction sites. If such
sites do not exist, the synthetic oligonucleotide adaptors or
linkers are used in accordance with conventional practice. A
nucleic acid is "operably linked" when it is placed into a
functional relationship with another nucleic acid sequence. For
instance, a promoter or enhancer is operably linked to a coding
sequence if it affects the transcription of the sequence. With
respect to transcription regulatory sequences, operably linked
means that the DNA sequences being linked are contiguous and, where
necessary to join two protein coding regions, contiguous and in
reading frame. For switch sequences, operably linked indicates that
the sequences are capable of effecting switch recombination.
[0146] 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
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, "expression vectors"). In general,
expression vectors of utility in recombinant DNA techniques are
often in the form of plasmids. The terms, "plasmid" and "vector"
may be used interchangeably. However, the invention is intended to
include such other forms of expression vectors, such as viral
vectors (e.g., replication defective retroviruses, adenoviruses and
adeno-associated viruses), which serve equivalent functions.
[0147] The term "recombinant host cell" (or simply "host cell"), as
used herein, is intended to refer to a cell into which a
recombinant expression vector has been introduced. It should be
understood that such terms are intended to refer not only to the
particular subject cell but to the progeny of such a cell. Because
certain modifications may occur in succeeding generations due to
either mutation or environmental influences, such progeny may not,
in fact, be identical to the parent cell, but are still included
within the scope of the term "host cell" as used herein.
[0148] The terms "treat," "treating," and "treatment," as used
herein, refer to therapeutic or preventative measures described
herein. The methods of "treatment" employ administration to a
subject, an antibody or antigen binding portion disclosed herein,
for example, a subject having a disease or disorder associated with
ErbB3 dependent signaling or predisposed to having such a disease
or disorder, in order to prevent, cure, delay, reduce the severity
of, or ameliorate one or more symptoms of the disease or disorder
or recurring disease or disorder, or in order to prolong the
survival of a subject beyond that expected in the absence of such
treatment.
[0149] The term "disease associated with ErbB3 dependent
signaling," or "disorder associated with ErbB3 dependent
signaling," as used herein, includes disease states and/or symptoms
associated with a disease state, where increased levels of ErbB3
and/or activation of cellular cascades involving ErbB3 are found.
It is understood that ErbB3 heterodimerizes with other ErbB
proteins such as, EGFR and ErbB2, when increased levels of ErbB3
are found. Accordingly, the term "disease associated with ErbB3
dependent signaling," also includes disease states and/or symptoms
associated with disease states where increased levels of EGFR/ErbB3
and/or ErbB2/ErbB3 heterodimers are found. In general, the term
"disease associated with ErbB3 dependent signaling," refers to any
disorder, the onset, progression or the persistence of the symptoms
of which requires the participation of ErbB3. Exemplary
ErbB3-mediated disorders include, but are not limited to, for
example, cancer.
[0150] The terms "cancer" and "cancerous" refer to or describe the
physiological condition in mammals that is typically characterized
by unregulated cell growth. 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, gastric
cancer, pancreatic cancer, glial cell tumors such as glioblastoma
and neurofibromatosis, cervical cancer, ovarian cancer, liver
cancer, bladder cancer, hepatoma, breast cancer, colon cancer,
melanoma, colorectal cancer, endometrial carcinoma, salivary gland
carcinoma, kidney cancer, renal cancer, prostate cancer, vulval
cancer, thyroid cancer, hepatic carcinoma and various types of head
and neck cancer. In a particular embodiment, a cancer treated or
diagnosed using the methods disclosed herein is selected from
melanoma, breast cancer, ovarian cancer, renal carcinoma,
gastrointestinal/colon cancer, lung cancer, and prostate
cancer.
[0151] The term "KRAS mutation", as used herein, refers to
mutations found in certain cancers in a human homolog of the
v-Ki-ras2 Kirsten rat sarcoma viral oncogene. Non-limiting examples
of human KRAS gene mRNA sequences include Genbank Accession Nos.
NM_004985 and NM_033360. It has been reported that KRAS mutations
are found in 73% of pancreatic tumors, 35% of colorectal tumors,
16% of ovarian tumors and 17% of lung tumors.
[0152] The term "PI3K mutation", as used herein, refers to
mutations found in certain cancers in a
phosphatidyl-inositol-3-kinase gene, typically leading to
activation of PI3K in the cancer cells. It has been reported that
PI3K mutations are found in 12% of colorectal tumors, 15% of head
and neck tumors and 26% of breast tumors.
[0153] The term "effective amount," as used herein, refers to that
amount of an antibody or an antigen binding portion thereof that
binds ErbB3, which is sufficient to effect treatment, prognosis or
diagnosis of a disease associated with ErbB3 dependent signaling,
as described herein, when administered to a subject. A
therapeutically effective amount will vary depending upon the
subject and disease condition being treated, the weight and age of
the subject, the severity of the disease condition, the manner of
administration and the like, which can readily be determined by one
of ordinary skill in the art. The dosages for administration can
range from, for example, about 1 ng to about 10,000 mg, about 5 ng
to about 9,500 mg, about 10 ng to about 9,000 mg, about 20 ng to
about 8,500 mg, about 30 ng to about 7,500 mg, about 40 ng to about
7,000 mg, about 50 ng to about 6,500 mg, about 100 ng to about
6,000 mg, about 200 ng to about 5,500 mg, about 300 ng to about
5,000 mg, about 400 ng to about 4,500 mg, about 500 ng to about
4,000 mg, about 1 .mu.g to about 3,500 mg, about 5 .mu.g to about
3,000 mg, about 10 .mu.g to about 2,600 mg, about 20 .mu.g to about
2,575 mg, about 30 to about 2,550 mg, about 40 .mu.g to about 2,500
mg, about 50 .mu.g to about 2,475 mg, about 100 .mu.g to about
2,450 mg, about 200 .mu.g to about 2,425 mg, about 300 .mu.g to
about 2,000, about 400 .mu.g to about 1,175 mg, about 500 .mu.g to
about 1,150 mg, about 0.5 mg to about 1,125 mg, about 1 mg to about
1,100 mg, about 1.25 mg to about 1,075 mg, about 1.5 mg to about
1,050 mg, about 2.0 mg to about 1,025 mg, about 2.5 mg to about
1,000 mg, about 3.0 mg to about 975 mg, about 3.5 mg to about 950
mg, about 4.0 mg to about 925 mg, about 4.5 mg to about 900 mg,
about 5 mg to about 875 mg, about 10 mg to about 850 mg, about 20
mg to about 825 mg, about 30 mg to about 800 mg, about 40 mg to
about 775 mg, about 50 mg to about 750 mg, about 100 mg to about
725 mg, about 200 mg to about 700 mg, about 300 mg to about 675 mg,
about 400 mg to about 650 mg, about 500 mg, or about 525 mg to
about 625 mg, of an antibody or antigen binding portion thereof,
according to the invention. Dosage regimen may be adjusted to
provide the optimum therapeutic response. An effective amount is
also one in which any toxic or detrimental effects (i.e., side
effects) of an antibody or antigen binding portion thereof are
minimized and/or outweighed by the beneficial effects. Additional
preferred dosages regimens are described further below in the
section pertaining to pharmaceutical compositions.
[0154] The term "patient" includes human and other mammalian
subjects that receive either prophylactic or therapeutic
treatment.
[0155] As used herein, the term "subject" or "patient" includes any
human or non-human animal. For example, the methods and
compositions disclosed herein can be used to treat a subject having
cancer. In a preferred embodiment, the subject is a human. The term
"non-human animal" includes all vertebrates, e.g., mammals and
non-mammals, such as non-human primates, sheep, dog, cow, etc.
[0156] The term "sample" refers to tissue, body fluid, or a cell
from a patient or a subject. Normally, the tissue or cell will be
removed from the patient, but in vivo diagnosis is also
contemplated. In the case of a solid tumor, a tissue sample can be
taken from a surgically removed tumor and prepared for testing by
conventional techniques. In the case of lymphomas and leukemias,
lymphocytes, leukemic cells, or lymph tissues can be obtained and
appropriately prepared. Other patient samples, including urine,
tear drops, serum, cerebrospinal fluid, feces, sputum, cell
extracts etc. can also be useful for particular tumors.
[0157] The terms "anti-cancer agent" and "antineoplastic agent"
refer to drugs used to treat malignancies, such as cancerous
growths. Drug therapy may be used alone, or in combination with
other treatments such as surgery or radiation therapy. Several
classes of drugs may be used in cancer treatment, depending on the
nature of the organ involved. For example, breast cancers are
commonly stimulated by estrogens, and may be treated with drugs
which inactive the sex hormones. Similarly, prostate cancer may be
treated with drugs that inactivate androgens, the male sex hormone.
Anti-cancer agents for use in certain methods of the present
invention include, among others, the following agents:
TABLE-US-00001 Anti-Cancer Agent Comments Examples Antibodies
Antibodies which bind A12 (fully humanized mAb) (a) antibodies
other IGF-1R (insulin-like 19D12 (fully humanized mAb) than
anti-ErbB3 growth factor type 1 CP751-871 (fully humanized mAb)
antibodies; and receptor), which is H7C10 (humanized mAb) (b)
anti-ErbB3 expressed on the cell alphaIR3 (mouse) antibodies which
surface of must human scFV/FC (mouse/human chimera) bind different
cancers EM/164 (mouse) epitopes AMG 479 (fully humanized mAb;
Amgen) IMCA 12 (fully humanized mAb; Imclone) NSC-742460 (Dyax)
MR-0646, F50035 (Pierre Fabre Medicament, Merck) Antibodies which
bind matuzumab (EMD72000) EGFR; Mutations Erbitux .RTM./cetuximab
(Imclone) affecting EGFR Vectibix .RTM./panitumumab (Amgen)
expression or activity can mAb 806 result in cancer nimotuzumab
(TheraCIM) INCB7839 (Incyte) panitumumab (Vectibix .RTM.; Amgen)
Antibodies which bind AVEO (AV299) (AVEO) cMET (mesenchymal AMG102
(Amgen) epithelial transition 5D5 (OA-5D5) (Genentech) factor); a
member of the MET family of receptor tyrosine kinases) Anti-ErbB3
antibodies Ab #14 described herein which bind different 1B4C3;
2D1D12 (U3 Pharma AG) epitopes U3-1287/AMG888 (U3 Pharma/Amgen)
Anti-ErbB2 (HER2) Herceptin .RTM. (trastuzumab; Genentech/Roche)
antibodies binds ectodomain Domain II of ErbB2; Omnitarg .RTM.
(pertuzumab; 2C4, R1273; Genentech/Roche) binds Domain IV of ErbB2
Small Molecules IGF-1R (insulin-like NVP-AEW541-A Targeting IGF1R
growth factor type 1 BMS-536,924 (1H-benzoimidazol-2-yl)-1H-
receptor), which is pyridin-2-one) expressed on the cell
BMS-554,417 surface of must human Cycloligan cancers TAE226 PQ401
Small Molecules EGFR; Mutations Iressa .RTM./gefitinib
(AstraZeneca) Targeting EGFR affecting EGFR CI-1033 (PD 183805)
(Pfizer) expression or activity can TYVERB/lapatinib
(GlaxoSmithKline) result in cancer Tykerb .RTM./lapatinib
ditosylate (SmithKline Beecham) Tarceva .RTM./Erlotinib HCL (OSI
Pharma) PKI-166 (Novartis) PD-158780 EKB-569 Tyrphostin AG
1478(4-(3-Chloroanillino)- 6,7-dimethoxyquinazoline) Small
Molecules ErbB2, also known as HKI-272 (neratinib; Wyeth) Targeting
ErbB2 HER2, a member of the KOS-953 (tanespimycin; Kosan
Biosciences) ErbB family of receptors, which is expressed on
certain cancer cells Small Molecules cMET (Mesenchymal PHA665752
Targeting cMET epithelial transition ARQ 197 (ArQule) factor); a
member of the ARQ-650RP (ArQule) MET family of receptor tyrosine
kinases) Antimetabolites An antimetabolite is a flourouracil (5-FU)
chemical with a similar capecitabine/XELODA .RTM. (HLR Roche)
structure to a substance (a 5-trifluoromethyl-2'-deoxyuridine
metabolite) required for methotrexate sodium (Trexall) (Barr)
normal biochemical raltitrexed/Tomudex .RTM. (AstraZaneca)
reactions, yet different pemetrexed/Alimta .RTM. (Lilly) enough to
interfere with tegafur the normal functions of cytosine arabinoside
(Cytarabine, Ara-C)/ cells, including cell tioguanine/Lanvis .RTM.
(GlaxoSmithKline) division. 5-azacytidine 6-mercaptopurine
(Mercaptopurine, 6-MP) azathioprine/Azasan .RTM. (AAIPHARMA LLC)
6-thioguanine (6-TG)/Purinethol .RTM. (TEVA) pentostatin/Nipent
.RTM. (Hospira Inc.) fludarabine phosphate/Fludara .RTM. (Bayer
Health Care) cladribine/Leustatin .RTM. (2-CdA, 2-
chlorodeoxyadenosine) (Ortho Biotech) floxuridine
(5-fluoro-2'-deoxyuridine)/ FUDR .RTM. (Hospira, Inc,) Alkylating
agents An alkylating Ribonucleotide Reductase Inhibitor (RNR)
antineoplastic agent is an cyclophosphamide/Cytoxan .RTM. (BMS)/
alkylating agent that Neosar .RTM. (TEVA) attaches an alkyl group
to ifosfamide/Mitoxana .RTM. (ASTA Medica) DNA. Since cancer cells
ThioTEPA (Bedford, Abraxis, Teva) generally proliferate
BCNU.fwdarw. 1,3-bis(2-chloroethyl)-1-nitosourea unrestrictively
more than CCNU.fwdarw. 1,-(2 -chloroethyl)-3-cyclohexyl-1- do
healthy cells they are nitrosourea (methyl CCNU) more sensitive to
DNA hexamethylmelamine (altretamine, HMM)/ damage, and alkylating
Hexalen .RTM. (MGI Pharma Inc.) agents are used clinically
busulfan/Myleran .RTM. (GlaxoSmithKline) to treat a variety of
procarbazine HCL/Matulane .RTM. (Sigma Tau) tumors. Dacarbazine
(DTIC .RTM.) chlorambucil/Leukaran .RTM. (SmithKline Beecham)
Melphalan/Alkeran .RTM. (GlaxoSmithKline) cisplatin (Cisplatinum,
CDDP)/Platinol (Bristol Myers) carboplatin/Paraplatin (BMS)
oxaliplatin/Eloxitan .RTM. (Sanofi-Aventis US) Bendamustine
carboquone carmustine chloromethine dacarbazine (DTIC) fotemustine
lomustine mannosulfan nedaplatin nimustine prednimustine
ranimustine satraplatin semustine streptozocin temozolomide
treosulfan triaziquone triethylene melamine triplatin tetranitrate
trofosfamide uramustine Topoisomerase Topoisomerase inhibitors
doxorubicin HCL/Doxil .RTM. (Alza) inhibitors are chemotherapy
agents daunorubicin citrate/Daunoxome .RTM. (Gilead) designed to
interfere with mitoxantrone HCL/Novantrone (EMD the action of
Serono) topoisomerase enzymes actinomycin D (topoisomerase I and
II), etoposide/Vepesid .RTM. (BMS)/Etopophos .RTM. which are
enzymes that (Hospira, Bedford, Teva Parenteral, Etc.) control the
changes in topotecan HCL/Hycamtin .RTM. DNA structure by
(GlaxoSmithKline) catalyzing the breaking teniposide (VM-26)/Vumon
.RTM. (BMS) and rejoining of the irinotecan HCL(CPT-11)/
phosphodiester backbone camptosar .RTM. (Pharmacia & Upjohn) of
DNA strands during camptothecin (CPT) the normal cell cycle.
belotecan rubitecan Microtubule Microtubules are one of
vincristine/Oncovin .RTM. (Lilly) targeting agents the components
of the vinblastine sulfate/Velban .RTM.(discontinued) cytoskeleton.
They have (Lilly) diameter of ~24 nm and vinorelbine
tartrate/Navelbine .RTM. length varying from (PierreFabre) several
micrometers to vindesine sulphate/Eldisine .RTM. (Lilly) possibly
millimeters in paclitaxel/Taxol .RTM. (BMS) axons of nerve cells.
docetaxel/Taxotere .RTM. (Sanofi Aventis US) Microtubules serve as
Nanoparticle paclitaxel (ABI-007)/ structural components Abraxane
.RTM. (Abraxis BioScience, Inc.) within cells and are
ixabepilone/IXEMPRA .TM. (BMS) involved in many cellular larotaxel
processes including ortataxel mitosis, cytokinesis, and tesetaxel
vesicular transport. vinflunine Kinase inhibitors Tyrosine kinases
are imatinib mesylate/Gleevec (Novartis) enzymes within the cell
sunitinib malate/Sutent .RTM. (Pfizer) that function to attach
sorafenib tosylate/Nexavar .RTM. (Bayer) phosphate groups to the
nilotinib hydrochloride monohydrate/ amino acid tyrosine. By
Tasigna .RTM. (Novartis) blocking the ability of AMG 386 (Amgen)
protein tyrosine kinases axitinib (AG-013736; Pfizer, Inc.) to
function, these bosutinib (SKI-606; Wyeth) compounds provide a tool
brivanib alalinate (BMS-582664; BMS) for controlling cancerous
cediranib (AZD2171; Recentin, AstraZeneca) cell growth. dasatinib
(BMS-354825: Sprycel .RTM.; BMS) lestaurtinib (CEP-701; Cephalon)
motesanib diphosphage (AMG-706; Amgen/Takeda) pazopanib HCL
(GW786034; Armala, GSK) semaxanib (SU5416; Pharmacia) vandetanib
(AZD647; Zactima; AstraZeneca) vatalanib (PTK-787; Novartis, Bayer
Schering Pharma) XL184 (NSC718781; Exelixis, GSK) Protein synthesis
Induces cell apoptosis L-asparaginase/Elspar .RTM. (Merck &
Co.) inhibitors Immunotherapeutic Induces cancer patients to Alpha
interferon agents exhibit immune Angiogenesis Inhibitor/Avastin
.RTM. responsiveness (Genentech) IL-2.fwdarw. Interleukin 2
(Aldesleukin)/ Proleukin .RTM. (Chiron) IL-12.fwdarw. Interleukin
12 Hormonal therapies Hormonal therapies Ttoremifene
citrate/Fareston .RTM. (GTX, Inc.) associated with
fulvestrant/Faslodex .RTM. (AstraZeneca) menopause and aging
raloxifene HCL/Evista .RTM. (Lilly) seek to increase the
anastrazole/Arimidex .RTM. (AstraZeneca) amount of certain
letrozole/Femara .RTM. (Novartis) hormones in the body to fadrozole
(CGS 16949A) compensate for age- or exemestane/Aromasin .RTM.
(Pharmacia & disease-related hormonal Upjohn) declines.
Hormonal leuprolide acetate/Eligard .RTM. (QTL USA) therapy as a
cancer Lupron .RTM. (TAP Pharm.) treatment generally either
goserelin acetate/Zoladex .RTM. (AstraZeneca) reduces the level of
one triptorelin pamoate/Trelstar .RTM. (Watson Labs) or more
specific buserelin/Suprefact .RTM. (Sanofi Aventis) hormones,
blocks a nafarelin hormone from interacting cetrorelix/Cetrotide
.RTM. (EMD Serono) with its cellular receptor bicalutamide/Casodex
.RTM. (AstraZeneca) or otherwise alters the nilutamide/Nilandron
.RTM. (Aventis Pharm.) cancer's ability to be megestrol
acetate/Megace .RTM. (BMS) stimulated by hormones somatostatin
Analogs (e.g., Octreotide acetate/ to grow and spread. Such
Sandostatin .RTM. (Novartis)) hormonal therapies thus abarelix
(Plenaxis .TM.; Amgen) include hormone abiraterone acetate (CB7630;
BTG plc) antagonists and hormone afimoxifene (TamoGel; Ascend
Therapeutics, synthesis inhibitors. In Inc.) some instances hormone
aromatase inhibitor (Atamestane plus agonists may also be used
toremifene; Intarcia Therapeutics, Inc.) as anticancer hormonal
arzoxifene (Eh Lilly & Co) therapies. Asentar .TM.; DN-101
(Novacea; Oregon Health Sciences U) flutamide (Eulexin .RTM.,
Schering; Prostacur, Laboratorios Almirall, S.A) letrozole
(CGS20267) (Femara .RTM., Chugai; Estrochek .RTM., (Jagsonpal
Pharmaceuticals Ltd;) Delestrogen .RTM., estradiol valerate
(Jagsonpal) magestrol acetate/Megace .RTM. medroxyprogesteone
acetate (Veraplex .RTM.; Combiphar) MT206 (Medisyn Technologies,
Inc.) nandrolone decanoate (Zestabolin .RTM.; Mankind Pharma Ltd)
tamoxifen (Taxifen .RTM., Yung Shin Pharmaceutical; Tomifen .RTM.,
Alkem Laboratories Ltd.) tamoxifen citrate (Nolvadex, AstraZeneca;
soltamox, EUSA Pharma Inc; tamoxifen citrate SOPHARMA, Sopharma
JSCo.) Glucocorticoids Anti-inflammatory drugs predinsolone used to
reduce swelling dexamethasone/Decadron .RTM. (Wyeth) that causes
cancer pain. prednisone (Deltasone, Orasone, Liquid Pred, Sterapred
.RTM.) Aromatase inhibitors Includes imidazoles ketoconazole mTOR
inhibitors The mTOR signaling sirolimus (Rapamycin)/Rapamune .RTM.
(Wyeth) pathway was originally Temsirolimus (CCI-779)/Torisel .RTM.
(Wyeth) discovered during studies Deforolimus (AP23573) (Ariad
Pharm.) of the Everolimus (RAD001)/Certican .RTM. (Novartis)
immunosuppressive agent
rapamycin. This highly conserved pathway regulates cell
proliferation and metabolism in response to environmental factors,
linking cell growth factor receptor signaling via
phosphoinositide-3- kinase (PI-3K) to cell growth, proliferation,
and angiogenesis. Chemotherapeutic adriamycin, 5-fluorouracil,
cytoxin, agents bleomycin, mitomycin C, daunomycin, carminomycin,
aminopterin, dactinomycin, mitomycins, esperamicins, clofarabine,
mercaptopurine, pentostatin, thioguanine, cytarabine, decitabine,
floxuridine, gemcitabine (Gemzar), enocitabine, sapacitabine
Protein Kinase B AKT Inhibitor Astex .RTM. (Astex Therapeutics)
(PKB) Inhibitors AKT Inhibitors NERVIANO (Nerviano Medical
Sciences) AKT Kinase Inhibitor TELIK (Telik Inc) AKT DECIPHERA
(Deciphera Pharmaceuticals, LLC) perifosine (KRX0401, D-21266;
Keryx Biopharmaceuticals Inc, AEterna Zentaris Inc) perifosine with
Docetaxel (Keryx Biopharmaceuticals Inc, AEterna Zentaris Inc)
perifosine with Gemcitabine (AEterna Zentaris Inc) perifosine with
paclitaxel (AEterna Zentaris Inc) protein kinase-B inhibitor
DEVELOGEN (DeveloGen AG) PX316 (Oncothyreon, Inc.) RX0183 (Rexahn
Pharmaceuticals Inc) RX0201 (Rexahn Pharmaceuticals Inc) VQD002
(VioQuest Pharmaceuticals Inc) XL418 (Exelixis Inc) ZEN027 (AEtema
Zentaris Inc) Phosphatidylinositol BEZ235 (Novartis AG) 3-Kinase
(PI3K) BGT226 (Novartis AG) Inhibitors CAL101 (Calistoga
Pharmaceuticals, Inc.) CHR4432 (Chroma Therapeutics Ltd) Erk/PI3K
Inhibitors ETERNA (AEterna Zentaris Inc) GDC0941 (Genentech
Inc/Piramed Limited/Roche Holdings Ltd) enzastaurin HCL (LY317615;
Enzastaurin; Eli Lilly) LY294002/Wortmannin PI3K Inhibitors
SEMAFORE (Semafore Pharmaceuticals) PX866 (Oncothyreon, Inc.)
SF1126 (Semafore Pharmaceuticals) VMD-8000 (VM Discovery, Inc.)
