Title of Invention

NOVEL ISOFORMS OF VASCULAR ENDOTHELIAL CELL GROWTH INHIBITOR

Abstract This invention discloses two new VEGI isoforms named VEGI-¿192a? and VEGI-192b consisting of 192 amino acid residues. These isoforms show endothelial cell-specific expression and share a C-terminal 151-residues segment with the previously described VEGI-174 and VEGI-751. Methods of using these isoforms of VEGI in diagnosing, screening agonist and antagonist of the isoforms, and treating various angiogenesis-related diseases are also disclosed.
Full Text NOVEL ISOFORMS OF VASCULAR ENDOTHELIAL CELL
GROWTH INHIBITOR
CROSS -REFERENCES TO RELATED APPLICATIONS
This application claims the priority benefit of U.S. provisional patent application serial
number 60/331,190, filed November 9,2001. The priority application is hereby incorporated
herein by reference in its entirety.
GOVERNMENT SUPPORT
This invention was made with U.S. Government support under Department of Defense
grant DAMD17-98-1-8093; National Institutes of Health grant NHLBIRO1 HL60660; and
National Cancer Institute grant CA58185-08. The Government has certain rights in the
invention.
FIELD OF THE INVENTION
The present invention relates to compositions that are useful in the treatment of
conditions in which it is advantageous that angiogenesis is inhibited, for example, in the
treatment of solid tumors, diabetic retinopathy, Kaposi's sarcoma, psoriasis, and rheumatoid
arthritis. In particular, the invention relates to novel isoforms of vascular endothelial growth
inhibitors (VEGIs), their DNA and associated protein sequences, compositions and variants
thereof, and their use in the treatment of angiogenesis-driven diseases.
BACKGROUND OF THE INVENTION
Under normal physiological conditions, humans and animals undergo angiogenesis, the
generation of new blood vessels into a tissue or organ, in very specific restricted situations.
For example, angiogenesis is normally observed in wound healing, embryonal development, and
formation of the corpus luteum, endometrium and placenta. The term "endothelium" means a
thin layer of flat epithelial cells that lines serous cavities, lymph vessels and blood vessels. The
term "anti-angiogenic" or "angiogenic inhibiting activity" means the capability of a molecule to
inhibit angiogenesis in general.
Both controlled and uncontrolled angiogenesis are thought to proceed in a similar
manner. Endothelial cells are actively involved in inflammation, cell adhesion, coagulation,
thrombosis, fibrinolysis, and angiogenesis. Endothelial cells and pericytes, surrounded by a
basement membrane, form capillary blood vessels. Angiogenesis begins with the erosion of the
basement membrane by enzymes released by endothelial cells and leukocytes. The endothelial
cells, which line the lumen of blood vessels, then protrude through the basement membrane.
Angiogenic stimulants induce the endothelial cells to migrate through the eroded basement
membrane. The migrating cells form a "sprout" off the parent blood vessel, where the endothelial
cells undergo mitosis and proliferate. The endothelial sprouts merge with each other to form
capillary loops, creating the new blood vessel.
Persistent unregulated angiogenesis occurs in a multiplicity of disease states, tumor
metastasis and abnormal growth by endothelial cells and supports the pathological damage seen
in these conditions. The diverse pathological disease states in which unregulated angiogenesis is
present have been grouped together as angiogenic dependent or angiogenic associated diseases.
During tumor growth, endothelial cells proliferate, invade the stroma, migrate toward the
source of angiogenic stimuli such as cancer cells, interact with perivascular cells and stromal
cells, and eventually form capillary vessels linking the tumor tissue to the circulation (J.
Folkman (1995) Nat. Med 1:27-31). Although the undoubtedly highly complex mechanism that
regulates angiogenesis is yet to be understood, it is becoming clear that the initiation or
termination of the process is a result of a balance between positive and negative regulators of
angiogenesis. A number of angiogenic factors, often markedly upregulated in tumor tissues,
have been described, including several members of the fibroblast growth factor family, such as
FGF-I(G. Gimenez-Gallego et al. (1985) Science 230. .1385), FGF-2 (L. Schweigerer et al.
(1987) Nature 325: 257), and those of the vascular endothelial cell growth factor family (VEGF)
(D. W. Leung et al. (1989) Science 246: 1306), as well as the receptors of these growth factors
(L. W. Burrus and B. B. Olwin (1989) JBiol. Chem. 264:18647; S. Wemistrom et al. (1991)
Growth Factors 4:197; B. Tennan et al (1992) Biochem. Biophys. Res. Comm. 187: 1579. C.
de Vries et al., (1992) Science 255: 989). Recently, two new protein factors, proliferin and a
proliferin-related protein, were found to participate in the regulation of the initiation and
cessation of neovascularization in mouse placenta (Jackson D, et al. Science 266,1581-4,1994).
All documents cited herein supra and infra are hereby expressly incorporated in their entirety by
reference thereto.
Several inhibitors of angiogenesis have also been reported, including thrombospondin
(D. J Good et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87:6624), angiostatin (M. S. O'Reilly et
al. (1994) Cell 79:315), endostatin (M.S. O'Reilly et al. (1997) Cell 88: 277) and platelet factor-4
(E. Maione et al. (1997) Science 247:77). It is apparent that normal angiogenesis is promptly
activated when required, and swiftly terminated when no longer needed, whereas pathological
angiogenesis, once initiated is often prolonged and difficult to stop. This indicates that the
negative regulation mechanism functioning in a normal angiogenesis process is missing or
suppressed in a pathological angiogenesis process. It has been suggested that proteolytic
activities that release angiogenesis inhibitors from a number of precursors may account partly for
down-regulation of angiogenesis, as indicated by the proteolytic activation of angiostatin from
plasminogen and that of endostatin from collagen XVIII (M. S. O'Reilly, (1997) Cell 88:277).
