Title of Invention

ANTI ALPHA-V BETA-6 ANTIBODIES

Abstract Monoclonal antibodies that specifically bind to M.96. Also included are methods of using these antibodies to treat mammals having or at risk of having 006-mediated diseases, or to diagnose %Qmediated diseases.
Full Text ANTI-αγβ6 ANTIBODIES
FIELD OF THE INVENTION
This invention relates generally to the field of molecular biology
and specifically to antibodies to αγβ6 integrins.
BACKGROUND OF THE INVENTION
Integrins are a superfamily of cell surface receptors that mediate
cell-cell and cell-matrix adhesion. These proteins are known to provide anchorage
as well as signals for cellular growth, migration and differentiation during
development and tissue repair. Integrins have also been implicated in cell
dedifferentiation and invasion, notably where cells lose their specialized form and
become metastasizing cancer cells.
Integrins are heterodimeric proteins composed of two noncovalently
linked subunits, α and β. The binding specificity of integrins is dictated by the
combination of some 18 different α chains with some 8 different β chains. The
αγβ6 integrin can bind to a number of ligands including fibronectin, tenascin,
vitronectin, and the recently identified latency associated peptide "LAP," a 278
amino acid peptide synthesized as part of the precursor TGF-β protein (Munger et
al., Cell 96(3):319-328 (1999)). LAP is cleaved from the mature form of TGF-β as
an N-terminal peptide during secretion but remains noncovalently associated with
TGF-β to maintain its latent state. This complex cannot bind to the TGF-jS
receptor and hence is not biologically active. The αγβ6 integrin can bind directly to
an RGD motif contained within LAP, resulting in release of LAP and activation of

TGF-β. Since αγβ6 binding to LAP may be important in the conversion of TGF-β
to its active state, blocking the binding may result in inhibition of αγβ6-mediated
activation of TGF-β and the associated fibrotic pathology.
SUMMARY OF THE INVENTION
This invention is based on the discovery and characterization of
high affinity antibodies against αγβ6, including the identification and analysis of
key amino acid residues in the complementary determining regions (CDRs) of such
antibodies.
This invention embraces a monoclonal antibody that (a) specifically
binds to αγβ6; (b) inhibits the binding of αγβ6 to its ligand such as LAP, fibronectin,
vitronectin, and tenascin with an IC50 value lower than that of 10D5 (International
Patent Application Publication WO 99/07405); (c) blocks activation of TGF-β; (d)
contains certain amino acid sequences in the CDRs (e.g., those shown in Figs. 7A
and 7B) that provide binding specificity to αγβ6; (e) specifically binds to the β6
subunit; and/or (f) recognizes αγβ6 in immunostaining procedures, such as
immunostaining of paraffin-embedded tissues.
It has been discovered that antibodies that bind to αγβ6 can be
grouped into biophysically distinct classes and subclasses. One class of antibodies
exhibits the ability to block binding of a ligand (e.g., LAP) to αγβ6 (blockers). This
class of antibodies can be further divided into subclasses of cation-dependent
blockers and cation-independent blockers. Some of the cation-dependent blockers
contain an arginine-glycine-aspartate (RGD) peptide sequence, whereas the cation-
independent blockers do not contain an RGD sequence. Another class of
antibodies exhibits the ability to bind to αγβ6 and yet does not block binding of
αγβ6 to a ligand (nonblockers).
Accordingly, in some embodiments of this invention, some
antibodies of this invention are divalent cation-dependent for binding to αγβ6, while
others are divalent cation-independent. Exemplary cations are Ca2+, Mg2+ and
Mn2+.

In some embodiments, the antibody comprises the same heavy and
light chain polypeptide sequences as an antibody produced by hybridoma 6.1A8,
6.3G9, 6.8G6, 6.2B1, 6.2B10, 6.2A1, 6.2E5, 7.1G10, 7.7G5, or 7.1C5.
In some embodiments, the antibodies comprise a heavy chain whose
complementarity determining regions (CDR) 1, 2 and 3 consist essentially (i.e.,
with the exception of some conservative variations) of the sequences of SEQ ID
Nos:l, 4 and 7, respectively, and/or a light chain whose CDRs 1, 2 and 3 consist
essentially of the sequences of SEQ ID NOs:10,13 and 15, respectively.
In some embodiments, the antibodies comprise a heavy chain whose
CDRs 1, 2 and 3 consist essentially of the sequences of SEQ ID NOs:3, 5 and 8,
respectively, and/or a light chain whose CDRs 1,2 and 3 consist essentially of the
sequences of SEQ ID NOs:l 1, l4 and 17, respectively.
In some embodiments, the antibodies comprise a heavy chain whose
CDRs 1,2 and 3 consist essentially of the sequences of SEQ ID NOs:3, 6 and 9,
respectively, and/or a light chain whose CDRs 1, 2 and 3 consist essentially of the
sequences of SEQ ID NOs:12,14 and 18, respectively.
In some embodiments, the antibodies comprise a heavy chain whose
CDRs 1, 2 and 3 consist essentially of the sequences of SEQ ID NOs:2, 46 and 47,
respectively, and/or a light chain whose CDRs 1, 2 and 3 consist essentially of the
sequences of SEQ ED NOs:48,13 and 16, respectively.
In some embodiments, the antibodies comprise a heavy chain whose
CDRs 1,2 and 3 consist essentially of the sequences of SEQ ID NOs:49,51 and
53, respectively, and/or a light chain whose CDRs 1, 2 and 3 consist essentially of
the sequences of SEQ ID NOs:55, 57 and 59, respectively.
In some embodiments, the antibodies comprise a heavy chain whose
CDRs 1, 2 and 3 consist essentially of the sequences of SEQ ID NOs:50, 52 and
54, respectively, and/or a light chain whose CDRs 1, 2 and 3 consist essentially of
the sequences of SEQ ID NOs:56, 58 and 60, respectively.
In some embodiments, the antibodies comprise a heavy chain
variable domain sequence of any one of SEQ ID NOs: 19-36 and 61-62.
In some embodiments, the antibodies comprise heavy and light
chain variable domain sequences of

(l)SEQ IDNOs:19and37;
(2) SEQ ID NO:20 or 21, and SEQ ID NO:38;
(3)SEQ ID NOs:22and43;
(4) SEQ ID NOs:23 and 44;
(5) SEQ ID NOs:24 and 45;
(6) SEQ ID NO:25 or 26 and SEQ ID NO:42;
(7) SEQ ID NO:27,28, or 29, and SEQ ID NO:39;
(8) SEQ ID NO:34 or 35, and SEQ ID NO:40;
(9)SEQ ID NOs:36and41;

(10) SEQ ID NOs:61 and 63; or
(11) SEQ ID NOs:62 and 64,
respectively.
In some embodiments, the antibodies specifically binds to αγβ6 but
does not inhibit the binding of αγβ6 to latency associated peptide (LAP). At least
some of these antibodies are capable of binding to αγβ6 in paraffin-embedded tissue
sections and therefore can be used for diagnostic purposes. Exemplary antibodies
include 6.2A1 and 6.2E5.
This invention also embraces antibodies that bind to the same
epitope as any of the above-described antibodies.
This invention also embraces compositions comprising one or more
antibodies of this invention, and a pharmaceutically acceptable carrier. In some of
these compositions, the antibodies are conjugated to a cytotoxic agent (i.e., an
agent that impairs the viability and/or the functions of a cell) such as a toxin or a
radionuclide. The antibodies in these compositions can be cation-dependent
antibodies. The compositions can be administered to a subject (e.g., a mammal
such as a human) having or at risk of having a disease mediated by αγβ6, so as to
treat (e.g., alleviating, mitigating, reducing, preventing, postponing the onset of)
the disease. Examples of such diseases include, but are not limited to: fibrosis
(e.g., scleroderma, scarring, liver fibrosis, lung fibrosis, and kidney fibrosis);
psoriasis; cancer (e.g., epithelial cancer; oral, skin, cervical, ovarian, pharyngeal,
laryngeal, esophageal, lung, breast, kidney, or colorectal cancer); Alport's
Syndrome; acute and chronic injuries of the lung, liver, kidney and other internal

organs; and sclerosis of the lung, liver, kidney and other internal organs. Risks of
having such diseases may result from genetic predisposition; certain lifestyles such
as smoking and alcoholism; exposure to environmental pollutants such as asbestos;
physiological conditions such as diabetes, hepatitis viral infection (e.g., hepatitis C
viral infection), autoimmune diseases; and medical treatments such as radiation
therapy.
This invention also embraces methods of detecting αγβ6 in a tissue
sample from a mammal (e.g., a human), comprising contacting the tissue sample
with the antibody of the invention, such as 6.2A1 and 6.2E5.
This invention also embraces cells of hybridomas 6.1A8, 6.2B10,
6.3G9, 6.8G6, 6.2B1, 6.2A1, 6.2E5,7.1G10, 7.7G5, and 7.1C5; isolated nucleic
acids comprising a coding sequence for any one of SEQ ID NOs: 19-45 and 61-64;
isolated polypeptides comprising an amino acid sequence of any one of SEQ ID
NOs:19-45 and 61-64.
An antibody of this invention refers to a full antibody, e.g., an
antibody comprising two heavy chains and two light chains, or to an antigen-
binding fragment of a full antibody such as a Fab fragment, a Fab' fragment, a
F(ab')2 fragment or a F(v) fragment. An antibody of this invention can be a murine
antibody or a homolog thereof, or a fully human antibody. An antibody of this
invention can also be a humanized antibody, a chimeric antibody or a single-
chained antibody.1 An antibody of this invention can be of any isotype and
subtype, for example, IgA (e.g., IgAl and IgA2), IgG (e.g., IgG1, IgG2, IgG3 and
IgG4), IgE, IgD, IgM, wherein the light chains of the immunoglobulin may be of
type kappa or lambda.
In some embodiments, the antibody of the invention may comprise
a mutation (e.g., deletion, substitution or addition) at one or more (e.g., 2, 3,4, 5,
or 6) of certain positions in the heavy chain such that the effector function of the
antibody (e.g., the ability of the antibody to bind to a Fc receptor or a complement
factor) is altered without affecting the antibody's antigen-binding ability. In other
embodiments, the antibody of this invention may contain a mutation at an amino
acid residue that is a site for glycosylation such that the glycosylation site is
eliminated. Such an antibody may have clinically beneficial, reduced effector

functions or other undesired functions while retaining its antigen-binding affinity.
Mutation of a glycosylation site can also be beneficial for process development (e. g. ,
protein expression and purification). In still other embodiments, the heavy or light chains
can contain mutations that increase affinity or potency.
Several of the Fusion #6 and Fusion #7 hybridomas were deposited at
the American Type Culture Collection("ATCC" ; P. O. Box 1549, Manassas, VA 20108,
USA) under the Budapest Treaty. Hybridoma clones 6.1A8, 6.2B10, 6.3G9, 6.8G6, and
6.2B1 were deposited on August 16,2001, and have accession numbers ATCCPTA-
3647,-3648,-3649,-3645, and-3646, respectively.
Hybridoma clones 6.2A1, 6.2E5, 7.1CH0, 7.7G5, and 7.1C5 were deposited on December
5,2001, and have accession numbers ATCCPTA-3896,-3897,-3898,- 3899, and-3900,
respectively. See Table 1, infra.
The antibodies of the invention are useful for treating any clinically undesirable
condition or disease (as discussed herein) that is mediated by binding of αγβ6, to its ligand,
such as LAP and fibronectin. These antibodies can be more potent, via higher affinity or
avidity, and cation dependency or independency of binding to ligand, than previously
known αγβ6 antibodies.
In addition to therapeutic applications of the antibodies of the invention,
especially the blockers, the nonblocker class of antibodies can be used for diagnostic
purposes, such as in antigen capture assays, enzyme-linked immunosorbent assays
(ELISAs), immunohistochemistry, and the like
Other features and advantages of the invention will be apparent from the
following detailed description, drawings, and claims.
BRIEF DESCRIPTION OF THE ACCOMPANYING DRAWINGS
Figs. 1A and 1B are bar graphs showing the results of a cell capture assay that
determined the ability of various anti- αγβ6 monoclonal antibodies ("mAb") to bind β6
transfected FDC-P1 cells (untransfected cells as control).
Fig. 2A is a graph showing the results of KLISA assays that determined
the ability of various purifiedanti- αγβ6"Fusion 6" monoclonal antibodies to
bind soluble recombinant humanavss6 ("hs αγβ6)- These antibodies were generated
by immunizing β6-/- mice with soluble human truncated αγβ6 The
Substituted Sheet