XL147 (Exelixis Inc) XL147 with XL647 (Exelixis Inc) XL765
(Exelixis Inc) PI-103 (Roche/Piramed) Cyclin Dependent CYC200,
R-roscovitine (Seliciclib; Cyclacel Kinase Inhibitors Pharma)
NSC-649890, L86-8275, HMR-1275 (alvocidib; NCI) TLr9, CD289 IMOxine
(Merck KGaA) HYB2055 (Idera) IMO-2055 (Isis Pharma) 1018 ISS
(Dynavax Technologies/UCSF) PF-3512676 (Pfizer) Enzyme Inhibitor
lonafarnib(SCH66336; Sarasar; SuperGen, U Arizona) Anti-TRAIL
AMG-655 (Aeterna Zentaris, Keryx Biopharma) Apo2L/TRAIL, AMG951
(Genentech, Amgen) APOMAB (fully humanized mAb; Genentech) MEK
Inhibitors [Mitogen-Activated ARRY162 (Array BioPharma Inc) Protein
Kinase Kinase 1 ARRY704 (Array BioPharma Inc) (MAP2K1); Mitogen-
ARRY886 (Array BioPharma Inc) Activated Protein Kinase AS703026
(Merck Serono S.A) Kinase 2 (MAP2K2)] AZD6244 (AstraZeneca Plc)
AZD8330 (AstraZeneca Plc) RDEA119 (Ardea Biosciences, Inc.) RDEA436
(Ardea Biosciences, Inc.) XL518 (Exelixis Inc; Genentech Inc)
Miscellaneous Imprime PGG (Biothera) Inhibitors CHR-2797
(AminopeptidaseM1 inhibitor; Chroma Therapeutics) E7820, NSC 719239
(Integrin-alpha2 inhibitor, Eisai) INCB007839 (ADAM 17, TACE
Inhibitor; Incyte) CNF2024, BIIB021 (Hsp90 Inhibitor; Biogen Idec)
MP470, HPK-56 (Kit/Mel/Ret Inhibitor; Schering-Plough)
SNDX-275/MS-275 (HDAC Inhibitor; Syndax) Zamestra .TM., Tipifarnib,
R115777 (Ras Inhibitor; Janssen Pharma) volociximab; Eos 200-4,
M200 (alpha581 integrin inhibitor; Biogen Idec; Eli Lilly/UCSF/PDL
BioPharma) apricoxib (TP2001; COX-2 Inhibitor, Daiichi Sankyo;
Tragara Pharma)
One or more anti-cancer agents may be administered either
simultaneously or before or after administration of an antibody or
antigen binding portion thereof disclosed herein.
[0158] Various aspects of the present invention are described in
further detail in the following subsections.
II. Methods for Producing Antibodies
[0159] (i) Monoclonal Antibodies
[0160] Monoclonal antibodies of the present disclosure can be
produced using a variety of known techniques, such as the standard
somatic cell hybridization technique described by Kohler and
Milstein (1975) Nature 256: 495, viral or oncogenic transformation
of B lymphocytes or phage display technique using libraries of
human antibody genes. In particular embodiments, the antibodies are
fully human monoclonal antibodies.
[0161] Accordingly, in one embodiment, a hybridoma method is used
for producing an antibody that binds ErbB3. In this method, a mouse
or other appropriate host animal can be immunized with a suitable
antigen in order to elicit lymphocytes that produce or are capable
of producing antibodies that will specifically bind to the antigen
used for immunization. Alternatively, lymphocytes may be immunized
in vitro. Lymphocytes can then be 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)). Culture medium in
which hybridoma cells are growing is assayed for production of
monoclonal antibodies directed against the antigen. 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, 1986 supra). 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. The monoclonal antibodies secreted by the subclones can be
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.
[0162] In another embodiment, antibodies and antibody portions that
bind ErbB3 can be isolated from antibody phage libraries generated
using the techniques described in, for example, McCafferty et al.,
Nature, 348:552-554 (1990). Clackson et al., Nature, 352:624-628
(1991), Marks et al., J. Mol. Biol., 222:581-597 (1991) and Hoet et
al (2005) Nature Biotechnology 23, 344-348; U.S. Pat. Nos.
5,223,409; 5,403,484; and 5,571,698 to Ladner et al.; U.S. Pat.
Nos. 5,427,908 and 5,580,717 to Dower et al.; U.S. Pat. Nos.
5,969,108 and 6,172,197 to McCafferty et al.; and U.S. Pat. Nos.
5,885,793; 6,521,404; 6,544,731; 6,555,313; 6,582,915 and 6,593,081
to Griffiths et al.. Additionally, production of high affinity (nM
range) human antibodies by chain shuffling (Marks et al.,
Bio/Technology, 10:779-783 (1992)), as well as combinatorial
infection and in vivo recombination as a strategy for constructing
very large phage libraries (Waterhouse et al., Nuc. Acids. Res.,
21:2265-2266 (1993)) may also be used.
[0163] In a particular embodiment, the antibody or antigen binding
portion thereof that binds ErbB3 is produced using the phage
display technique described by Hoet et al., supra. This technique
involves the generation of a human Fab library having a unique
combination of immunoglobulin sequences isolated from human donors
and having synthetic diversity in the heavy-chain CDRs is
generated. The library is then screened for Fabs that bind to
ErbB3.
[0164] In yet another embodiment, human monoclonal antibodies
directed against ErbB3 can be generated using transgenic or
transchromosomic mice carrying parts of the human immune system
rather than the mouse system (see e.g., Lonberg, et al. (1994)
Nature 368(6474): 856-859; Lonberg, N. et al. (1994), supra;
reviewed in Lonberg, N. (1994) Handbook of Experimental
Pharmacology 113:49-101; Lonberg, N. and Huszar, D. (1995) Intern.
Rev. Immunol. 13: 65-93, and Harding, F. and Lonberg, N. (1995)
Ann. N.Y. Acad. Sci. 764:536-546. See further, U.S. Pat. Nos.
5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,789,650; 5,877,397;
5,661,016; 5,814,318; 5,874,299; and 5,770,429; all to Lonberg and
Kay; U.S. Pat. No. 5,545,807 to Surani et al.; PCT Publication Nos.
WO 92/03918, WO 93/12227, WO 94/25585, WO 97/13852, WO 98/24884 and
WO 99/45962, all to Lonberg and Kay; and PCT Publication No. WO
01/14424 to Korman et al.).
[0165] In another embodiment, human antibodies disclosed herein can
be raised using a mouse that carries human immunoglobulin sequences
on transgenes and transchomosomes, such as a mouse that carries a
human heavy chain transgene and a human light chain transchromosome
(see e.g., PCT Publication WO 02/43478 to Ishida et al.).
[0166] Still further, alternative transgenic animal systems
expressing human immunoglobulin genes are available in the art and
can be used to raise anti-ErbB3 antibodies or fragments thereof of
the invention. For example, an alternative transgenic system
referred to as the XENOMOUSE (Abgenix, Inc.) can be used; such mice
are described in, for example, U.S. Pat. Nos. 5,939,598; 6,075,181;
6,114,598; 6, 150,584 and 6,162,963 to Kucherlapati et al.
[0167] Moreover, alternative transchromosomic animal systems
expressing human immunoglobulin genes are available in the art and
can be used to raise anti-ErbB3 antibodies or fragments thereof of
the invention. For example, mice carrying both a human heavy chain
transchromosome and a human light chain transchromosome can be
used; as described in Tomizuka et al. (2000) Proc. Natl. Acad. Sci.
USA 97:722-727. Furthermore, cows carrying human heavy and light
chain transchromosomes have been described in the art (Kuroiwa et
al. (2002) Nature Biotechnology 20:889-894) and can be used to
raise anti-ErbB3 antibodies or fragments thereof of the
invention.
[0168] In yet another embodiment, antibodies disclosed herein can
be prepared using a transgenic plant and/or cultured plant cells
(such as, for example, tobacco, maize and duckweed) that produce
such antibodies. For example, transgenic tobacco leaves expressing
antibodies or antigen binding portions thereof can be used to
produce such antibodies by, for example, using an inducible
promoter (see, e.g., Cramer et al., Curr. Top. Microbol. Immunol.
240:95 118 (1999)). Also, transgenic maize can be used to express
such antibodies and antigen binding portions thereof (see, e.g.,
Hood et al., Adv. Exp. Med. Biol. 464:127 147 (1999)). Antibodies
can also be produced in large amounts from transgenic plant seeds
including antibody portions, such as single chain antibodies (e.g.,
scFvs), for example, using tobacco seeds and potato tubers (see,
e.g., Conrad et al., Plant Mot Biol. 38:101 109 (1998)). Methods of
producing antibodies or antigen binding portions in plants can also
be found in, e.g., Fischer et al., Biotechnol. Appl. Biochem. 30:99
108 (1999), Ma et al., Trends Biotechnol. 13:522 7 (1995); Ma et
al., Plant Physiol. 109:341 6 (1995); Whitelam et al., Biochem.
Soc. Trans. 22:940 944 (1994) and U.S. Pat. Nos. 6,040,498 and
6,815,184.
[0169] The binding specificity of antibodies or portions thereof
that bind ErbB3 prepared using any technique including those
disclosed here, can be determined by immunoprecipitation or by an
in vitro binding assay, such as radioimmunoassay (RIA) or
enzyme-linked immunoabsorbent assay (ELISA). The binding affinity
of a antibody or portion thereof also can be determined by the
Scatchard analysis of Munson et al., Anal. Biochem., 107:220
(1980).
[0170] In certain embodiments, an ErbB3 antibody or portion thereof
produced using any of the methods discussed above may be further
altered or optimized to achieve a desired binding specificity
and/or affinity using art recognized techniques, such as those
described herein.
[0171] In one embodiment, partial antibody sequences derived from
an ErbB3 antibody may be used to produce structurally and
functionally related antibodies. For example, antibodies interact
with target antigens predominantly through amino acid residues that
are located in the six heavy and light chain complementarity
determining regions (CDRs). For this reason, the amino acid
sequences within CDRs are more diverse between individual
antibodies than sequences outside of CDRs. Because CDR sequences
are responsible for most antibody-antigen interactions, it is
possible to express recombinant antibodies that mimic the
properties of specific naturally occurring antibodies by
constructing expression vectors that include CDR sequences from the
specific naturally occurring antibody grafted onto framework
sequences from a different antibody with different properties (see,
e.g., Riechmann, L. et al., 1998, Nature 332:323-327; Jones, P. et
al., 1986, Nature 321:522-525; and Queen, C. et al., 1989, Proc.
Natl. Acad. See. U.S.A. 86:10029-10033). Such framework sequences
can be obtained from public DNA databases that include germline
antibody gene sequences.
[0172] Thus, one or more structural features of an anti-ErbB3
antibody or fragment thereof of the invention, such as the CDRs,
can be used to create structurally related anti-ErbB3 antibodies
that retain at least one functional property of other antibodies or
fragments thereof of the invention, e.g., inhibiting EGF-like
ligand mediated phosphorylation of ErbB3; inhibiting one or more of
heregulin, epiregulin, epigen or biregulin-mediated signaling
through ErbB3; inhibiting proliferation or cells expressing ErbB3;
and/or decreasing levels of ErbB3 on cell surfaces.
[0173] In a particular embodiment, one or more CDR regions selected
from SEQ ID NOs:7-12, SEQ ID NOs:13-18, SEQ ID NOs:19-24, SEQ ID
NOs:39-44, and SEQ ID NOs:45-50 is combined recombinantly with
known human framework regions and CDRs to create additional,
recombinantly-engineered, anti-ErbB3 antibodies or fragments
thereof of the invention. The heavy and light chain variable
framework regions can be derived from the same or different
antibody sequences.
[0174] It is well known in the art that antibody heavy and light
chain CDR3 domains play a particularly important role in the
binding specificity/affinity of an antibody for an antigen (see,
Hall et al., J. Imunol., 149:1605-1612 (1992); Polymenis et al., J.
Immunol., 152:5318-5329 (1994); Jahn et al., Immunobiol.,
193:400-419 (1995); Klimka et al., Brit. J. Cancer, 83:252-260
(2000); Beiboer et al., J. Mol. Biol, 296:833-849 (2000); Rader et
al., Proc. Natl. Acad. Sci. USA, 95:8910-8915 (1998); Barbas et
al., J. Am. Chem. Soc., 116:2161-2162 (1994); Ditzel et al., J.
Immunol., 157:739-749 (1996)). Accordingly, in certain embodiments,
antibodies are generated that include the heavy and/or light chain
CDR3s of the particular antibodies described herein (e.g., SEQ ID
NOs:9, 15, 21, 41, 47 and/or SEQ ID NOs:12, 18, 24, 44, 50). The
antibodies can further include the heavy and/or light chain CDR1
and/or CDR2s of the antibodies specifically disclosed herein (e.g.,
SEQ ID NOs:7-8 and/or SEQ ID NOs:10-11; SEQ ID NOs:13-14 and/or SEQ
ID NOs:16-17; SEQ ID NOs:20-21 and/or SEQ ID NOs:22-23; SEQ ID
NOs:39-40 and/or SEQ ID NOs:42-43; or SEQ ID NOs:45-46 and/or SEQ
ID NOs:48-49).
[0175] The CDR1, 2, and/or 3 regions of the engineered antibodies
described above can comprise the exact amino acid sequence(s) as
those disclosed herein (e.g., CDRs of Ab #6, Ab #3, Ab #14, Ab #17,
or Ab #19, set forth in SEQ ID NOs:7-12, 13-18, 19-24, 39-44, and
45-50, respectively). However, the ordinarily skilled artisan will
appreciate that some deviation from the exact CDR sequences may be
possible while still retaining the ability of the antibody to bind
ErbB3 effectively (e.g., conservative amino acid substitutions).
Accordingly, in another embodiment, the engineered antibody may be
composed of one or more CDRs that are, for example, 90%, 95%, 98%,
99% or 99.5% identical to one or more CDRs of Ab #6, Ab #3 or Ab
#14.
[0176] In another embodiment, one or more residues of a CDR may be
altered to modify binding to achieve a more favored on-rate of
binding. Using this strategy, an antibody having ultra high binding
affinity of, for example, 10.sup.10 M.sup.-1 or more, can be
achieved. Affinity maturation techniques, well known in the art and
those described herein, can be used to alter the CDR region(s)
followed by screening of the resultant binding molecules for the
desired change in binding. Accordingly, as CDR(s) are altered,
changes in binding affinity as well as immunogenicity can be
monitored and scored such that an antibody optimized for the best
combined binding and low immunogenicity are achieved.
[0177] As described in further detail in Example 20, mutagenesis
(e.g., alanine scanning mutagenesis) has been conducted on the
heavy and light chain CDRs of Ab #6 to identify amino acid residues
involved in binding to ErbB3 to thereby define the paratope of the
antibody.
[0178] Paratope CDR sequences for anti-ErbB3 antibodies are shown
in FIGS. 37A and 37B, based on this mutagenesis analysis. As
illustrated in FIG. 37A, an anti-ErbB3 antibody or fragment thereof
of the invention can comprise a heavy chain paratope comprising
CDR1, CDR2 and CDR3 sequences as shown in SEQ ID NOs: 63, 64 and
65, respectively, and a light chain paratope comprising CDR1, CDR2
and CDR3 sequences as shown in SEQ ID NOs: 69, 70 and 71,
respectively. As illustrated in FIG. 37B, an anti-ErbB3 antibody or
fragment thereof of the invention can comprise a heavy chain
paratope comprising CDR1, CDR2 and CDR3 sequences as shown in SEQ
ID NOs: 76, 64 and 65, respectively, and a light chain paratope
comprising CDR1, CDR2 and CDR3 sequences as shown in SEQ ID NOs:
78, 70 and 80, respectively. In yet another embodiment, the
invention provides an anti-ErbB3 antibody comprising a heavy chain
paratope comprising CDR1, CDR2 and CDR3 sequences as shown in SEQ
ID NOs: 63 or 76 (CDR1), 64 (CDR2) and 65 (CDR3), respectively. In
yet another embodiment, the invention provides an anti-ErbB3
antibody comprising a light chain paratope comprising CDR1, CDR2
and CDR3 sequences as shown in SEQ ID NOs: 69 or 78 (CDR1), 70
(CDR2) and 71 or 80 (CDR3), respectively.
[0179] Consensus CDR sequences for anti-ErbB3 antibodies or
fragments thereof of the invention also are shown in FIGS. 37A and
37B, based on this mutagenesis analysis. As illustrated in FIG.
37A, an anti-ErbB3 antibody or fragment thereof of the invention
can comprise a heavy chain variable region comprising CDR1, CDR2
and CDR3 sequences as shown in SEQ ID NOs: 60, 61 and 62,
respectively, and a light chain variable region comprising CDR1,
CDR2 and CDR3 sequences as shown in SEQ ID NOs: 66, 67 and 68,
respectively. As illustrated in FIG. 37B, an anti-ErbB3 antibody or
fragment thereof of the invention can comprise a heavy chain
variable region comprising CDR1, CDR2 and CDR3 sequences as shown
in SEQ ID NOs: 75, 61 and 62, respectively, and a light chain
variable region comprising CDR1, CDR2 and CDR3 sequences as shown
in SEQ ID NOs: 77, 67 and 79, respectively. In yet another
embodiment, the invention provides an anti-ErbB3 antibody
comprising a heavy chain variable region comprising CDR1, CDR2 and
CDR3 sequences as shown in SEQ ID NOs: 60 or 75 (CDR1), 61 (CDR2)
and 62 (CDR3), respectively. In yet another embodiment, the
invention provides an anti-ErbB3 antibody comprising a light chain
variable region comprising CDR1, CDR2 and CDR3 sequences as shown
in SEQ ID NOs: 66 or 77 (CDR1), 67 (CDR2) and 68 or 79 (CDR3),
respectively.
[0180] In addition to, or instead of, modifications within the
CDRs, modifications can also be made within one or more of the
framework regions, FR1, FR2, FR3 and FR4, of the heavy and/or the
light chain variable regions of an antibody, so long as these
modifications do not eliminate the binding affinity of the
antibody.
[0181] In another embodiment, the antibody is further modified with
respect to effector function, so as to enhance the effectiveness of
the antibody in treating cancer, for example. For example cysteine
residue(s) may be introduced in the Fc region, thereby allowing
interchain disulfide bond formation in this region. The homodimeric
antibody thus generated may have improved internalization
capability and/or increased complement-mediated cell killing and
antibody-dependent cellular cytotoxicity (ADCC). See Caron et al.,
J. Exp Med. 176:1191-1195 (1992) and Shopes, B. J. Immunol.
148:2918-2922 (1992). Homodimeric antibodies with enhanced
anti-tumor activity may also be prepared using heterobifunctional
cross-linkers as described in Wolff et al. Cancer Research
53:2560-2565 (1993). Alternatively, an antibody can be engineered
which has dual Fc regions and may thereby have enhanced complement
lysis and ADCC capabilities. See Stevenson et al. Anti-Cancer Drug
Design 3:219-230 (1989).
[0182] Mutagenesis of one or more residues in the CDRs, framework
regions, Fc regions, or other antibody regions as disclosed herein
can be accomplished using standard recombinant DNA techniques,
including but not limited to site-directed mutagenesis and
PCR-mediated mutagenesis. Screening of the effects of mutation on
antigen binding (e.g., binding to ErbB3) and other functional
characteristics also can be accomplished using standard methods.
For example, the antibody (e.g., an scFv version) containing the
mutated CDRs can be expressed on the surface of cells, such as
mammalian cells, yeast cells or bacterial cells (e.g., using a
phage display system) and binding of the antigen to the cells can
be determined using standard methods, for example flow cytometry in
which antigen bound to the cells is detected, e.g., using a labeled
secondary antibody. Additionally or alternatively, the antibody can
be expressed in soluble form and the binding of the antibody to the
antigen can be assessed using a standard binding assay such as
ELISA or BIACORE analysis. Detailed descriptions of the foregoing
and related techniques for such purposes may be found in numerous
well known textbooks and laboratory manuals, for example: Handbook
of Therapeutic Antibodies Vols. 1-3, Stefan Dubel, ed., Wiley-VCH
2007; Making and Using Antibodies: A Practical Handbook, Gary C.
Howard, CRC 2006; Antibody Engineering: Methods and Protocols,
Benny K. C. Lo, Humana Press 2003; Therapeutic Antibodies: Methods
and Protocols, Antony S. Dimitrov, ed., Humana Press 2009; Antibody
Phage Display: Methods and Protocols, 2nd ed. Robert Aitken, ed.,
Humana Press 2009; Flow Cytometry Protocols, 2nd ed. Teresa S.
Hawley and Robert G. Hawley, eds., Humana Press 2004; Flow
Cytometry: Principles and Applications, Marion G. Macey, ed.,
Humana Press 2007. Also see "Selecting and Screening Recombinant
Antibody Libraries," H. R. Hoogenboom, Nature Biotechnol.
23:1105-1116; 2005.
[0183] Also encompassed by the present invention are bispecific
antibodies and immunoconjugates, as discussed below.
[0184] (ii) Bispecific Antibodies
[0185] Bispecific antibodies of the present disclosure include at
least one binding specificity for ErbB3 and at least one binding
specificity for another antigen, such as the product of an
oncogene. Bispecific antibodies can be prepared as full length
antibodies or antibody fragments (e.g. F(ab')2 bispecific
antibodies).
[0186] Methods for making bispecific antibodies are well known in
the art (see, e.g., WO 05117973 and WO 06091209). For example,
production of full length bispecific antibodies can be based on the
coexpression of two immunoglobulin heavy chain-light chain pairs,
where the two chains have different specificities (see, e.g.,
Millstein et al., Nature, 305:537-539 (1983)). Further details of
generating bispecific antibodies can be found, for example, in
Suresh et al., Methods in Enzymology, 121:210 (1986) and in Brennan
et al., Science, 229: 81 (1985), which describes a chemical linkage
process for making bispecific antibodies. 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
(see, e.g., Kostelny et al., J. Immunol., 148(5):1547-1553 (1992)).
Another strategy for making bispecific antibody fragments by the
use of single-chain Fv (scFv) dimers has also been reported (see,
e.g., Gruber et al., J. Immunol., 152:5368 (1994)).
[0187] In a particular embodiment, the bispecific antibody
comprises a first antibody or binding portion thereof which binds
to ErbB3 and a second antibody or binding portion thereof which
binds to ErbB2, ERbB3, ErbB4, EGFR, IGF1-R, C-MET, Lewis Y, MUC-1,
EpCAM, CA125, prostate specific membrane antigen, PDGFR-.alpha.,
PDGFR-.beta., C-KIT, or any of the FGF receptors.
[0188] (iii) Immunoconjugates
[0189] Immunoconjugates of the present disclosure can be formed by
conjugating the antibodies or antigen binding portions thereof
described herein to another therapeutic agent. Suitable agents
include, for example, a cytotoxic agent (e.g., a chemotherapeutic
agent), a toxin (e.g. an enzymatically active toxin of bacterial,
fungal, plant or animal origin, or fragments thereof), and/or a
radioactive isotope (i.e., a radioconjugate). Chemotherapeutic
agents useful in the generation of such immunoconjugates have been
described above. 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. A variety of radionuclides are available for
the production of radioconjugated anti-ErbB3 antibodies. Examples
include .sup.212Bi, .sup.131I, .sup.131In, .sup.90Y and
.sup.186Re.
[0190] Immunoconjugates of the invention can be made using a
variety of bifunctional protein coupling agents such as
N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP),
2-iminothiolane (IT), bifunctional derivatives of imidoesters (such
as dimethyl adipimidate HCL), active esters (such as disuccinimidyl
suberate), aldehydes (such as glutareldehyde), bis-azido compounds
(such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium
derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine),
diisocyanates (such as tolyene 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, e.g., WO94/11026).
[0191] (iv) Antibodies Raised Against ErbB3 Ectodomain Peptides
[0192] Those if skill will recognize that monoclonal and
monospecific polyclonal antibodies having various of the desireable
properties of Ab #6 (e.g., antibodies that inhibit cancer cell
proliferation and downregulate ErbB3 on cells), or that compete
with Ab #6 for binding to ErbB3, can be readily obtained using
conventional immunization methods using peptides (e.g., synthetic
peptides), or conjugates thereof (e.g., KLH conjugates), as
immunogens. Peptide for use as immunogens in this embodiment are
those comprising any 10 or more contiguous amino acid residues from
residues1-183 of SEQ ID NO: 73. Preferably the 10 or more
contiguous amino acid residues are from Domain I of the ectodomain
of ErbB3, preferably the residues at least partially fall within or
span residues 92-104 of SEQ ID NO: 73.
III. Methods for Screening Antibodies
[0193] Subsequent to producing antibodies or antigen binding
portions that bind ErbB3, such antibodies, or portions thereof, can
be screened for various properties, such as those described herein,
using a variety of assays that are well known in the art.
[0194] In one embodiment, the antibodies or antigen binding
portions thereof are screened for the ability to inhibit EGF-like
ligand mediated phosphorylation of ErbB3. This can be done by
treating cells expressing ErbB3 with an EGF-like ligand in the
presence and absence of the antibody or antigen binding portion
thereof. The cells can then be lysed and the crude lysates can be
centrifuged to remove insoluble material. ErbB3 phosphorylation can
be measured, for example, by Western blotting followed by probing
with an anti-phosphotyrosine antibody as described in Kim et al.,
supra and the Examples below.