Many of the known angiogenesis regulators are pleiotrophic and can act on other cell types as
well as the one that produces the regulators, although it is conceivable that endothelial cells may
produce autocrine factors to suppress an angiogenic process or maintain the quiescence of a
mature vasculature. It is therefore an object of the present application to describe novel autocrine
negative regulators of angiogenesis of a class called Vascular Endothelial Cell Growth Inhibitors
(VEGI) that are specifically expressed by endothelial cells.
Published PCT Application WO 99/23105 discloses a VEGI protein (VEGI-m) and a
splice variant VEGI-251 and their corresponding nucleotide sequences, the disclosure of which is
hereby expressly incorporated into the present application by reference in its entirety. Anti-
angiogenic activity of N-terminal truncated forms of VEGI-174 was described. The protein
VEGI-174 exhibited 20-30% sequence homology to human TNFa, TNFß, and the Fas ligand. A
protein with a molecular weight of 22 kD was produced in an in vitro transcription and
translation experiment using a cDNA clone as a template, consistent with the predicted open
reading frame of 174 amino acids. This protein is herein referred to as VEGI-174.
Hydrophobicity analysis of the protein predicted a 12-amino acid hydrophobic region
immediately following the N-terminal segment of 14 non-hydrophobic amino acids. This was
consistent with the structure of a type II transmembrane protein, similar to TNFs (B. B.
Aggarwal and K. Natarajan (1996) Eur.Cytolane News. 7:93). An isoform of VEGI was also
described. This protein is herein referred to as VEGI-251 which was predicted to be a membrane
protein.
Recent Northern analysis of total RNA preparations from 22 different types of cultured
cells of various lineages indicated that transcripts for this protein can only be detected in two
lines of endothelial cells: HUVE cells and human venous endothelial cells of an early passage. A
mRNA was not detected in human venous endothelial cells of a later passage, nor was it seen in
human artery cells. In sharp contrast, the TNF family members are mostly expressed in immune
cells (B. B. Aggarwal and K. Natarajan (1996), supra). For instance, TNFa is produced by
macrophages, monocytes, neutrophils, and T cells, while TNFß is predominantly produced by
mitogen-stimulated T lymphocytes and leukocytes. Similarly, the ligands for Fas and other TNF
family members, CD27, CD30, CD40, OX40, and 4-1 BB, are all expressed in cell types in the
immune system. Using multiple tissue Northern blots, an EGI transcript was found to be
expressed in placenta, lung, kidney, skeletal muscle, brain, liver, thymus, testis, ovary and
peripheral blood lymphocytes.
Inhibition of angiogenesis in a tumor is an important approach for the treatment of cancer
such as breast and other solid tumors. First of all, tumor growth and metastasis are dependent on
angiogenesis. It has been shown in a model system that blocking the capillaries of the tumor
neovasculature by specifically induced coagulation gives rise to the eradication of the tumor
vasculature and leads to abrogation of the tumors. In addition, it has been suggested that
endothelial cells are highly proliferative in tumor tissues but are mostly quiescent in normal
tissues. This makes the tumor neovasculature a specific and attractive target. Furthermore,
while the characteristics of cancer cells may vary greatly in different tumors, the endothelial cell
population in most solid tumors is likely to be untransformed, and thus remains homogeneous.
This would apply for both human and animal subjects. It may therefore be possible to develop an
antiangiogenic therapeutic agent that could be applied universally for the treatment of many
different cancers.
In addition to solid tumors, other important angiogenesis-driven diseases include diabetic
retinopathy, Kaposi's sarcoma, psoriasis, rheumatoid arthritis. Patients who suffer from these
diseases may benefit from an anti-angiogenic therapeutic approach.
The present invention identifies and describes sequences, functions, compositions, and
therapeutic uses of novel isoforms of members of the VEGI family of proteins. Two new
isoforms that are termed VEGI-192a, and VEGI-192b respectively, comprise a novel N-terminal
sequence that substantially alters the properties of the protein with respect to its expression,
secretion, and anti-angiogenic properties.
There are disclosed two new VEGI isoforms named VEGI192aand VEG192b, both
consisting of 192 amino acid residues. Both isoforms show endothelial cell-specific expression
and share a C-terminal 151-residues segment with the previously described VEGI-174 and VEGI-
251. The isoforms are generated from a 17 kb human gene by alternative splicing. VEGI251, the
most abundant isoform, contains a putative secretion signal. VEGI protein is detected in
conditioned media of endothelial cells, human sera and VEGI251-transfected mammalian cells.
Subcellular localization pattern of VEGI251 is suggestive of a secretory protein. Overexpression
of VEGI251 in endothelial cells causes dose-dependent cell death. VEGI251-transfected cancer
cells gave rise to xenograft tumors of reduced growth rate and microvessel density compared
with tumors of VEGI174 transfectants. The invention provides a view that endothelial cell-
secreted VEGI can function as an autocrine inhibitor of angiogenesis and a naturally existing
modulator of vascular homeostasis.
All publications cited herein are hereby incorporated by reference in their entirety.
SUMMARY OF THE INVENTION
The present invention relates to inhibitors of endothelial cell proliferation in general and
inhibitors of angiogenesis in particular, and their methods of use. The complete nucleotide
sequences of VEGI-192a, VEGI-192b, and VEGI-251 are shown in Table 1 (SEQ ID NO: 1), Table 2
(SEQ ID NO:2), and Table 3 (SEQ ID NO:3), and the deduced amino acid sequences are shown
in Table 4 (SEQ ID NO:4), Table (SEQ ID NO:5), and Table 6 (SEQ ID NO:6), respectively.