numbers in the legend indicate the clone numbers. For the corresponding clone
names, see Table 2.
Fig. 2B is a graph showing the results of ELISA assays that
determined the ability of various purified anti-αγβ6 "Fusion 7" monoclonal
antibodies to bind soluble recombinant hsαγβ6. These antibodies were generated
by immunizing β6-/- mice with β6-transfected NIH 3T3 cells (Fusion #7).
Figs. 3A-F are graphs showing the differential cation dependence of
the binding of various anti-αγβ6 monoclonal antibodies to hsαγβ6.
Figs. 4A and 4B are graphs showing that Fusion #6 and Fusion #7
monoclonal antibodies, respectively, inhibit the binding of biotin-hsαγβ6 to LAP.
Figs. 5 A-E are graphs showing that exemplary monoclonal
antibodies of the invention inhibit the binding of β6-transfected FDC-P1 cells to
LAP. Figs. 5A and 5B display the results from Fusion #6 antibodies. Figs. 5C-E
display the results from Fusion #7 antibodies.
Figs. 6A and 6B are graphs showing that Fusion #6 and Fusion #7
antibodies, respectively, inhibit the αγβ6-mediated activation of TGF-β, using a
PAI-1 luciferase reporter gene assay to monitor TGF-β activation.
Fig. 7A depicts the amino acid sequences of the variable domains of
the heavy chains of αγβ6 monoclonal antibodies 6.1A8, 6.8G6 (subclones A and B),
7.7G5, 6.2B1, 6.3G9, 6.2B10 (subclones A and B), 6.2G2, 6.2A1, 6.4B4
(subclones A, B and C), 7.10H2, 7.9H5, 7.4A3 (subclones A and B), 7.1C5
(subclones A and B) and 7.1G10. Antibodies 6.1A8, 6.8G6 and 7.7G5 are cation-
dependent in binding to αγβ6, while antibodies 6.2B1, 6.2A1, 6.3G9, 6.2B10,
6.4B4, 7.1C5 and 7.1G10 are cation-independent (infra). The numbers in
parentheses denote amino acid residue positions. The CDRs are in the large boxes,
while the small boxes containing italicized amino acids represent polymorphism in
different clones of a particular antibody.
Fig. 7B depicts the amino acid sequences of the variable domains of
the light chains of αγβ6 monoclonal antibodies 6.1A8,6.8G6,6.4B4,6.2A1, 7.1C5,
7.1G10,6.2B10, 7.7G5, 6.2B1 and 6.3G9.

Fig. 8 is a scatter plot showing the expression of αγβ6 in human
breast cancer and human squamous carcinoma tissue sections. Normal human
tissues show only negligible expression levels of αγβ6.
Figs. 9A and 9B are quadratic curve graphs depicting the solution
binding affinities of two anti-αγβ6 antibodies, 6.8G6 and 6.3G9, respectively, for
soluble αγβ6.
Figs. 10A and 10B are bar graphs demonstrating the ability of
purified monoclonal antibodies to compete with biotinylated 6.3G9 and
biotinylated 6.8G6, respectively, for binding to αγβ6.
Fig. 11 is a bar graph showing percent smooth actin staining in
kidneys from UUO animals treated with anti-αγβ6 mAb treatment.
Fig. 12 shows αγβ6 expression on tumor cell lines by FACS analysis
(right side of figure) and inhibition of tumor cell lines binding to the LAP ligand
by mAbs 6.3G9 and 6.4B4 (left side of figure).
Fig. 13 is a bar graph demonstrating inhibition of three tumor cell
lines binding to the LAP ligand by anti-αγβ6 mAbs 6.3G9,6.8G6 and 6.4B4. The
mAb binding was compared to total binding without the addition of test mAbs
(TB) and nonspecific binding to BSA control alone (NSB).
Figs. 14A and 14B are graphs showing the effects of anti-αγβ6 mAb
6.3G9 and 6.4B4, respectively, over a 33 day study period on tumors arising from
subcutaneously implanted Detroit 562 cells.
Figs. 15A-C are graphs showing the effects of anti-αγβ6 mAb on
bleomycin-induced lung fibrosis. (A) Antibody treatment using 6.3G9 mAb was
started on day 0 at the time of bleomycin administration and was monitored over a
30 day period; (B) Antibody treatment using 6.3G9 mAb was started 15 days after
bleomycin treatment and was monitored over a 30 day period; (C) Antibody
treatment using 6.3G9, 6.8G6 and 6.4B4 mAbs was started 15 days after
bleomycin treatment and was monitored over an extended 60 day period. In both
Figs. 15 A and 15B, the bar graphs on the left represent μg hydroxyproline/lung
while the bar graphs on right show percent increase in hydroxyproline above saline
treated mice (no bleomycin). In Fig. 15C, the graph shows hydroxyproline content
per lung.

DETAILED DESCRIPTION OF THE INVENTION
This invention features classes and subclasses of antibodies that are
specific for the integrin αγβ6. At least one class of the antibodies (blockers) are
capable of blocking the binding of αγβ6 to LAP or preventing the activation of
TGF-β.
The following describes the various methods of making the
antibodies of this invention. Methods that are known in the art but not specifically
described herein are also within the scope of this invention. For instance,
antibodies of this invention can also be identified using phage-displayed antibody
libraries, such as those described in Smith, Science 228:1315-7 (1985); U.S.
Patents 5,565,332, 5,733,743, 6,291,650, and 6,303,313. Additional antibodies of
this invention can be made by coupling the heavy chains identified herein with a
noncognate light chain, e.g., a light chain identified by phage display technology. .
Non-Human Hvbridoma Antibodies
The monoclonal antibodies of this invention can be generated by
well known hybridoma technology. To do so, β6 -I- animals (e.g., mice, rats or
rabbits) are immunized with purified or crude αγβ6 preparations, cells transfected
with cDNA constructs encoding αγ, β6 or both antigens, cells that constitutively
express αγβ6, and the like. The antigen can be delivered as purified protein, protein
expressed on cells, protein fragment or peptide thereof, or as naked DNA or viral
vectors encoding the protein, protein fragment, or peptide. Sera of the immunized
animals are then tested for the presence of anti-αγβ6 antibodies. B cells are isolated
from animals that test positive, and hybridomas are made with these B cells.
Antibodies secreted by the hybridomas are screened for their ability
to bind specifically to αγβ6 (e.g., binding to β6-transfected cells and not to
untransfected parent cells) and for any other desired features, e.g., having the
desired CDR consensus sequences, inhibiting (or not inhibiting in the case of
nonblockers) the binding between LAP and αγβ6 with an IC50 value lower than that
of known anti-αγβ6 antibody 10D5, or inhibiting TGF-β activation.
Hybridoma cells that test positive in the screening assays are
cultured in a nutrient medium under conditions that allow the cells to secrete the

monoclonal antibodies into the culture medium. The conditioned hybridoma
culture supernatant is then collected and antibodies contained in the supernatant are
purified. Alternatively, the desired antibody may be produced by injecting the
hybridoma cells into the peritoneal cavity of an unimmunized animal (e.g., a
mouse). The hybridoma cells proliferate in the peritoneal cavity, secreting the
antibody which accumulates as ascites fluid. The antibody may then be harvested
by withdrawing the ascites fluid from the peritoneal cavity with a syringe.
The monoclonal antibodies can also be generated by isolating the
antibody-coding cDNAs from the desired hybridomas, transfecting mammalian
host cells (e.g., CHO or NSO cells) with the cDNAs, culturing the transfected host
cells, and recovering the antibody from the culture medium.
Chimeric Antibodies
The monoclonal antibodies of this invention can also be generated
by engineering a cognate hybridoma (e.g., murine, rat or rabbit) antibody. For
instance, a cognate antibody can be altered by recombinant DNA technology such
that part or all of the hinge and/or constant regions of the heavy and/or light chains
are replaced with the corresponding components of an antibody from another
species (e.g., human). Generally, the variable domains of the engineered antibody
remain identical or substantially so to the variable domains of the cognate
antibody. Such an engineered antibody is called a chimeric antibody and is less
antigenic than the cognate antibody when administered to an individual of the
species from which the hinge and/or constant region is derived (e.g., a human).
Methods of making chimeric antibodies are well known in the art.
The chimeric antibodies embraced in this invention may contain a
heavy chain variable domain having a sequence identical (or substantially so) to
any one of SEQ ID NOs: 19-36 and/or a light chain variable domain having a
sequence identical (or substantially so) to any one of SEQ ID NOs:37-45.
Preferred human constant regions include those derived from IgGl
and IgG4.
Fully Human Antibodies
The monoclonal antibodies of this invention also include fully
human antibodies. They may be prepared using in vitro-primed human

splenocytes, as described by Boeraer et al., J. Immunol. 147:86-95 (1991), or
using phage-displayed antibody libraries, as described in, e.g., U.S. Patent
6,300,064.
Some other methods for producing fully human antibodies involve
the use of non-human animals that have inactivated endogenous Ig loci and are
transgenic for un-rearranged human antibody heavy chain and light chain genes.
Such transgenic animals can be immunized with αγβ6 and hybridomas are then
made from B cells derived therefrom. These methods are described in, e.g., the
various GenPharm/Medarex (Palo Alto, CA) publications/patents concerning
transgenic mice containing human Ig miniloci (e.g., Lonberg U.S. Patent
5,789,650); the various Abgenix (Fremont, CA) publications/patents with respect
to XENOMICE (e.g., Kucherlapati U.S. Patents 6,075,181, 6,150,584 and
6,162,963; Green et al., Nature Genetics 7:13-21 (1994); and Mendez et al.,
15(2):146-56 (1997)); and the various Kirin (Japan) publications/patents
concerning "transomic" mice (e.g., EP 843 961, and Tomizuka et al., Nature
Genetics 16:133-1443 (1997)).
Humanized Antibodies
The monoclonal antibodies of this invention also include humanized
versions of cognate anti-αγβ6 antibodies derived from other species. A humanized
antibody is an antibody produced by recombinant DNA technology, in which some
or all of the amino acids of a human immunoglobulin light or heavy chain that are
not required for antigen binding (e.g., the constant regions and the framework
regions of the variable domains) are used to substitute for the corresponding amino
acids from the light or heavy chain of the cognate, nonhuman antibody. By way of
example, a humanized version of a murine antibody to a given antigen has on both
of its heavy and light chains (1) constant regions of a human antibody; (2)
framework regions from the variable domains of a human antibody; and (3) CDRs
from the murine antibody. When necessary, one or more residues in the human
framework regions can be changed to residues at the corresponding positions in the
murine antibody so as to preserve the binding affinity of the humanized antibody to
the antigen. This change is sometimes called "back mutation." Humanized
antibodies generally are less likely to elicit an immune response in humans as

compared to chimeric human antibodies because the former contain considerably
fewer non-human components.
The methods for making humanized antibodies are described in,
e.g., Winter EP 239 400; Jones et al., Nature 321:522-525 (1986); Riechmann et
al., Nature 332:323-327 (1988); Verhoeyen et al., Science 239: 1534-1536 (1988);
Queen et al., Proc. Nat. Acad. Sci. USA 86:10029 (1989); U.S. Patent 6,180,370;
and Orlandi et al., Proc. Natl. Acad. Sci. USA 86:3833 (1989). Generally, the
transplantation of murine (or other non-human) CDRs onto a human antibody is
achieved as follows. The cDNAs encoding heavy and light chain variable domains
are isolated from a hybridoma. The DNA sequences of the variable domains,
including the CDRs, are determined by sequencing. The DNAs encoding the
CDRs are transferred to the corresponding regions of a human antibody heavy or
light chain variable domain coding sequence by site directed mutagenesis. Then
human constant region gene segments of a desired isotype (e.g., γ1 for CH and k
for CL) are added. The humanized heavy and light chain genes are co-expressed in
mammalian host cells (e.g., CHO or NSO cells) to produce soluble humanized
antibody. To facilitate large scale production of antibodies, it is often desirable to
produce such humanized antibodies in bioreactors containing the antibody-,
expressing cells, or to produce transgenic mammals (e.g., goats, cows, or sheep)
that express the antibody in milk (see, e.g., U.S. Patent 5,827,690).
At times, direct transfer of CDRs to a human framework leads to a
loss of antigen-binding affinity of the resultant antibody. This is because in some
cognate antibodies, certain amino acids within the framework regions interact with
the CDRs and thus influence the overall antigen binding affinity of the antibody.
In such cases, it would be critical to introduce "back mutations" (supra) in the
framework regions of the acceptor antibody in order to retain the antigen-binding
activity of the cognate antibody.
The general approach of making back mutations is known in the art.
For instance, Queen et al. (supra), Co et al., Proc. Nat. Acad. Sci. USA 88:2869-
2873 (1991), and WO 90/07861 (Protein Design Labs Inc.) describe an approach
that involves two key steps. First, the human V framework regions are chosen by
computer analysis for optimal protein sequence homology to the V region