[0195] In other embodiments, the antibodies and antigen binding
portions are further screened for one or more of the following
properties: (1) inhibition of ErbB3-ligand (e.g., heregulin,
epiregulin, epigen or biregulin) mediated signaling through ErbB3;
(2) inhibition of proliferation of cells expressing ErbB3; (3) the
ability to decrease levels of ErbB3 on cell surface (e.g., by
inducing internalization of ErbB3), (4) inhibition of VEGF
secretion of cells expressing ErbB3; (5) inhibition of the
migration of cells expressing ErbB3; (6) inhibition of spheroid
growth of cells expressing ErbB3; and/or (7) binding to an epitope
located on Domain I of the ectodomain of ErbB3, each of which can
be readily measured using art recognized techniques and those
discussed herein.
[0196] Inhibition of one or more of heregulin, epiregulin, epigen
or biregulin-mediated signaling through ErbB3 can be readily
measured using routine assays, such as, described in Horst et al.
supra. For example, the ability of an antibody or antigen binding
portion thereof to inhibit heregulin, epiregulin, epigen or
biregulin-mediated signaling through ErbB3 can be measured by
kinase assays for known substrates of ErbB3 such as, for example,
SHC and PI3K, as described in, for example, Horst et al. supra,
Sudo et al., (2000) Methods Enzymol, 322:388-92; and Morgan et al.
(1990) Eur. J. Biochem., 191:761-767, following stimulation by one
or more of heregulin, epiregulin, epigen or biregulin. Accordingly,
cells expressing ErbB3 can be stimulated with one or more of
heregulin, epiregulin, epigen or biregulin, and incubated with a
candidate antibody or antigen-binding portion thereof. Cell lysates
subsequently prepared from such cells can be immunoprecipitated
with an antibody for a substrate of ErbB3 (or a protein in a
cellular pathway involving ErbB3) such as, for example, an
anti-JNK-1 antibody, and assayed for kinase activity (e.g., JNK
kinase activity or PI3-kinase activity) using art recognized
techniques. A decrease in or complete disappearance in level or
activity (e.g., kinase activity) of a ErbB3 substrate or protein in
a pathway involving ErbB3 in the presence of the antibody or
antigen binding portion thereof, relative to the level or activity
in the absence of the antibody or antigen binding portion thereof,
is indicative of an antibody or antigen binding portion which
inhibits one or more of heregulin, epiregulin, epigen or
biregulin-mediated signaling.
[0197] In certain embodiments, the antibody or antigen binding
portion thereof inhibits ErbB3-ligand (e.g., heregulin, epiregulin,
epigen or biregulin) mediated signaling by decreasing the binding
of one or more of heregulin, epiregulin, epigen or biregulin to
ERbB3.
[0198] In order to select for those antibodies or antigen binding
portions thereof which inhibit the binding of one or more of
heregulin, epiregulin, epigen or biregulin to ErbB3, cells which
express ErbB3 (e.g. MALME-3M cells, as described in the Examples
infra), can be contacted with a labeled ErbB3-ligand (e.g.,
radiolabeled heregulin, epiregulin, epigen or biregulin) in the
absence (control) or presence of the anti-ErbB3 antibody or antigen
binding portion thereof. If the antibody or antigen binding portion
thereof inhibits heregulin, epiregulin, epigen or biregulin binding
to ErbB3, then a statistically significantly decrease in the amount
of label recovered (e.g., radiolabeled heregulin, epiregulin,
epigen or biregulin), relative to the amount in the absence of the
antibody or antigen binding portion thereof, will be observed.
[0199] The antibody or antigen binding portion thereof may inhibit
the binding of the ErbB3-ligand (e.g., heregulin, epiregulin,
epigen or biregulin) by any mechanism. For example, the antibody or
antigen binding portion thereof may inhibit binding of the ErbB3
ligand (e.g., one or more of heregulin, epiregulin, epigen or
biregulin) to ErbB3 by binding to the same site or an overlapping
site on ErbB3 as the ErbB3 ligand. Alternatively, the antibody or
antigen binding portion thereof may inhibit binding of an ErbB3
ligand by altering or distorting the conformation of ErbB3, such
that it is unable to bind to the ErbB3 ligand.
[0200] Antibodies and antigen binding portions thereof that
decrease levels of ErbB3 on cell surfaces can be identified by
their ability to downregulate ErbB3 on tumor cells. In certain
embodiments, the antibodies or antigen binding portions thereof
decrease ErbB3 cell surface expression by inducing internalization
(or increasing endocytosis) of Erbb3. To test this, ErbB3 can be
biotinylated and the number of ErbB3 molecules on the cell surface
can be readily determined, for example, by measuring the amount of
biotin on a monolayer of cells in culture in the presence or
absence of an antibody or antigen binding portion thereof, for
example, as described in, e.g., Waterman et al., J. Biol. Chem.
(1998), 273:13819-27, followed by immunoprecipitation of ErbB3 and
probing with streptavidin. A decrease in detection of biotinylated
ErbB3 over time in the presence of an antibody or antigen binding
portion is indicative of an antibody which decreases ErbB3 levels
on cell surfaces.
[0201] Antibodies or antigen binding portions thereof of the
present disclosure can also be tested for their ability to inhibit
proliferation of cells expressing ErbB3, for example, tumor cells,
using art recognized techniques, such as the
CellTiter-Glo.RTM.Assay described in the Examples below (also see,
e.g., Macallan et al., Proc. Natl. Acad. Sci. (1998) 20;
95(2):708-13; Perez et al. (1995) Cancer Research 55, 392-398).
[0202] In another embodiment, the antibodies or antigen binding
portions thereof are screened for the ability to inhibit VEGF
secretion of cells expressing ErbB3. This can be done by using
well-known assays, such as the VEGF ELISA kit available from
R&D Systems, Minneapolis, Minn., # DY293B. Similarly, the
antibodies or portions can be screened for the ability to inhibit
the migration of cells expressing ErbB3 (e.g., MCF-7 cells) using a
trans-well assay (Millipore Corp., Billerica, Mass., # ECM552) as
described herein.
[0203] In another embodiment, the antibodies or antigen binding
portions thereof are screened for the ability to inhibit spheroid
growth of cells expressing ErbB3. This can be done by using an
assay which approximates conditions of a developing tumor growth
(see, e.g., Herman et al. (2007) Journal of Biomolecular Screening
Electronic publication) as described herein.
[0204] Antibodies or antigen binding portions thereof that bind to
the same or overlapping epitopes as one or more antibodies
specifically disclosed herein can also be identified using standard
techniques known in the art and described herein. For example, in
order to screen for antibodies which bind to the same or an
overlapping epitope on ErbB3 bound by an antibody of interest, a
cross-blocking assay, such as that described in Antibodies, A
Laboratory Manual, Cold Spring Harbor Laboratory, Ed Harlow and
David Lane (1988), can be performed.
IV. Pharmaceutical Compositions
[0205] In another aspect, the present invention provides a
composition, e.g., a pharmaceutical composition, containing one or
a combination of antibodies, or antigen-binding portion(s) thereof
disclosed herein, formulated together with a pharmaceutically
acceptable carrier. In one embodiment, the compositions include a
combination of multiple (e.g., two or more) isolated antibodies,
which bind different epitopes on ErbB3.
[0206] As used herein, "pharmaceutically acceptable carrier"
includes any and all solvents, dispersion media, coatings,
antibacterial and antifungal agents, isotonic and absorption
delaying agents, and the like that are physiologically compatible.
Preferably, the carrier is suitable for intravenous, intramuscular,
subcutaneous, parenteral, spinal or epidermal administration (e.g.,
by injection or infusion). Depending on the route of
administration, the active agent, i.e., antibody, antibody
fragment, bispecific and multispecific molecule, may be coated in a
material to protect the agent from the action of acids and other
natural conditions that may inactivate it.
[0207] A "pharmaceutically acceptable salt" refers to a salt that
retains the desired biological activity of the parent compound and
does not impart any undesired toxicological effects (see e.g.,
Berge, S. M., et al. (1977) J. Pharm. Sci. 66:1-19). Examples of
such salts include acid addition salts and base addition salts.
Acid addition salts include those derived from nontoxic inorganic
acids, such as hydrochloric, nitric, phosphoric, sulfuric,
hydrobromic, hydroiodic, phosphorous and the like, as well as from
nontoxic organic acids such as aliphatic mono- and dicarboxylic
acids, phenyl-substituted alkanoic acids, hydroxy alkanoic acids,
aromatic acids, aliphatic and aromatic sulfonic acids and the like.
Base addition salts include those derived from alkaline earth
metals, such as sodium, potassium, magnesium, calcium and the like,
as well as from nontoxic organic amines, such as
N,N'-dibenzylethylenediamine, N-methylglucamine, chloroprocaine,
choline, diethanolamine, ethylenediamine, procaine and the
like.
[0208] Pharmaceutical compositions of the invention can comprise
other agents. For example, the composition can include at least one
or more additional therapeutic agents, such as the anti-cancer
agents described infra. The pharmaceutical compositions can also be
administered in conjunction with radiation therapy and/or surgery.
Alternately a composition of the invention can be separately
co-administered with at least one or more additional therapeutic
agents, such as the anti-cancer agents described infra.
[0209] A composition of the present disclosure can be administered
by a variety of methods known in the art. As will be appreciated by
the skilled artisan, the route and/or mode of administration will
vary depending upon the desired results. The active agents can be
prepared with carriers that will protect the agents against rapid
release, such as a controlled release formulation, including
implants, transdermal patches, and microencapsulated delivery
systems. Biodegradable, biocompatible polymers can be used, such as
ethylene vinyl acetate, polyanhydrides, polyglycolic acid,
collagen, polyorthoesters, and polylactic acid. Many methods for
the preparation of such formulations are patented or generally
known to those skilled in the art. See, e.g., Sustained and
Controlled Release Drug Delivery Systems, J. R. Robinson, ed.,
Marcel Dekker, Inc., New York, 1978.
[0210] To administer an antibody or fragment thereof of the
invention by certain routes of administration, it may be necessary
to coat it with, or co-administer it with, a material to prevent
its inactivation. For example, it may be administered to a subject
in an appropriate carrier, for example, liposomes, or a diluent.
Pharmaceutically acceptable diluents include saline and aqueous
buffer solutions. Liposomes include water-in-oil-in-water CGF
emulsions as well as conventional liposomes (Strejan et al. (1984)
J. Neuroimmunol. 7:27).
[0211] Pharmaceutically acceptable carriers include sterile aqueous
solutions or dispersions and sterile powders or lyophylysates for
the extemporaneous preparation of sterile injectable solutions or
dispersion. The use of such media and agents for pharmaceutically
active antibodies is known in the art. Except insofar as any
conventional media or agent is incompatible with the active agent,
use thereof in the pharmaceutical compositions of the invention is
contemplated. Supplementary active compounds can also be
incorporated into the compositions.
[0212] Therapeutic compositions typically must be sterile and
stable under the conditions of manufacture and storage. The
composition can be formulated as a solution, microemulsion,
liposome, or other ordered structure suitable to high drug
concentration. The carrier can be a solvent or dispersion medium
containing, for example, water, ethanol, polyol (for example,
glycerol, propylene glycol, and liquid polyethylene glycol, and the
like), and suitable mixtures thereof. The proper fluidity can be
maintained, for example, by the use of a coating such as lecithin,
by the maintenance of the required particle size in the case of
dispersion and by the use of surfactants. In many cases, it will be
preferable to include isotonic agents, for example, sugars,
polyalcohols such as mannitol, sorbitol, or sodium chloride in the
composition. Prolonged absorption of the injectable compositions
can be brought about by including in the composition an agent that
delays absorption, for example, monostearate salts and gelatin.
[0213] Sterile injectable solutions can be prepared by
incorporating the active agent in the required amount in an
appropriate solvent with one or a combination of ingredients
enumerated above, as required, followed by sterilization
microfiltration. Generally, dispersions are prepared by
incorporating the active agent into a sterile vehicle that contains
a basic dispersion medium and the required other ingredients from
those enumerated above. In the case of sterile powders for the
preparation of sterile injectable solutions, the preferred methods
of preparation are vacuum drying and freeze-drying (lyophilization)
that yield a powder of the active ingredient plus any additional
desired ingredient from a previously sterile-filtered solution
thereof.
[0214] Dosage regimens are adjusted to provide the optimum desired
response (e.g., a therapeutic response). For example, a single
bolus may be administered, several divided doses may be
administered over time or the dose may be proportionally reduced or
increased as indicated by the exigencies of the therapeutic
situation. For example, the human antibodies disclosed herein may
be administered once or twice weekly by subcutaneous injection or
once or twice monthly by subcutaneous injection.
[0215] Non-limiting examples of suitable dosage ranges and regimens
include 2-50 mg/kg (body weight of the subject) administered once a
week, or twice a week or once every three days, or once every two
weeks, and 1-100 mg/kg administered once a week, or twice a week or
once every three days, or once every two weeks. In various
embodiments, an antibody is administered at a dosage of 3.2 mg/kg,
6 mg/kg, 10 mg/kg, 15 mg/kg, 20 mg/kg, 25 mg/kg, 30 mg/kg, 35 mg/kg
or 40 mg/kg at a timing of once a week, or twice a week or once
every three days, or once every two weeks. Additional dosage ranges
include: 1-1000 mg/kg, 1-500 mg/kg, 1-400 mg/kg, 1-300 mg/kg and
1-200 mg/kg. Suitable dosage schedules include once every three
days, once every five days, once every seven days (i.e., once a
week), once every 10 days, once every 14 days (i.e., once every two
weeks), once every 21 days (i.e., once every three weeks), once
every 28 days (i.e., once every four weeks) and once a month.
[0216] As demonstrated in the Examples, use of an antibody
disclosed herein in combination with an additional therapeutic
agent can lead to an additive effect for anti-tumor activity.
Accordingly, for combination therapy, suboptimal dosages of the
antibody or the second therapeutic agent, or both, can be used to
achieve a desired therapeutic outcome due to the additive effects
of the agents. For example, when use din combination with another
therapeutic agent, in various embodiments an antibody or fragment
thereof of the invention may be administered at a dosage that is
90%, or 80%, or 70% or 60% or 50% of the dosage used when the
antibody is administered alone.
[0217] It is especially advantageous to formulate parenteral
compositions in dosage unit form for ease of administration and
uniformity of dosage. Dosage unit form as used herein refers to
physically discrete units suited as unitary dosages for the
subjects to be treated; each unit contains a predetermined quantity
of active agent calculated to produce the desired therapeutic
effect in association with the required pharmaceutical carrier. The
specification for the dosage unit forms of the invention are
dictated by and directly dependent on (a) the unique
characteristics of the active agent and the particular therapeutic
effect to be achieved, and (b) the limitations inherent in the art
of compounding such an active agent for the treatment of
sensitivity in individuals.
[0218] Examples of pharmaceutically-acceptable antioxidants
include: (1) water soluble antioxidants, such as ascorbic acid,
cysteine hydrochloride, sodium bisulfate, sodium metabisulfite,
sodium sulfite and the like; (2) oil-soluble antioxidants, such as
ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated
hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol,
and the like; and (3) metal chelating agents, such as citric acid,
ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid,
phosphoric acid, and the like.
[0219] For the therapeutic compositions, formulations of the
present disclosure include those suitable for oral, nasal, topical
(including buccal and sublingual), rectal, vaginal and/or
parenteral administration. The formulations may conveniently be
presented in unit dosage form and may be prepared by any methods
known in the art of pharmacy. The amount of active ingredient which
can be combined with a carrier material to produce a single dosage
form will vary depending upon the subject being treated, and the
particular mode of administration. The amount of active ingredient
which can be combined with a carrier material to produce a single
dosage form will generally be that amount of the composition which
produces a therapeutic effect. Generally, out of one hundred
percent, this amount will range from about 0.001 percent to about
ninety percent of active ingredient, preferably from about 0.005
percent to about 70 percent, most preferably from about 0.01
percent to about 30 percent.
[0220] Formulations of the present disclosure which are suitable
for vaginal administration also include pessaries, tampons, creams,
gels, pastes, foams or spray formulations containing such carriers
as are known in the art to be appropriate. Dosage forms for the
topical or transdermal administration of compositions of this
invention include powders, sprays, ointments, pastes, creams,
lotions, gels, solutions, patches and inhalants. The active agent
may be mixed under sterile conditions with a pharmaceutically
acceptable carrier, and with any preservatives, buffers, or
propellants which may be required.
[0221] The phrases "parenteral administration" and "administered
parenterally" as used herein means modes of administration other
than enteral and topical administration, usually by injection, and
includes, without limitation, intravenous, intramuscular,
intraarterial, intrathecal, intracapsular, intraorbital,
intracardiac, intradermal, intraperitoneal, transtracheal,
subcutaneous, subcuticular, intraarticular, subcapsular,
subarachnoid, intraspinal, epidural and intrasternal injection and
infusion.
[0222] Examples of suitable aqueous and nonaqueous carriers which
may be employed in the pharmaceutical compositions of the invention
include water, ethanol, polyols (such as glycerol, propylene
glycol, polyethylene glycol, and the like), and suitable mixtures
thereof, vegetable oils, such as olive oil, and injectable organic
esters, such as ethyl oleate. Proper fluidity can be maintained,
for example, by the use of coating materials, such as lecithin, by
the maintenance of the required particle size in the case of
dispersions, and by the use of surfactants.
[0223] These compositions may also contain adjuvants such as
preservatives, wetting agents, emulsifying agents and dispersing
agents. Particular examples of adjuvants which are well-known in
the art include, for example, inorganic adjuvants (such as aluminum
salts, e.g., aluminum phosphate and aluminum hydroxide), organic
adjuvants (e.g., squalene), oil-based adjuvants, virosomes (e.g.,
virosomes which contain a membrane-bound hemagglutinin and
neuraminidase derived from the influenza virus).
[0224] Prevention of presence of microorganisms may be ensured both
by sterilization procedures, supra, and by the inclusion of various
antibacterial and antifungal agents, for example, paraben,
chlorobutanol, phenol sorbic acid, and the like. It may also be
desirable to include isotonic agents, such as sugars, sodium
chloride, and the like into the compositions. In addition,
prolonged absorption of the injectable pharmaceutical form may be
brought about by the inclusion of agents which delay absorption
such as aluminum monostearate and gelatin.
[0225] When the antibodies of the present disclosure are
administered as pharmaceuticals, to humans and animals, they can be
given alone or as a pharmaceutical composition containing, for
example, 0.001 to 90% (more preferably, 0.005 to 70%, such as 0.01
to 30%) of active ingredient in combination with a pharmaceutically
acceptable carrier.
[0226] Regardless of the route of administration selected, the
antibodies of the present disclosure, which may be used in a
suitable hydrated form, and/or the pharmaceutical compositions of
the present disclosure, are formulated into pharmaceutically
acceptable dosage forms by conventional methods known to those of
skill in the art.
[0227] Actual dosage levels of the active ingredients in the
pharmaceutical compositions of the present disclosure may be varied
so as to obtain an amount of the active ingredient which is
effective to achieve the desired therapeutic response for a
particular patient, composition, and mode of administration,
without being toxic to the patient. The selected dosage levels will
depend upon a variety of pharmacokinetic factors including the
activity of the particular compositions employed, or, for compounds
co-administered with antibodies or fragments thereof provided
herein, the ester, salt or amide thereof, the route of
administration, the time of administration, the rate of excretion
of the particular agent being employed, the duration of the
treatment, other drugs, compounds and/or materials used in
combination with the particular compositions employed, the age,
sex, weight, condition, general health and prior medical history of
the patient being treated, and like factors well known in the
medical arts. A physician or veterinarian having ordinary skill in
the art can readily determine and prescribe the effective amount of
the pharmaceutical composition required. For example, the physician
or veterinarian could start doses of the antibodies or fragments
thereof of the invention employed in the pharmaceutical composition
at levels lower than that required in order to achieve the desired
therapeutic effect and gradually increase the dosage until the
desired effect is achieved. In general, a suitable daily dose of a
composition of the invention will be that amount which provides the
lowest dose effective to produce a therapeutic effect. Such an
effective dose will generally depend upon the factors described
above. It is preferred that administration be intravenous,
intramuscular, intraperitoneal, or subcutaneous, preferably
administered proximal to the site of the target. If desired, the
effective daily dose of a therapeutic composition may be
administered as two, three, four, five, six or more sub-doses
administered separately at appropriate intervals throughout the
day, optionally, in unit dosage forms. While it is possible for a
antibody of the present disclosure to be administered alone, it is
preferable to administer the antibody as a pharmaceutical
formulation (composition).
[0228] Therapeutic compositions can be administered with medical
devices known in the art. For example, in a preferred embodiment, a
therapeutic composition of the invention can be administered with a
needleless hypodermic injection device, such as the devices
disclosed in U.S. Pat. Nos. 5,399,163, 5,383,851, 5,312,335,
5,064,413, 4,941,880, 4,790,824, or 4,596,556. Examples of
well-known implants and modules useful in the present invention
include: U.S. Pat. No. 4,487,603, which discloses an implantable
micro-infusion pump for dispensing medication at a controlled rate;
U.S. Pat. No. 4,486,194, which discloses a therapeutic device for
administering medications through the skin; U.S. Pat. No.
4,447,233, which discloses a medication infusion pump for
delivering medication at a precise infusion rate; U.S. Pat. No.
4,447,224, which discloses a variable flow implantable infusion
apparatus for continuous drug delivery; U.S. Pat. No. 4,439,196,
which discloses an osmotic drug delivery system having
multi-chamber compartments; and U.S. Pat. No. 4,475,196, which
discloses an osmotic drug delivery system. Many other such
implants, delivery systems, and modules are known to those skilled
in the art.
[0229] In certain embodiments, compositions disclosed herein can be
formulated to ensure proper distribution in vivo. For example, the
blood-brain barrier (BBB) excludes many highly hydrophilic
compounds. To ensure that therapeutic compounds in compositions of
the invention cross the BBB (if desired), they can be formulated,
for example, in liposomes. For methods of manufacturing liposomes,
see, e.g., U.S. Pat. Nos. 4,522,811; 5,374,548; and 5,399,331. The
liposomes may comprise one or more moieties which are selectively
transported into specific cells or organs, thus enhance targeted
drug delivery (see, e.g., V. V. Ranade (1989) J. Clin. Pharmacol.
29:685). Exemplary targeting moieties include folate or biotin
(see, e.g., U.S. Pat. No. 5,416,016 to Low et al.); mannosides
(Umezawa et al., (1988) Biochem. Biophys. Res. Commun. 153:1038);
antibodies (P. G. Bloeman et al. (1995) FEBS Lett. 357:140; M.
Owais et al. (1995) Antimicrob. Agents Chemother. 39:180);
surfactant protein A receptor (Briscoe et al. (1995) Am. J.
Physiol. 1233:134), different species of which may comprise the
formulations of the invention, as well as components of the
invented molecules; p 120 (Schreier et al. (1994) J. Biol. Chem.
269:9090); see also K. Keinanen; M. L. Laukkanen (1994) FEBS Lett.
346:123; J. J. Killion; I. J. Fidler (1994) Immunomethods
4:273.
V. Methods of Using Antibodies
[0230] The present invention also provides methods of using
antibodies and antigen-binding portions thereof that bind ErbB3 in
a variety of ex vivo and in vivo diagnostic and therapeutic
applications. For example, antibodies disclosed herein can be used
for treating a disease associated with ErbB3 dependent signaling,
including a variety of cancers.
[0231] In one embodiment, the present invention provides a method
for treating a disease associated with ErbB3 dependent signaling by
administering to a subject an antibody or antigen binding portion
thereof of the invention in an amount effective to treat the
disease. Suitable diseases include, for example, a variety of
cancers including, but not limited to, melanoma, breast cancer,
ovarian cancer, renal carcinoma, gastrointestinal cancer, colon
cancer, lung cancer (e.g., non-small cell lung cancer), and
prostate cancer.
[0232] In a preferred embodiment, a tumor sample obtained from the
patient is tested and treatment is provided in accordance with the
methods disclosed in International Application No. PCT/US09/054051,
filed Aug. 17, 2009, titled "Methods, Systems And Products For
Predicting Response Of Tumor Cells To A Therapeutic Agent And
Treating A Patient According To The Predicted Response" which is
incorporated herein by reference. For example, the patient is to be
treated for a malignant tumor, a sample of the tumor is obtained, a
level of phosoho-ErbB3 (pErbB3) in the sample is determined, and at
least one antineoplastic therapeutic agent is subsequently
administered to the patient, however, if the level of pErbB3
determined in the sample is no lower than 50% of a level of pErbB3
measured in a culture of ACHN cells following culture for 20-24
hours in serum-free medium then the at least one antineoplastic
therapeutic agent subsequently administered to the patient
comprises an anti-ErbB3 antibody of the present invention, e.g., Ab
#6, and if the level of pErbB3 determined in the sample is lower
than 50% of the level of pErbB3 measured in the culture of ACHN
cells then the at least one antineoplastic therapeutic agent
subsequently administered to the patient does not comprise an
anti-ErbB3 antibody.