Accordingly, in one embodiment, the invention provides an isolated polynucleotide that
comprises the sequence shown in Table 1 (SEQ ID NO:1), or their complement. The invention
also provides an isolated polynucleotide that comprises at least 10, at least 15, at least 18, at least
20, at least 25, at least 30, at least 50, and at least 100 or more contiguous nucleotides of SEQ ID
NO:1, wherein the contiguous nucleotides are within nucleotides 1-93 of SEQ ID NO:1. The
invention also provides an isolated polynucleotide that comprises at least 10, at least 15, at least
18, at least 20, at least 25, at least 30, at least 50, and at least 100 or more contiguous nucleotides
of SEQ ID NO:1, wherein the contiguous nucleotides comprise nucleotides 93 and 94 of SEQ ID
NO:1.
In other embodiments, the invention provides an isolated polynucleotide that comprises
the sequence shown in Table 2 (SEQ ID NO:2), or their complement. The invention also
provides an isolated polynucleotide that comprises at least 10, at least 15, at least 18, at least 20,
at least 25, at least 30, at least 50, and at least 100 or more contiguous nucleotides of SEQ ID
NO:2, wherein the contiguous nucleotides are within nucleotides 1-386 of SEQ ID NO:2. The
invention also provides an isolated polynucleotide that comprises at least 10, at least 15, at least
18, at least 20, at least 25, at least 30, at least 50, and at least 100 or more contiguous nucleotides
of SEQ ID NO:2, wherein the contiguous nucleotides comprise nucleotides 386 and 387 of SEQ
ID NO:2.
In some embodiments, the invention provides an isolated polynucleotide that comprises a
sequence encoding the polypeptide of SEQ ID NO:4. The present invention also provides an
isolated polynucleotide that comprises a polynucleotide encoding at least 5, at least 10, at least
15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:4, wherein the
contiguous amino acids are within amino acids 1-26 of SEQ ID NO:4. The invention also
provides an isolated polynucleotide that comprises a polynucleotide encoding at least 5, at least
10, at least 15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:4, wherein
the contiguous amino acids comprise amino acids 26 and 27 of SEQ ID NO:4. In some
embodiments, the contiguous amino acids are amino acids about 5-192,10-192,15-192,20-192,
or 25-192 of the sequence shown in Table 4 (SEQ ID NO:4).
In some embodiments, the invention provides an isolated polynucleotide that comprises a
sequence encoding the polypeptide of SEQ ID NO:5. The present invention also provides an
isolated polynucleotide that comprises a polynucleotide encoding at least 5, at least 10, at least
15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:5, wherein the
contiguous amino acids are within amino acids 1-26 of SEQ ID NO:5. The invention also
provides an isolated polynucleotide that comprises a polynucleotide encoding at least 5, at least
10, at least 15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:5, wherein
the contiguous amino acids comprise amino acids 26 and 27 of SEQ ID NO:5. In some
embodiments, the contiguous amino acids are amino acids about 5-192,10-192,15-192,20-192,
or 25-192 of the sequence shown in Table 5 (SEQ ID NO:5).
In some embodiments, the polynucleotide of the invention provides sequence encoding
functionally-preserved variants of the nucleic acid sequences disclosed herein, which include
nucleic acid substitutions, additions, and/or deletions. Variants include naturally occurring
variants of the polynucleotide sequence (e.g. degenerate variants, allelic variants, etc.)
In some embodiments, the invention provides an isolated polynucleotide having at least
85%, at least 88%, at least 90%, at least 92%, at least 94%, at least 96 %, at least 98%, or at least
99% sequence identity with the polynucleotides of the invention as described herein. One
embodiment provides an isolated polynucleotide having at least 85%, at least 88%, at least 90%,
at least 92%, at least 94%, at least 96 %, at least 98%, or at least 99% sequence identity with the
sequence of nucleotides 1-93 shown in Table 1 (SEQ ID NO:1) or nucleotides 1-386 shown in
Table 2(SEQ ID NO:2).
In some embodiments, the polynucleotides of the invention further comprise a detectable
label. In some embodiments, the polynucleotide of the invention is immobilized on a surface. In
some embodiments of the invention, the polynucleotide of the invention is single stranded. In
some embodiments of the invention, the polynucleotide of the invention is selected from the
group consisting of DNA and RNA. In some embodiments of the invention, the polynucleotide
of the invention is prepared in part by chemical synthesis.
It is understood that (unless otherwise specified or required), any embodiment of the
invention described herein that is a polynucleotide encompasses both the double-stranded form
and each of two complementary single-stranded forms known or predicted to make up the double
stranded form.
It is further understood that the invention provides embodiments "consisting of or
"consisting essentially of the polynucleotide, polypeptides, and/or antibodies described herein.
In another aspect, the invention provides vectors and expression vectors comprising any
of the polynucleotides described herein.
In still other aspects, the invention provides a host cell comprising any of the
polynucleotide or vectors described herein. In some embodiments, the host cell is prokaryotic,
such as E. coli. In some embodiments, the host cell is eukaryotic, such as Chinese hamster ovary
(CHO) cells.
The present invention also encompasses cells containing recombinant polynucleotides
which comprises a VEGI-192a or VEGI-192b polynucleotide or variants of VEGI-192a or VEGI-192b
polynucleotide. In one embodiment, the invention provides a genetically engineered mammalian
cell or bacterial cell, such as E. coli, comprising a recombinantly modified VEGI-192a or VEGI-
192b polynucleotide, such that the polynucleotide is overexpressed. In another embodiment, the
invention provides cells comprising a variant of VEGI-992a or VEGI-192b polynucleotide. In
another embodiment, a VEGI-192a or VEGI-192b polynucleotide is operatively linked to an
inducible promoter. In still other embodiments, the genetically engineered cells possess a variant
VEGI-192a or VEGI-192b gene instead of a native VEGI-192a or VEGI-192b gene.