framework of the cognate murine antibody. Then, the tertiary structure of the
murine V region is modeled by computer in order to visualize framework amino
acid residues that are likely to interact with the murine CDRs, and these murine
amino acid residues are then superimposed on the homologous human framework.
Under this two-step approach, there are several criteria for
designing humanized antibodies. The first criterion is to use as the human acceptor
the framework from a particular human immunoglobulin that is usually
homologous to the non-human donor immunoglobulin, or to use a consensus
framework from many human antibodies. The second criterion is to use the donor
amino acid rather than the acceptor if the human acceptor residue is unusual and
the donor residue is typical for human sequences at a specific residue of the
framework. The third criterion is to use the donor framework amino acid residue
rather than the acceptor at positions immediately adjacent to the CDRs.
One may also use a different approach as described in, e.g.,
Tempest, Biotechnology 9:266-271 (1991). Under this approach, the V region
frameworks derived from NEWM and REI heavy and light chains, respectively,
are used for CDR-grafting without radical introduction of mouse residues. An
advantage of using this approach is that the three-dimensional structures of NEWM
and REI variable regions are known from X-ray crystallography and thus specific
interactions between CDRs and V region framework residues can be readily
modeled.
Other Moieties
The monoclonal antibodies of this invention may further comprise
other moieties to effect the desired functions. For instance, the antibodies may
include a toxin moiety (e.g., tetanus toxoid or ricin) or a radionuclide (e.g.,111In or
90Y) for killing of cells targeted by the antibodies (see, e.g., U.S. Patent 6,307,026)
The antibodies may comprise a moiety (e.g., biotin, fluorescent moieties,
radioactive moieties, histidine tag or other peptide tags) for easy isolation or
detection. The antibodies may also comprise a moiety that can prolong their serum
half life, for example, a polyethylene glycol (PEG) moiety.

Diseased Conditions And Animal Models
The antibodies of the invention are useful in the treatment,
including prevention, of αγβ6-mediated diseases. For example, these antibodies
can be used to treat fibrosis (e.g., lung fibrosis, acute lung injury, kidney fibrosis,
liver fibrosis, Alport's Syndrome, and scleroderma) by blocking the activation of
TGF-β or blocking the binding of αγβ6 to any other ligands, such as fibronectin,
vitronectin, and tenascin. The novelty of this approach includes: (1) it blocks the
activation of TGF-β rather than the binding of TGF-β to its receptor, (2) it can
inhibit TGF-β locally (i.e., at sites of αγβ6 upregulation) rather than systemically,
and (3) it inhibits binding of αγβ6 to a ligand. Other than fibrotic diseases or
conditions, the antibodies of the invention are useful in treating cancer or cancer
metastasis (including tumor growth and invasion), particularly epithelial cancers.
A subset of epithelial cancers is squamous cell carcinoma, e.g., head and neck,
oral, breast, lung, prostate, cervical, pharyngeal, colon, pancreatic and ovarian
cancers. Our studies using the new αγβ6 monoclonal antibodies demonstrated that
αγβ6 is highly expressed in many epithelial cancers, especially on the leading edge
of the tumors. The new antibodies can also be used to any other diseases mediated
by αγβ6, including psoriasis.
The treatments of this invention are effective on both human and
animal subjects afflicted with these conditions. Animal subjects to which the
invention is applicable extend to both domestic animals and livestock, raised either
as pets or for commercial purposes. Examples are dogs, cats, cattle, horses, sheep,
hogs and goats.
The efficacy of the antibodies of the invention can be tested in
various animal models. Mouse models for lung fibrosis include bleomycin- (Pittet
et al., J. Clin. Invest. 107(12):1537-1544 (2001); and Munger et al., supra) and
irradiation- inducible lung fibrosis (Franko et al., Rod. Res. 140:347-355 (1994)).
In bleomycin-treated mice, the expression of αγβ6 increases in the epithelial
alveolar cells of the lungs. But β6 knockout mice are protected from bleomycin-
induced injury and fibrosis.
Mouse models for kidney fibrosis include COL4A3 -/- mice (see,
e.g., Cosgrove et al., Amer. J. Path. 157:1649-1659 (2000), mice with adriamycin-

induced injury (Wang et al., Kidney International 58: 1797-1804 (2000); Deman et
al., Nephrol Dial Transplant 16: 147-150 (2001)), db/db mice (Ziyadeh et al.,
PNAS USA 97:8015-8020 (2000)), and mice with unilateral ureteral obstruction
(Fogo et al., Lab Investigation 81:189A (2001); and Fogo et al., Journal of the
American Society of Nephrology 12:819A (2001)). In all of these models, the mice
develop kidney injury and fibrosis that can progress to renal failure, αγβ6 is
upregulated in the epithelial lining of the ascending and descending tubules of the
kidneys of the COL4A3 -/- mice, adriamycin-treated mice, and mice that undergo
unilateral ureteral obstruction. It is likely that αγβ6 expression also increases in a
variety of kidney injury models.
Anti-αγβ6 monoclonal antibodies can also be tested for their ability
to inhibit tumor growth, progression, and metastasis in such animal models as the
standard in vivo tumor growth and metastasis models. See, e.g., Rockwell et al., J.
Natl. Cancer Inst. 49:735 (1972); Guy et al., Mol. Cell Biol. 12:954(1992);
Wyckoff et al., Cancer Res. 60:2504 (2000); and Oft et al., Curr. Biol. 8:1243
(1998). Important αγβ6 ligands in cancer may include TGF-β, which is involved in
metastasis (for review see Akhurst et al., Trends in Cell Biology 11 :S44-S51
(2001)), fibronectin and vitronectin.
The efficacy of the treatments of this invention may be measured by
a number of available diagnostic tools, including physical examination, blood tests,
proteinuria measurements, creatinine levels and creatinine clearance, pulmonary
function tests, plasma blood urea nitrogen (BUN) levels, observation and scoring
of scarring or fibrotic lesions, deposition of extracellular matrix such as collagen,
smooth muscle actin and fibronectin, kidney function tests, ultrasound, magnetic
resonance imaging (MRI), and CT scan.
Pharmaceutical Compositions
The pharmaceutical compositions of this invention comprise one or
more antibodies of the present invention, or pharmaceutically acceptable
derivatives thereof, optionally with any pharmaceutically acceptable carrier. The
term "carrier" as used herein includes known acceptable adjuvants and vehicles.
According to this invention, the pharmaceutical compositions may
be in the form of a sterile injectable preparation, for example a sterile injectable

aqueous or oleaginous suspension. This suspension may be formulated according
to techniques known in the art using suitable dispersing, wetting, and suspending
agents.
The pharmaceutical compositions of this invention may be given
orally, topically, intravenously, subcutaneously, intraperitoneally, intramuscularly,
intramedullarily, intra-articularly, intra-synovially, intrasternally, intrathecally,
intrahepatically, or intracranially as desired, or just locally at sites of inflammation
or tumor growth. The pharmaceutical compositions of this invention may also be
administered by inhalation through the use of, e.g., a nebulizer, a dry powder
inhaler or a metered dose inhaler.
The dosage and dose rate of the antibodies of this invention
effective to produce the desired effects will depend on a variety of factors, such as
the nature of the disease to be treated, the size of the subject, the goal of the
treatment, the specific pharmaceutical composition used, and the judgment of the
treating physician. Dosage levels of between about 0.001 and about 100 mg/kg
body weight per day, for example between about 0.1 and about 50 mg/kg body
weight per day, of the active ingredient compound are useful. For instance, an
antibody of the invention will be administered at a dose ranging between about
0.01 mg/kg body weight/day and about 20 mg/kg body weight/day, e.g., ranging
between about 0.1 mg/kg body weight/day and about 10 mg/kg body weight/day,
and at intervals of every one to fourteen days. In another embodiment, the
antibody is administered at a dose of about 0.3 to 1 mg/kg body weight when
administered intraperitoneally. In yet another embodiment, the antibody is
administered at a dose of about 5 to 12.5 mg/kg body weight when administered
intravenously. In one embodiment, an antibody composition is administered in an
amount effective to provide a plasma level of antibody of at least 1 mg/ml.
Diagnostic Methods
The antibodies of this invention can be used to diagnose diseased
conditions associated with altered αγβ6 expression levels. A tissue sample from a
subject, such as a tissue biopsy, body fluid sample or lavage (e.g., alveolar lavage),
can be tested in an antigen capture assay, ELIS A, immunohistochemistry assay,

and the like using the antibodies. A tissue sample from a normal individual is used
as control.
Practice of the present invention will employ, unless indicated
otherwise, conventional techniques of cell biology, cell culture, molecular biology,
microbiology, recombinant DNA, protein chemistry, and immunology, which are
within the skill of the art. Such techniques are described in the literature. See, for
example, Molecular Cloning: A Laboratory Manual, 2nd edition (Sambrook et al.,
Eds.), 1989; Oligonucleotide Synthesis, (M.J. Gait, Ed.), 1984; U.S. Patent
4,683,195 to MuUis et al.; Nucleic Acid Hybridization, (B.D. Hames and S.J.
Higgins), 1984; Transcription and Translation, (B.D. Hames and S. J. Higgins),
1984; Culture of Animal Cells (R.I. Freshney, Ed.), 1987; Immobilized Cells and
Enzymes, IRL Press, 1986; A Practical Guide to Molecular Cloning (B. Perbal),
1984; Methods in Enzymology, Volumes 154 and 155 (Wu et al., Eds.), Academic
Press, New York; Gene Transfer Vectors for Mammalian Cells (J.H. Miller and
M.P. Calos, Eds.), 1987; Immunochemical Methods in Cell and Molecular Biology
(Mayer and Walker, Eds.), 1987; Handbook of Experiment Immunology, Volumes
I-IV (D.M. Weir and C.C. Blackwell, Eds.), 1986; Manipulating the Mouse
Embryo, 1986.
Unless otherwise defined, all technical and scientific terms used
herein have the same meaning as commonly understood by one of ordinary skill in
the art to which this invention pertains. Exemplary methods and materials are
described below, although methods and materials similar or equivalent to those
described herein can also be used in the practice of the present invention. All
publications and other references mentioned herein are incorporated by reference
in their entirety. In case of conflict, the present specification, including definitions,
will control. The materials, methods, and examples are illustrative only and not
intended to be limiting. Throughout this specification, the word "comprise," or
variations such as "comprises" or "comprising" will be understood to imply the
inclusion of a stated integer or group of integers but not the exclusion of any other
integer or group of integers.