[0233] In one embodiment, the cancer comprises a KRAS mutation. As
demonstrated in Example 17, antibodies disclosed herein (e.g., Ab
#6) are capable of inhibiting the growth of tumor cells that
comprise a KRAS mutation, either when used as a single agent
(monotherapy) or in combination with another therapeutic agent. In
another embodiment, the cancer comprises a PI3K mutation. As
demonstrated in Example 19, antibodies disclosed herein (e.g., Ab
#6) are capable of inhibiting the growth of tumor cells that
comprise a PI3K mutation, either when used as a single agent
(monotherapy) or in combination with another therapeutic agent.
[0234] The antibody can be administered alone or with another
therapeutic agent which acts in conjunction with or synergistically
with the antibody to treat the disease associated with ErbB3
mediated signaling. Such therapeutic agents include, for example,
the anticancer agents described infra (e.g., cytotoxins,
chemotherapeutic agents, small molecules and radiation). As
demonstrated in Examples 16, 17 and 19, antibodies disclosed herein
(e.g., Ab #6) when used in combination with another therapeutic
agent can exhibit increased tumor growth inhibition as compared to
when used in monotherapy. Preferred therapeutic agents for
combination therapy include erlotinib (Tarceva.RTM.), paclitaxel
(Taxol.RTM.) and cisplatin (CDDP).
[0235] In certain aspects, antibodies disclosed herein are
administered to patients
[0236] In another embodiment, the present invention provides a
method for diagnosing a disease (e.g., a cancer) associated with
ErbB3 upregulation in a subject, by contacting antibodies or
antigen binding portions disclosed herein (e.g., ex vivo or in
vivo) with cells from the subject, and measuring the level of
binding to ErbB3 on the cells. Abnormally high levels of binding to
ErbB3 indicate that the subject has a disease associated with ErbB3
upregulation.
[0237] Also within the scope of the present invention are kits
comprising antibodies and antigen binding portions thereof of the
invention. The kits may include a label indicating the intended use
of the contents of the kit and optionally including instructions
for use of the kit in treating or diagnosing a disease associated
with ErbB3 upregulation and/or ErbB3 dependent signaling, e.g.,
treating a tumor. The term label includes any writing, marketing
materials or recorded material supplied on or with the kit, or
which otherwise accompanies the kit.
[0238] The present invention is further illustrated by the
following examples which should not be construed as further
limiting. The contents of Sequence Listing, figures and all
references, patents and published patent applications cited
throughout this application are expressly incorporated herein by
reference.
EXAMPLES
[0239] Materials and Methods
[0240] Throughout the examples, the following materials and methods
were used unless otherwise stated.
[0241] In general, the practice of the various aspects of the
present invention employs, unless otherwise indicated, conventional
techniques of chemistry, molecular biology, recombinant DNA
technology, immunology (especially, e.g., antibody technology), and
standard techniques in polypeptide preparation. See, e.g.,
Sambrook, Fritsch and Maniatis, Molecular Cloning: Cold Spring
Harbor Laboratory Press (1989); Antibody Engineering Protocols
(Methods in Molecular Biology), 510, Paul, S., Humana Pr (1996);
Antibody Engineering: A Practical Approach (Practical Approach
Series, 169), McCafferty, Ed., Irl Pr (1996); Antibodies: A
Laboratory Manual, Harlow et al., C. S. H. L. Press, Pub. (1999);
and Current Protocols in Molecular Biology, eds. Ausubel et al.,
John Wiley & Sons (1992). In vitro and in vivo model systems
for assaying HCV biology are described, for example, in Cell
culture models and animal models of viral hepatitis. Part II:
hepatitis C, Lab. Anim. (NY); 34(2):39-47 (2005) and in The
chimpanzee model of hepatitis C virus infections, ILAR J.;
42(2):117-26 (2001).
[0242] Heregulin
[0243] As used in these Examples and in the Figures, HRG refers to
the isoform of heregulin variously known as heregulin 1 beta 1,
HRG1-B, HRG-.beta.1, neuregulin 1, NRG1, neuregulin 1 beta 1,
NRG1-b1, HRG ECD, and the like. HRG is commercially available,
e.g., R&D Systems #377-HB-050/CF.
[0244] Cell Lines
[0245] All the cell lines used in the experiments described below
are obtained, as indicated, from American Type Culture Collection
(ATCC, Manassas, Va.), National Cancer Institute (NCI,
www.cancer.gov) e.g., from the Division of Cancer Treatment and
Diagnostics (DCTD), or from investigator(s), as indicated by
citation of publication.
[0246] MCF7--ATCC cat. No. HTB-22
[0247] T47D--ATCC cat. No. HTB-133
[0248] Colo357--Kolb, et al., (2006) Int. J. Cancer,
120:514-523.
[0249] Also see Morgan, et al., (1980) Int. J. Cancer,
25:591-598.
[0250] Du145--ATCC cat. No. HTB-81
[0251] OVCAR8--NCI
[0252] H1975--ATCC cat. No. CRL-5908
[0253] A549--ATCC cat. No. CCL-185
[0254] MALM-3M--NCI
[0255] AdrR--NCI
[0256] ACHN--ATCC cat. No. CRL-1611
[0257] Pulverization of Tumor Cells
[0258] A cryopulverizer (Covaris Inc) is used for the pulverization
of tumors. Tumors are stored in special bags (pre-weighed before
the addition of the tumor) and placed in liquid nitrogen while
handling them. For small tumors, 200 uL of Lysis buffer is first
added to the bag containing the tumor, frozen in liquid nitrogen
and then pulverized to improve the recovery of the tumor from the
bag. Pulverized tumors are transferred to 2 mL EPPENDORF tubes and
placed in liquid nitrogen until ready for further processing
[0259] Lysis of Tumor Cells
[0260] Tumors are lysed in Lysis buffer supplemented with protease
and phosphatase inhibitors. Lysis Buffer is added to the tumor
aliquots in a final concentration of about 62.5 mg/mL. Tumor
samples are homogenized by vortexing for 30 sec and incubating on
ice for about 30 min. The lysates are spun for about 10 min in
QIAGEN QIASHREDDER columns for further homogenization of the
samples. Cleared lysates are aliquoted into fresh tubes for further
processing.
[0261] BCA Assay
[0262] BCA assay (Pierce) is performed following the manufacturer's
protocol on all tumor samples. The total protein concentration (in
mg/mL) of each tumor sample is later used in the normalization of
the ELISA results
[0263] ELISA Assay
[0264] All ELISA reagents for the total and phospho-ErbB3 ELISAs
are purchased from R&D Systems as DUOSET kits. 96-well NUNC
MAXISORB plates are coated with 50 uL of an antibody and incubated
overnight at room temperature. Next morning, plates are washed 3
times with 1000 .mu.l/well in the BIOTEK plate washer with
Dulbecco's phosphate buffered saline without calcium or magnesium
(PBS) with added Tween detergent (PBST) (0.05% Tween-20). Plates
are subsequently blocked for about an 1 hr at room temperature with
2% BSA in PBS. The plates are washed 3 times with 1000 .mu.l/well
in the BIOTEK plate washer with PBST (0.05% Tween-20). 50 .mu.L of
cell lysates and standards diluted in 50% Lysis buffer and 1% BSA
are used in duplicates for further processing. Samples are
incubated for 2 hrs at 4.degree. C. on a plate shaker and washed as
before. About 50 .mu.l of a detection antibody diluted in 2% BSA,
PBST is added and incubated for about 1 hr at room temperature. For
phosphor-ErbB3, the detection antibody is directly conjugated to
horseradish peroxidase (HRP) and incubated for 2 hrs at room
temperature. The plate is washed as before. About 50 .mu.l of
Streptavidin-HRP is added and incubate for 30 min at room
temperature (except for pErbB3). The plates are washed as before.
About 50 .mu.L of SUPERSIGNAL ELISA Pico (Thermo Scientific)
substrate is added and the plate is read using a FUSION plate
reader. The data are analyzed using EXCEL. Duplicate samples are
averaged and the error bars are used to represent the standard
deviation between the two replicates.
Example 1: Production of Antibodies Using Phage Display
[0265] In order to obtain human anti-ErbB3 antibodies referred to
herein as Ab #6, Ab #3, Ab #14, Ab #17, and Ab #19, a human
Fab-phage library including a unique combination of immunoglobulin
sequences obtained from human donors (Hoet et al., supra) is
initially screened for ErbB3 binders.
[0266] Using purified ErbB3 and a Chinese hamster ovary (CHO) cell
line expressing cell surface ErbB3, 73 unique Fab sequences from
the library (obtained using the methods described above or minor
variations thereof) were identified. These 73 clones are then
reformatted as Fab only without the phage. Using high throughput
methods, these Fabs are expressed on a small scale and tested for
binding using ELISA and the FLEXCHIP method which is a
high-throughput surface plasmon resonance (SPR) technology. The 73
Fabs without the phage are spotted on a chip surface and the
binding kinetics and epitope blocking to a ErbB3-his fusion target
protein or a ErbB3-Fc protein (R & D Systems) are measured. The
equilibrium binding constant and on/off rates for the Fabs are
calculated from the data obtained.
[0267] Binding of the various Fabs to MALME-3M cells is next
examined using about 500 nM of the Fabs and a 1:750 dilution of a
goat anti-human Alexa 647 secondary antibody. As shown in FIGS. 1A
and 1B, data obtained using the methods described above or minor
variations thereof indicate that several candidate Fabs exhibited
appreciable staining of MALME-3M cells.
Example 2: Optimization of Anti-ErbB3 Fabs
[0268] Subsequent to the identification of Fabs which block the
binding of ErbB3 ligand, heregulin, to ErbB3, the VH and VL
sequences of the Fabs are codon-optimized as follows.
[0269] The VH and VL regions are reformatted using expression
constructs for expression as an IgG1 or IgG2 isotype. The
constructs include a SELEXIS backbone which has a cassette designed
for substitution of the appropriate heavy and light chain
sequences. The SELEXIS vectors include a CMV promoter and a
matching poly-A signal.
[0270] The nucleic acid sequences for the codon-optimized VH and VL
of Ab #6 (obtained using the methods described above or minor
variations thereof) are set forth in SEQ ID NOs:25 and 26,
respectively, and those for Ab #3 are set forth in SEQ ID NOs:27
and 28, respectively, as shown in FIG. 22.
Example 3: Binding Affinity for ErbB3
[0271] The dissociation constants of the anti-ErbB3 antibodies are
measured using two independent techniques, i.e., a Surface Plasmon
Resonance Assay and a cell binding assay using MALME-3M cells.
[0272] Surface Plasmon Resonance Assay
[0273] The Surface Plasmon Resonance Assay (e.g., a FLEXCHIP assay)
is performed substantially as described in Wassaf et al. (2006)
Analytical Biochem., 351:241-253, in a BIACORE 3000 instrument or
the like using recombinant ErbB3 as the analyte and the subject
antibody as the ligand. The K.sub.D value is calculated based on
the formula K.sub.D=K.sub.d/K.sub.a.
[0274] The K.sub.D values of Ab #6 and Ab #3, respectively, as
measured using the Surface Plasmon Resonance Assay using the
methods described above or minor variations thereof, are depicted
in FIGS. 2A and 2B. Ab #6 exhibited a K.sub.D value of about 4 nM
and Ab #3 exhibited a K.sub.D value of about 8 nM. Furthermore,
surface plasmon resonance demonstrated that Ab #6 competes with HRG
for binding to ErbB3.
[0275] Cell Binding Assay
[0276] The cell binding assay for determining the K.sub.D values of
Ab #6 and Ab #3 is performed as follows.
[0277] MALME-3M cells are detached with 2 mLs trypsin-EDTA+2 mLs
RMPI+5 mM EDTA at room temperature for 5 minutes. Complete RPMI (10
mLs) is added immediately to the trypsinized cells, resuspended
gently and spun down in a Beckman tabletop centrifuge at 1100 rpm
for 5 minutes. Cells are resuspended in BD stain buffer (PBS+2%
FBS+0.1% sodium azide, Becton Dickinson) at a concentration of
2.times.10.sup.6 cells per ml and 50 .mu.l (1.times.10.sup.5 cells)
aliquots are plated in a 96-well titer plate.
[0278] A 150 .mu.l solution of 200 nM anti-ErbB3 antibody (Ab #6 or
Ab #3) in BD stain buffer is prepared in an EPPENDORF tube and
serially diluted 2-fold into 75 .mu.l BD stain buffer. The
concentrations of the diluted antibody ranged from 200 nM to 0.4
nM. 50 .mu.l aliquots of the different protein dilutions are then
added directly to the 50 ul cell suspension giving the final
concentrations of 100 nM, 50 nM, 25 nM, 12 nM, 6 nM, 3 nM, 1.5 nM,
0.8 nM, 0.4 nM and 0.2 nM of the antibody.
[0279] Aliquoted cells in the 96-well plate are incubated with the
protein dilutions for 30 minutes at room temperature on a platform
shaker and washed 3 times with 300 .mu.l BD stain buffer. Cells are
then incubated with 100 .mu.l of a 1:750 dilution of Alexa
647-labeled goat anti-human IgG in BD stain buffer for 45 minutes
on a platform shaker in the cold room. Finally, cells are washed
twice, pelleted and resuspended in 250 .mu.l BD stain buffer+0.5
.mu.g/ml propidium iodide. Analysis of 10,000 cells is done in a
FACSCALIBUR flow cytometer using the FL4 channel. MFI values and
the corresponding concentrations of the anti-ErbB3-antibodies are
plotted on the y-axis and x-axis, respectively. The K.sub.D of the
molecule is determined using GraphPad PRISM software using the
one-site binding model for a non-linear regression curve.
[0280] The K.sub.D value is calculated based on the formula
Y=Bmax*X/K.sub.D+X (Bmax=fluorescence at saturation. X=antibody
concentration. Y=degree of binding). As calculated from the data
shown in FIGS. 2C and 2D, Ab #6 and Ab #3 had K.sub.D values of
about 4 nM and 1.3 nM, respectively, were obtained (using the
methods described above or minor variations thereof) in a cell
binding assay using MALME-3M cells.
[0281] KinExA.RTM. Assay
[0282] In additional experiments to study the binding kinetics of
Ab #6, a Kinetic Exclusion Assay (KinExA.RTM.) is used to determine
the association and dissociation rates for Ab #6. An association
rate of 1.43.times.10.sup.5 M.sup.-1s.sup.-2 and a dissociation
rate of 1.10.times.10.sup.-4 s.sup.-1 was measured using a
KinExA.RTM. instrument (Sapidyne Instruments, Boise, Id.), with the
dissociation constant (K.sub.d) determined to be 769 pM.
Example 4: Binding Specificity/Epitope Binding for ErbB3
[0283] The binding specificity of an IgG2 isotype of Ab #6 to ErbB3
is assayed using ELISA as follows. Identification of the epitope
bound by Ab #6 is also analyzed. 96-well NUNC MAXISORB plates are
coated by overnight incubation at room temperature with 50
.mu.l/well of 5 .mu.g/ml of individual proteins. The proteins are
recombinant human EGFR ectodomain, BSA, recombinant human ErbB3
ectodomain and TGF-.alpha.. The next morning, plates are washed 3
times with 1000 .mu.l/well of PBST (0.05% Tween-20) in the BIOTEK
plate washer. The wells are blocked for 1 hr at room temperature
with 2% BSA in PBS and washed again as before. About 50 .mu.L of
the Ab #6 is added at several dilutions (1 .mu.M and serial 2 fold
dilutions) in 2% BSA, PBST. All samples are run in duplicate and
incubated for 2 hrs at 4.degree. C. on a plate shaker. The plates
are washed again as before. 50 .mu.l of human IgG-Fc detection
antibody (HRP conjugated, Bethyl Laboratories, Inc; 1:75000
dilution in 2% BSA, PBST) is added and the plates are incubated for
1 hr at room temperature. The plates are washed again as before. 50
.mu.L of SUPERSIGNAL ELISA Pico substrate is added and the plate is
read on the FUSION plate reader (Packard/Perkin Elmer). The data is
analyzed using the EXCEL program. Duplicate samples are averaged
and the error bars represent the standard deviation between the two
replicates.
[0284] As shown in FIG. 3, data obtained using the methods
described above or minor variations thereof indicate that Ab #6
bound recombinant ErbB3 in an ELISA, but did not show any
appreciable binding to EGFR, BSA or TGF-.alpha..
[0285] A DNA fragment encoding an ErbB3 ectodomain fragment
corresponding to amino acid residues 1-183 of mature ErbB3 (SEQ ID
NO: 73) is cloned into the yeast display vector pYD2 (a modified
version of pYD1 (Invitrogen) with a stop codon engineered in front
of the His tag) between the Nhe and BsiWI restriction sites. The
plasmid is transformed into the yeast strain EBY100 (Invitrogen)
and clones containing the plasmid selected on Trp-selective medium.
The clone is grown in glucose containing medium overnight at
30.degree. C. and expression of the ErbB3 truncation mutant is
induced by transfer to a galactose-containing medium for 2 days at
18.degree. C. Yeast displaying the ErbB3 truncation mutant are
stained with 50 nM of Ab #6, followed by a goat anti-human antibody
labeled with Alexa dye-647. A separate sample is stained with the
goat anti-human antibody only to show that there is no non-specific
binding to yeast of the secondary antibody. Analysis is performed
by flow cytometry on the FACSCALIBUR cell sorter (BD
Biosciences).
[0286] As shown by the data (obtained using the methods described
above or minor variations thereof) presented in FIG. 39, Ab #6
bound to the ErbB3 ectodomain, i.e., amino acid residues 1-183 of
mature ErbB3 (SEQ ID NO: 73).
Example 5: Downregulation of Total ErbB3 on Tumor Cells
[0287] The ability of Ab #6 to downregulate ErbB3 expression both
in vitro and in vivo in tumor cells is tested as follows.
[0288] MALME-3M cells are seeded in 96 well tissue culture plates
and grown in RPMI-1640 media supplemented with antibiotics, 2 mM
L-glutamine and 10% fetal bovine serum (FBS) for 24 hours at
37.degree. C. and 5% carbon dioxide. Media are then switched to the
same medium without FBS and with and without the antibody at
concentrations of 1 uM, 250 nM, 63 nM, 16 nM, 4.0 nM, 1.0 nM, 240
pM, 61 pM and 15 pM. Medium containing no FBS or antibody is used
as control. Cells are grown for 24 hours at 37.degree. C. and 5%
carbon dioxide, washed with cold PBS, then harvested with mammalian
protein extract (MPER) lysis buffer (Pierce, 78505) to which 150 mM
NaCl, 5 mM sodium pyrophosphate, 10 uM bpV (phen), 50 uM
phenylarsine, 1 mM sodium orthovanadate, and protease inhibitor
cocktail (Sigma, P2714) is added. Cell lysates are diluted two-fold
with 4% bovine serum albumin in PBST (0.1% tween-20), then analyzed
by ELISA with mouse anti-human ErbB3 capture antibody and
biotinylated mouse anti-human ErbB3 secondary detection antibody.
Signal is generated with streptavidin conjugated to
horseradish-peroxidase reacted with SUPERSIGNAL ELISA Pico
chemiluminescent substrate (Pierce, 37070). ELISAs are quantitated
using a luminometer.
[0289] As shown in FIG. 4, data obtained using the methods
described above or minor variations thereof indicate that Ab #6
decreased total ErbB3 levels by about 46.9% in MALME-3M cells in
vitro, as measured by ELISA.
[0290] In a further experiment, the downregulation of ErbB3
receptors on MALME-3M cells using IgG1 and IgG2 isotypes of Ab #6
is examined using FACS analysis. MALME-3M cells are trypsinized
from a 15 cm dish and washed once with RPMI+10% FBS. Cell pellets
are resuspended at a density of 1.times.10.sup.6 cells per ml. Two
aliquots of 2.times.10.sup.5 cells are added to separate wells in a
12-well tissue culture plate and each resuspended in a final volume
of 800 ul RPMI+10% FBS. To one well, Ab #6 IgG1 or Ab #6IgG2
isotype is added to a final concentration of 100 nM (treated
sample) and to the other well, an equivalent volume of PBS
(untreated sample) is added.
[0291] The following day, treated and untreated cells are
trypsinized, washed and incubated with 100 nM of Ab #6 in BD stain
buffer for 30 minutes on ice. Cells are washed twice with 1 ml BD
stain buffer and incubated with 100 ul of a 1:500 dilution of Alexa
647-labeled goat anti-human Alexa 647 for 45 minutes on ice. Cells
are then washed and resuspended in 300 ul BD stain buffer+0.5 ug/ml
propidium iodide. Analysis of 10,000 cells is done in a FACSCALIBUR
flow cytometer using the FL4 channel.
[0292] As shown in FIGS. 5A and 5B, data obtained using the methods
described above or minor variations thereof indicate that both IgG1
and IgG2 isotypes of Ab #6 downregulated ErbB3 on MALME-3M cells by
about 62% and about 66%, respectively.
[0293] In order to determine whether this downregulation of ErbB3
is due to internalization of the ErbB3 receptor on the surface of
MALME-3M cells, a cell surface fluorescence quenching assay is
preformed. MALME-3M cells are plated overnight on 6-well plates
(0.2.times.10.sup.6 per well) in RPMI+10% FBS. The following day,
old medium is removed and cells are preincubated for 60 minutes on
ice in RPMI+2% FBS containing 100 nM of Ab #6 conjugated to the
fluorescent dye Alexa 488. Cells are then returned to a 37.degree.
C. incubator and incubated for 0.5 h, 2 h or 24 h. At the end of
each timepoint, cells are trypsinized, washed with PBS+2% BSA+0.1%
sodium azide (FACS stain buffer) and stored on ice until all
samples are ready. For a 0 h timepoint, cells are immediately
trypsinized after the 60 minute preincubation and stored on ice.
After cells are harvested from all timepoints, samples from each
timepoint are divided into two tubes. One set of tubes is incubated
with 25 ug/ml anti-Alexa 488 antibody for 60 minutes on ice to
quench any fluorescence source (i.e., Alexa 488-conjugated Ab #6)
on the cell surface. The other set of tubes is left unquenched and
stored on ice during this incubation period. At the end of the
quenching period, cells are washed twice with FACS stain buffer and
resuspended in a final volume of 300 ul FACS stain buffer. For each
sample 10,000 events are collected and analyzed with a FACSCALIBUR
flow cytometer. This protocol gives an indication of what
proportion of AB #6 (as measured by fluorescence) remains on the
cell surface (indicated by the differential between the
fluorescence of the quenched and unquenched cells at each
timepoint) and how much is internalized (indicated by the level of
fluorescence of quenched cells).
[0294] As shown in FIG. 6, downregulation of ErbB3 in the presence
of Ab #6 was measured at 0 hour (FIG. 6A), 0.5 hour (FIG. 6B), 2
hour (FIG. 6C) and 24 hours (FIG. 6D). As shown in FIG. 6A-6D, of
the cell surface ErbB3 receptors were downregulated by about 50%
after about 30 minutes and were downregulated by about 93% at about
24 hours.
[0295] The ability of Ab #6 to cause ErbB3 downregulation in vivo
in melanoma cells was also examined as follows.
[0296] T-cell deficient nu/nu mice (3-4 week old female mice
originated at NIH; outbred; albino background) were purchased from
Charles River Labs (Wilmington, Mass.). MALME-3M cells for
implantation were grown in culture (RPMI media, 10% FBS,
L-glutamine and antibiotics, 37.degree. C., 5% CO2) to about 80%
confluency before harvesting. Cells were kept on ice until
implantation. Mice were implanted via subcutaneous injection with
100 ul MALME-3M cells (3.5.times.10.sup.6 cells in PBS) via
subcutaneous injection on the right flank and allowed to recover
while being monitored for initial tumor growth.
[0297] The tumors were measured (length by width) by digital
caliper and the mice were pretreated with murine IgG2a (Sigma,
M7769--5 mg) by intravenous injection to block in vivo depletion of
tested antibodies by murine Fc receptors. Mice were dosed
intra-peritoneally every other day with either 15 .mu.g or 100
.mu.g of Ab #1, Ab #6, Ab #11, and Ab #13, each separately in both
IgG1 and IgG2 form, and tumors were measured three times per week
and the measurements recorded in a Microsoft EXCEL spreadsheet.