The invention also provides VEGI-192a polypeptides. Therefore, the invention provides
an isolated polypeptide comprising the sequence of SEQ ID NO:4. The invention also provides
an isolated polypeptide comprising a polypeptide encoded by any of the polynucleotides of the
invention, as described herein. In other embodiments, the present invention also provides an
isolated polypeptide that comprises at least about 5, at least 10, at least 15, at least 20, at least 25,
or more contiguous amino acids of a sequence depicted in Table 4 (SEQ ID NO:4), wherein the
contiguous amino acids are within amino acids 1-26 of the sequence shown in Table 4 (SEQ ID
NO:4). In other embodiments, the present invention also provides an isolated polypeptide that
comprises at least about 5, at least 10, at least 15, at least 20, at least 25, or more contiguous
amino acids of a sequence depicted in Table 4 (SEQ ID NO:4), wherein the contiguous amino
acids comprise amino acids 26 and 27 of SEQ ID NO:4. In some embodiments, the contiguous
amino acids are amino acids about 5-192,10-192,15-192,20-192,25-192 of SEQ ID NO:4.
The invention also provides VEGI-192b polypeptides. Therefore, the invention provides
an isolated polypeptide comprising the sequence of SEQ ID NO:5. The invention also provides
an isolated polypeptide comprising a polypeptide encoded by any of the polynucleotides of the
invention, as described herein. In other embodiments, the present invention also provides an
isolated polypeptide that comprises at least about 5, at least 10, at least 15, at least 20, at least 25,
or more contiguous amino acids of a sequence depicted in Table 5 (SEQ ID NO:5), wherein the
contiguous amino acids are within amino acids 1-26 of the sequence shown in Table 5 (SEQ ID
NO:5). In other embodiments, the present invention also provides an isolated polypeptide that
comprises at least about 5, at least 10, at least 15, at least 20, at least 25, or more contiguous
amino acids of a sequence depicted in Table 5 (SEQ ID NO:5), wherein the contiguous amino
acids comprise amino acids 26 and 27 of SEQ ID NO:5. In some embodiments, the contiguous
amino acids are amino acids about 5-192,10-192,15-192,20-192,25-192 of SEQ ID NO:5.
In other embodiments, the invention provides any polypeptide described herein, wherein
the polypeptide includes an epitope. In other embodiments, the invention provides any
polypeptide described herein, wherein the polypeptide is immobilized on a solid support.
In other embodiments, the invention provides polypeptides that retains a biological
activity of VEGI-192a and/or VEGI-192b and/or VEGI-251. As shown in the Examples, VEGI-192a
inhibits vascular endothelial cell growth; and VEGI-251 upon expression inhibits vascular
endothelial cell growth, the formation of capillary-like tubes in an in vitro angiogenesis model,
and also inhibits the growth of xenograft tumors in athymic nude mice.
The invention also provides antibodies that selectively bind VEGI-192a and/or VEGI-192b.
Accordingly, the invention provides an antibody that selectively binds to any of the VEGI-192a
and/or VEGI-192b polypeptides described herein. In one embodiment, the antibody is capable of
binding selectively to VEGI-192a or VEGI-192b. In other embodiment, the antibody is capable of
binding selectively to both VEGI-192a and VEGI-192b, but not to other isoforms of VEGI. In some
embodiments, the antibody binds to a polypeptide encoded by any of the polynucleotides
described herein. In one embodiment, the invention provides an antibody capable of binding to a
polypeptide of this invention. In another embodiment, the antibody is capable of specifically
binding to a polypeptide comprising (a) the sequence shown in Table 4 (SEQ ID NO:4) and/or
Table 5 (SEQ ID NO:5); or (b) at least 10 contiguous amino acids of SEQ ID NO:4 and/or SEQ
ID NO: 5, wherein the contiguous amino acids are within amino acids 1-26 shown in Table 4
(SEQ ID NO:4) and/or Table 5 (SEQ ID NO:5). The present invention also provides an antibody
that is capable of binding to a region of the polypeptide shown in Table 4 (SEQ ID NO:4) and/or
Table 5 (SEQ ID NO:5), wherein said region is at least about 5, at least 10, at least 15, at least
20, at least 25, or more contiguous amino acids of SEQ ID NO:4 and/or SEQ ID NO:5, and said
region comprise amino acids 26 and 27 of SEQ ID NO:4 and/or SEQ ID NO:5.
In some embodiments, the antibody is a polyclonal antibody. In other embodiments, the
antibody is a monoclonal antibody. In still other embodiments, the antibody is immobilized on a
solid support. In still other embodiments, the antibody further comprises a detectable label.
The present invention also provides compositions, including pharmaceutical,
compositions, comprising the polynucleotides, polypeptides, antibodies, recombinant vectors,
and host cells of the invention. In some embodiments, the invention provides a pharmaceutical
composition comprising the polypeptide of SEQ ID NO:4, or a fragment thereof, wherein the
fragment comprises amino acids 26 and 27, in a pharmaceutically acceptable excipient.
The present invention also provides an angiogenesis inhibitor, where the inhibitor
comprises VEGI-192a, VEGI-192b, or VEGI-251 polynucleotides, polypeptides or derivatives in a
pharmaceutically acceptable carrier, in a pharmaceutically acceptable amount.
In another embodiment, the present invention provides a repressor or inhibitor of cancer
growth composition comprising substantially purified VEGI isoform (i.e., VEGI-192a, VEGI-192b,
or VEGI-251) polynucleotides or polypeptides of the invention.
In another embodiment, the present invention provides an accelerator of angiogenesis. the
accelerator comprising an antibody, an antisense oligonucleotide, an antagonist, a ribozyme,
drug or agent which reduces or eliminates VEGI-192a, VEGI-192b, or VEGI-251 function when
supplied in a pharmaceutically acceptable carrier, in a pharmaceutically acceptable amount.