Examples
The following examples are meant to illustrate the methods and
materials of the present invention. Suitable modifications and adaptations of the
described conditions and parameters normally encountered in the antibody art that
are obvious to those skilled in the art are within the spirit and scope of the present
invention.
In the following examples, the β6 -I- mice were generated as
described in Huang et al., J. Cell Biol. 133:921 (1996). Recombinant human LAP
was purchased from R & D Systems (Minneapolis, MN). Antibody 10D5 was
purchased from Chemicon (Temecula, CA). The L230 hybridoma was purchased
from ATCC and the secreted antibody was purified from the supernatant of
saturated cultures by affinity chromatography on immobilized protein A. Isotyping
of antibodies was carried out using the ISOSTRIP kit (Roche Diagnostics)
according to the manufacturer's instructions. The β6-transfected SW480 cell line
was prepared as described in Weinacker et al., J. Biol. Chem. 269:6940-6948
(1994).
Example 1: Generation of β6-transfected stable cell lines
β6-transfected MH 3T3 and FDC-P1 cells were generated by
electroporating parent cell lines with a DNA construct containing full length
murine β6 cDNA and a neomycin selectable marker. Stably transfected cells were
selected by passaging cells in culture medium containing G418 for 14 days
followed by fluorescent activated cell sorting (FACS) to isolate cells expressing
the highest level of surface β6. Transfected FDC-Pl cells were cultured in DMEM
supplemented with 4 mM L-glutamine adjusted to contain 1.5 g/L sodium
bicarbonate, 4.5 g/1 glucose, and 1.0 mM sodium pyruvate, 10% FBS, 2.5% mouse
IL-3 culture supplement, and 1.5 mg/ml active G418. Transfected NIH 3T3 cells
were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine,
penicillin/streptomycin, and 1 mg/ml active G418.
Example 2: Purification of human soluble αγβ6
The αγβ6 protein was purified essentially as described in Weinacker,
supra. A CHO cell line expressing hsαγβ6 was cultured, and the resultant
supernatant collected by centrifugation. The integrin was purified by affinity

chromatography using anti-αγ antibody L230. Purified L230 was cross-linked to
CNBr-activated Sepharose 4B (Sigma) at a ratio of 4.8 mg antibody/ml resin. The
αγβ6, supernatant was loaded at 0.5 mg antibody/ml resin onto the L230 affinity
column, and the column was washed with 10 column volumes of each of (1) 50
mM Tris-Cl, pH 7.5,1 M NaCl, 1 mM MgCl2; (2) 50 mM Tris-Cl, pH 7.5, 50 mM
Nad, 1 mM MgCl2; and (3) 10 mM Na3PO4, pH 7.0. Hsαγβ6 was eluted with 100
mM glycine, pH 2.5 into 1:10 volume of 1 M Na3PO4, pH 8.0. The protein was
dialyzed with several changes against phosphate buffered saline (PBS) and stored
at-20°C.
Example 3: Immunization of β6 -/- mice
β6 -/- mice were immunized by intraperitoneal (IP) injection with 25
g of purified recombinant human αγβ6 emulsified in complete Freund's adjuvant
(CFA) at a volume ratio of 1:1 in a total volume of 200 μl. Alternatively,β6-/-
mice were immunized via IP injection with 4 X 106 β6-transfected NIH 3T3 cells
resuspended in 100 μl of PBS supplemented with 1 mg/ml of CaCl2 and 1 mg/ml
MgCl2, and the same mice were injected at an adjacent site with 100 μl of CFA.
Two weeks and four weeks after the initial immunization, the mice were boosted
similarly with the same reagents with the exception that incomplete Freund's
adjuvant was used in place of CFA. The mice were bled 7 days after the final
boost and anti-β6 titers were determined by binding of the serum to purified
recombinant human αγβ6 or to β6-transfected cells. In the case of mice immunized
with purified recombinant human αγβ6, mice were rested for 3 months and
reimmunized with the same antigen mixed with ImmunEasy (Qiagen). Three days
prior to isolating spleens for hybridoma fusions, the mice were immunized with
12.5 μg of purified recombinant human αγβ6 protein by both IP and intravenous
injection. On day of fusion, the animals were sacrificed, and their spleens were
removed and teased into single cell suspensions. The splenocytes were
immortalized by fusion to a drug-selectable cell fusion partner.
Example 4:- Screening of hvbridomas
Two groups of antibodies were generated through the immunization
of β6 -/- mice. One set of antibodies were generated through immunization with
soluble human truncated αγβ6 (Fusion #6). The other set of antibodies were

generated through immunization with murine β6-transfected NIH 3T3 cells (Fusion
#7). Screening for anti-αγβ6 antibodies was carried out using both cell-based and
cell-free binding and functional assays as described below. Initial selection of
positive clones was based on binding to purified hsαγβ6 and β6-transfected human
and murine cells (untransfected cells as control). Selected clones were expanded
and terminal cultures were re-evaluated for binding to both β6-transfected and
untransfected cells in cell capture assays (Example 5b, infra) (representative
examples shown in Figs. 1A and 1B, where the prefixes "6." or "7." of the mAb
names, which denote Fusion 6 and Fusion 7, respectively, are omitted; see also
Table 2 below). Some antibodies bound preferentially to the β6-transfected cells,
while others bound to both transfected and untransfected cells, indicating that only
a subset of the antibodies had a preference for β6 (Figs. 1A and 1B). Further
selection was based on the ability of the antibodies to block binding of both
biotinylated hsαγβ6 and β6-transfected murine cells to LAP. Select clones were
subcloned using FACS and stored frozen until use.
Monoclonal antibodies were screened for specificity of binding to
αγβ6 based on their ability to bind β6-transfected cells and not untransfected parent
cells. Monoclonal antibodies were further confirmed as specific binders of αγβ6
and not of other αγ integrins or non-specific integrins (i.e., non-αγ integrins that
bind to RGD-containing ligands) based on their lack of binding to cell lines
expressing αγβ3, αγβ8, αγβ1, αγβ1 or αγβ1. These included stably transfected cells as
well as untransfected JY, K562, SW480, NIH3T3, and FDCPl cell lines.
Some of the antibodies that have been deposited with the ATCC are
listed below in Table 1.



Example 5: Assays for screening and characterization
a. αγβ6ELISA
A 96-well microtiter plate (Coming COSTAR EASY-WASH) was
coated with 50 μl/well of 5 μg/ml hsαγβ6 at 4°C overnight. The plate was washed
with wash buffer (0.1% TWEEN-20 in PBS) four times in an automated plate
washer. Then 180 l/well of 3% BSA in TBS was added and incubated for 1 hr at
25°C to block nonspecific binding. The plate was washed as above, and dilutions
of either hybridoma supernatant (for screening assays) or purified antibody (for
characterization) in TBS containing 1 mg/ml BSA, 1 mM CaCh, and 1 mM MgCl2
were added (50 μl/well). The plate was incubated for 1 hr at 25°C, washed, and
then incubated for 1 hr with 50 l/well of peroxide-conjugated goat anti-mouse
IgG+A+M antibody (Cappel). Bound antibody was detected using 3,3',5,5'-
tetramethylbenzidine (TMB). Binding was indicated by the absorbency measured at 450 nm.
b. Cell capture assay
A 96-well microtiter plate was coated with 50 μ^well of secondary
antibody (donkey anti-mouse IgG (Jackson Immunoresearch); 5 μg/ml diluted in
50 mM sodium bicarbonate, pH 9.2) at 4°C overnight. Plates were washed twice with 100 μl/well of assay buffer (RPMI + 2% BSA) and then blocked with 100
μl/well of the assay buffer at 37°C for 1 hr. For FDC-Pl cells and β6-transfected
FDC-P1 cells, plates were blocked with anti-mouse Ig (Jackson ImmunoResearch;

20 μg/ml) for 10 min at room temperature to decrease non-specific Fc receptor
binding by secondary antibody (omitted for other cell types). While the plates
were being blocked, the cells were labeled with 2 μM fluorescent dye (Calcein-
AM, Molecular Probes) in the assay buffer at 5 X 106 cells/ml. The cells were
incubated with the dye in the assay buffer with gentle shaking in a 37ºC water bath
for 15 min, collected by centrifugation, and resuspended in assay buffer to 5 X 106
cells/ml. Following the blocking step, the buffer was discarded by flicking the
plate, and 25 μg/well of supernatant or purified antibody was added to the plate.
Following a 15 min incubation at 37°C, 25 μl/well of labeled cells were added, and
the plate was incubated for 1 hr at 37°C. The plate was washed 3-5 times with the
assay buffer (100 μg/well) and fluorescence emitted by captured cells on the plate
was recorded. Percent binding was determined by comparing the fluorescence
prior to the final wash step (i.e., total cells added) to that after washing (i.e. bound
cells).
c. FACS
Cells were harvested by trypsinization, washed one time in PBS,
and then resuspended in FACS buffer (IX PBS, 2% FBS, 0.1% NaN3, 1 mM
CaCl2, and 1 mM MgC12). 0.2 X lO5 cells were then incubated on ice for 1 hr in
FACS buffer containing hybridoma supernatant in a total volume of 100 μl. After
incubation, the cells were washed two times with ice cold FACS buffer,
resuspended in 100 μl of FACS buffer containing 5 μg/ml donkey anti-mouse IgG
PE (Jackson ImmunoResearch), and incubated on ice for 30 min. The cells were
then washed twice with ice cold FACS buffer and resuspended in 200 μl of FACS
buffer. Binding of the PE labeled secondary antibody was monitored by flow
cytometry.
d. Binding of biotin-hsαγβ6 to LAP
96-well microtiter plates (Corning COSTAR EASY-WASH) were
coated with 0.3 g/ml recombinant human LAP (R&D Systems, Cat. # 246-LP)
diluted in PBS (50 μg/well) at 4°C overnight. After the coating solution was
removed, the plates were blocked with 180 μg/well of 3% BSA/TBS at 25°C for 1
hr. In a separate 96-well round-bottom plate, 60 μl/well of a 2X stock (0.5 g/ml
(1.25 nM) of biotin-αγβ6, 2 mM CaCl2, and 2 mM MgCl2 in TBS containing 1

mg/ml BSA) was combined with 60 μ^well of a 2X stock of either a hybridoma
supernatant (for screening) or a purified antibody (also in TBS containing 1 rng/inl
BSA) and incubated at 25°C for 1 hr. After washing the LAP-coated plate with
wash buffer (0.1% TWEEN-20 in PBS) 4 times in an automated plate washer, 100
l of the antibody-αγβ6 mixture was transferred to the plate, and incubated for 1 hr
at 25°C. The plate was washed as above and incubated with 50 μl/well of a 1:1000
dilution of extravidin-horseradish peroxidase conjugate (Sigma) in TBS (1 mg/ml
BSA) for 1 hr at 25°C. Bound protein was detected using the TMB substrate.
e. Adhesion of β6-FDC-Pl cells to LAP
A 96-well microtiter plate was coated with 50 μl/well of 0.5 μg/ml
recombinant human LAP (R&D Systems) diluted in 50 mM sodium bicarbonate,
pH 9.2 at 4°C overnight. The plate was washed twice with PBS (100 μl/well) and
blocked with 1% BSA in PBS (100 μg/well) for 1 hr at 25°C. The plate was
washed twice with 100 μg/well of assay buffer (TBS complete plus 1 mM CaCl2
and 1 mM MgCl2). Next, to the individual wells of the plate were added 25 μl of a
hybridoma supernatant (or a purified antibody) and 25 μl of β6-FDC-Pl cells (5X
106 cells/ml, labeled with Calcein AM as described above). The plate was
incubated at 25°C for 1 hr, and then washed 4-6 times with the assay buffer (100
μl/well). The fluorescence emitted from cells captured on the plate was recorded.
Percentage binding was determined by comparing the fluorescence signal prior to
the final wash step (i.e., total cells added) to that after washing (i.e., bound cells).
f. TGF-β bioassay
The TGF-β bioassay used herein was a variation of the Mink lung
epithelial cell (MLEC) PAI-1 luciferase coculture assay described in Abe et al.,
Anal. Biochem. 216:276-284 (1994), in which β6-transfected cells were cocultured
with the reporter cells to monitor activation of TGF-β by αvβ6 (Munger, supra). It
is a quantitative bioassay for TGF-β based on its ability to induce the expression of
plasminogen activator inhibitor-1 (PAI-1). In this assay, MLEC cells are stably
transfected with an expression construct containing a truncated PAI-1 promoter
fused to the firefly luciferase reporter gene. Exposure of the transfected MLEC
cells to active TGF-β (0.2 to > 30 pM) results in a dose-dependent increase in
luciferase activity in the cell lysates.

To conduct this assay, TMLC (mink lung epithelial cell line Mv 1
Lu) cells were transfected with the PAI-1-luciferase construct. The transfected
cells were grown in DMEM + 10% FBS with L-Gln, Pen/Strep and 200 μg/ml
G418. SW480 cells transfected with an integrin & construct ("β6-SW480" or
"SW480 β6" cells) were grown in DMEM + 10% FBS with L-Gln and Pen/Strep.
Cells were lifted from flasks with PBS + 5 mM EDTA, washed in PBS + 0.5%
BSA, counted by hemocytometer and plated in 96-well plates. SW480-β6 cells
were plated at 4 X 104 cells/well in the wash buffer. Monoclonal antibodies were
diluted in DMEM (serum-free), added to the SW480-β6 cells and pre-incubated for
20 min at room temperature. TMLC cells were then added at 2 X 104 cells/well to
a final volume of 100 l. The plates were incubated for 20 hr in a humidified,
CO2-enriched incubator. Supernatant from the plates was discarded and replaced
with 100 μl of PBS + 1 mM Ca2+ and 1 mM Mg2+. Cells in the plates were then
lysed, and the level of luciferase activity was detected with the glow-type reaction
Packard LUCLITE kit (#6016911) and TROPIX microplate luminometer.
Example 6: Antibody purification
Eight hybridoma clones from Fusion #6 (denoted by the prefix "6.")
and fourteen hybridoma clones from Fusion #7 (denoted by the prefix "7.") were
selected for further scale-up and characterization (Table 2).
A small-scale culture (150 ml) of each hybridoma was prepared,
and the supernatant was collected by centrifugation. Antibodies were purified
from these supematants using Protein A affinity chromatography. For the IgG2a
isotype antibodies, the supernatant was directly loaded onto Protein A Sepharose 4
Fast Flow (Amersham Pharmacia Biotech, AB, Uppsala, Sweden) (1 ml settled bed
volume). The column was washed with PBS, and the IgG fraction was eluted
using 25 mM phosphoric acid, 100 mM NaCl, pH 2.8 into 1:20 volume of 0.5 M
Na3PO4, pH 8.6. For the murine IgG1 antibodies, the supernatant was adjusted to
1.5 M glycine, 3 M NaCl, pH 8.9 prior to loading, and the column was washed
with 25 mM Na3PO4, 3 M NaCl, pH 8.6 prior to elution. These preparations were
used for the in vitro biochemical characterization described herein.