[0298] Final tumor measurements (L.times.W) were taken, the mice
were euthanized by CO2 asphyxiation and tumors were excised, snap
frozen in liquid nitrogen, and were stored at -80.degree. C. (for
biochemical analysis). Final tumor measurements were analyzed and
graphed by tumor area and tumor volume as described, for example,
in Burtrum et al., (2003) Cancer Res., 63:8912-8921. The data was
also analyzed by "normalized` and "non-normalized" means for both
tumor volume and tumor area. For the "normalization" of the data,
at each time point of measurement, each tumor in each group was
divided by the initial tumor size determined by caliper
measurement.
[0299] As shown in FIG. 7, PBS was used as a control and the
various antibodies tested in this xenograft model included Ab #11
in IgG2 isotype and each of AB #1, Ab #6, and Ab #13 in both IgG1
and IgG2 isotypes. Of these, only Ab #6 caused significant
downregulation of total ErbB3, an effect that was seen as soon as
24 hours post-injection in tumors treated with either IgG1 or IgG2
isotype versions of Ab #6.
[0300] In a further experiment, the ability of Ab #6 to
downregulate ErbB3 in AdrR xenografts in vivo was examined.
[0301] Briefly, the samples were pulverized in a cryopulverizer
(Covaris Inc). Tumors were stored in special bags (pre-weighed
before the addition of the tumor) and placed in liquid nitrogen
while handling them. For small tumors, 200 .mu.L of Lysis buffer
was first added to the bag with the tumor, frozen in liquid
nitrogen and then pulverized to improve the recovery of the tumor
from the bag. Pulverized tumors were transferred to 2 ml EPPENDORF
tubes and placed in liquid nitrogen until lysed. Tumors were lysed
in Lysis buffer supplemented with protease and phosphatase
inhibitors. Lysis Buffer was added to the tumor aliquots in a final
concentration of 62.5 mg/ml. Tumor samples were homogenized by
vortexing for 30 seconds and letting them sit on ice for 30 min.
The lysates were spun for 10 minutes in QIAGEN QIASHREDDER columns
for further homogenization of the samples. Cleared lysates were
aliquoted into fresh tubes.
[0302] The BCA assay is performed as set forth substantially as
described in the materials and methods section supra.
[0303] The total levels of ErbB3 were determined by ELISA. The
ELISA reagents were purchased from R&D Systems as DUOSET kits.
96-well NUNC MAXISORB plates were coated with 50 .mu.l of
respective capture antibody and incubated overnight at room
temperature. The next morning, the plates were washed 3 times with
1000 .mu.l/well in a BIOTEK plate washer with PBST (0.05% Tween-20)
and then blocked for 1 hour at room temperature with 2% BSA in PBS.
The plates were then washed again as before. Lysates (50 .mu.l) and
standards were diluted in 50% Lysis buffer and 1% BSA; all samples
were run in duplicate. Plates were incubated for 2 hours at
4.degree. C. on a plate shaker and then washed again as before.
Fifty microliters of detection antibody diluted in 2% BSA, PBST was
added and the plates were incubated for 1 hour at room temperature.
Plates were washed again as before. Fifty microliters of
Streptavidin-HRP was added and the plates were incubated for 30
minutes at room temperature. Plates were washed again as before.
Fifty microliters of SUPERSIGNAL ELISA Pico substrate was added and
readout was performed on a Fusion plate reader. Data was analyzed
using Microsoft EXCEL. Duplicate samples were averaged and the
error bars represent the standard deviation between the two
replicates.
[0304] The results of this experiment are shown in FIG. 8. As shown
in FIG. 8, Ab #6 downregulated ErbB3 in AdrR xenografts in
vivo.
Example 6: Inhibition of Tumor Cell Proliferation
[0305] The ability of Ab #6 to inhibit cellular proliferation of
cells expressing ErbB3 (e.g., cancer cells) is examined as
follows.
[0306] MALME3M, ACHN and NCI/AdrR cells are seeded in 96 well
tissue culture plates and grown in RPMI-1640 media supplemented
with antibiotics, 2 mM L-glutamine and 10% FBS for 24 hours at 37
degrees Celsius and 5% carbon dioxide. Media are then switched to
RPMI-1640 media with antibiotics and 2 mM L-glutamine without FBS
in the presence or absence of Ab #6 at 1 uM, 250 nM, 63 nM, 16 nM,
4.0 nM, 1.0 nM, 240 pM, 61 pM and 15 pM concentrations. Cells are
grown for 96 hours at 37.degree. C. and 5% carbon dioxide, then
harvested with CellTiter-Glo.RTM. Luminescent Cell Viability Assay
(Promega, G7573) and analyzed on a luminometer. Media containing no
serum and antibody is used as control.
[0307] As shown in FIGS. 9, 10 and 11, data obtained using the
methods described above or minor variations thereof indicate that
Ab #6 inhibited proliferation of MALME-3M cells (FIG. 9), AdrR
ovarian cancer cells (FIG. 10) and ACHN cells (FIG. 11) which
express ErbB3. Specifically, Ab #6 inhibited proliferation of
MALME-3M cells by about 19.6%, as measured using the
CellTiter-Glo.RTM. assay, and inhibited proliferation of AdrR
ovarian cancer cells by about 30.5%. Also, as shown in FIG. 11, Ab
#6 inhibited proliferation of ACHN cells by about 25.4%.
Example 7: Inhibition of ErbB3 Phosphorylation in Tumor Cells
[0308] The ability of Ab #6 to inhibit ErbB3 phosphorylation in
vivo is examined as follows.
[0309] The samples are pulverized substantially as described in
Example 5 supra, with respect to FIG. 8. The BCA assay is performed
substantially as set forth in the Materials and Methods section
supra, and the ELISA assay is performed substantially as described
in Example 5 supra with respect to FIG. 8.
[0310] The results of this experiment (obtained using the methods
described above or minor variations thereof) are shown in FIG. 12.
As shown in FIG. 12, Ab #6 significantly inhibited ErbB3
phosphorylation in AdrR ovarian xenografts in vivo, as measured by
the amount of phosphorylated ErbB3 (pErbB3) in ng/mg of total
protein.
[0311] Inhibition of BTC or HRG induced ErbB3 phosphorylation by Ab
#6 is examined in vitro as follows.
[0312] Ovarian AdrR cells are preincubated with Ab #6 for 30
minutes prior to stimulation with 50 mM BTC, 10 mM HRG or 333 nM
TGF-.alpha.. Following pre incubation, the media are removed and
the cells are stimulated for 5 minutes at 37.degree. C., 5% CO2
with 50 nM BTC or 333 nM TGF-.alpha.. HRG controls (5 minutes, 5
nM), 10% serum and 0% serum controls are also used. Cells are
washed with 1.times. cold PBS and lysed in 30 .mu.l cold lysis
buffer (M-PER buffer (Pierce) plus sodium vanadate (NaVO4, Sigma),
2-glycerophosphate, phenylarsine oxide, BpV and protease
inhibitors) by incubating on ice for 30 minutes. Lysates are stored
overnight at -80.degree. C.
[0313] As shown in FIGS. 13A-13C, data obtained using the methods
described above or minor variations thereof indicate that Ab #6
significantly inhibited both betacellulin and heregulin-mediated
phosphorylation of ErbB3.
[0314] In a further experiment, the ability of Ab #6 to inhibit
ErbB3 phosphorylation in ovarian tumor cell lines OVCAR 5 and OVCAR
8 was examined as follows.
[0315] The OVCAR 5 and OVCAR 8 cell lines are obtained from the
National Cancer Institute, Division of Cancer Treatment and
Diagnostics ("DCTD"). The ELISA is performed as substantially as
described in the Materials and Methods section supra.
[0316] The results of this experiment (obtained using the methods
described above or minor variations thereof) are depicted in FIGS.
14A and 14B. As there depicted, Ab #6 inhibited ErbB3
phosphorylation in both OVCAR 5 and OVCAR 8 ovarian cancer cell
lines.
[0317] As discussed above, Ab #6 inhibits betacellulin-mediated
phosphorylation of ErbB3. In order to investigate whether
betacellulin-mediated phosphorylation of ErbB3 occurs through ErbB1
or ErbB3, the following experiment was performed.
[0318] AdrR cells or MALME-3M cells (1.times.10.sup.5) are
pre-incubated with 25 .mu.M of anti-ErbB3 Ab #6 or 25 .mu.M of
cetuximab (anti-ErbB1) in 50 .mu.l BD stain buffer for 30 minutes
on ice. After 30 minutes, 50 .mu.l of 400 nM biotinylated BTC is
added to the cells and incubated for another 30 minutes on ice.
This yields a final concentration of 12.5 .mu.M antibodies and 200
nM BTC. Cells are then washed twice with 500 .mu.l BD stain buffer
and incubated with 100 .mu.l of a 1:200 dilution of streptavidin-PE
(PE=phycoerythrin) (Invitrogen) in BD stain buffer for 45 minutes.
Finally, cells are washed twice, resuspended in 300 .mu.l of BD
stain buffer and analyzed in a FACSCALIBUR flow cytometer. As a
positive control, 1.times.10.sup.5 AdrR or MALME-3M cells are
incubated with 200 nM BTC for 30 minutes on ice, washed twice and
incubated with a 1:200 dilution of streptavidin-PE for 45 minutes.
To assess background staining from the streptavidin-PE conjugate,
cells are incubated with 100 .mu.l of a 1:200 dilution of
streptavidin-PE only for 45 minutes.
[0319] The results of this experiment (obtained using the methods
described above or minor variations thereof) are depicted in FIGS.
15A-15C. As shown in FIG. 15A, BTC does not show any appreciable
binding to ErbB1 negative MALME-3M cells. However, as depicted in
FIGS. 15B and 15C, BTC does show binding to ErbB1 positive AdrR
cells.
[0320] Also, as shown in FIGS. 15B and 15C, binding to ErbB1 was
blocked by cetuximab (Erbitux.RTM.), which is an anti-EGFR antibody
which specifically binds EGFR and was included as a control to
demonstrate that EGF-like ligands bind to EGFR, and which is
described in e.g., Adams et al. (2005), Nature Biotechnology 23,
1147-1157.
Example 8: Inhibition of Heregulin-Mediated Signaling in Tumor
Cells
[0321] The ability of Ab #6 to inhibit heregulin-mediated tumor
cell signaling is investigated as follows.
[0322] MALME-3M cells and OVCAR8 cells are separately seeded in 96
well tissue culture plates (35,000 cells per well) and grown in
RPMI-1640 media supplemented with antibiotics, 2 mM L-glutamine and
10% FBS for 24 hours at 37.degree. C. and 5% carbon dioxide. Cells
are serum-starved in RPMI-1640 media with antibiotics and 2 mM
L-glutamine for 24 hours at 37.degree. C. and 5% carbon dioxide.
Cells are pre-treated with and without the anti-ErbB3 antibody
(IgG2 isotype of Ab #6) at 250 nM, 63 nM, 16 nM, 4.0 nM, 1.0 nM,
240 pM, 61 pM and 15 pM concentrations for 30 minutes then
stimulated with 5 nM HRG for 10 minutes at 37.degree. C. and 5%
carbon dioxide. Controls are HRG without added antibody and
untreated cells (no HRG and no Ab). Cells are washed with cold PBS
then harvested with mammalian protein extract (M-PER) lysis buffer
(Pierce, 78505) containing 150 mM NaCl, 5 mM sodium pyrophosphate
(Sigma, 221368-100G), 10 uM bpV(phen) (Calbiochem, 203695), 50
.mu.M oxophenylarsine (Calbiochem, 521000), 1 mM sodium
orthovanadate (Sigma, 56508-10G), and protease inhibitor cocktail
(Sigma, P2714). Cell lysates are diluted two-fold with 4% bovine
serum albumin in PBST (0.2% tween-20), then analyzed by ELISA for
phosphorylation of either ErbB3, or AKT (a downstream effector of
ErbB3).
[0323] In order to test for AKT phosphorylation, lysates are run on
an ELISA plate with a capture antibody specific to AKT and
biotinylated detection antibody specific to phospho-serine 473 of
phospho-AKT (pAKT). Signal is generated with streptavidin
conjugated to horseradish-peroxidase reacted with SUPERSIGNAL ELISA
Pico chemiluminescent substrate (Pierce, 37070). In order to assay
for ErbB3 phosphorylation, lysates are run on an ELISA plate with a
capture antibody specific for ErbB3 and an anti-phosphotyrosine
detection antibody conjugated to horseradish-peroxidase. This is
then reacted with the same chemiluminescent substrate. Luminescent
signal on the ELISAs is measured using a luminometer.
[0324] As shown by the data presented in FIGS. 16A-D (obtained
using the methods described above or minor variations thereof), Ab
#6 is a potent inhibitor of heregulin-mediated signaling in
MALME-3M cells and OVCAR8 cells, as measured by decreased
phosphorylation of ErbB3 (FIG. 16A) and AKT (FIG. 16B). Notably,
essentially complete inhibition of the phosphorylation of each of
AKT and ErbB3 by Ab #6 is observed.
Example 9: Inhibition of Ovarian, Prostate, and Pancreatic Tumor
Growth
[0325] To assess the efficacy of Ab #6 in vivo, several xenograft
models of human cancer are established in nude mice and the
inhibition of tumor growth is assessed at multiple doses of Ab #6.
For example, T-cell deficient nu/nu mice (3-4 week old female mice
originated at NIH; outbred; albino background) are purchased from
Charles River Labs (Wilmington, Mass.) for xenograft studies. AdrR
cells for implantation are grown in culture (RPMI media, 10% FBS,
L-glutamine and antibiotics, 37.degree. C., 5% CO2) to about 85%
confluency before harvesting. Cells are kept on ice until
implantation. Mice are implanted via subcutaneous injection with
100 .mu.l AdrR cells (6.times.10.sup.6 cells in PBS) on the right
flank and allowed to recover while being monitored for initial
tumor growth.
[0326] Tumors are measured (length by width) by digital caliper and
the mice are dosed with IgG2a (Sigma, M7769--5 MG) by intravenous
injection. Mice are dosed intra-peritoneally every third day with
either 30 .mu.g or 300 .mu.g of Ab #6 and tumors are measured three
times per week and recorded in a Microsoft Excel spreadsheet.
[0327] Final tumor measurements (L.times.W) are taken, the mice are
euthanized by CO2 asphyxiation and tumors are excised, snap frozen
in liquid nitrogen, and are stored at -80.degree. C. (for
biochemical analysis). Final tumor measurements are analyzed and
graphed by tumor area and tumor volume, as described in Burtrum et
al., supra. The data are also analyzed by "normalized` and
"non-normalized" means for both tumor volume and tumor area. For
the "normalization" of the data, at each time point of measurement,
each tumor in each group is divided by the initial tumor size
determined by caliper measurement.
[0328] The data (obtained using the methods described above or
minor variations thereof) from three different models derived from
human tumor cell lines, AdrR (ovarian), Du145 (prostate) and OvCAR8
(ovarian) data are shown in FIGS. 17A-C and Colo357 (pancreatic)
xenograft study data are shown in FIG. 17D. In each of these
figures, the right hand panel shows serum levels achieved at
specified dosages of Ab #6 and the left hand panel shows tumor
volume changes with different treatments. The data from these
studies demonstrate that a 300 ug dose of Ab #6 every three days
(Q3d) results in significant inhibition of tumor growth (p<0.05
for multiple time points during the studies). Moreover, this
inhibitory effect of Ab #6 is further elevated when the dose is
increased to 600 ug Q3d, in the Du145 prostate cancer model as well
as a renal (ACHN) and a pancreatic carcinoma (COLO357) xenograft
model. However, further elevating the dose to 1500 ug Q3d did not
result in increased efficacy (OvCAR8-FIG. 17C; COLO357-FIG. 17D)
suggesting that the 600 ug is saturating for tumor growth
inhibition. Pharmacokinetic (PK) analyses of the serum from the
animals from these studies demonstrate a dose-dependent increase in
the serum retention of Ab #6. Similarly, biochemical analysis of
the intra-tumoral levels of Ab #6 from these different studies
showed a dose-dependent range of 0 to .about.6 pg Ab #6/ug of total
tumor lysate.
Example 10: Inhibition of Binding of ErbB3 Ligands to ErbB3 on
Tumor Cells
[0329] In a further experiment, the specificity of Ab #6 and Ab #3
to inhibit the binding of ErbB3 ligands to ErbB3, and not EGF-like
ligands to EGFR, is investigated as follows.
[0330] In one experiment, the specificity of Ab #6 and a Fab
version of Ab #3 (Ab/Fab #3) to inhibit the binding of ErbB3
ligands (e.g., heregulin and epiregulin) to ErbB3 is investigated
in order to investigate the ability of Ab #6 and Ab/Fab #3 to
inhibit the binding of heregulin to ErbB3.
[0331] MALME3M cells (1.times.10.sup.5) are incubated with 10 .mu.M
of an anti-ErbB3 antibody (e.g., Ab #6 or Ab/Fab #3) in 50 .mu.l BD
stain buffer for 30 minutes on ice. After 30 minutes, 50 .mu.l of
40 nM biotinylated heregulin EGF is added to the cells and
incubated for another 10 minutes on ice. This yields a final
concentration of 5 .mu.M antibody and 20 nM heregulin EGF. Cells
are then washed twice with 500 .mu.l BD stain buffer and incubated
with 100 .mu.l of a 1:200 dilution of streptavidin-PE
(PE=phycoerythrin) (Invitrogen) in BD stain buffer for 45 minutes.
Finally, cells are washed twice, resuspended in 300 .mu.l of BD
stain buffer and analyzed in a FACSCALIBUR flow cytometer. As a
positive control, 1.times.10.sup.5 MALME3M cells are incubated with
20 nM heregulin EGF for 10 minutes on ice, washed twice and
incubated with a 1:200 dilution of streptavidin-PE for 45 minutes.
In order to assess background staining from the streptavidin-PE
conjugate, 1.times.10.sup.5 MALME3M cells are incubated with 100
.mu.l of a 1:200 dilution of streptavidin-PE only for 45
minutes.
[0332] The results of this experiment (obtained using the methods
described above or minor variations thereof) are shown in FIGS. 18A
and 18B. As depicted in FIGS. 18A and 18B, both Ab #6 and Ab/Fab #3
are able to inhibit heregulin binding to ErbB3.
[0333] Similarly, the ability of Ab #6 to inhibit the binding of
another ErbB3-ligand, epiregulin, to ErbB3, is examined as
follows.
[0334] AdrR cells (1.times.10.sup.5) are pre-incubated with 25
.mu.M of the anti-ErbB3 antibody, Ab #6, or 25 .mu.M of the
anti-ErbB1 antibody cetuximab, or with no added antibody (as
control) in 50 .mu.l BD stain buffer for 30 minutes on ice. After
30 minutes, 50 .mu.l of 2 biotinylated Epi is added to the cells
and incubated for another 30 minutes on ice. This yields a final
concentration of 12.5 .mu.M antibodies and 1 .mu.M Epi. Cells are
then washed twice with 500 .mu.l BD stain buffer and incubated with
100 .mu.l of a 1:200 dilution of streptavidin-PE (PE=phycoerythrin,
a fluorescent protein) (Invitrogen) in BD stain buffer for 45
minutes. Finally, cells are washed twice, resuspended in 300 .mu.l
of BD stain buffer and analyzed in a FACSCALIBUR flow cytometer. As
a positive control, 1.times.10.sup.5 AdrR cells are incubated with
1 .mu.M Epi for 30 minutes on ice, washed twice and incubated with
a 1:200 dilution of streptavidin-PE for 45 minutes. To assess
background staining from the streptavidin-PE conjugate, cells are
incubated with 100 .mu.l of a 1:200 dilution of streptavidin-PE
only for 45 minutes.
[0335] The results of this experiment (obtained using the methods
described above or minor variations thereof) are depicted in FIGS.
19A and 19B. As shown in FIG. 19A, epiregulin binds to ErbB3
positive AdrR cells. Further, as shown in FIG. 19B, this binding is
inhibited by both cetuximab and Ab #6, suggesting that epiregulin
may bind to both EGFR and ErbB3.
[0336] A further experiment is performed to investigate whether Ab
#6 is able to inhibit the binding of an EGF-like ligand (e.g.,
HB-EGF) to tumor cells.
[0337] AdrR cells (1.times.10.sup.5) are pre-incubated with 2504 of
Ab #6 or 25 .mu.M of cetuximab (as control) in 50 .mu.l BD stain
buffer for 30 minutes on ice. After 30 minutes, 50 .mu.l of 400 nM
biotinylated HB-EGF is added to the cells and incubated for another
30 minutes on ice. This yields a final concentration of 12.5 .mu.M
antibodies and 200 nM HB-EGF. Cells are then washed twice with 500
.mu.l BD stain buffer and incubated with 100 .mu.l of a 1:200
dilution of streptavidin-PE (PE=phycoerythrin) (Invitrogen) in BD
stain buffer for 45 minutes. Finally, cells are washed twice,
resuspended in 300 .mu.l of BD stain buffer and analyzed in a
FACSCALIBUR flow cytometer. As a positive control, 1.times.10.sup.5
AdrR cells are incubated with 200 nM HB-EGF for 30 minutes on ice,
washed twice and incubated with a 1:200 dilution of streptavidin-PE
for 45 minutes. To assess background staining from the
streptavidin-PE conjugate, cells are incubated with 100 .mu.l of a
1:200 dilution of streptavidin-PE only for 45 minutes.
[0338] As shown by the data set forth in FIG. 20 (obtained using
the methods described above or minor variations thereof), HB-EGF
binds to AdrR cells, presumably to either or both of ErbB1 and
ErbB4 on AdrR cells. Ab #6 does not inhibit this binding,
evidencing that Ab #6 is specific for inhibiting the binding of
ErbB3 ligands (e.g., heregulin and epiregulin) to ErbB3.
Example 11: Inhibition of VEGF Secretion in Tumor Cells
[0339] The ability of Ab #6 to inhibit VEGF secretion of cells
expressing ErbB3 (e.g., cancer cells) is examined using VEGF
secretion assay (VEGF ELISA, R&D Systems DY293B) as described
under "ELISA Assay" in Materials and Methods, above. First, the
ability of Ab #6 to inhibit VEGF secretion in untreated and HRG
treated MCF-7, T47D and COLO-357 cells is analyzed. As shown in
FIG. 24A, these studies revealed that COLO-357 secrete the highest
amount of VEGF into the media. As these cells also exhibit very
high HRG levels, addition of HRG to the media does little to induce
VEGF secretion. In contrast, HRG is able to induce more than a
doubling of VEGF secretion in MCF-7 and T47D cells. Ab #6 shows a
potent inhibitory effect at high levels in all three cell lines
with the highest being in COLO-357 (FIG. 24A, FU=Fluorescence
Units).
[0340] Ab #6 also shows a similar effect in vivo by inhibiting VEGF
secretion in three different xenografts, the highest being in
COLO-357 xenograft (FIG. 24B). Inhibition of VEGF correlates with
inhibition of ErbB3 phosphorylation (FIG. 24 C). It has been
demonstrated that myeloma cell-secreted factors, such as VEGF and
bFGF, trigger angiogenesis (see, e.g., Leung et al. (1989) Science
246(4935):1306-9; Yen et al. (2000) Oncogene 19(31):3460-9).
Inhibition of VEGF secretion is also known in the art to correlate
with inhibition of tumor induced angiogenesis, a facilitator of
tumor growth.
Example 12: Inhibition of Cell Migration
[0341] The ability of Ab #6 to inhibit the migration of cells
expressing ErbB3 (e.g., MCF-7 cells) is examined using a trans-well
assay (Millipore Corp., Billerica, Mass., # ECM552). First, MCF-7
cells are serum-starved overnight and then incubated in the
presence or absence of Ab #6 (8 uM final concentration) for 15
minutes at room temperature. The cells are then transferred to an
upper chamber that is separated from a lower chamber by a collagen
type I-coated membrane through which the cells can migrate. 10% FBS
is added to media in the lower chamber to act as a chemoattractant
in the presence of absence of Ab #6. The chambers are incubated at
37.degree. C. for 16 hours and then the cells that migrate through
the membrane into the lower chamber are removed using a detachment
buffer and incubated with a cell-binding fluorescent dye.
Fluorescence is quantitated using a fluorescent plate reader. The
average fluorescence .+-.SEM (n=2) is shown in FIG. 25.
[0342] As shown by the data presented in FIG. 25 (obtained using
the methods described above or minor variations thereof), 10% FBS
stimulates cell migration (lane 3) as compared to untreated control
(lane 1) and 8 uM Ab #6 inhibits the FBS induced cell migration
(lane 4).
Example 13: Inhibition of Spheroid Growth
[0343] The ability of Ab #6 to inhibit the spheroid growth of cells
expressing ErbB3 is examined using an assay which approximates
conditions of developing tumor growth (Herrmann et al. J Biomol
Screen. 2008 January; 13(1):1-8. Epub 2007 Nov. 26) AdrR (an
ovarian cancer cell line) and DU145 (a prostate cancer cell line)
spheroids are initiated at a frequency of 1 spheroid per well of a
96 well plate using a hanging drop method (Herrmann et al., supra).