The invention also provides kits, arrays comprising any of the polynucleotides,
polypeptides and antibodies described herein. In one embodiment, the invention provides kits or
arrays for assessing amount of polynucleotide in a sample comprising any of the polynucleotides
described herein. In other embodiment, the invention provides kits or arrays for assessing level
of polypeptide in a sample comprising any of the antibodies described herein.
In another embodiment, the present invention provides a method for inhibiting
angiogenesis which comprises administering to an individual (such as a human or animal) a
composition comprising a substantially purified VEGI-192a, VEGI-192b, or VEGI-251
polynucleotide, polypeptides of the invention, or a modified form of these disclosed VEGI
isoforms described herein in a dosage sufficient to inhibit angiogenesis. In one embodiment, the
composition comprises a gene delivery vector comprising the polynucleotide shown in Table 3
(SEQ ID NO.3) or a polynucleotide encoding the polypeptide of SEQ ID NO:6. In some
embodiments, the polynucleotide is operably associated with a regulatory sequence that controls
gene expression. In other embodiment, the composition comprising substantially purified VEGI-
192a polypeptide of the sequence shown in Table 4 (SEQ ID NO.4), or a functional fragment,
wherein the fragment comprises amino acids 26 and 27 of SEQ ID NO.4 or comprises at least
one amino acids from amino acids 1-26 of SEQ ID NO:4.
In another embodiment, the invention provides a method for the treatment or
amelioration of disease and processes that are mediated by uncontrolled angiogenesis,
comprising the step of administering to an individual a composition comprising a VEGI-192a,
VEGI-192b, or VEGI-251 polynucleotide, polypeptides, or a modified form of these disclosed
VEGI isoforms described herein in a dosage sufficient to control angiogenesis. In one
embodiment, the composition comprises a gene delivery vector comprising the polynucleotide
shown in Table 3 (SEQ ID NO:3) or a polynucleotide encoding the polypeptide of SEQ ID
NO:6. In some embodiments, the polynucleotide is operably associated with a regulatory
sequence that controls gene expression. In other embodiment, the composition comprising
substantially purified VEGI-192a polypeptide of the sequence shown in Table 4 (SEQ ID NO:4),
or a functional fragment, wherein the fragment comprises amino acids 26 and 27 of SEQ ID
NO:4 or comprises at least one amino acids from amino acids 1-26 of SEQ ID NO:4.
In another embodiment, the present invention provides a method for treating cancer or
suppressing tumor growth which comprises administering to an individual a composition
comprising a VEGI-192a, VEGI-192b, or VEGI-251 polynucleotide, polypeptides, or a modified
form of these disclosed VEGI isoforms described herein in a dosage sufficient to suppress tumor
growth. In one embodiment, the composition comprises a gene delivery vector comprising the
polynucleotide shown in Table 3 (SEQ ID NO:3) or a polynucleotide encoding the polypeptide
of SEQ ID NO:6. In some embodiments, the polynucleotide is operably associated with a
regulatory sequence that controls gene expression. In other embodiment, the composition
comprising substantially purified VEGI-192a polypeptide of the sequence shown in Table 4 (SEQ
ID NO:4), or a functional fragment, wherein the fragment comprises amino acids 26 and 27 of
SEQ ID NO:4 or comprises at least one amino acids from amino acids 1-26 of SEQ ID NO:4.
In another embodiment, the present invention provides a method for accelerating
angiogenesis which comprises administering to a human or animal a composition comprising an
antibody, an antisense oligonucleotide, an antagonist, a ribozyme, a drug, or agent which reduces
or eliminates activity of VEGI-192a, VEGI-192b, and/or VEGI-251.
In yet another embodiment, the present invention provides a therapeutic method and
composition for the treatment or amelioration of diseases and processes that are mediated by
angiogenesis, including, but not limited to, hemangioma, solid tumors, leukemia, metastasis,
telangiectasia, psoriasis sclerodemia, pyogenic granuloma, myocardial anaiogenesis, plagie
neovascularization, coronary collaterals, ischemic limb anciogenesis, comeal diseases, rubeosis,
neovascular glaucoma, diabetic retinopathy, retrolental fibroplasia, arthritis, diabetic
neovascularization, uveitis, retinopathy of prematurity, macular degeneration, comeal graft
neovascularization, graft versus host disease, inflammatory bowel disease, myelosuppression,
and restenosis; wherein angiogenesis is uncontrolled or excessive and requires inhibition, the
method comprising providing to an individual in need of such treatment an effective amount of
VEGI isoform (i.e., VEGI-192a, VEGI-192b, or VEGI-251) polynucleotides or polypeptides of the
invention such that angiogenesis is inhibited.
In yet another embodiment, the present invention provides a therapeutic method and
composition for the treatment or amelioration of diseases such as macular degeneration, wound
healing, peptic ulcer, fractures, keloids, vasculogenesis, hematopoiesis, ovulation, menstruation,
and placentation, in which angiogenesis is desired, the method comprising administering to an
individual in need of such treatment, an antagonist of VEGI isoform (i.e., VEGI-192a, VEGI-192b,
or VEGI-251) polynucleotides or polypeptides of the present invention; antisense oligonucleotides
specific for VEGI isoform polynucleotides, or anti-VEGI antibodies, agents, or drugs which
reduce or eliminate VEGI function in a pharmaceutically acceptable carrier, in a
pharmaceutically acceptable amount.
In another embodiment, the present invention provides a method for detecting VEGI
isoform polypeptide (VEGI-192a, or VEGI-192b) comprising contacting a sample from an
individual with an antibody described herein which selectively binds to the VEGI polypeptide of
the invention, and detecting the presence or absence of a complex formed between a polypeptide
in the sample and the antibody. These detection methods are also applicable to detecting any of
the VEGI-192a or VEGI-192b described herein.