*: A blocker is defined as an antibody that blocks the binding of αvβ6 to LAP as
determined by blocking of ligand binding either to purified hsαvβ6 or to β6-
expressing cells.
For use in animal models, hybridoma clones were scaled up to 2L of
media and grown for 4 weeks in Lifecell Culture Bags-PL732 (Nexell, Cat. No.
R4R2113). Antibodies from the hybridomas were purified first by Protein A
affinity chromatography as described above, followed by an ion-exchange step on
Q Sepharose (Amersham Pharmacia). The eluate from the Protein A
chromatographic step was adjusted to pH 8.6 using 2 M Tris base, diluted 10-fold
with water, and loaded onto a Q Sepharose column (20 mg protein/ml resin) that
had been equilibrated in 10 mM Na3PO4, 25 mM NaCl, pH 8.6. The column was
washed with 5 column volumes of equilibration buffer, and bound protein was
eluted using 25 mM Na3PO4, 150 mM NaCl, pH 7.2. The eluted proteins were
sterile-filtered (0.45 μm) and stored at -70°C until use.
Example 7: Characterization of purified antibodies
The purified antibodies (Table 2, supra) were characterized
quantitatively with respect to their ability to (1) bind hsαvβ6, (2) bind β6-transfected
SW480 and FDC-Pl cells, (3) inhibit binding of biotin-αvβ6 to LAP, (4) inhibit
binding of β6-transfected FDC-Pl cells to LAP, and (5) block αvβ6-mediated
activation of TGF-β in the MLEC assay (supra). The relative potency in each of
these assays was compared to that of the known αvβ6 antibody 10D5 (Huang et al,
J. Cell Sci. 111:2189 (1998)) and, in some cases, the anti-αv antibody L230. For
the characterization of Fusion #7 antibodies, the Fusion #6 antibody 6.8G6 was
also used as a positive control.
An initial binding experiment (Example 5a, supra), carried out in
the presence of 1 mM Ca2+ and 1 mM Mg2+, indicated that a majority of the
purified antibodies bound to hsαvβ6 (Figs. 2A and 2B). Unexpectedly, however, no
binding was observed for 10D5 and clones 7.2F5 and 7.10D7. A subsequent
experiment established that binding of 10D5 (Fig. 3E), 7.2F5, and 7.10D7 was
supported only weakly by Ca2+/Mg2+, but much more strongly by 1 mM MnCl2.
Among the new clones, three (6.1 A8 (Fig. 3A), 7.7G5, and 6.8G6 (Fig. 3C))
showed a requirement for divalent cations, although no difference between the
Ca2+/Mg2+ state and the Mn2+-bound state was observed.

The remaining clones showed no requirement for divalent cations,
i.e. could bind to the antigen in the presence of 10 mM EDTA (Figs. 3B, 3D and
3F). FACS analysis of antibody binding to β6-transfected NIH 3T3 cells or SW480
cells revealed a similar pattern, with the exception that 10D5, in this context,
bound equivalently in the Ca2+/Mg2+ and Mn2+ states. The requirements for
binding to soluble αvβ6 may differ from those for binding to cell surface-expressed
αvβ6 due to a difference in protein conformation or avidity effects.
These results suggest that there are at least 3 different classes of β6-
blocking antibodies in this group. One of the classes (10D5) distinguishes between
the Ca2+/Mg2+ and Mn2+ conditions. Another class (including 6.1 A8, 7.7G5, and
6.8G6) requires cation but does not distinguish between Ca2+/Mg2+ and Mn2+. The
last class (including anti-ct, antibody L230, 6.2B10, 6.3G9 (Fig. 3B), and 6.2B1
(Fig. 3D), 7.1C5, and 7..1G10) is cation-independent.
The purified antibodies were next evaluated for their ability to
inhibit the αvβ6-LAP interaction. In the cell-free assay of Example 5d, supra,
antibodies 6.1A8, 6.2B1, 6.3G9, and 6.8G6 showed IC50 values lower than that of
10D5 (Fig. 4A; Table 3). 6.2B10 showed a higher IC50 but still gave complete
inhibition (Fig. 4A). 6.4B4 showed only partial inhibition, whereas 6.6B5 and
6.8B4 showed no inhibition (Fig. 4A). Using the same assay system, antibodies
7.1C5, 7.1G10, 7.2A1, 7.4A3, 7.7G5, 7.9G8, 7.9H5, and 7.10H2 showed IC50
values lower than that of 10D5 (Fig. 4B; Table 3). Antibodies 7.2F5, 7.2H2 and
7.8H12 displayed nearly identical or higher IC50 values and yet still gave complete
inhibition (Fig. 4B).
In the cellular assay described in Example 5e, supra, a similar trend
was observed, with the exceptions of 6.1 A8,6.2B10 and 7.9D4, which were much
less potent on cells than on purified protein (Figs. 5A-E; Table 3).
Collectively, these results indicate that we have successfully
generated antibodies that specifically inhibit the interaction of both human and
murine αvβ6 with LAP. Some of these antibodies bound to αvβ6 with high affinity
(apparent Kd's ≥0.3 nM, as determined by flow cytometry), inhibited binding of
β6-transfected cells to LAP with an IC50 of ≥0.05 nM (8 ng/mL), and prevented
αvβ6-mediated activation of TGF-β1 with an IC50 of ≥0.58 nM (87 ng/mL).

Finally, the purified antibodies were evaluated for their ability to
block αvβ6-mediated activation of TGF-/3 in the PAI-1/luciferase reporter gene
assay (Example 5f, supra). Once again, 6.3G9, 6.8G6,6.2B1,7.1G10, and 7.7G5
were able to inhibit αvβ6-mediated activation of TGF-β with IC50 values lower than
10D5, while the remaining antibodies appeared to be significantly less potent in
this assay (Figs. 6A and 6B; Table 3). Thus, the ability to block αvβ6's interaction
with LAP correlates with the ability to inhibit activation of TGF-β in vitro.



dilutions of the soluble integrin (1 X 10-8 M to 2.4 X 10-12 M) were incubated with
1X 10-10 M of the antibody for 3 h. These samples were then passed through
polymethylmethacrylate beads coated with the integrin using a KinExA instrument
(Sapidynelnstruments, Inc., Boise, Idaho). In the case of 6.8G6, 1mM CaCl2 and
1mM MgCl2 were included in the incubation and assay buffers. The amounts of
bound and free antibody were determined using a Cy5-labeled anti-mouse
secondary antibody. Quadratic curve fitting was performed using the KinExA
software to attain a dissociation constant (Kd) for each interaction. The Kd's
determined using this method were 15.6 pM for 6.3G9 and 22.8 pM for 6.8G6
(Figs. 9 A and 9B). Thus, both of these antibodies had very high affinities for αvβ6-
We further identified classes of anti-αvβ6 antibodies that recognized
"activated" states of the integrin. There are two potential activation states of αvβ6-
In the first state, the activated integrin is defined as having a higher affinity for its
ligand. Antibodies specific for this activated state showed enhanced binding to the
integrin in the presence of activating cations such as 1 mM MnCl2. A comparison
of the extent of binding in 1 mM MnCl2 and 1 mM MgCl2 (non-activating cation)
by flow cytometry indicated that some of the αvβ6 antibodies described here,
including 6.1 A8 and 6.6B5, showed significantly enhanced binding in the presence
of MnCl2.

In a second activated state of αvβ6, the integrin can activate latent
TGF-β as described above. A cell line expressing truncated αvβ6 (SW480(β6-
770T)) was prepared. The cell line was able to bind LAP but could not activate
TGF-β in the TMLC luciferase assay (Munger et al., supra). Antibodies which
bind to the full length β6-transfected SW480 cells, but not to the 770T truncated
transfected cells, were thus specific to the form of αvβ6 that is able to activate
TGF-β. Antibodies 7.8B3 and 7.8C9 met this criteria.
Example 8: Epitope mapping by antibody competition
The purified monoclonal antibodies were also tested for their ability
to compete with 6.8G6 for binding to biotinylated αvβ6 in an ELISA format. In this
assay, 6.8G6 was coated on an ELISA plate, and a mixture of the competing
antibody and biotinylated αvβ6 was added in a buffer containing 1 mM each of Ca2+
and Mg2+. Bound integrin was detected using extravidin-HRP conjugate, and
competing antibodies were scored for their ability to block binding. All consensus
blockers (Table 2) except 6.2B10 (a weak blocker) were shown to be able to
compete with 6.8G6 to various degrees (Table 4). These data confirm that these
consensus blockers bind to the same or overlapping epitope as 6.8G6.



The purified monoclonal antibodies were tested for their ability to
compete with biotinylated 6.3G9 or biotinylated 6.8G6 for binding to αvβ6 in
ELISA. In this assay, unlabeled αvβ6 was coated on an ELISA plate, and a mixture
of the competing antibody and the biotinylated antibody was added in a buffer
containing 1 mM each of Ca2+ and Mg2+. Bound biotinylated antibody was
detected by using neutravidin-HRP conjugate. The data showed that the most
potent blocking antibodies (e.g., 6.2B1, 7.1C5, and 7.1G10) competed with both
6.3G9 and 6.8G6 for binding to αvβ6 (Table 4.1, and Figs. 10A and 10B).
Antibodies 6.1A8 and 7.7G5 showed less competition, probably due to their lower
affinity for αvβ6. None of the non-blocking antibodies or the anti-αv antibody
L230 showed any competition with 6.3G9 or 6.8G6 in this assay. These results
indicate that the αvβ6-specific blocking antibodies bind to the same or overlapping
epitopes on αvβ6.



Example 9: CDR sequences
The cDNAs for some of the purified monoclonal antibodies were
isolated and sequenced using standard techniques as described in Coligan et al.
(eds), Current Protocols in Immunology, Wiley, Media, PA (2001). The deduced
amino acid sequences are shown in Figs. 7A and 7B.
Amino acid sequences of the heavy chain CDRs of high affinity
binders 6.8G6,6.1A8,6.2B1,6.3G9 and 6.2A1 and of nonblocker 6.2G2 are
compared as follows (dashes indicate gaps).
CDRl
6.8G6 SYTFTDYAMH (SEQ ID NO:1)
G.1A8 SYTFTDYTMH (SEQ ID NO:2)
6.2B1 GFTFSRYVMS (SEQ ID NO:3)
6.3G9 GFTFSRYVMS (SEQ ID NO:3)
6.2A1 GYDFNNDLIE (SEQ ID NO:4 9)
6.2G2 GYAFTNYLIE (SEQ ID NO:50)
CDR2
6.8G6 VISTYYGNTNYNQKFKG (SEQ ID NO:4)
6.1A8 VIDTYYGKTNYNQKFEG (SEQ ID NO:46)
6.2B1 SISSG-GSTYYPDSVKG (SEQ ID NO:5)
6.3G9 SISSG-GRMYYPDTVKG (SEQ ID NO:6)
6.2A1 VINPGSGRTNYNEKFKG (SEQ ID NO:51)
6.2G2 VISPGSGIINYNEKFKG (SEQ ID NO:52)
CDR3
6.8G6 GGLRRGDRPSLRYAMDY (SEQ ID NO:7)
6.1A8 GGFRRGDRPSLRYAMDS (SEQ ID NO:47)
6.2B1 GAIYDG YYVFAY (SEQ ID NO: 8)
6.3G9 GSIYDG YYVFPY (SEQ ID NO: 9)
6.2A1 IYYGPH SYAMDY (SEQ ID NO: 53)
6.2G2 ID-YSG PYAVDD (SEQ ID NO: 54)