Subconfluent cells are trypsinized, counted, and resuspended in
filtered medium. The cell concentration is adjusted to 100,000
cells/ml, and one 20 ul drop (containing 2000 cells) is added to
each ring on the underside of the lid of a 96-well plate. The lids
with these hanging droplets are then placed back on the original
96-well plate, which contained 100 ul of PBS in each well to
maintain moisture. Four days after initial plating, the hanging
droplets containing the spheroids are replated into new 96-well
plates. This replating involves transferring the lid containing the
hanging droplets to a fresh 1% agarose/RPMI-coated 96-well plate
that contains 150 ul of medium per well. The plate and lid are then
centrifuged together at 500 rpm for 1 minute to transfer the
spheroid-containing drops from the lids to the wells. Plates are
then further incubated at 37.degree. C. in a humidified CO2
incubator. Spheroids are photographed in an inverted phase contrast
microscope. A micrometer scale is also photographed at the same
magnification to determine spheroid size. The diameter of the
spheroids is determined using Metamorph Analysis software (MDS
Analytical Technologies).
[0344] Individual spheroids thus obtained are then treated with
either Ab #6 (8 uM final concentration), heregulin-.beta.1 EGF
domain (R&D Systems, 396-HB, 3.4 nM final concentration), or a
combination of both. The diameters of the spheroids are measured
using light microscopy (10.times. objective) at day 1 and day
13.
[0345] Data (obtained using the methods described above or minor
variations thereof) presented in FIGS. 26A and 26B show that Ab #6
inhibits spheroid growth in AdrR cells and that 3.4 nM HRG
stimulates spheroid growth while Ab #6 inhibits the HRG effect
(FIG. 26B). Data (obtained using the methods described above or
minor variations thereof) presented in FIG. 26C show that spheroids
derived from DU145 do not increase in size during 13 days of the
experiment; however, growth is significantly stimulated by HRG. In
these cells, 8 uM Ab #6 inhibits HRG induced spheroid growth.
[0346] In additional experiments, the ability of Ab #6 to inhibit
spheroid growth of OVCAR8 cells, another human ovarian cancer cell
line, is examined. Multicellular tumor spheroids are generated as
before. To test the effect of Ab #6 on spheroid growth, the
antibody is added to a final concentration of 25 .mu.g/ml on days 1
and 4 of spheroid formation. Data obtained using the methods
described above or minor variations thereof showed that Ab #6
caused a 30-40% decrease in OVCAR8 spheroid area.
Example 14: Inhibition of Signaling
[0347] The ability of Ab #6 to inhibit the signaling induced by
different ligands is examined. For example, the effect of Ab #6 on
HRG and BTC binding to AdrR cells expressing ErbB3 receptor is
tested. As shown by the FACS analysis results presented in FIGS.
27A and B, Ab #6 competes with HRG but not BTC for binding to AdrR
cells. Accordingly, since Ab #6 does not activate HRG-induced
signaling (as is indicated by experiments below) blocking of HRG
binding to ErbB3 by Ab #6 will prevent signaling induced by
HRG.
[0348] Various ligands are tested for inducement of ErBb3
phosphorylation. At least three ligands, HRG, BTC, and HGF, are
able to stimulate ErbB3 induced phosphorylation in AdrR cells,
while EGF can not. As shown in FIG. 28, Ab #6 inhibits HGF induced
ErbB3 phosphorylation in AdrR cells. Further, as known in the art
(see, e.g., Wallenius et al. (2000) Am J Pathol. 156 (3):821-9),
enhanced HGF signaling has been reported in various epithelial and
non-epithelial tumors.
[0349] ErbB3/c-MET Interaction and the Role of Ab #6 in Modulating
this Interaction
[0350] It has been shown that non-small-cell lung cancers carrying
activating mutations in EGFR develop resistance to tyrosine kinase
inhibitors by recruiting c-MET and HER3 and thus activating the
PI3K-AKT cell survival pathway (Engelmann et al. (2007) Science
316: 1039-1043; Gou (2007) PNAS: 105(2): 692-697). The association
between EGFR and c-MET in cell lines that carry activating EGFR
mutations has been well established by co-immunoprecipitation
(Engelmann et al. 2007; Gou 2007). Guo et al. recently used
co-immunoprecipitation to demonstrate that c-MET and ErbB3 also
exist in a complex in a gastric cell line MKN45 known to be
dependent on amplified c-MET.
[0351] c-MET-ErbB3 interactions also occur in AdrR cells carrying
the wild type EGFR and is not dependent on amplified c-MET. HGF
(Hepatocyte Growth Factor) induces ErbB3 phosphorylation in AdrR
cells in a dose dependent manner as shown in FIG. 28. In addition,
Ab #6 inhibits HGF induced erbB3 phosphorylation.
[0352] The effect of HRG and BTC on both ErbB1 and ErbB3
phosphorylation has also been investigated, and HRG and BTC are
found to induce phosphorylation of both ErbB1 and ErbB3. HRG is
found to be a more potent inducer of ErbB3 phosphorylation while
BTC is a potent inducer of ErbB1 phosphorylation (FIG. 29A). This
phosphorylation is likely to be driven by the complex between ErbB1
and ErbB3. HRG binding to ErbB3 induces complex formation between
ErbB1 and ErbB3, leading to the activation of both receptors. The
same phenomenon appears likely for BTC, where BTC binding to ErbB1
stimulates complex formation between ErbB1 and ErbB3, leading to
the phosphorylation of both ErbB1 and ErbB3.
[0353] Inhibition of HRG, BTC, EGF, and HGF Stimulated ErbB3
Phosphorylation.
[0354] The ability of Ab #6 to inhibit ligand (HRG, BTC, EGF, and
HGF) induced ErbB3 phosphorylation is examined by the following
method: [0355] 1. AdrR cells are plated into 96 well plate at a
density of 30,000 cells/well/100 uL in RPMI medium containing 10%
FBS and allowed to grow overnight; [0356] 2. The next day, cells
are serum-starved by changing medium to FBS-free medium and allowed
to grow overnight; [0357] 3. Cells are pre-treated with different
concentrations of Ab #6 (from 0.01 nM to 100 nM), or buffer
(un-pretreated, "0"), for 2 hours; [0358] 4. Pretreated and
un-pretreated cells are then stimulated with 10 nM HRG or HGF for
10 minutes, or 10 nM BTC or EGF for 5 minutes, and separate wells
of un-pretreated cells are left unstimulated ("Control"); [0359] 5.
The reaction is stopped by removing the culture medium and washing
the cells once with ice cold PBS; [0360] 6. The cells are then
lysed in 25 mM Tris, pH+7.5, 150 mM NaCl, 1 mM EDTA, 1.0% Triton
X-100, 1.0% CHAPS, 10% v/v glycerol, containing 1.times. protease
inhibitor and 1.times. phosphatase inhibitor; and [0361] 7. ErbB3
phosphorylation is measured in cell lysates using Human
Phospho-ErbB3 [0362] ELISA kit (R&D Systems, DYC1769) according
to manufacturer's instructions. Results obtained by the methods
described above or minor variations thereof are set forth in FIGS.
38A-D.
[0363] Antibody Inhibition of ErbB2-ErbB3 Protein Complex
Formation.
[0364] AdrR cells are pre-incubated with buffer (control), or 250
nM Ab #6 for 60 minutes at room temperature, then treated with 10
nM HRG or 10 nM BTC or control buffer for 10 minutes. The cells are
lysed in 25 mM Tris, pH+7.5, 150 mM NaCl, 1 mM EDTA, 1.0% Triton
X-100, 1.0% CHAPS, 10% v/v glycerol, containing 0.2 mM PMSF, 50
mTU/mL aprotinin, and 100 uM leupeptin, and the crude lysate are
centrifuged briefly to remove insoluble material. Supernatant is
transferred to a new EPPENDORF tube, and anti-ErbB3 antibody (Santa
Cruz sc-285) is added at 1:500 dilution. Supernatants are incubated
overnight with gentle shaking at 4 C. 60 ul of Immobilized Protein
A/G agarose beads (Pierce, Rockford, Ill., #20421) is first washed
with 1.times.PBS. The cell lysate-antibody mixture is added to the
PBS washed beads, and incubated for 2 hours with gentle shaking at
4.degree. C. The immunoprecipitates are then washed with ice-cold
lysis buffer 3 times, resuspended in 30 ul of 2.times.SDS sample
buffer, heat denatured at 95.degree. C. for 7 minutes and run on
4-12% Bis-Tris Gels. SDS-PAGE and electro-transferred to PVDF
membrane in Tri-Glycine buffer with 10% MeOH. The membrane is
blocked for 1 hour in 10 ml of blocking buffer (Li-Cor Biosciences,
Lincoln, Nebr., #927-40000) and then incubated with the anti-ErbB2
antibody at 1:1000 (Cell Signaling Technology, Danvers, Mass.,
#29D8) in 10 ml of blocking buffer (Li-Cor Biosciences,
#927-40000). The signal is detected using goat anti-rabbit IRDye800
at 1:5000 (2 ul) in 10 ml of blocking buffer (Li-Cor Biosciences,
#927-40000).
[0365] By the methods described above or minor variations thereof,
Ab #6 was shown to completely inhibit HRG stimulated ErbB2/3
complex formation (FIG. 29B).
Example 15: Inhibition Profile of Ab #6 is Distinct from Cetuximab,
Lapatinib and Pertuzumab
[0366] In this example, inhibitor dose response studies are
performed with AdrR cells stimulated with either HRG or BTC in the
presence of either Ab #6, cetuximab, lapatinib or pertuzumab. Serum
starved AdrR cells are pre-incubated for 30 minutes with 4-fold
serial dilutions of Ab #6, lapatinib or cetuximab from 2 mM to 7.6
pM or of pertuzumab from 100 nM to 1.5 pM and then stimulated for
10 minutes with 25 nM of HRG or BTC. Phosphorylation of ErbB3 is
measured by ELISA (R&D Systems, DYC1769-5, per manufacturers
protocol) and IC.sub.50 values are determined using Prism (GraphPad
Software Inc.).
[0367] Data obtained using the methods described above or minor
variations thereof showed that: [0368] Ab #6 inhibited both
HRG-induced ErbB3 phosphorylation and BTC-induced ErbB3
phosphorylation, with IC.sub.50s of 2.4 nM and 5.9 nM, respectively
(with 95% confidence intervals of 1.5-3.8 nM and 2.5-13.6 nM,
respectively). [0369] Lapatinib (a reversible tyrosine kinase
inhibitor of ErbB1 and ErbB2) inhibited HRG and BTC-induced ErbB3
phosphorylation with IC.sub.50s of 150 nM and 360 nM, respectively
(with 95% confidence intervals of 46-504 nM and 119-1069 nM,
respectively). [0370] Cetuximab (an anti-ErbB1 antibody) inhibited
BTC-induced ErbB3 phosphorylation with an IC.sub.50 of 1.8 nM (with
a 95% confidence interval of 0.9-3.8 nM). but cetuximab did not
inhibit HRG-induced ErbB3-induced ErbB3 phosphorylation, confirming
earlier observations that HRG signaling is mediated primarily by
ErbB2/ErbB3 and not ErbB 1/ErbB3 heterodimers. [0371] Pertuzumab (a
monoclonal antibody that sterically hinders ErbB2's recruitment
into ErbB ligand complexes) inhibited HRG-induced ErbB3
phosphorylation with an IC.sub.50 of 3.6 nM (with a 95% confidence
interval of 1.0-13.5 nM), but did not inhibit BTC-induced ErbB3
phosphorylation.
[0372] Thus, Ab #6 was the only inhibitor tested that is capable of
potently inhibiting ErbB3 phosphorylation with low nanomolar
IC.sub.50 values for both HRG and BTC stimulation.
Example 16: Combination Therapy with Ab #6 and Other Therapeutic
Agents
[0373] In this example, the efficacy of Ab #6 in inhibiting tumor
growth in xenograft tumor models is assessed in combination with
other therapeutic agents, namely erlotinib or taxol.
[0374] In a first experiment, mice bearing ACHN (a renal tumor cell
line) xenograft tumors are prepared by establishing tumors
subcutaneously in the flanks of nude mice (Charles River
Laboratories). The tumor-bearing mice are dosed intraperitoneally
(IP) every three days with either a suboptimal dose of 300 .mu.g Ab
#6 or vehicle. Erlotinib (25 mg/kg) is administered orally once
daily, either alone or in combination with the Ab #6 treatment.
Tumor size (length.times.width) is measured twice a week and
measurements are used to calculate tumor volume (p/6 (L.times.W2).
The data presented in FIG. 30 (obtained using the methods described
above or minor variations thereof) demonstrate that while Ab #6 or
erlotinib alone inhibit tumor growth, inhibition by the combination
therapy (Ab #6 plus erlotinib) is greater than either single agent
alone resulting in an additive effect.
[0375] In a second experiment, mice bearing DU145 (a prostate tumor
cell line) xenograft tumors are prepared by establishing tumors
subcutaneously in the flanks of nude mice (Charles River
Laboratories). The tumor-bearing mice are dosed intraperitoneally
(IP) every three days with Ab #6 (300 .mu.g) or vehicle. Taxol (20
mg/kg) is administered IP once per week, either alone or in
combination with the Ab #6 treatment. Again, tumor size is measured
twice a week and measurements are used to calculate tumor volume.
The data presented in FIG. 31 (obtained using the methods described
above or minor variations thereof) demonstrate that while Ab #6 or
taxol alone inhibited tumor growth, inhibition by the combination
therapy (Ab #6 plus taxol) is greater than either single agent
alone resulting in an additive effect.
Example 17: Inhibition of Growth of KRAS Mutant Tumor Cells
[0376] In this example, the ability of Ab #6, either alone or in
combination with other agents, to inhibit the growth of tumor cells
that comprise a KRAS mutation is examined.
[0377] A549 is a lung cancer cell line that comprises a G12S KRAS
mutation, a mutation in codon 12 of the human KRAS gene, in which
the codon is changed from one coding for glycine (G) to one coding
for serine (S). This cell line is insensitive to treatment with
erlotinib or taxol alone. To test the ability of Ab #6 alone to
inhibit growth of A549 cells in vitro, the cells are grown as
multicellular tumor spheroids (2000 cells/spheroid/well of a 96
well plate) and then treated with 0, 0.001, 0.01, 0.1 or 1 .mu.M Ab
#6 for seven days. The area of the spheroid is measured under
4.times. magnification using METAMORPH software on day 1 and day 7
and the percent change in spheroid area is calculated ((Initial
Area-Final Area/Initial Area.times.100). The results (obtained
using the methods described above or minor variations thereof) are
shown in the graph of FIG. 32A ("-4" on the x axis of the graph
corresponds to the "0" dose), and the photographs of FIG. 32B. The
data of FIG. 32A demonstrate that Ab #6 treatment alone is
sufficient to inhibit the growth of the KRAS mutant A549 tumor
cells in vitro and that there is a linear dose response result
regarding the percent decrease in spheroid area with the indicated
ten-fold increases in Ab #6 concentration. Photographs of
representative spheroids are shown in FIG. 32B. Untreated spheroids
grew approximately 5% in 7 days versus a 35% reduction in size of
spheroids treated with 1 .mu.M Ab #6.
[0378] To test the ability of Ab #6 alone to inhibit the growth of
the KRAS mutant A549 cells in vivo, nude mice bearing A549
subcutaneous xenograft tumors are treated with 600 .mu.g of Ab #6
every three days, followed by measurement of tumor volume. The
results (obtained using the methods described above or minor
variations thereof) are shown in the graph of FIG. 32C, which
demonstrates significant tumor growth inhibition by Ab #6 treatment
alone, which growth inhibition is retained after dosing stopped on
day 22. Thus, Ab #6 alone was able to inhibit the growth of KRAS
mutant tumor cells in vivo.
[0379] To test the ability of Ab #6 in combination with either
erlotinib or taxol to inhibit the growth of the KRAS mutant A549
cells in vivo, nude mice bearing A549 subcutaneous xenograft tumors
are treated with either: (i) 300 .mu.g of Ab #6 alone every three
day; (ii) 25 mg/kg erlotinib alone every day; (iii) 20 mg/kg taxol
alone every 7 days; (iv) Ab #6 and erlotinib in combination (at the
same dosing); or (v) Ab #6 and taxol in combination (at the same
dosing). The results for the erlotinib experiment and the taxol
experiment (all obtained using the methods described above or minor
variations thereof) are shown in FIGS. 33A and 33B. The results
from both experiments demonstrate that the KRAS mutant A549
xenografts are insensitive to treatment with either erlotinib or
taxol alone, that growth of the KRAS mutant xenografts is inhibited
by Ab #6 treatment alone and that combining Ab #6 treatment with
either erlotinib or taxol treatment led to even greater tumor
growth inhibition that observed with Ab #6 monotherapy.
Example 18: Epitope Mapping of Ab #6 Binding to ErbB3
[0380] In this example, alanine scanning mutagenesis is used to map
the epitope within ErbB3 to which Ab #6 binds.
[0381] Since Ab #6 inhibits HRG binding to ErbB3, alanine
mutagenesis analysis is commenced focusing on the predicted HRG
binding site in the extracellular domain (the ectodomain) of ErbB3,
and in particular Domain I of the ectodomain, of ErbB3. To assist
in selection of which residues to mutate, the crystal structure of
EGFR complexed with TGF.alpha. (Garret et al. (2002) Cell
110:763-773) was used as a model, since the crystal structure of
ErbB3 complexed with HRG was not available. ErbB3 and EGFR are
homologous in structure and thus even if the interacting residues
are not identical, the structural elements (certain loops or helix
faces) should be the same. Accordingly, the residues in EGFR
specified to be involved in ligand binding as described in Garret
et al., supra, are identified and sequence alignment of ErbB3 and
EGFR reveal the corresponding ErbB3 residues. In addition to the
ligand binding sites, other faces of Domain I of the ErbB3
ectodomain are mutated using the crystal structure of ErbB3 as a
guide (Cho and Leahy (2002) Science 297:1330-1333).
[0382] Accordingly, the following ErbB3 point mutations are made:
L14A, N15A, L17A, S18A, V19A, T20A, N25A, K32A, L33A, V47A, L48A,
M72A, Y92A, Y92P, D93A, M101A, L102A, Y104A, Y104P, N105A, T106A,
Y129A, Y129P, K132A, Q59A, T77A, Q90A, Q114A, Q119A, R145A, R151A,
V156A, H168A, K172A and L186A. In this notation, which uses the
standard single letter amino acid abbreviations, L14A, for example,
indicates that leucine (L) at amino acid position 14 of mature
ErbB3 (SEQ ID NO: 73) is specifically mutated to alanine (A), with
other substitution mutations indicated in the same fashion.
Mutagenesis is accomplished using standard methods known in the art
and the ErbB3 mutants, within the context of the ErbB3 ectodomain
Domain I, are expressed on the surface of yeast cells using
standard methods known in the art. All mutants expressed well on
the surface of the yeast at levels identical to those of the wild
type ErbB3 Domain I. Expression of the ErbB3 Domain I mutants on
yeast allows for the examination of binding of Ab #6 to mutants
using FACS without first purifying the recombinant proteins.
[0383] Binding of Ab #6 to ErbB3 ectodomain Domain I fragments
comprising single mutations is determined by standard FACS
analysis. A second anti-ErbB3 antibody (SGP1; Lab Vision), which
binds an epitope on ErbB3 which does not overlap with the epitope
bound by Ab #6 (as evidenced by lack of competition for binding to
ErbB3), is used as a control to ensure that the mutations are not
just generally destabilizing the ErbB3 structure. Thus, ErbB3
mutations that affect the binding of both antibodies are excluded
from further characterization. For FACS analysis, yeast cells
expressing the different mutant version of ErbB3 Domain I on their
surface are labeled simultaneously with Ab #6 (followed by a goat
anti-human Ab-Alexa 488 as secondary antibody) and with SGP1-Alexa
647. Data (obtained using the methods described above or minor
variations thereof) indicate that four of the alanine point
mutations described above inhibit Ab #6 binding to ErbB3 ectodomain
Domain I while not inhibiting the binding of the control anti-ErbB3
antibody (SGP1). These four point mutations are: D93A, M101A, L102A
and Y104A.
[0384] To further confirm that the Ab #6 epitope comprises residues
93, 101, 102 and 104 of mature ErbB3 (SEQ ID NO: 73), these four
mutations (D93A, M101A, L102A, Y104A), are expressed in the context
of the full length mature ErbB3 following stable transfection into
CHO K1 cells in order to examine their effects in this context. CHO
K1 cells expressing wild type full-length ErbB3 serve as a positive
control. High expressing clones are selected for each mutant and
labeled for standard FACS analysis either with Ab #6 or SGP1 (to
confirm proper folding of ErbB3). SGP1 is directly labeled with
Alexa 647 dye and Ab #6 is directly labeled with Alexa 488 dye.
[0385] The results (obtained using the methods described above or
minor variations thereof) are shown in FIGS. 34A-34E, which show
the binding of SGP1 or Ab #6 to wild type ErbB3, the D93A mutant,
the M101A mutant, the L102A mutant or the Y104A mutant,
respectively. The results demonstrate that the control anti-ErbB3
antibody (SGP1) is able to bind all four mutants, whereas Ab #6
displays essentially no binding to three of the mutants (D93A,
L102A and Y104A) and only very minimal binding to the fourth mutant
(M101A). Thus, full-length ErbB3 CHO cell expression experiments
demonstrate that the Ab #6 epitope on ErbB3 comprises residues 93,
101, 102 and 104 of the mature, human ErbB3 sequence shown in SEQ
ID NO: 73. These four residue are located on strand 3 of a 5 stand
parallel beta-sheet within ErbB3. Further experiments performed in
analogous fashion yielded data indicating that the epitope further
comprises residues 92, 99 and 129 of the mature, human ErbB3
sequence shown in SEQ ID NO: 73. Thus, the epitope bound by Ab #6
may be viewed as comprising the sequence spanning residues 92-104
and 129 (which lies adjacent to 92-104 in the folded protein), of
the mature, human ErbB3 sequence shown in SEQ ID NO: 73.
Example 19: Inhibition of Growth of PI3K Mutant Tumor Cells
[0386] In this example, the ability of Ab #6, either alone or in
combination with another agent, to inhibit the growth of tumor
cells that comprise a PI3K mutation is examined.
[0387] SKOV3 (SKOV-3) is an ovarian cancer cell line that comprises
a mutation that upregulates PI3K expression. To test the ability of
Ab #6 alone to inhibit the growth of the PI3K mutant SKOV3 cells in
vivo, nude mice bearing SKOV3 subcutaneous xenograft tumors (tumor
volume of 150-200 mm.sup.3) are treated with 600 .mu.g of Ab #6
every three days, followed by measurement of tumor volume. The
results (obtained using the methods described above or minor
variations thereof) are shown in the graph of FIG. 35A, and
demonstrate that Ab #6 treatment alone results in partial tumor
growth inhibition. In this experiment, a "lag phase" in tumor
growth of approximately 30 days was observed even in the
vehicle-treated mice, indicating that this tumor is slow to grow in
vivo. Nevertheless, the decrease in the tumor volume after 30 days
in the Ab #6 treated mice as compared to the vehicle treated mice
demonstrates that Ab #6 treatment alone is able to inhibit the
growth of PI3K mutant tumor cells in vivo.
[0388] To test the ability of Ab #6 in combination with cisplatin
to inhibit the growth of the PI3K mutant SKOV3 cells in vivo, nude
mice bearing SKOV3 subcutaneous xenograft tumors are treated with
either: (i) 300 .mu.g of Ab #6 alone every three day (a suboptimal
dose of Ab #6); (ii) 1.5 mg/kg cisplatin (CDDP) alone; or (iii) Ab
#6 and cisplatin in combination (at the same dosing). Given the 30
day "lag phase" observed in the Ab #6 monotherapy experiment
described above, dosing with Ab #6 in the combination experiment is
not begun until after the 30 day lag phase had elapsed. The results
for the combination therapy experiment (obtained using the methods
described above or minor variations thereof) are shown in FIG. 35B.
The results demonstrate that both Ab #6 and cisplatin alone are
able to inhibit the growth of the SKOV3 xenografts and that the
combination treatment led to even greater tumor growth inhibition
than either agent alone, thereby demonstrating the enhanced
effectiveness of Ab #6 treatment when combined with a second
therapeutic agent, such as cisplatin.