In another embodiment, the present invention also provides a method for detecting VEGI
isoform (VEGI-192a, or VEGI-192b) polynucleotides comprising contacting a sample from an
individual with a polynucleotide (such as an oligonucleotide) which selectively binds to the
VEGI polynucleotide of the invention; and detecting the presence or absence of a duplex formed
between the oligonucleotide and a polynucleotide in the sample. These methods are also
applicable to detecting any of the VEGI-192a or VEGI-192b polynucleotides described herein.
In yet another embodiment, the present invention provides a method for the diagnosis of
conditions involving pathological angiogenesis, where the method comprises detecting the
presence or absence of polypeptides derived from VEGI-192a or VEGI-192b, in a sample, the
method comprising the steps of:
(i) contacting a sample from a subject suspected of having pathological angiogenesis with
antibodies that are specific for the VEGI-192a and/or VEGI-192b polypeptides of the invention; and
(ii) detecting the presence or absence of a complex formed between VEGI-192a, and/or
VEGI-192b, and the antibodies.
In yet another embodiment, the present invention provides a method for the diagnosis of?
pathological angiogenesis comprising detecting the presence or absence of VEGI-192a or VEGI-
192b, polynucleotides (preferably RNA) in a sample, the method comprising the steps of.
(i) contacting a sample from a subject suspected of having pathological angiogenesis with
polynucleotides (such as oligonucleotides) that specifically bind VEGI-192a or VEGI-192b
polynucleotides of the invention (for example, RNA); and
(ii) detecting the presence or absence of a duplex formed between polynucleotides and
oligonucleotides derived from VEGI-192a, or VEGI-192b.
In another embodiment, the present invention provides a method for the diagnosis of
pathological angiogenesis using the polymerase chain reaction (PCR), the method comprising
designing primers using the nucleotide sequence of VEGI isoform (i.e. VEGI-192a, VEGI-192b) as
shown in SEQ ID NO:1, and SEQ ID NO:2, wherein the polymerase chain reaction specifically
amplifies a region of VEGI as the basis for detection. The primers can be used to amplify VEGI
DNA or VEGI RNA, the latter amplification occurring after RNA is converted into
complementary DNA (cDNA) by reverse transcription of the RNA. The PCR assay can be made
quantitative by comparing the amplified product to a standard, which can be generated using
methods known in the art.
In yet another embodiment, the present invention provides a method for the detection of
VEGI isoform (i.e. VEGI-192a, or VEGI-192b) polynucleotides in a sample, the method comprising
assaying for the presence or absence of VEGI-192a, or VEGI-192b isoform RNA or DNA in a
sample by hybridization assay.
In a further embodiment, the present invention provides a diagnostic or prognostic kit
comprising antibodies that bind VEGI isoform (i.e. VEGI-192a, or VEGI-192b) polynucleotides or
polypeptides of the invention; oligonucleotides that hybridize to VEGI DNA or RNA; and/or
PCR primers for amplification of VEGI DNA or RNA, and ancillary reagents suitable for use in
detecting the presence of VEGI isoform in a sample. Since VEGI may function as a membrane
protein, a naturally existing soluble form of membrane-bound VEGI may function as its
antagonist, and methods for detecting the soluble form are included in another embodiment of
the present invention.
In yet another embodiment, the present invention provides a diagnostic assay comprising
detecting the presence or absence of a mutation in VEGI isoform (i.e. VEGI-192a, or VEGI-192b)
polynucleotides, which results in the decrease or increase of VEGI isoform expression or
function. Such an assay would include hybridization assay, restriction map polymorphism
assays, and gene sequencing, to name a few.
In yet another embodiment, the present invention provides a method for testing possible
agents or drugs for angiogenic inhibitory activity by testing whether or not the drug or agent is
capable of upregulating VEGI isoform (i.e., VEGI-192a, or VEGI-1921,) expression and/or activity.
Since VEGI isoforms, like other angiogenic inhibitors, are activated by proteases which release
the protein from the cell membrane, proteases, as well as other agents that facilitate such
activation such as metal ions would be useful as agents for increasing the expression of VEGI
isoforms.
In another embodiment, the present invention provides a method for testing possible
antitumor agents or drugs by testing whether or not the drug or agent is capable of inhibiting
angiogenesis by upregulating VEGI isoform expression and/or activity.
In still another embodiment, the present invention provides a method for testing possible
drugs or agent which promote angiogenesis by testing whether or not the agent or drug can block
and/or inhibit VEGI function (for example, inhibition of angiogenesis). In this case, inhibition of
proteases which activate VEGI isoforms as discussed above or agents required for, or agents
which facilitate such activation such as metal ions, can be used to down-regulate VEGI, thereby
enhancing angiogenesis.
BRIEF DESCRIPTION OF THE ACCOMPANYING FIGURES:
Figure 1. Serum VEGI level in normal adults. Serum from 40 normal volunteers (20 male, 20
female) were measured by ELIS A with an anti-VEGI antibody. Each point represents a single
value. Purified recombinant VEGI was used to generate a standard curve. The horizontal bars
among the spots indicate the median values for each gender group.
Figure 2. VEGI is expressed as multiple transcripts in human tissue. VEGI expression in adult
human tissues was determined by multi-tissue Northern blotting analysis, using 32P-labeled full
length VEGI-174 cDNA as a probe. Three distinct VEGI-related messages of the indicated sizes
are detected.
Figure 3. Isolation of novel VEGI cDNAs. A. Scheme showing synthesis of 5'RACE products
followed by cDNA library screening to isolate full-length VEGI cDNAs from various human
tissues. Shaded boxes represent ligated 5' adaptors present in the RACE panel. PCR primers are
denoted by arrows with open arrowheads. PCR products of different sizes are visualized by
ethidium bromide staining. The PCR products were isolated and subjected to sequencing. L=
lung; U=uterus; B=brain. A 1 Kb DNA molecular weight ladder is shown between the L and U
lanes. B. Amino acid sequence alignment of three VEGI isoforms. The putative hydrophobic
regions of VEGI-251 and VEGI-174 are underlined. Asterisk denotes the start of homologous
sequences.