In SEQ ID NO: 7, the "R" in boldface (the twelfth residue) indicates
that it is subject to polymorphism and can be, for example, a Q.
Amino acid sequences of the light chain CDRs of these four high
affinity binders and of nonblocker 6.2G2 are compared as follows.
CDRl
6.8G6 RASQSVSTSS-YSYMY (SEQ ID NO:10)
6.1A8 RASQSVSIST-YSYIH (SEQ ID NO-.48)
6.2B1 SASSSVSSS YLY (SEQ ID NO:11)
6.3G9 SANSSVSSS YLY (SEQ ID NO: 12)
6.2A1 KASLDVRTAVA (SEQ ID NO:55)
6.2G2 KASQAVNTAVA (SEQ ID NO:56)
CDR2
6.8G6 YASNLES (SEQ ID NO:13)
6.1A8 YASNLES (SEQ ID NO:13)
6.2B1 STSNLAS (SEQ ID NO:14)
6.3G9 STSNLAS (SEQ ID NO:14)
6.2A1 SASYRYT (SEQ ID NO:57)
6.2G2 SASYQYT (SEQ ID NO:58)
CDR3
6.8G6 QHNWEIPFT (SEQ ID NO:15)
6.1A8 QHSWEIPYT (SEQ ID NO:16)
6.2B1 HQWSSYPPT (SEQ ID NO:17)
6.3G9 HQWSTYPPT (SEQ ID NO:18)
6.2A1 QQHYGIPWT (SEQ ID NO:59)
6.2G2 QHHYGVPWT (SEQ ID NO:60)
As shown in Figs. 7A and 7B, the mAbs that fall into the divalent
cation-dependent class (e.g., 6.1A8 and 6.8G6) seem to contain very similar amino
acid sequences within the CDRs, while the divalent cation-independent mAbs
(e.g., 6.2B1 and 6.3G9) contain another set of motifs in their CDRs.

The potency and specificity of ami-αvβ6 monoclonal antibodies may
be governed by subtly different amino acid residues. In the case of 6.1A8 and
6.8G6, the amino acid sequences of the variable domains are very similar,
containing 10 amino acid differences in the heavy chain, three of which are
conservative, and 11 amino acid differences in the light chain. Yet these
antibodies have a roughly 100-fold difference in activity in in vitro assays. The
amino acid differences are dispersed throughout the variable domains of the
polypeptide chains and these residues may function alone or synergistically with
residues on the same chain or the partner chain to affect the potency of the
antibodies. In the heavy chain, seven residues are located such that they are likely
to be in close proximity to, or play an active role in binding to, αvβ6.
An RGD motif is found in a number of integrin-binding proteins
(ligands). This motif has been shown to mediate their interaction with integrins by
directly contacting the binding pocket on the integrin. Because RGD itself is fairly
common among integrin-binding proteins, flanking residues outside the motif must
play a role in conferring binding specificity to the integrin-ligand interaction. In
6.1A8 and 6.8G6, one such flanking residue is at position 101 in the heavy chain,
within CDR3. This amino acid residue flanks the RGD motif and may be located
at the site of antigen recognition, contributing to binding potency and specificity.
Other different residues within the same heavy chain CDRs of
6.1A8 and 6.8G6 include those at positions 33 (CDR1); positions 52, 57, and 65
(CDR2); and position 115 (CDR3). Another difference in the heavy chain lies at
position 4 in framework 1, which is near the N-terminus. This residue is predicted
by crystallographic models to fold close to the CDRs of the antibody and may play
an important role in αvβ6 binding. The three remaining differences between 6.1A8
and 6.8G6 are conservative differences at positions 20 (framework 1), 44
(framework 2) and 82 (framework 3).
The amino acid sequences of the cation-independent antibodies are
also highly homologous. They can be divided into two classes: those that compete
with the RGD-containing antibody 6.8G6 (i.e., 6.2B1, 6.3G9, 7.10H2, 7.9H5,
7.1C5,7.1G10, and 7.4A3); and those that do not (i.e., 6.2A1, 6..2B10 and 6.4B4).
The 6.8G6-competing class contains a FXY motif in CDR3 of the heavy chain,

whereas the noncompeting class does not. This difference suggests that the FXY
motif is important for mediating cation-independent binding to αvβ6. Additionally,
this FXY-containing class of antibodies probably bind to an epitope on αvβ6 that is
overlapping with, yet distinct from, the RGD-binding pocket. Antibodies 6.2B10
and 6.4B4 do not contain an FXY motif and are poor αvβ6 blockers. They were
shown to bind to the αvβ6 I-domain-like portion and define yet another epitope to
which anti-αvβ6 antibodies bind. Interestingly, the monoclonal antibody 6.2A1
belongs to the cation-independent class but does not contain the RGD sequence, as
with other cation-independent mAbs.
Monoclonal antibody 7.7G5 belongs to the cation-dependent class.
However, the light chain sequence of 7.7G5 is highly homologous to the cation-
independent, I-domain binding antibody 6.2B10. The heavy chain of 7.7G5 is also
similar to cation-independent antibodies in CDRl. Yet its CDR2 and CDR3 are
more similar to those of the cation-dependent class. This observation suggests that
specific CDRs confer specificity to an antibody. This is particularly true for CDR3
of the heavy chain, presumably due to the high degree of variability within this part
of the antibody. In fact, two out of three cation-dependent and seven out of nine
cation-independent antibodies contain heavy chain CDR3 sequences that are likely
to play an important role in αvβ6 recognition. Of note, 7.7G5 lacks an RGD motif
but contains an XGD motif in its heavy chain CDR2. This XGD motif may
function in a similar fashion to RGD and confer binding affinity/specificity to
7.7G5.
The above sequence observations and inferences made therefrom
provide a basis for rational design of specific variable region amino acid sequences
that confer specific binding properties.
Example 10: Diagnostic antibodies
Antibodies that can detect αvβ6 expression in paraffin-embedded
tissue sections or other tissue samples may be useful as diagnostics. These
diagnostic tools can be used to, e.g., detect upregulated αvβ6 in tissue sections for
such indications as cancer or fibrosis.
In order to identify antibodies that detect αvβ6 in paraffin-embedded
tissues, we first screened a panel of antibodies for binding to HPLC-purified β6

subunit. Antibodies which bind this subunit are likely recognizing linear peptide
epitopes, and were therefore expected to have a greater likelihood for success in
paraffin-embedded tissues. Binding to purified β6 subunit was carried out using an
ELISA format identical to that described for measuring αv binding (supra),
except with the purified β6 integrin, rather than the αvβ6 protein, immobilized on
the plate. Using this method, a number of Fusion 6 antibodies capable of binding
both the purified αvβ6 protein and the purified β6 subunit were identified. See
Table 5, infra, where the prefix "6." in the clone names is omitted.







As shown above, some antibodies bound to purified β6 subunit.
They will have a high likelihood to bind to denatured αvβ6 and thus can be useful in
detecting αvβ6 in paraffin-embedded tissue sections. Other antibodies bound to
soluble αvβ6 but not the β6 subunit. Both types of antibodies were used to stain
denatured paraffin-embedded β6-transfected SW480 cells and untransfected parent
cells, and the data are shown in Table 6.
To stain paraffin-embedded tissues or cells, the sample slides were
first de-paraffinized by incubation in the following solutions: (1) Xylene, 5 min,
twice; (2) 100% ethanol, 2 min, twice; (3) 95% ethanol, 2 min, twice; (4) 50%
ethanol, 2 min, once; and (5) distilled water, 2 min, once. The slides were then
incubated in a solution consisting of 200 ml of methanol and 3 ml of 30% H2O2 for
15 min to block endogenous peroxidase. The slides were rinsed twice in PBS for 2
min each time. The paraffin sections on the slides were then unmasked with
pepsin (Zymed 00-3009) for 5 min at 37°C. The slides were rinsed again twice in
PBS for 2 min each time. Next, the slides were blocked with avidin and then
biotin (Vector SP-2001; Vector Laboratories, Burlingame, CA), 10 min each at
room temperature, with washing between each incubation as described above.
After the blocking solution was drained off the slides, the primary antibody
(hybridoma culture supernatant) diluted in PBS/0.1% BSA was applied to the
slides and incubated overnight at 4°C.

The next day, the slides were rinsed in PBS as described above.
Meanwhile, the avidin-biotin complex-horseradish peroxidase solution (ABC
reagent) was prepared as follows: 1 ml of PBS was mixed with 20 /l of solution A
(1:50) and 20 l of solution B (1:50) from Vector Kit PK-6102; and the mixture
was incubated for 30 min at room temperature before use. During this time, the
slides were incubated for 30 min at room temperature with anti-mouse-biotinylated
antibody (1:200) from the Vector Kit with 15 μl/ml normal serum. The slides were
then rinsed twice in PBS, 2 min each time. Then the above-described ABC reagent
was applied to the slides and incubated for 30 min at room temperature. The slides
were rinsed again as described above. Then the substrate (Vector SK-4100), 100
μl of DAB (3,3'-diaminobenzidine), were applied to the slides and incubated for 5
min at room temperature. DAB was prepared as follows: to 5 ml of H2O, add 2
drops of Buffer Stock Solution, mix well; then add 4 drops of DAB Stock solution,
mix well; and then add 2 drops of H2O2 Solution, mix well. Then the slides were
rinsed in running water for 2 min. Next, the DAB signal was enhanced for all
slides as follows: rinse the paraffin sections in 0.05 M sodium bicarbonate, pH 9.6,
for 10 min; blot excess buffer, apply the DAB Enhancing Solution 15 seconds; and
then quickly rinse with water for 1 min to stop reaction. The slides were then
stained in Mayer's Hematoxylin (a nuclear counterstain) for 1 min. The slides
were rinsed in running water for 1 min, and then submerged in PBS for 1 min so
that the hematoxylin turned blue. The slides were then rinsed again in running
water for 1 min and dehydrated and cleared as follows: submerge in (1) 95%
ethanol for 1 min, twice; (2) 100% ethanol for 1 min, twice; and (3) Xylene for 2
min, twice. Coverslips were then applied to the slides using permount.
The results suggested that Fusion 6 antibodies 1A1, 2C4, 3B2,
3B11, 5D6, 5G9, 5H3, 6D12, 7C7, 9B5, 9B7, 9D11, 9F5, 10E4, 10H11, 6H8, 7A5,
7G9, 9A3, 2A1, 2E5,4E4, 4H4, 8B4, 2G2, and 4E6, all of which could bind to
purified β6 subunit (Table 5), indeed stained paraffin-embedded β6-transfected
SW480 cells strongly, while not staining untransfected parent cells (Table 6).