Example 20: Paratope Mapping of Ab #6
[0389] In this example, paratope mapping of Ab #6 is performed
using a single chain (scFv) version of the antibody. In this scFv
version (SEQ ID NO: 72) the V.sub.H region (SEQ ID NO: 1) and the
V.sub.L region (SEQ ID NO: 2) are connected with a (G4S).sub.3
linker (amino acids 123-137 of SEQ ID NO: 72; the linker sequence
is also shown in SEQ ID NO: 74), and this scFv still retains the
ability to specifically bind ErbB3. This format is used to
investigate the effect on ErbB3 binding of alanine (and in some
cases phenylalanine) substitution mutations in the CDR loops.
[0390] To predict which residues in the CDR loops of Ab #6 are
surface exposed, the crystal structures of two very homologous
antibodies were examined, since the crystal structure of Ab #6 had
yet to be empirically determined. The antibodies for which crystal
structures are available that appeared to be most homologous to Ab
#6 are 1 mhp (anti-alphal integrin, Karpusas et al., J. Mol. Biol.
327:1031 (2003)) for the V.sub.H chain and 1 mco (Guddat et al.,
Proc. Natl. Acad. Sci. USA 90:4271 (1993)) for the V.sub.L chain.
Shown below in Table 1 are the CDR loops of Ab #6, with the
residues chosen for mutation highlighted in boldface and
underlined. Also shown in Table 1 are the sequences of the V.sub.H
CDRs of the 1 mhp antibody and of the V.sub.L CDRs of the 1 mco
antibody, with the number of amino acid mismatches compared to Ab
#6 shown in parentheses following the SEQ ID NO for each CDR and
the surface residues highlighted in italics, boldface and
underlined.
TABLE-US-00002 TABLE 1 CDR Loops in Antibody #6 VH Ab #6 CDR H1
HYVMA (SEQ ID NO: 7) CDR H2 SISSSGGWTLYADSVKG (SEQ ID NO: 8) CDR H3
GLKMATIFDY (SEQ ID NO: 9) VL Ab #6 CDR L1 TGTSSDVGSYNVVS (SEQ ID
NO: 10) CDR L2 EVSQRPS (SEQ ID NO: 11) CDR L3 CSYAGSSIFVI (SEQ ID
NO: 12) VH 1mhp CDR H1 MS (SEQ ID NO: 54) (3) CDR H2 T -GG YLDSVKG
(SEQ ID NO: 55) (6) CDR H3 G G F V (SEQ ID NO: 56) (7) VL 1mco CDR
L1 TG VG VS (SEQ ID NO: 57) (2) CDR L2 PS (SEQ ID NO: 58) (2) CDR
L3 S EG FV (SEQ ID NO: 59) (5)
[0391] The mutations made in Ab #6 are summarized below in Table 2.
The amino acid residue numbering for the mutations corresponds to
the linear numbering of the V.sub.H and V.sub.L residues within the
scFv format, not to Kabat numbering. The notation Thr28Ala
indicates that threonine (Thr) at amino acid position 28 of the
scFv is specifically mutated to alanine (Ala), with the rest of the
substitution mutations indicated in the same fashion.
TABLE-US-00003 TABLE 2 Ab #6 Mutations CDR Mutation Name
Substitution H1 M1 Thr28Ala M2 Ser30Ala M3 His31Ala M4 Tyr32Ala M5
Tyr32Phe M6 Val33Ala H2 M7 Ser52Ala M8 Ser53Ala M9 Ser54Ala M10
Trp57Ala M11 Thr58Ala M12 Leu59Ala H3 M13 Leu100Ala M14 Lys101Ala
M15 Met102Ala M16 Thr104Ala M17 Ile105Ala M18 Asp107Ala L1 M19
Thr162Ala M20 Ser163Ala M21 Ser164Ala M22 Asp165Ala M23 Ser168Ala
M24 Tyr169Ala M25 Tyr169Phe M26 Asn170Ala M27 Val171Ala L2 M28
Glu189Ala M29 Val190Ala M30 Ser191Ala M31 Gln192Ala M32 Arg193Ala
L3 M33 Ser229Ala M34 Tyr230Ala M35 Tyr230Phe M36 Ser233Ala M37
Ser234Ala M38 Ile235Ala
[0392] As shown in Table 2, all of the mutations are to alanine
except that the tyrosine residues are also mutated to phenylalanine
because Phe and Tyr are structurally very similar (e.g., both are
aromatic) and such mutations are thus expected to be less
disruptive in regard to antigen binding. In addition to the
mutations made within the CDRs proper, heavy chain residues 28 and
30, outside of the CDRs, are also mutated (mutations M1 and M2 in
Table 2) as they fall in the CDR loop regions. All of the mutations
are made using standard recombinant DNA techniques and binding of
the mutants to ErbB3 is tested using standard screening techniques
known in the art.
[0393] As shown in FIG. 36, several mutations were identified that
preferentially affected binding of the scFv to the ErbB3 domain
more than they altered the binding of the scFv to Protein A (which
binding does not involve the CDRs). Their identities and effects
(based on the three groupings shown in FIG. 36) are indicated below
in Table 3. "No effect on binding" indicates either that binding to
ErbB3 is not substantially affected or that there is a
corresponding decrease in binding to Protein A attributed to
destabilization of the scFv protein. The majority of the binding
residues are located in the H1, H2 and H3 loops and some in the L1
and L3 loops. As seen in many other antibody antigen complexes, the
L2 CDR does not directly contribute to binding.
TABLE-US-00004 TABLE 3 Effect on ErbB3 Binding of Ab #6 Mutations
H1 M1 Thr28Aal no effect on binding M2 Ser30Ala no effect on
binding M3 His31Ala no effect on binding M4 Tyr32Ala large decrease
in binding M5 Tyr32Phe no effect on binding M6 Val33Ala large
decrease in binding H2 M7 Ser52Ala no effect on binding M8 Ser53Ala
no effect on binding M9 Ser54Ala no effect on binding M10 Trp57Ala
large decrease in binding M11 Thr58Ala no effect on binding M12
Leu59Ala no effect on binding H3 M13 Leu100Ala no effect on binding
M14 Lys101Ala no effect on binding M15 Met102Ala large decrease in
binding M16 Thr104Ala large decrease in binding M17 Ile105Ala small
decrease in binding M18 Asp107Ala no effect on binding L1 M19
Thr162Ala no effect on binding M20 Ser163Ala no effect on binding
M21 Ser164Ala no effect on binding M22 Asp165Ala small decrease in
binding M23 Ser168Ala no effect on binding M24 Tyr169Ala large
decrease in binding M25 Tyr169Phe no effect on binding M26
Asn170Ala no effect on binding M27 Val171Ala no effect on binding
L2 M28 Glu189Ala no effect on binding M29 Val190Ala no effect on
binding M30 Ser191Ala no effect on binding M31 Gln192Ala no effect
on binding M32 Arg193Ala no effect on binding L3 M33 Ser229Ala no
effect on binding M34 Tyr230Ala large decrease in binding M35
Tyr230Phe no effect on binding M36 Ser233Ala no effect on binding
M37 Ser234Ala no effect on binding M38 Ile235Ala no effect on
binding
[0394] Based on the results shown in Table 3, consensus sequences
for each of the heavy and light chain CDRs were derived. These
consensus sequences are shown in FIGS. 37A and 37B, below the wild
type CDR sequences. The consensus sequences differ from the wild
type CDR sequences in that those amino acid residues that are
mutated to alanine and found not to substantially affect binding
have been genericized to allow any amino acid (Xaa) at those
positions. Additionally, for those amino acid positions containing
an aromatic tyrosine residue in which mutation to aromatic
phenylalanine did not affect binding, but mutation to alanine did
affect binding, any of the aromatic amino acids tyrosine,
histidine, tryptophan and phenylalanine are allowed at that
position in the consensus sequences shown in FIG. 37A, while in the
consensus sequences shown in FIG. 37B those amino acid positions
are allowed to be either tyrosine or phenylalanine.
[0395] Furthermore, based on the results shown in Table 3, paratope
sequences for each of the heavy and light chain CDRs were derived.
These paratope sequences are shown in FIGS. 37A and 37B, below the
wild type and consensus CDR sequences. The paratope sequences
correspond to those amino acid residue positions within the CDRs
that were shown to substantially decrease binding to ErbB3 when
mutated to alanine, thereby suggesting a substantial role for these
positions in antigen binding. Additionally, for those amino acid
positions containing an aromatic tyrosine residue in which mutation
to aromatic phenylalanine did not affect binding, but mutation to
aliphatic alanine did affect binding, any of the aromatic amino
acids tyrosine, histidine, tryptophan and phenylalanine in FIG. 37A
(or alternately tyrosine and phenylalanine in FIG. 37B) are allowed
at each such position in the paratope. The other amino acid
positions within the CDRs that do not appear to be directly
involved in antigen binding are allowed to be any amino acid
residue (Xaa) within the paratope.
[0396] The wild-type heavy chain CDR1, CDR2 and CDR3 sequences for
Ab #6 are also shown in SEQ ID NOs: 7, 8 and 9, respectively, and
the wild type light chain CDR1, CDR2 and CDR3 sequences for Ab #6
are also shown in SEQ ID NOs: 10, 11 and 12, respectively. The
consensus heavy chain CDR1, CDR2 and CDR3 sequences for Ab #6 are
also shown in SEQ ID NOs: 60 and 75 (CDR1), 61 (CDR2) and 62
(CDR3), respectively, and the consensus light chain CDR1, CDR2 and
CDR3 sequences for Ab #6 are also shown in SEQ ID NOs: 66 and 77
(CDR1), 67 (CDR2) and 68 and 79 (CDR3), respectively. The heavy
chain CDR1, CDR2 and CDR3 paratope sequences for Ab #6 are also
shown in SEQ ID NOs: 63 and 76 (CDR1), 64 (CDR2) and 65 (CDR3),
respectively, and the light chain CDR1, CDR2 and CDR3 paratope
sequences for Ab #6 are also shown in SEQ ID NOs: 69 and 77 (CDR1),
70 (CDR2) and 71 and 80 (CDR3), respectively.
EQUIVALENTS
[0397] Those skilled in the art will recognize, or be able to
ascertain and implement using no more than routine experimentation,
many equivalents of the specific embodiments of the invention
described herein. Such equivalents are intended to be encompassed
by the following claims. Any combination of the embodiments
disclosed in the dependent claims are contemplated to be within the
scope of the invention.
INCORPORATION BY REFERENCE
[0398] The disclosure of each and every US and foreign patent and
pending patent application and publication referred to herein is
hereby incorporated herein by reference in its entirety.
Sequence CWU 1
1
801119PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 1Glu Val Gln Leu Leu Glu Ser Gly Gly Gly Leu
Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly
Phe Thr Phe Ser His Tyr 20 25 30Val Met Ala Trp Val Arg Gln Ala Pro
Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Ser Ile Ser Ser Ser Gly Gly
Trp Thr Leu Tyr Ala Asp Ser Val 50 55 60Lys Gly Arg Phe Thr Ile Ser
Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75 80Leu Gln Met Asn Ser
Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95Thr Arg Gly Leu
Lys Met Ala Thr Ile Phe Asp Tyr Trp Gly Gln Gly 100 105 110Thr Leu
Val Thr Val Ser Ser 1152111PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 2Gln Ser Ala Leu Thr Gln
Pro Ala Ser Val Ser Gly Ser Pro Gly Gln1 5 10 15Ser Ile Thr Ile Ser
Cys Thr Gly Thr Ser Ser Asp Val Gly Ser Tyr 20 25 30Asn Val Val Ser
Trp Tyr Gln Gln His Pro Gly Lys Ala Pro Lys Leu 35 40 45Ile Ile Tyr
Glu Val Ser Gln Arg Pro Ser Gly Val Ser Asn Arg Phe 50 55 60Ser Gly
Ser Lys Ser Gly Asn Thr Ala Ser Leu Thr Ile Ser Gly Leu65 70 75
80Gln Thr Glu Asp Glu Ala Asp Tyr Tyr Cys Cys Ser Tyr Ala Gly Ser
85 90 95Ser Ile Phe Val Ile Phe Gly Gly Gly Thr Lys Val Thr Val Leu
100 105 1103118PRTArtificial SequenceDescription of Artificial
Sequence Synthetic polypeptide 3Glu Val Gln Leu Leu Glu Ser Gly Gly
Gly Leu Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser Cys Ala Ala
Ser Gly Phe Thr Phe Ser Ala Tyr 20 25 30Asn Met Arg Trp Val Arg Gln
Ala Pro Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Val Ile Tyr Pro Ser
Gly Gly Ala Thr Arg Tyr Ala Asp Ser Val 50 55 60Lys Gly Arg Phe Thr
Ile Ser Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75 80Leu Gln Met
Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95Ala Arg
Gly Tyr Tyr Tyr Tyr Gly Met Asp Val Trp Gly Gln Gly Thr 100 105
110Leu Val Thr Val Ser Ser 1154110PRTArtificial SequenceDescription
of Artificial Sequence Synthetic polypeptide 4Gln Ser Val Leu Thr
Gln Pro Pro Ser Ala Ser Gly Thr Pro Gly Gln1 5 10 15Arg Val Thr Ile
Ser Cys Ser Gly Ser Asp Ser Asn Ile Gly Arg Asn 20 25 30Tyr Ile Tyr
Trp Tyr Gln Gln Phe Pro Gly Thr Ala Pro Lys Leu Leu 35 40 45Ile Tyr
Arg Asn Asn Gln Arg Pro Ser Gly Val Pro Asp Arg Ile Ser 50 55 60Gly
Ser Lys Ser Gly Thr Ser Ala Ser Leu Ala Ile Ser Gly Leu Arg65 70 75
80Ser Glu Asp Glu Ala Glu Tyr His Cys Gly Thr Trp Asp Asp Ser Leu
85 90 95Ser Gly Pro Val Phe Gly Gly Gly Thr Lys Leu Thr Val Leu 100
105 1105122PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 5Glu Val Gln Leu Leu Glu Ser Gly Gly Gly Leu
Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly
Phe Thr Phe Ser Ala Tyr 20 25 30Gly Met Gly Trp Val Arg Gln Ala Pro
Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Tyr Ile Ser Pro Ser Gly Gly
His Thr Lys Tyr Ala Asp Ser Val 50 55 60Lys Gly Arg Phe Thr Ile Ser
Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75 80Leu Gln Met Asn Ser
Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95Ala Lys Val Leu
Glu Thr Gly Leu Leu Val Asp Ala Phe Asp Ile Trp 100 105 110Gly Gln
Gly Thr Met Val Thr Val Ser Ser 115 1206106PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
6Gln Tyr Glu Leu Thr Gln Pro Pro Ser Val Ser Val Tyr Pro Gly Gln1 5
10 15Thr Ala Ser Ile Thr Cys Ser Gly Asp Gln Leu Gly Ser Lys Phe
Val 20 25 30Ser Trp Tyr Gln Gln Arg Pro Gly Gln Ser Pro Val Leu Val
Met Tyr 35 40 45Lys Asp Lys Arg Arg Pro Ser Glu Ile Pro Glu Arg Phe
Ser Gly Ser 50 55 60Asn Ser Gly Asn Thr Ala Thr Leu Thr Ile Ser Gly
Thr Gln Ala Ile65 70 75 80Asp Glu Ala Asp Tyr Tyr Cys Gln Ala Trp
Asp Ser Ser Thr Tyr Val 85 90 95Phe Gly Thr Gly Thr Lys Val Thr Val
Leu 100 10575PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 7His Tyr Val Met Ala1 5817PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 8Ser
Ile Ser Ser Ser Gly Gly Trp Thr Leu Tyr Ala Asp Ser Val Lys1 5 10
15Gly910PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 9Gly Leu Lys Met Ala Thr Ile Phe Asp Tyr1 5
101014PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 10Thr Gly Thr Ser Ser Asp Val Gly Ser Tyr Asn Val
Val Ser1 5 10117PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 11Glu Val Ser Gln Arg Pro Ser1
51211PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 12Cys Ser Tyr Ala Gly Ser Ser Ile Phe Val Ile1 5
10135PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 13Ala Tyr Asn Met Arg1 51417PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 14Val
Ile Tyr Pro Ser Gly Gly Ala Thr Arg Tyr Ala Asp Ser Val Lys1 5 10
15Gly159PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 15Gly Tyr Tyr Tyr Tyr Gly Met Asp Val1
51613PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 16Ser Gly Ser Asp Ser Asn Ile Gly Arg Asn Tyr Ile
Tyr1 5 10177PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 17Arg Asn Asn Gln Arg Pro Ser1
51811PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 18Gly Thr Trp Asp Asp Ser Leu Ser Gly Pro Val1 5
10195PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 19Ala Tyr Gly Met Gly1 52017PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 20Tyr
Ile Ser Pro Ser Gly Gly His Thr Lys Tyr Ala Asp Ser Val Lys1 5 10
15Gly2113PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 21Val Leu Glu Thr Gly Leu Leu Val Asp Ala Phe Asp
Ile1 5 102211PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 22Ser Gly Asp Gln Leu Gly Ser Lys Phe
Val Ser1 5 10238PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 23Tyr Lys Asp Lys Arg Arg Pro Ser1
5249PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 24Gln Ala Trp Asp Ser Ser Thr Tyr Val1
525357DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 25gaggtgcagc tgctggagag cggcggaggg
ctggtccagc caggcggcag cctgaggctg 60tcctgcgccg ccagcggctt caccttcagc
cactacgtga tggcctgggt gcggcaggcc 120ccaggcaagg gcctggaatg
ggtgtccagc atcagcagca gcggcggctg gaccctgtac 180gccgacagcg
tgaagggcag gttcaccatc agcagggaca acagcaagaa caccctgtac
240ctgcagatga acagcctgag ggccgaggac accgccgtgt actactgcac
caggggcctg 300aagatggcca ccatcttcga ctactggggc cagggcaccc
tggtgaccgt gagcagc 35726333DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 26cagtccgccc
tgacccagcc cgccagcgtg agcggcagcc caggccagag catcaccatc 60agctgcaccg
gcaccagcag cgacgtgggc agctacaacg tggtgtcctg gtatcagcag
120caccccggca aggcccccaa gctgatcatc tacgaggtgt cccagaggcc
cagcggcgtg 180agcaacaggt tcagcggcag caagagcggc aacaccgcca
gcctgaccat cagcggcctg 240cagaccgagg acgaggccga ctactactgc
tgcagctacg ccggcagcag catcttcgtg 300atcttcggcg gagggaccaa
ggtgaccgtc cta 33327354DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 27gaggtgcagc
tgctggaaag cggcggaggg ctggtgcagc caggcggcag cctgaggctg 60tcctgcgccg
ccagcggctt caccttcagc gcctacaaca tgagatgggt gcggcaggcc
120ccaggcaagg gcctggaatg ggtgtccgtg atctacccca gcggcggagc
caccagatac 180gccgacagcg tgaagggcag gttcaccatc agcagggaca
acagcaagaa caccctgtac 240ctgcagatga acagcctgag ggccgaggac
accgccgtgt actactgcgc caggggctac 300tactactacg gcatggacgt
gtggggccag ggcaccctgg tgaccgtgag cagc 35428330DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
28cagagcgtgc tgacccagcc cccaagcgcc agcggcaccc caggccagag ggtgaccatc
60agctgcagcg gcagcgacag caacatcggc aggaactaca tctactggta tcagcagttc
120cccggcaccg cccccaagct gctgatctac aggaacaacc agaggcccag
cggcgtgccc 180gacaggatca gcggcagcaa gagcggcacc agcgccagcc
tggccatcag cggcctgaga 240agcgaggacg aggccgagta ccactgcggc
acctgggacg acagcctgag cggcccagtg 300ttcggcggag ggaccaagct
gaccgtccta 33029366DNAArtificial SequenceDescription of Artificial
Sequence Synthetic polynucleotide 29gaagttcaat tgttagagtc
tggtggcggt cttgttcagc ctggtggttc tttacgtctt 60tcttgcgctg cttccggatt
cactttctct gcttacggta tgggttgggt tcgccaagct 120cctggtaaag
gtttggagtg ggtttcttat atctctcctt ctggtggcca tactaagtat
180gctgactccg ttaaaggtcg cttcactatc tctagagaca actctaagaa
tactctctac 240ttgcagatga acagcttaag ggctgaggac acggccgtat
attactgtgc gaaagtactg 300gaaactggct tattggttga tgcttttgat
atctggggcc aagggacaat ggtcaccgtc 360tcaagc 36630318DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
30cagtacgaat tgactcagcc accctcagtg tccgtgtacc caggacagac agccagcatc
60acctgctctg gagatcaatt ggggagtaaa tttgtttcct ggtatcagca gaggccaggc
120cagtcccctg tgttggtcat gtataaagat aaaaggcggc cgtcagagat
ccctgagcga 180ttctctggct ccaactctgg gaacacagcc actctgacca
tcagcgggac ccaggctata 240gatgaggctg actattattg tcaggcgtgg
gacagcagca cttatgtctt cggcactggg 300accaaggtca ccgtccta
31831357DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 31gaagttcaat tgttagagtc tggtggcggt
cttgttcagc ctggtggttc tttacgtctt 60tcttgcgctg cttccggatt cactttctct
cattacgtta tggcttgggt tcgccaagct 120cctggtaaag gtttggagtg
ggtttcttct atctcttctt ctggtggctg gactctttat 180gctgactccg
ttaaaggtcg cttcactatc tctagagaca actctaagaa tactctctac
240ttgcagatga acagcttaag ggctgaggac acagccgtgt attactgtac
tagaggtctc 300aagatggcta caatttttga ctactggggc cagggcaccc
tggtcaccgt ctcaagc 35732333DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 32cagagcgctt
tgactcagcc tgcctccgtg tctgggtctc ctggacagtc gatcaccatc 60tcctgcactg
gaaccagcag tgatgttggg agttataatg ttgtctcctg gtaccaacaa