Figure 4. Differential expression of VEGI-174 and VEGI-251 in human tissues. Northern blotting
analysis of VEGI expression in adult human tissues were performed with cDNA fragments
specific for VEGI-251 and VEGI-174. A 2 kb transcript is detected with the VEGI-174 probe, while
a 7.5 kb message is detected with the VEGI-251 probe. The human tissues examined were as
follows: 1. Peripheral blood leukocytes, 2. Lung, 3. Placenta, 4. Small intestine, 5. Liver, 6.
Kidney, 7. Spleen, 8. Thymus, 9. colon, 10. Skeletal muscle, 11. Heart, 12. Brain.
Figure 5. Ribonuclease protection analysis of VEGI isoforms in various cultured cells. Total
RNA from each culture shown was hybridized with isoform-specific VEGI probes and (i-actin
for loading control. Full-length undigested probes are shown in the probes lane (P), indicated by
solid arrowheads, and products of RNase protection are indicated by open arrowheads. Y=yeast
RNA, Hc=human coronary artery endothelial cells, Hm = human dermal microvascular
endothelial cells, Hu= human umbilical vein endothelial cells, Sm= human Coronary artery
smooth muscle cells, 3T= NIH3T3 embryonic mouse cell line, Ba= adult bovine aortic
endothelial cells, Bh= fetal bovine heart endothelial cells, Hy= EA.Hy926 human hybridoma
cells, bE=bEND.3 mouse brain endothelioma cells.
Figure 6. Gene structure of human VEGI and proposed generation of isoforms. The segments
numbered 1 through 9 represent the PCR fragments generated during gene mapping, with
specific primer pairs listed in Materials and Methods. Boxes with roman numerals above
represent exons and horizontal lines represent intronic sequence. The putative transcription start
site is indicated by a double arrowhead. R denotes the 5' untranslated sequence unique to each
respective transcript, and stippled boxes represent the common 3' untranslated region.
Approximate sizes of the introns are indicated. VEGI-251, VEGI-192a, or VEGI-174 specific
sequences are labeled 251', '192' or '174'. Exon Illb encodes residues shared by both VEGI-251 and
VEGI-192a. The introns 5' of exons III and IV are dashed because the 5' ends or initiation sites of
VEGI-192a and VEGI-174 transcripts have not been determined. 'COM' denotes the coding region
of the last exon that is common to all three isoforms.
Figure 7. TNFa induces VEGI isoform expression in both microvessel and large vessel
endothelial cells. Ribonuclease protection assays showing parallel induction of VEGI expression.
Arrows indicate protected RNAs. A. HMVE cells treated with TNFa at 15, 50 and 90 ng/ml over
24 hr. B. Induction of VEGI gene expression by TNFa in HUVE cells. HUVE cells were treated
(+) with 20 ng/ml TNFa for 4,8 and 24 hr. Controls (-) received corresponding vehicle
treatments.
Figure 8. Intracellular localization of recombinant VEGI-174 and VEGI-251 in transfected
endothelial cells. A. VEGI-174-myc and VEGI-251-myc (B) were detected in transfected ABAE
cells by Texas Red staining of the associated myc tags. C. Double staining of VEGI-251-myc
(red) and von Willebrand Factor (green) in transfected HUVE cells. The diagram in D depicts
VEGI expression constructs with a C-terminal myc tag. E-J. N-terminal tagged GFP-VEGI
constructs showed distinct distribution in ABAE cells. Cells transfected with vector plasmid (E)
showed GFP throughout the cell whereas three VEGI constructs (F, H-J) resulted in localized
GFP distributions. In I and J, VEGI-251 1-99 directed GFP distribution in the plasma membrane.
K. The GFP tags in the expression constructs used in F through J are located at the amino termini
of the VEGI fragments.
Figure 9 Detection by Western analysis of VEGI-251 in medium conditioned by transfected
MB231 cells and untransfected HUVE cells. A. Conditioned medium from stable transfectants of
MDA-MB231. Lane 1 = pcDNA3 vector only, Lanes 2 and 3 = two independent clones
expressing VEGI-251. B. Lane 1= HUVE cell-conditioned medium, Lane 2= HUVE cell lysate. In
both experiments, conditioned media were concentrated with Centricon columns (MW cutoff
10,000), immunoprecipitated using polyclonal antibody, then subjected to SDS-PAGE and
Western detection using monoclonal antibody 1-8F against the common C-terminal region of
VEGI (residues 29-174). Both panels show VEGI peptides of approximately 25 kD.
Figure 10. Overexpression of VEGI-251 causes endothelial cell death and interferes with tumor
neovascularization. A. Lentivirus delivery of secreted VEGI is lethal to HUVE cells. Dose-
dependent cytotoxicity of lentiviral stock expressing VEGI-251 and sVEGI compared with VEGI-
174. Twenty four hours following viral infection, adherent cells remaining in culture were counted
by Coulter counting. Viral p24 levels were estimated and viral dose is expressed as multiplicity
of infection (MOI). Values shown are mean ± SEM of three independent experiments. B.
Retardation of xenograft MDA-MB231 breast tumor growth by VEGI-251 and sVEGI.. Pools of
stably transfected MDA-MB231 cells expressing the indicated construct were injected
subcutaneously into mammary fat pads of female athymic mice, and tumor sizes monitored in a
blind manner. Control mice received MDA-MB231 cells transfected with empty pcDNA3
vector. Attenuation of tumor growth was observed for both VEGI-251 and sVEGI, but not for full
length VEGI-174. C. VEGI-251 and sVEGI transfection result in reduced microvessel densities in
MB231 xenograft tumors. Paraffin sections (5um) from tumors were taken from mice described
in Figure 10.4. Vessels were identified by CD31 immunostaining as described in Materials and
Methods. One-way analysis of variance was used, a: P xenografts with vector pcDNA3.