Example 11: Diagnosis of cancer
αvβ6 is normally expressed at negligible to low levels in healthy
adult tissues. However, αvβ6 expression is upregulated in injury, fibrosis, and
cancer (see, e.g., Thomas et al. J. Invest. Dermatology 117:67-73 (2001); Brunton
et al., Neoplasia 3: 215-226 (2001); Agrez et al., Int. J. Cancer 81:90-97 (1999);
Breuss, J. Cell Science 108:2241-2251 (1995)). Thus, antibodies that bind
specifically to αvβ6 expressed on paraffin-embedded tissues can be used in standard
immunohistochemistry techniques to detect αvβ6 expression for diagnosis of
fibrosis, cancer and any other diseases in which αvβ6 is upregulated.
As described above, certain antibodies of the present invention bind
to HPLC-purified β6 integrin and paraffin-embedded and fixed β6-transfected cells.
These antibodies were also shown to bind to representative squamous and breast
cancer tissues in immunostaining. See, e.g., Fig. 8, where monoclonal antibody
6.2A1 was used to show relative staining of paraffin-embedded breast and
squamous carcinomas. Thus, these new antibodies are useful as diagnostic tools.
Example 12: Effects of anti-αvβ6 blocking mAbs in Alport mice
The collagen 4A3 (COL4A3) knockout (Alport) mice have been
established as an in vivo model for kidney fibrosis and used to test the therapeutic
effects of pharmacological agents (supra). We tested mAb 6.8G6 (cation-
dependent) and 6.3G9 (cation-independent) in Alport mice to determine if they
would inhibit the fibrosis normally observed in seven week old Alport mice. As
shown above, these two antibodies were found to inhibit αvβ6 binding to LAP and
to inhibit activation of TGF-β in a bioassay. Antibody 1E6 was used as a negative
control.
Three week old Alport mice were given intraperitoneal injections 3
times a week with one of the following antibodies: (1) 6.8G6,4mg/kg (7 mice); (2)

6.3G9,4 mg/kg (4 mice); and (3) 1E6, 1mg/kg (6 mice). The injections were
continued for 4 weeks. The mice were then sacrificed, and their kidneys retrieved.
Paraffin-embedded sections of the kidneys were made as described
above, and then stained to detect smooth muscle actin, a marker for myoblasts and
matrix deposition in kidney fibrosis. We found a significant decrease in smooth
muscle actin staining in both the interstitial and glomerular regions of the kidney
from the Alport mice treated with mAb 6.8G6 or 6.3G9, as compared to mice
treated with 1E6.
Figs. 11A and 11B show a dot plot of smooth muscle actin staining
in the glomerular and interstitial regions of the Alport kidney. There was
significantly reduced smooth muscle actin staining in the kidneys of the Alport
mice treated with 6.8G6 and 6.3G9, as compared to negative control lE6-treated
mice.
Example 13: Effectiveness of anti-αvβ6 mAbs in preventing unilateral ureteral
obstruction-induced nephrosclerosis
We used another mouse model for renal fibrotic progression to test
the antifibrotic efficacy of 6.8G6 and 6.3G9. In this mouse model, a ureter of the
animal is ligated, resulting in unilateral ureteral obstruction (UUO). UUO causes
progressive nephrosclerosis without near-term renal failure in mice because the
unobstructed kidney can maintain relatively normal renal function. While the
obstructed kidney undergoes rapid global fibrosis, the unobstructed kidney
undergoes adaptive hypertrophy.
This study quantitated morphometrically the impact of anti-αvβ6
treatment on UUO-induced renal fibrosis. Male, 8-12 week old, viral antigen-free
C57BL mice of 25.5±0.2 g in weight (Jackson Laboratories, Bar Harbor, ME) were
used. The mice were allowed to accommodate for seven days prior to beginning
the study. The mice had ad libitum access to irradiated standard mouse chow and
sterile water throughout the accommodation and experimental period. Body
weight was measured at intervals as part of animal health monitoring. The results
showed that age-matched unoperated mice gained about 10% body weight over the
two-week study period. UUO mice lost about 9% body weight by day 2 but

gradually regained the lost body weight by day 14. This weight change pattern
occurred irrespective of therapeutic treatment.
To induce renal fibrosis, the left ureter was aseptically isolated via a
left-of-midline laparotomy under ketamine:xylazine (100:10 mg/kg s.c.)
anesthesia. Two tight, occlusive 6-0 silk ligatures were placed on the ureter at the
level of the lower pole of the kidney, and the ureter cut between the ligatures. The
abdominal wall was closed with 4-0 Vicryl suture and the skin closed with 4-0
nylon. The animals were allowed to recover on a heating pad and given 0.05
mg/kg s.c. buprenorphine twice daily on days 0 and 1. The procedure was adapted
from Ma et al., Kidney Int. 53 (4):937-944 (1998).
The mice were then divided into the following study groups:

All animals except those in Group 5 were dosed twice weekly beginning on the
day before surgery.
The animals were then euthanized with carbon dioxide at day 10
after ligation and dissected. In UUO mice, the renal pelvis and ureter were
markedly swollen and fluid-filled above the obstructing ligature. The degree of
swelling and extent of remaining renal tissue mass varied among treatment groups.
Group 2 showed about half as much swelling as negative control groups. Ligated
kidneys were pale in color. Contralateral kidneys were bright red and enlarged by
about one third.
Next, both kidneys (left ligated, right unligated) of the animals were
removed and halved transversely through the center of the renal pelvis. One half
of each kidney was placed in 10% neutral buffered formalin for fixed-tissue

staining. The other half of each kidney was placed in 15% sucrose, followed by
30% sucrose, for immunohistochemical staining.
Formalin-fixed kidney sections were immunostained for
myofibroblasts (smooth muscle actin), a marker of fibrosis. Images were captured
using standardized lighting conditions and digital cameral exposure settings,
corrected for background, and calibrated to distance standards. Images of
contiguous fields covering the entire left kidney section were taken from each
animal for quantitation.
Smooth muscle actin was expressed as a percent of total tissue area
within the measured fields. These included all cortical and medullary tissue from
the section except the renal papilla.
In conclusion, mice treated with 6.3G9 and 6.8G6 show a
significant reduction in fibrosis.
Example 14: Effectiveness of anti-αvβ6 blocking mAbs against bleomycin-induced
lung fibrosis in mice
Bleomycin-induced lung fibrosis in mice has been established as an
in vivo model for lung fibrosis and used to test the therapeutic effects of
pharmacological agents. Inflammation is normally evident 5-15 days following
bleomycin treatment. In 129 strain mice, the degree of pulmonary fibrosis
progressively increases for up to 60 days after bleomycin treatment. Matrix
accumulation usually becomes detectable around day 15. In this example, mAb
6.3G9 was injected intraperitoneally at a concentration of 4 mg/kg/dose into mice
with bleomycin-induced lung fibrosis starting at day 0 or day 15, three times
weekly. Lung fibrosis was induced at day 0 by administering a single intratracheal
dose of bleomycin at a concentration of 0.03 units/kg in 50 μl of sterile saline. The
animals were sacrificed at day 30 and the extent of lung fibrosis was assessed.
Antibody 1E6 was used as a negative control.
Lungs were harvested from each animal and hydroxyproline content
was measured as an index of lung collagen deposition, as described in Monger et
al., supra. As shown in Fig. 15 A, treatment with 6.3G9 beginning at day 0
significantly inhibited the bleomycin-induced increase in lung hydroxyproline
content. Importantly, the 6.3G9 treatment was at least as effective when it began

15 days after bleomycin administration, a time when collagen deposition had
already begun.
We also examined the effects of 6.3G9, cation-dependent 6.8G6,
and the non-blocking antibody 6.4B4 in inhibiting more substantial degrees of lung
fibrosis in an extended bleomycin-induced fibrosis protocol (lasting 60 days). To
do this, we started the antibody treatments 15 days after bleomycin administration
(day 15). Lungs were then harvested at day 60 to determine hydroxyproline
content. As shown by Fig. 15C, treatment with 6.8G6 significantly inhibited
bleomycin-induced fibrosis (a more than 70% reduction in hyrdroxyproline content
compared to animals treated with bleomycin and saline). Treatment with 6.3G9
also showed a trend toward protection, but these results did not reach statistical
significance (Fig. 15C).
In conclusion, both cation-dependent and cation-independent anti-
αvβ6 blocking mAbs reduced lung fibrosis in mice treated with bleomycin.
Furthermore, this intervention was effective even when antibody treatment was not
initiated until after the initial onset of fibrosis.
Example 15: Upregulation of αvβ6 in human psoriasis lesions
In order to determine whether αvβ6 is involved in psoriasis, αvβ6
expression was examined on lesional and nonlesional skin biopsies from five
psoriasis patients and four normal individuals. Using mAb 6.2A1 immunostaining,
we found a significant increase in αvβ6 expression in psoriatic lesions, as compared
to nonlesional skin from psoriatic patients and normal controls. Thus, the
upregulation of αvβ6 in psoriatic lesions suggests both diagnostic and therapeutic
implication for the use of anti-αvβ6 antibodies.
Example 16: Upregulation of αvβ6 in mouse and human liver with biliary duct
disease
As previously discussed, αvβ6 expression has been implicated in
tissue injury. In this study, expression of αvβ6 was investigated in mouse and
human liver injured by biliary duct disease.
Hepatic injury in mice was induced by ligation of the biliary duct.
See, e.g., George et al., PNAS 96:12719-24 (1999); George et al., Am J Pathol

156:115-24 (2000). Using xnAb 6.2G2, we found that expression of αvβ6 was
significantly elevated at days 9,14 and 16 following biliary duct ligation.
Similarly, human liver sections from patients with biliary duct
disease displayed upregulated expression of αvβ6, as determined by
immunohistochemistry using the mAb 6.2G2. Elevated expression of αvβ6 was
observed for example, in liver samples from a 44 year old male with acute
cholestasis, a post-transplant 59 year old male with acute bile duct obstruction, a
22 year old male with biliary atresia, and a 24 year old male with chronic bile duct
obstruction.
In sum, the new anti-αvβ6 antibodies are useful diagnostic and
therapeutic tools for liver diseases.
Example 17: Upreeulation of αvβ6 in various human cancers
Integrin αvβ6 is normally expressed at negligible to low levels in
healthy adult tissues. A variety of human tumor tissues was evaluated for αvβ6
expression using the antibody 6.2A1 and methods generally described herein. The
results showed that αvβ6 integrin expression was significantly upregulated in
several human epithelial cancers. Notably, immunohistology showed that αvβ6
was expressed especially prominently on the edges of tumor islands in many of the
epithelial cancers. To further study expression of αvβ6 in epithelial cancer cells,
Detroit 562 cells (pharynx carcinoma) and SCC-14 cells (tongue squamous cell
carcinoma) as well as SW480β6 cells (supra) were stained with 6.3G9 and 6.4B4
and analyzed by flow cytometry.
The right side of Fig. 12 shows αvβ6 expression on the different
tumor cell lines as indicated by 6.3G9 binding in fluorescence activated cell sorting
(FACS). The solid peak represents 6.3G9 binding while the open peak represents
background binding of the secondary mAb alone. The line graph on the left side of
Fig. 12 shows inhibition of the tumor cell lines' binding to the LAP ligand by
increasing concentrations of 6.3G9 or 6.4B4. 6.4B4 was a significantly less potent
inhibitor of αvβ6 binding to LAP, compared to 6.3G9 (> 10-fold IC50 for Detroit
562, > 30-fold IC50 for SW480B6, and > 100-fold IC50 for SCC-14). This is
consistent with previous in vitro results indicating that 6.3G9 is a potent blocking
mAb and 6.4B4 is a weak blocking mAb. This data is also consistent with

negligible inhibitory activity of 6.4B4 in the Detroit xenograft model (Fig. 14B).
Fig. 13 further shows the relative inhibition of tumor cell lines' binding to LAP by
various anti-αvβ6 mAbs. Both 6.3G9 and 6.8G6 displayed equivalent inhibiting
activity (consistent with all previous data) while 6.4B4 was a significantly less
potent inhibitor of αvβ6 binding to LAP.
Example 18: Effects of anti-αvβ6 blocking mAbs in a human tumor xenograft
model
Immunodeficient animals (e.g., nude mice and SCID mice)
transplanted with human tumor xenografts have been established as a useful in vivo
model system to test the therapeutic effects of anti-cancer agents (see, e.g., van
Weerden et al., Prostate 43(4):263-71 (2000); Bankert et al., Front Biosci 7x44-62
(2002)). Thus, the blocking anti-αvβ6 monoclonal antibodies of the present
invention can be tested in vivo in a xenograft model for their ability to inhibit
tumor growth. In this experiment, we tested the ability of some of the new αvβ6
antibodies to inhibit tumor growth in athymic nude female mice transplanted with
cancerous human pharyngeal (Detroit 562 cell line) xenograft.
To do this, Detroit 562 cells (ATCC) were passed in vitro in
Minimum essential medium (Eagle) with 2 mM L-glutamine and Earle's BSS
adjusted to contain 1.5 g/L sodium bicarbonate, 0.1 mM nonessential amino acids,
and 1.0 mM sodium pyruvate, and 10% fetal bovine serum, without antibiotics.
About 5X106 cells/0.2 mi media (without serum) were implanted subcutaneously
into nude mice on the right flank. Three to four days later, tumor size
measurements were started and continued until the tumors were about 5 mm
(length) by 5 mm (width). The mice were randomized and injected
intraperitoneally with the test antibodies or control solutions on day 1, followed by
three injections weekly for a period of 33 days. The test antibodies and control
solutions were: (1) 6.3G9,1 mg/kg, 10 mice; (2) 6.3G9, 4 mg/kg, 10 mice; (3)
6.3G9,10 mg/kg, 10 mice; (4) 6.4B4,1 mg/kg, 10 mice; (5) 6.4B4, 4 mg/kg, 10
mice; (6) 6.4B4,10 mg/kg, 10 mice; and (7) vehicle control (PBS), 0.2 ml/per
mouse, 30 mice. In addition, cis-platinum was injected into 10 mice
subcutaneously at 2 mg/kg as a chemotherapeutical control. The cis-platinum
injections were done on day 1 and then every 2 days for a total of six treatments.
At the end of the 33 day period, animal weights and tumor sizes were measured,