120cacccaggca aagcccccaa actcatcatt tatgaggtca gtcagcggcc
ctcaggggtt 180tctaatcgct tctctggctc caagtctggc aacacggcct
ccctgacaat ctctgggctc 240cagactgagg acgaggctga ttattactgc
tgctcatatg caggtagtag tattttcgtg 300atattcggcg gagggaccaa
ggtgaccgtc cta 33333354DNAArtificial SequenceDescription of
Artificial Sequence Synthetic polynucleotide 33gaagttcaat
tgttagagtc tggtggcggt cttgttcagc ctggtggttc tttacgtctt 60tcttgcgctg
cttccggatt cactttctct gcttacaata tgcgttgggt tcgccaagct
120cctggtaaag gtttggagtg ggtttctgtt atctatcctt ctggtggcgc
tactcgttat 180gctgactccg ttaaaggtcg cttcactatc tctagagaca
actctaagaa tactctctac 240ttgcagatga acagcttaag ggctgaggac
acggccgtgt attactgtgc gagagggtac 300tactactacg gtatggacgt
ctggggccaa ggcaccctgg tcaccgtctc aagc 35434330DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
34cagagcgtct tgactcagcc accctcagcg tctgggaccc ccgggcagag ggtcaccatc
60tcgtgttctg gaagcgactc caacatcgga agaaattata tatattggta ccagcaattc
120ccaggaacgg cccccaagct cctcatctat aggaataatc agcggccctc
aggggtccct 180gaccgaatct ctggctccaa gtctggcacc tcagcctccc
tggccatcag tgggctccgg 240tccgaggatg aggctgagta tcactgtgga
acatgggatg acagcctgag tggtccggta 300ttcggcggag ggactaagct
gaccgtccta 33035118PRTArtificial SequenceDescription of Artificial
Sequence Synthetic polypeptide 35Glu Val Gln Leu Leu Glu Ser Gly
Gly Gly Leu Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser Cys Ala
Ala Ser Gly Phe Thr Phe Ser Trp Tyr 20 25 30Gly Met Gly Trp Val Arg
Gln Ala Pro Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Tyr Ile Ser Pro
Ser Gly Gly Ile Thr Val Tyr Ala Asp Ser Val 50 55 60Lys Gly Arg Phe
Thr Ile Ser Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75 80Leu Gln
Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95Ala
Arg Leu Asn Tyr Tyr Tyr Gly Leu Asp Val Trp Gly Gln Gly Thr 100 105
110Thr Val Thr Val Ser Ser 11536108PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
36Gln Asp Ile Gln Met Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser Val1
5 10 15Gly Asp Arg Ile Thr Ile Thr Cys Gln Ala Ser Gln Asp Ile Gly
Asp 20 25 30Ser Leu Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Arg
Leu Leu 35 40 45Ile Tyr Asp Ala Ser Asn Leu Glu Thr Gly Val Pro Pro
Arg Phe Ser 50 55 60Gly Ser Gly Ser Gly Thr Asp Phe Thr Phe Thr Phe
Arg Ser Leu Gln65 70 75 80Pro Glu Asp Ile Ala Thr Tyr Phe Cys Gln
Gln Ser Ala Asn Ala Pro 85 90 95Phe Thr Phe Gly Pro Gly Thr Lys Val
Asp Ile Lys 100 10537119PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 37Glu Val Gln Leu Leu Glu
Ser Gly Gly Gly Leu Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser
Cys Ala Ala Ser Gly Phe Thr Phe Ser Arg Tyr 20 25 30Gly Met Trp Trp
Val Arg Gln Ala Pro Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Tyr Ile
Gly Ser Ser Gly Gly Pro Thr Tyr Tyr Val Asp Ser Val 50 55 60Lys Gly
Arg Phe Thr Ile Ser Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75
80Leu Gln Met Asn Ser Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys
85 90 95Ala Gly Gly Arg Gly Thr Pro Tyr Tyr Phe Asp Ser Trp Gly Gln
Gly 100 105 110Thr Leu Val Thr Val Ser Ser 11538110PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
38Gln Tyr Glu Leu Thr Gln Pro Ala Ser Val Ser Gly Ser Pro Gly Gln1
5 10 15Ser Ile Thr Ile Ser Cys Thr Gly Thr Ser Ser Asp Ile Gly Arg
Trp 20 25 30Asn Ile Val Ser Trp Tyr Gln Gln His Pro Gly Lys Ala Pro
Lys Leu 35 40 45Met Ile Tyr Asp Val Ser Asn Arg Pro Ser Gly Val Ser
Asn Arg Phe 50 55 60Ser Gly Ser Lys Ser Gly Asn Thr Ala Ser Leu Thr
Ile Ser Gly Leu65 70 75 80Gln Ala Glu Asp Glu Ala Asp Tyr Tyr Cys
Ser Ser Tyr Thr Ser Ser 85 90 95Ser Thr Trp Val Phe Gly Gly Gly Thr
Lys Leu Thr Val Leu 100 105 110395PRTArtificial SequenceDescription
of Artificial Sequence Synthetic peptide 39Trp Tyr Gly Met Gly1
54017PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 40Tyr Ile Ser Pro Ser Gly Gly Ile Thr Val Tyr Ala
Asp Ser Val Lys1 5 10 15Gly419PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 41Leu Asn Tyr Tyr Tyr Gly Leu
Asp Val1 54211PRTArtificial SequenceDescription of Artificial
Sequence
Synthetic peptide 42Gln Ala Ser Gln Asp Ile Gly Asp Ser Leu Asn1 5
10437PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 43Asp Ala Ser Asn Leu Glu Thr1 5449PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 44Gln
Gln Ser Ala Asn Ala Pro Phe Thr1 5455PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 45Arg
Tyr Gly Met Trp1 54617PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptide 46Tyr Ile Gly Ser Ser Gly Gly
Pro Thr Tyr Tyr Val Asp Ser Val Lys1 5 10 15Gly4710PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 47Gly
Arg Gly Thr Pro Tyr Tyr Phe Asp Ser1 5 104814PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 48Thr
Gly Thr Ser Ser Asp Ile Gly Arg Trp Asn Ile Val Ser1 5
10497PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 49Asp Val Ser Asn Arg Pro Ser1 55010PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 50Ser
Ser Tyr Thr Ser Ser Ser Thr Trp Val1 5 1051111PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
51Gln Ser Ala Leu Thr Gln Pro Ala Ser Val Ser Gly Ser Pro Gly Gln1
5 10 15Ser Ile Thr Ile Ser Cys Thr Gly Thr Ser Ser Asp Val Gly Ser
Tyr 20 25 30Asn Val Val Ser Trp Tyr Gln Gln His Pro Gly Lys Ala Pro
Lys Leu 35 40 45Met Ile Tyr Glu Val Ser Lys Arg Pro Ser Gly Val Ser
Asn Arg Phe 50 55 60Ser Gly Ser Lys Ser Gly Asn Thr Ala Ser Leu Thr
Ile Ser Gly Leu65 70 75 80Gln Ala Glu Asp Glu Ala Asp Tyr Tyr Cys
Cys Ser Tyr Ala Gly Ser 85 90 95Ser Ile Phe Val Ile Phe Gly Gly Gly
Thr Lys Val Thr Val Leu 100 105 11052108PRTArtificial
SequenceDescription of Artificial Sequence Synthetic polypeptide
52Gln Asp Ile Gln Met Thr Gln Ser Pro Ser Ser Leu Ser Ala Ser Val1
5 10 15Gly Asp Arg Ile Thr Ile Thr Cys Gln Ala Ser Gln Asp Ile Gly
Asp 20 25 30Ser Leu Asn Trp Tyr Gln Gln Lys Pro Gly Lys Ala Pro Arg
Leu Leu 35 40 45Ile Tyr Asp Ala Ser Asn Leu Glu Thr Gly Val Pro Pro
Arg Phe Ser 50 55 60Gly Ser Gly Ser Gly Thr Asp Phe Thr Phe Thr Phe
Arg Ser Leu Gln65 70 75 80Pro Glu Asp Ile Ala Thr Tyr Phe Cys Gln
Gln Ser Ala Asn Ala Pro 85 90 95Phe Thr Phe Gly Pro Gly Thr Lys Val
Asp Ile Arg 100 10553110PRTArtificial SequenceDescription of
Artificial Sequence Synthetic polypeptide 53Gln Tyr Glu Leu Thr Gln
Pro Ala Ser Val Ser Gly Ser Pro Gly Gln1 5 10 15Ser Ile Thr Ile Ser
Cys Thr Gly Thr Ser Ser Asp Ile Gly Arg Trp 20 25 30Asn Ile Val Ser
Trp Tyr Gln Gln His Pro Gly Lys Ala Pro Lys Leu 35 40 45Met Ile Tyr
Asp Val Ser Asn Arg Pro Ser Gly Val Ser Asn Arg Phe 50 55 60Ser Gly
Ser Lys Ser Gly Asn Thr Ala Ser Leu Thr Ile Ser Gly Leu65 70 75
80Gln Ala Glu Asp Glu Ala Asp Tyr Tyr Cys Ser Ser Tyr Thr Ser Ser
85 90 95Ser Thr Val Val Phe Gly Gly Gly Thr Lys Leu Thr Val Leu 100
105 110545PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 54Arg Tyr Thr Met Ser1 55516PRTArtificial
SequenceDescription of Artificial Sequence Synthetic peptide 55Thr
Ile Ser Gly Gly Gly His Thr Tyr Tyr Leu Asp Ser Val Lys Gly1 5 10
155610PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 56Gly Phe Gly Asp Gly Gly Tyr Phe Asp Val1 5
105714PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 57Thr Gly Thr Ser Ser Asp Val Gly Gly Tyr Asn Tyr
Val Ser1 5 10587PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptide 58Glu Val Asn Lys Arg Pro Ser1
55910PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 59Ser Ser Tyr Glu Gly Ser Asp Asn Phe Val1 5
10605PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(1)Any amino acidMOD_RES(2)..(2)Tyr,
Phe, Trp or His 60Xaa Xaa Val Met Ala1 56117PRTArtificial
SequenceDescription of Artificial Sequence Synthetic
peptideMOD_RES(3)..(5)Any amino acidMOD_RES(9)..(9)Thr or Ala 61Ser
Ile Xaa Xaa Xaa Gly Gly Trp Xaa Leu Tyr Ala Asp Ser Val Lys1 5 10
15Gly6210PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(3)..(3)Any amino acidMOD_RES(9)..(9)Any
amino acid 62Gly Leu Xaa Met Ala Thr Ile Phe Xaa Tyr1 5
10635PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(1)Any amino acidMOD_RES(2)..(2)Tyr,
Phe, Trp or HisMOD_RES(4)..(5)Any amino acid 63Xaa Xaa Val Xaa Xaa1
56417PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(7)Any amino acidMOD_RES(9)..(9)Thr or
AlaMOD_RES(11)..(17)Any amino acid 64Xaa Xaa Xaa Xaa Xaa Xaa Xaa
Trp Xaa Leu Xaa Xaa Xaa Xaa Xaa Xaa1 5 10 15Xaa6510PRTArtificial
SequenceDescription of Artificial Sequence Synthetic
peptideMOD_RES(1)..(1)Any amino acidMOD_RES(3)..(3)Any amino
acidMOD_RES(5)..(5)Any amino acidMOD_RES(8)..(10)Any amino acid
65Xaa Leu Xaa Met Xaa Thr Ile Xaa Xaa Xaa1 5 106614PRTArtificial
SequenceDescription of Artificial Sequence Synthetic
peptideMOD_RES(3)..(5)Any amino acidMOD_RES(9)..(9)Any amino
acidMOD_RES(10)..(10)Tyr, Phe, Trp or HisMOD_RES(11)..(11)Any amino
acid 66Thr Gly Xaa Xaa Xaa Asp Val Gly Xaa Xaa Xaa Val Val Ser1 5
10677PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(5)Any amino acid 67Xaa Xaa Xaa Xaa
Xaa Pro Ser1 56811PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptideMOD_RES(3)..(3)Tyr, Phe, Trp or
HisMOD_RES(6)..(8)Any amino acid 68Cys Ser Xaa Ala Gly Xaa Xaa Xaa
Phe Val Ile1 5 106914PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptideMOD_RES(1)..(5)Any amino
acidMOD_RES(7)..(9)Any amino acidMOD_RES(10)..(10)Tyr, Phe, Trp or
HisMOD_RES(11)..(11)Any amino acidMOD_RES(13)..(14)Any amino acid
69Xaa Xaa Xaa Xaa Xaa Asp Xaa Xaa Xaa Xaa Xaa Val Xaa Xaa1 5
10707PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(7)Any amino acid 70Xaa Xaa Xaa Xaa
Xaa Xaa Xaa1 57111PRTArtificial SequenceDescription of Artificial
Sequence Synthetic peptideMOD_RES(1)..(2)Any amino
acidMOD_RES(3)..(3)Tyr, Phe, Trp or HisMOD_RES(4)..(11)Any amino
acid 71Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa1 5
1072248PRTArtificial SequenceDescription of Artificial Sequence
Synthetic polypeptide 72Glu Val Gln Leu Leu Glu Ser Gly Gly Gly Leu
Val Gln Pro Gly Gly1 5 10 15Ser Leu Arg Leu Ser Cys Ala Ala Ser Gly
Phe Thr Phe Ser His Tyr 20 25 30Val Met Ala Trp Val Arg Gln Ala Pro
Gly Lys Gly Leu Glu Trp Val 35 40 45Ser Ser Ile Ser Ser Ser Gly Gly
Trp Thr Leu Tyr Ala Asp Ser Val 50 55 60Lys Gly Arg Phe Thr Ile Ser
Arg Asp Asn Ser Lys Asn Thr Leu Tyr65 70 75 80Leu Gln Met Asn Ser
Leu Arg Ala Glu Asp Thr Ala Val Tyr Tyr Cys 85 90 95Thr Arg Gly Leu
Lys Met Ala Thr Ile Phe Asp Tyr Trp Gly Gln Gly 100 105 110Thr Leu
Val Thr Val Ser Ser Ala Ser Thr Gly Gly Gly Gly Ser Gly 115 120
125Gly Gly Gly Ser Gly Gly Gly Gly Ser Gln Ser Ala Leu Thr Gln Pro
130 135 140Ala Ser Val Ser Gly Ser Pro Gly Gln Ser Ile Thr Ile Ser
Cys Thr145 150 155 160Gly Thr Ser Ser Asp Val Gly Ser Tyr Asn Val
Val Ser Trp Tyr Gln 165 170 175Gln His Pro Gly Lys Ala Pro Lys Leu
Ile Ile Tyr Glu Val Ser Gln 180 185 190Arg Pro Ser Gly Val Ser Asn
Arg Phe Ser Gly Ser Lys Ser Gly Asn 195 200 205Thr Ala Ser Leu Thr
Ile Ser Gly Leu Gln Thr Glu Asp Glu Ala Asp 210 215 220Tyr Tyr Cys
Cys Ser Tyr Ala Gly Ser Ser Ile Phe Val Ile Phe Gly225 230 235
240Gly Gly Thr Lys Val Thr Val Leu 245731323PRTHomo sapiens 73Ser
Glu Val Gly Asn Ser Gln Ala Val Cys Pro Gly Thr Leu Asn Gly1 5 10
15Leu Ser Val Thr Gly Asp Ala Glu Asn Gln Tyr Gln Thr Leu Tyr Lys
20 25 30Leu Tyr Glu Arg Cys Glu Val Val Met Gly Asn Leu Glu Ile Val
Leu 35 40 45Thr Gly His Asn Ala Asp Leu Ser Phe Leu Gln Trp Ile Arg
Glu Val 50 55 60Thr Gly Tyr Val Leu Val Ala Met Asn Glu Phe Ser Thr
Leu Pro Leu65 70 75 80Pro Asn Leu Arg Val Val Arg Gly Thr Gln Val
Tyr Asp Gly Lys Phe 85 90 95Ala Ile Phe Val Met Leu Asn Tyr Asn Thr
Asn Ser Ser His Ala Leu 100 105 110Arg Gln Leu Arg Leu Thr Gln Leu
Thr Glu Ile Leu Ser Gly Gly Val 115 120 125Tyr Ile Glu Lys Asn Asp
Lys Leu Cys His Met Asp Thr Ile Asp Trp 130 135 140Arg Asp Ile Val
Arg Asp Arg Asp Ala Glu Ile Val Val Lys Asp Asn145 150 155 160Gly
Arg Ser Cys Pro Pro Cys His Glu Val Cys Lys Gly Arg Cys Trp 165 170
175Gly Pro Gly Ser Glu Asp Cys Gln Thr Leu Thr Lys Thr Ile Cys Ala
180 185 190Pro Gln Cys Asn Gly His Cys Phe Gly Pro Asn Pro Asn Gln
Cys Cys 195 200 205His Asp Glu Cys Ala Gly Gly Cys Ser Gly Pro Gln
Asp Thr Asp Cys 210 215 220Phe Ala Cys Arg His Phe Asn Asp Ser Gly
Ala Cys Val Pro Arg Cys225 230 235 240Pro Gln Pro Leu Val Tyr Asn
Lys Leu Thr Phe Gln Leu Glu Pro Asn 245 250 255Pro His Thr Lys Tyr
Gln Tyr Gly Gly Val Cys Val Ala Ser Cys Pro 260 265 270His Asn Phe
Val Val Asp Gln Thr Ser Cys Val Arg Ala Cys Pro Pro 275 280 285Asp
Lys Met Glu Val Asp Lys Asn Gly Leu Lys Met Cys Glu Pro Cys 290 295
300Gly Gly Leu Cys Pro Lys Ala Cys Glu Gly Thr Gly Ser Gly Ser
Arg305 310 315 320Phe Gln Thr Val Asp Ser Ser Asn Ile Asp Gly Phe
Val Asn Cys Thr 325 330 335Lys Ile Leu Gly Asn Leu Asp Phe Leu Ile
Thr Gly Leu Asn Gly Asp 340 345 350Pro Trp His Lys Ile Pro Ala Leu
Asp Pro Glu Lys Leu Asn Val Phe 355 360 365Arg Thr Val Arg Glu Ile
Thr Gly Tyr Leu Asn Ile Gln Ser Trp Pro 370 375 380Pro His Met His
Asn Phe Ser Val Phe Ser Asn Leu Thr Thr Ile Gly385 390 395 400Gly
Arg Ser Leu Tyr Asn Arg Gly Phe Ser Leu Leu Ile Met Lys Asn 405 410
415Leu Asn Val Thr Ser Leu Gly Phe Arg Ser Leu Lys Glu Ile Ser Ala
420 425 430Gly Arg Ile Tyr Ile Ser Ala Asn Arg Gln Leu Cys Tyr His
His Ser 435 440 445Leu Asn Trp Thr Lys Val Leu Arg Gly Pro Thr Glu
Glu Arg Leu Asp 450 455 460Ile Lys His Asn Arg Pro Arg Arg Asp Cys
Val Ala Glu Gly Lys Val465 470 475 480Cys Asp Pro Leu Cys Ser Ser
Gly Gly Cys Trp Gly Pro Gly Pro Gly 485 490 495Gln Cys Leu Ser Cys
Arg Asn Tyr Ser Arg Gly Gly Val Cys Val Thr 500 505 510His Cys Asn
Phe Leu Asn Gly Glu Pro Arg Glu Phe Ala His Glu Ala 515 520 525Glu
Cys Phe Ser Cys His Pro Glu Cys Gln Pro Met Glu Gly Thr Ala 530 535
540Thr Cys Asn Gly Ser Gly Ser Asp Thr Cys Ala Gln Cys Ala His
Phe545 550 555 560Arg Asp Gly Pro His Cys Val Ser Ser Cys Pro His
Gly Val Leu Gly 565 570 575Ala Lys Gly Pro Ile Tyr Lys Tyr Pro Asp
Val Gln Asn Glu Cys Arg 580 585 590Pro Cys His Glu Asn Cys Thr Gln
Gly Cys Lys Gly Pro Glu Leu Gln 595 600 605Asp Cys Leu Gly Gln Thr
Leu Val Leu Ile Gly Lys Thr His Leu Thr 610 615 620Met Ala Leu Thr
Val Ile Ala Gly Leu Val Val Ile Phe Met Met Leu625 630 635 640Gly
Gly Thr Phe Leu Tyr Trp Arg Gly Arg Arg Ile Gln Asn Lys Arg 645 650
655Ala Met Arg Arg Tyr Leu Glu Arg Gly Glu Ser Ile Glu Pro Leu Asp
660 665 670Pro Ser Glu Lys Ala Asn Lys Val Leu Ala Arg Ile Phe Lys
Glu Thr 675 680 685Glu Leu Arg Lys Leu Lys Val Leu Gly Ser Gly Val
Phe Gly Thr Val 690 695 700His Lys Gly Val Trp Ile Pro Glu Gly Glu
Ser Ile Lys Ile Pro Val705 710 715 720Cys Ile Lys Val Ile Glu Asp
Lys Ser Gly Arg Gln Ser Phe Gln Ala 725 730 735Val Thr Asp His Met
Leu Ala Ile Gly Ser Leu Asp His Ala His Ile 740 745 750Val Arg Leu
Leu Gly Leu Cys Pro Gly Ser Ser Leu Gln Leu Val Thr 755 760 765Gln
Tyr Leu Pro Leu Gly Ser Leu Leu Asp His Val Arg Gln His Arg 770 775
780Gly Ala Leu Gly Pro Gln Leu Leu Leu Asn Trp Gly Val Gln Ile
Ala785 790 795 800Lys Gly Met Tyr Tyr Leu Glu Glu His Gly Met Val
His Arg Asn Leu 805 810 815Ala Ala Arg Asn Val Leu Leu Lys Ser Pro
Ser Gln Val Gln Val Ala 820 825 830Asp Phe Gly Val Ala Asp Leu Leu
Pro Pro Asp Asp Lys Gln Leu Leu 835 840 845Tyr Ser Glu Ala Lys Thr
Pro Ile Lys Trp Met Ala Leu Glu Ser Ile 850 855 860His Phe Gly Lys
Tyr Thr His Gln Ser Asp Val Trp Ser Tyr Gly Val865 870 875 880Thr
Val Trp Glu Leu Met Thr Phe Gly Ala Glu Pro Tyr Ala Gly Leu 885 890
895Arg Leu Ala Glu Val Pro Asp Leu Leu Glu Lys Gly Glu Arg Leu Ala
900 905 910Gln Pro Gln Ile Cys Thr Ile Asp Val Tyr Met Val Met Val
Lys Cys 915 920 925Trp Met Ile Asp Glu Asn Ile Arg Pro Thr Phe Lys
Glu Leu Ala Asn 930 935 940Glu Phe Thr Arg Met Ala Arg Asp Pro Pro
Arg Tyr Leu Val Ile Lys945 950 955 960Arg Glu Ser Gly Pro Gly Ile
Ala Pro Gly Pro Glu Pro His Gly Leu 965 970 975Thr Asn Lys Lys Leu
Glu Glu Val Glu Leu Glu Pro Glu Leu Asp Leu 980 985 990Asp Leu Asp
Leu Glu Ala Glu Glu Asp Asn Leu Ala Thr Thr Thr Leu 995 1000
1005Gly Ser Ala Leu Ser Leu Pro Val Gly Thr Leu Asn Arg Pro Arg
1010 1015 1020Gly Ser Gln Ser Leu Leu Ser Pro Ser Ser Gly Tyr Met
Pro Met 1025 1030 1035Asn Gln Gly Asn Leu Gly Glu Ser Cys Gln Glu
Ser Ala Val Ser 1040 1045 1050Gly Ser Ser Glu Arg Cys Pro Arg Pro
Val Ser Leu His Pro Met 1055 1060 1065Pro Arg Gly Cys Leu Ala Ser
Glu Ser Ser Glu Gly His Val Thr 1070 1075 1080Gly Ser Glu Ala Glu
Leu Gln Glu Lys Val Ser Met Cys Arg Ser 1085 1090
1095Arg Ser Arg Ser Arg Ser Pro Arg Pro Arg Gly Asp Ser Ala Tyr
1100 1105 1110His Ser Gln Arg His Ser Leu Leu Thr Pro Val Thr Pro
Leu Ser 1115 1120 1125Pro Pro Gly Leu Glu Glu Glu Asp Val Asn Gly
Tyr Val Met Pro 1130 1135 1140Asp Thr His Leu Lys Gly Thr Pro Ser
Ser Arg Glu Gly Thr Leu 1145 1150 1155Ser Ser Val Gly Leu Ser Ser
Val Leu Gly Thr Glu Glu Glu Asp 1160 1165 1170Glu Asp Glu Glu Tyr
Glu Tyr Met Asn Arg Arg Arg Arg His Ser 1175 1180 1185Pro Pro His
Pro Pro Arg Pro Ser Ser Leu Glu Glu Leu Gly Tyr 1190 1195 1200Glu
Tyr Met Asp Val Gly Ser Asp Leu Ser Ala Ser Leu Gly Ser 1205 1210
1215Thr Gln Ser Cys Pro Leu His Pro Val Pro Ile Met Pro Thr Ala
1220 1225 1230Gly Thr Thr Pro Asp Glu Asp Tyr Glu Tyr Met Asn Arg
Gln Arg 1235 1240 1245Asp Gly Gly Gly Pro Gly Gly Asp Tyr Ala Ala
Met Gly Ala Cys 1250 1255 1260Pro Ala Ser Glu Gln Gly Tyr Glu Glu
Met Arg Ala Phe Gln Gly 1265 1270 1275Pro Gly His Gln Ala Pro His
Val His Tyr Ala Arg Leu Lys Thr 1280 1285 1290Leu Arg Ser Leu Glu
Ala Thr Asp Ser Ala Phe Asp Asn Pro Asp 1295 1300 1305Tyr Trp His
Ser Arg Leu Phe Pro Lys Ala Asn Ala Gln Arg Thr 1310 1315
13207415PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptide 74Gly Gly Gly Gly Ser Gly Gly Gly Gly Ser Gly Gly
Gly Gly Ser1 5 10 15755PRTArtificial SequenceDescription of
Artificial Sequence Synthetic peptideMOD_RES(1)..(1)Any amino
acidMOD_RES(2)..(2)Tyr or Phe 75Xaa Xaa Val Met Ala1
5765PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(1)Any amino acidMOD_RES(2)..(2)Tyr or
PheMOD_RES(4)..(5)Any amino acid 76Xaa Xaa Val Xaa Xaa1
57714PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(3)..(5)Any amino acidMOD_RES(9)..(9)Any
amino acidMOD_RES(10)..(10)Tyr or PheMOD_RES(11)..(11)Any amino
acid 77Thr Gly Xaa Xaa Xaa Asp Val Gly Xaa Xaa Xaa Val Val Ser1 5
107814PRTArtificial SequenceDescription of Artificial Sequence
Synthetic peptideMOD_RES(1)..(5)Any amino acidMOD_RES(7)..(9)Any
amino acidMOD_RES(10)..(10)Tyr or PheMOD_RES(11)..(11)Any amino
acidMOD_RES(13)..(14)Any amino acid 78Xaa Xaa Xaa Xaa Xaa Asp Xaa
Xaa Xaa Xaa Xaa Val Xaa Xaa1 5 107911PRTArtificial
SequenceDescription of Artificial Sequence Synthetic
peptideMOD_RES(3)..(3)Tyr or PheMOD_RES(6)..(8)Any amino acid 79Cys
Ser Xaa Ala Gly Xaa Xaa Xaa Phe Val Ile1 5 108011PRTArtificial
SequenceDescription of Artificial Sequence Synthetic
peptideMOD_RES(1)..(2)Any amino acidMOD_RES(3)..(3)Tyr or
PheMOD_RES(4)..(11)Any amino acid 80Xaa Xaa Xaa Xaa Xaa Xaa Xaa Xaa
Xaa Xaa Xaa1 5 10
* * * * *
References