αvβ6 expression assessed by immunohistology, and serum anti- αvβ6 levels
measured.
Immunohistological staining showed that the implanted tumor cells
strongly expressed αvβ6 in vivo. Tumor weight data further showed that blocking
mAb 6.3G9 effectively inhibited tumor growth at all three concentrations tested
(Fig. 14A). In contrast, weak blocking mAb 6.4B4 did not inhibit tumor growth
(Fig. 14B).
In sum, blocking antibodies inhibited tumor growth by 40-50% in
the treated mice. In contrast, a weak blocking anti-αvβ6 antibody did not inhibit
tumor growth.
Example 19: αvβ6 antibody internalization
Antibodies that are internalized by cells offer an advantage for
certain clinical indications such as cancer, because the antibodies can then be
conjugated with toxins, radioactive compounds or other anti-cancer agents to
selectively target and inhibit growth of cancer cells. The ability of anti-αvβ6
antibodies to be internalized was studied in SW480β6 (supra) and SCC-14 cells.
Cells were split 1:5 and plated onto 4-chambered glass slides for
overnight incubation at 37°C, 5% CO2. The next day, mAbs 6.8G6,6.1 A8,6.3G9,
7.1C5,6.4B4,10D5, and 8B3 were diluted to a final concentration of 20 g/mL.
The mAbs or medium alone were added to appropriate wells. A time course of
internalization was run from 0 h to 48 h. Time points included were 0, 5,10 and
30 min, and 1,4,24 and 48 h. A secondary antibody (anti-murine-Alexa 594) was
added as a negative control. Internalization was stopped at each time point by
removing the antibody and washing the cell layer with buffer. Wheat Germ
Agglutinin-Alexa-488 was added for 20 min at 18°C to stain the outer edge of the
cells with green fluorescence. After the cells were washed, Cytofix/Cytoperm
solution was added for 20 min at 18°C to fix and permeabilize the cells. The cells
were washed again and the secondary anti-mouse-Alexa 594 (red fluorescence)
was added for 20 min at 18°C to label the bound or internalized murine αvβ6
antibody. The cells were then washed and fixed by addition of 2%
paraformaldehyde and examined by confocal microscopy. Images were then taken
with a Leitz Plan-Apochromatic 63x (1.32 numerical aperture, ail immersion)

objective (Leica) with a 2x digital zoom. Each frame represented a single optical
section from the middle section of the cells observed for internalization under all
conditions. There was no staining observed in the nucleus.
Internalization was observed for cation-dependent mAbs (RGD-
containing ligand mimetics) such as 6.8G6 and 6.1A8. No internalization was
observed for cation-independent mAbs such as 6.3G9, 7.1C5, and 6.4B4.

We Claim:
1. A monoclonal antibody that (a) specifically binds to αvβ6; and (b) inhibits the binding
latency associated peptide (LAP) with an 1C50 value lower than that of
antibody 10D5. wherein the monoclonal antibody comprises same heavy and light chain
complementarity determining region. CDR is an antibody produced by a hybridoma,
or wherein the CDRs have an amino acid mutation such that a site for glycosylation is
eliminated, wherein the hybridoma is selected from the group consisting of hybridoma
6.1A8 (ATCC Accession No. PTA 3647), 6.3G9 (ATCC Accession No PTA-3649),
6.8G6 (ATCC Accession No PTA-3645), 6 2B1 (ATCC Accession No PTA 3646),
7.1G10 (ATCC Accession No PTA-3898), 7.7G5 (ATCC Accession No PTA-3899), and
7.1C5 (ATCC Accession No PTA-3900).
2. The antibody of claim 1, wherein the binding between the antibody and αvβ6 is
divalent cation-dependent.
3 The antibody of claim 2, wherein the divalent cation is Ca2+, Mg2+ or Mn2+.
4. The antibody of claim 1, wherein the binding between the antibody and αvβ6 is
divalent cation-independent.
5. An anti- αvβ6 antibody selected from the group consisting of
a) an antibody whose heavy chain complementarity determining regions
(CDRs) 1, 2, and 3 consist essentially of SEQ ID NOs: 1, 4, and 7 respectively, and
whose light chain CDRs consist essentially of SEQ ID NOs 10, 13 and 15, respectively;
b) an antibody whose heavy chain complementarity determining regions
(CDRs) 1, 2, and 3 consist essentially of SEQ ID NOs: 3, 5, and 8 respectively, and
whose light chain CDRs consist essentially of SEQ ID NOs 11, 14 and 17, respectively;
c). an antibody whose heavy chain complementarity determining regions
(CDRs) 1, 2, and 3 consist essentially of SEQ ID NOs: 3, 6, and 9 respectively, and
whose light chain CDRs consist essentially of SEQ ID NOs 12, 14 and 18, respectively;

d) an antibody whose heavy chain complementarity determining regions
(CDIRs) 1, 2, and 3 consist essentially of SEQ ID NOs 2, 46, and 47 respectively and
whose light chain CDRs consist essenlially of SEQ ID NOs 48, 13 and 16, respectively;
e) an antibody whose heavy chain complementarity determining regions
(CDIRs) 1, 2, and 3 consist essentially of SEQ ID NOs: 49, 51, and 53 respectively, and
whose light chain CDRs consist essentially of SEQ ID NOs 55, 57 and 59, respectively;
f) an antibody whose heavy chain complementarity determining regions
(CDRs) 1, 2, and 3 consist essentially of SEQ ID NOs: 50, 52, and 54 respectively, and
who se light chain CDRs consist essentially of SEQ ID NOs 56, 58 and 60, respectively;
or
g) an antibody of any of steps (a) through (f) wherein the CDRs have an amino
acid mutation such that a site for glycosylation is eliminated.
6. The anti-αvβ6, antibody as claimed in claim 1 comprising a heavy chain variable
domain sequence of any one of SEQ ID NOs: 19-36 and 61-62.
7. An anti- αvβ6 antibody comprising a heavy chain variable domain sequence and a
light chain variable domain sequence consisting essentially of sequences selected from
the group consisting of:
a) a heavy chain variable domain sequence of SEQ ID NO: 19 and a light
chain variable domain sequence of SEQ ID NO:37;
b) a heavy chain variable domain sequence of SEQ ID NO:20 or 21 and a
light chain variable domain sequence of SEQ ID NO:38;
c) a heavy chain variable domain sequence of SEQ ID NO:22 and a light
chain variable domain sequence of SEQ ID NO:43;
d) a heavy chain variable domain sequence of SEQ ID NO:23 and a light
cha in variable domain sequence of SEQ ID NO:44;
e) a heavy chain variable domain sequence of SEQ ID NO:24 and a light
chain variable domain sequence of SEQ ID NO:45;

f) a heavy chaiin variable domain sequence of SEQ ID NO:25 or 26 and a
light chain variable domain sequence of SEQ ID NO.42;
g) a heavy chain variable domain sequence of SEQ ID NO:27, 28 or 29 and a
light chain variable domain sequence of SEQ ID NO:39;
h) a heavy chain variable domain sequence of SEQ ID NO:34 or 35 and a
light chain variable domain sequence of SEQ ID NO:40:
i) a heavy chain variable domain sequence of SEQ ID NO:36 and a light
chain variable domain sequence of SEQ ID NO:41;
j) a heavy chain variable domain sequence of SEQ ID NO:61 and a light
chain variable domain sequence of SEQ ID NO:63;
k) a heavy chain variable domain sequence of SEQ ID NO:62 and a light
chain variable domain sequence of SEQ ID NO:64;
8. An antibody as claimed in any one of the claims 1 to 7 for use in preventing or treating
a disease mediated by αvβ6 a subject.
9. An antibody as claimed in any one of the claims 1 to 7 for use in treating a subject
having or at risk of having a disease mediated by αvβ6.
10. An antibody of any one of the claims 1 to 7 for use in the manufacture of a
medicament for preventing or treating a disease mediated by αvβ6 in a subject.
11. The antibody as claimed in any one of the claims 8-10, wherein the antibody is
optionally conjugated to a cytotoxic agent.
12. The antibody as claimed in any one of the claims 8-10, wherein the disease is fibrosis,
psoriasis, cancer or Alport's Syndrome.
13. The antibody as claimed in claim 12, wherein the fibrosis is scleroderma, scarring,
liver fibrosis, kidney fibrosis, or lung fibrosis.

14. The antibody as claimed in claim 12, wherein the cancer is epithelial, oral, skin,
cervical, ovarian, pharyngeal, laryngeal, esophageal, lung, breast, kidney, or colorectal
cancer.
15. An in vitro method of detecting αvβ6 in a tissue sample from a subject, comprising
contacting the tissue sample with the antibody of any of the claims 1 to 7.
16. A nucleic acid comprising a coding sequence for any one of SEQ ID NOs: 19-45 and
61-64.
17. A polypeptide comprising an amino acid sequence of any one of SEQ ID NOs: 19-45
and 61-64.
18. A monoclonal antibody comprising same heavy and light chain polypeptide
sequences as an antibody produced by hybridoma 6. 2B10 (ATCC accession number
PTA-3648).
19. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 6.3G9 (ATCC Accession No PTA-
3649) cells.
20. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 6.8G6 (ATCC Accession No PTA-
3649) cells.
21. A process of producing the monocloaal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 6.1A8 (ATCC Accession No PTA
3647) cells.

22. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said' antibody produced from hybridoma 6 2B1 (ATCC Accession No PTA
3646) cells.
23. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 7.1G10 (ATCC Accession No PTA-
3898) cells.
24. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 7.7G5 (ATCC Accession No PTA-
3899) cells.
25. A process of producing the monoclonal antibody as claimed in claim 1 comprising
isolating said antibody produced from hybridoma 7.1C5 (ATCC Accession No PTA-
3900) cells.
26. A process of producing the monoclonal antibody as claimed in claim 18 comprising
isolating said antibody produced from hybridoma 6.2B10 (ATCC accession number
PTA-3648) cells.

Monoclonal antibodies that specifically bind to M.96. Also included are methods of using these antibodies to treat
mammals having or at risk of having 006-mediated diseases, or to diagnose %Qmediated diseases.

Documents:

1305-KOLNP-2004-CORRESPONDENCE.pdf

1305-KOLNP-2004-CORRESPONDENCE_1.1.pdf

1305-KOLNP-2004-FORM 27_.pdf

1305-KOLNP-2004-FORM-27.pdf

1305-kolnp-2004-granted-abstract.pdf

1305-kolnp-2004-granted-assignment.pdf

1305-kolnp-2004-granted-claims.pdf

1305-kolnp-2004-granted-correspondence.pdf

1305-kolnp-2004-granted-description (complete).pdf

1305-kolnp-2004-granted-drawings.pdf

1305-kolnp-2004-granted-examination report.pdf

1305-kolnp-2004-granted-form 1.pdf

1305-kolnp-2004-granted-form 13.pdf

1305-kolnp-2004-granted-form 18.pdf

1305-kolnp-2004-granted-form 2.pdf

1305-kolnp-2004-granted-form 26.pdf

1305-kolnp-2004-granted-form 3.pdf

1305-kolnp-2004-granted-form 5.pdf

1305-kolnp-2004-granted-gpa.pdf

1305-kolnp-2004-granted-reply to examination report.pdf

1305-kolnp-2004-granted-sequence listing.pdf

1305-kolnp-2004-granted-specification.pdf

1305-KOLNP-2004-OTHERS.pdf


Patent Number 226395
Indian Patent Application Number 1305/KOLNP/2004
PG Journal Number 51/2008
Publication Date 19-Dec-2008
Grant Date 17-Dec-2008
Date of Filing 08-Sep-2004
Name of Patentee BIOGEN INDEC MA INC.
Applicant Address 14 COMBRIDGE CENTER, COMBRIDGE, MA
Inventors:
# Inventor's Name Inventor's Address
1 VIOLETTE. SHELIA, M. 91 SIMONDS ROAD, LEXINGTON. MA 02420
2 WEINREB. PAUL, H. 18 BRUNDRETT AVENUE, ANDVER, MA 01810
3 SIMON, KENNETH, J 454 WINDSOR STREET, COMBRIDGE, MA 02141
4 SHEPPARD, DEAN 1006 HUBERT ROAD, OAKLAND, CA 94610
5 LEONE, DIANE. R. 24 EUGENE DRIVE, WINCHESTER MA 01890
PCT International Classification Number C12N
PCT International Application Number PCT/US03/08048
PCT International Filing date 2003-03-13
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/426,286 2002-11-13 U.S.A.
2 60/364,991 2002-03-13 U.S.A.