Figure 11. Photograph of the results of a multi-tissue Northern blotting analysis of the
expression of VEGI in various human organs, using P-32-labeled VEGI-174 cDNA as a probe.
VEGI mRNA signals of different sizes are visible.
Figure 12. A scheme illustrating RACE-PCR procedures used to search for possible VEGI
isoforms. ADP1 and ADP2 indicate adapter-specific primers. GSP1 and GSP2 indicate gene-
specific primers.
Figure 13. Photograph of the results of agarose gel electrophoresis of RACE-PCR products.
Four PCR products of different sizes from different human tissues are visualized by using
ethidium bromide staining. The PCR products were isolated and subjected to sequencing.
Figure 14. Photograph of a Western blotting analysis of the conditioned media of MDA-MB-
231 cells transfected with an empty vector (lane 1) or VEGI-251 cDNA (lane 2). The conditioned
media is subjected to a gel-filtration chromatography and fractions with a molecular weight
range of 10 - 50 kD were collected and subjected to SDS-PAGE. Panel A: Coomassie blue
staining of the gel. Panel B: Western blotting with a monoclonal antibody (13-2D) to VEGI.
Figure 15. Graph showing inhibition of the growth of xenograft tumors formed by MDA-MB-
231 cells transfected with VEGI-174, VEGI-251, IL6/VEGI, or an empty pCDNA-3 vector. One
million stably transfected cells are injected into the mammary fat pads of female athymic nude
mice. There are 2 injection sites per animal and 5 animal per group. The groups are coded and
the sizes of the xenograft tumors are monitored in a blinded manner. Statistically significant
inhibition of the growth of the tumors are observed for the VEGI-251 or the IL6-VEGI
overexpressing cells. VEGI-174 overexpression has no effect on the tumor growth.
Figure 16. Immunohistochernical analysis of the tumor samples obtained from the experiments
described in Figure 7, using mAb 13-2D against human VEGI. VEGI-overexpressing cells are
stained brown. Panels on the left are photographs of sections of tumor formed by the VEGI-251
transfected cells. Levels of VEGI-251 production were apparently highly variable, as evident from
the intensive staining of some of the tumor sections (G9-1R), which suggests high levels of
VEGI production, versus markedly less staining of some tumors of the same group (G9-2R).
Panels on the right are photographs of sections of tumors formed by vector-control cells. Brown-
staining in the control tumor sections are likely to be the results of antibody cross-reaction to the
intrinsic VEGI molecules on the mouse endothelium.
Figure 17. Graph showing the growth rate of the tumors formed by the VEGI-251 transfected
MDA-MB-231 cancer cells vary in accordance to the amount of VEGI produced by the cancer
cells. Tumors in which VEGI level is higher (G9-1R) grow much more slowly than those with
low VEGI levels (G9-2R).
Figure 18. Northern blotting analysis of VEGI transcripts. Panel A, VEGI expression in human
cells: Jurkat, human T cell leukemia cell; L923, human embryonic kidney cell; HL60, human
promyelocytic leukemia; V.E, human venous endothelial cell (10th passage); A431, human
epidermoid carcinoma; V.E.-2, human venous endothelial cell (20th passage); Raji, human
Burkitt's lymphoma; A.E, human artery endothelial cell; THP-1, human monocytic leukemia;
CCD-29Lu, human lung emphysema; CAMA1, breast cancer; AN3CA, uterine cancer; SK.UT.1,
uterine cancer; MG63, osteoblastoma; HOS, osteoblastoma; MCF7, breast cancer; OVCAR-3,
ovarian cancer; CAOV-3, ovarian cancer; HUVE, human umbilical vein endothelial cell;
AOSMIC, smooth muscle. The estimated message size is 6.5 kb. Panel B, VEGI expression in
adult human tissues using multiple tissue Northern blots (Clonetech): Three separate blots were
carried out. Positive results from any of the three experiments are shown.
Figure 19. Graph showing effect of VEGI on the proliferation of endothelial cell and breast
cancer cells. The number of cells is plotted against VEGI concentration as indicated. Inhibition
of the growth of ABAE cells (closed circles) but not that of MDA-MB-231 (open circles) or
MDA-MB-435 (triangles) cells, is shown. Cancer cells and ABAE cells are seeded at 2000 and
8000 cells/well, respectively, in triplicate in 24-well plates. The culture media contained IMEM
(Gibco) and 10% FCS. FGF-2 (1 ng/ml) is added to the media for ABAE cells. The cultures
were maintained at 37°C, 5% CO2, for 6 days. The cells are then trypsinized, and the number of
cells determined by using a Coulter counter. One fifth of the total number of recovered ABAE
cells is shown in order to normalize the comparison with the cancer cells.
Figure 20. Expression of VEGI in proliferating or quiescent endothelial cells. The VEGI
mRNA levels in cultured HUVE cells are determined by Northern blotting analysis. Identical
amount of total RNA (15 µg) is loaded on each lane, as indicated by the intensity of ß-actin.
Total RNA is prepared at the indicated time point (days post-seeding). The number of cells in
each culture flask is determined simultaneously. The experiment is carried out in duplicate.
Cells were seeded at 125,000 cells per flask (T-25) in IMEM, 10% FCS, 6 ng/ml FGF-2, and
cultured at 37°C, 5% CO2.
Figure 21. Graph showing the effect of VEGI on the ability of ABAE cells to form
capillary-like tubes on collagen gels. The ability of the recombinant VEGI to inhibit the
formation of capillary-like tubes by ABAE cells is shown. The p-values (t-test) given above the
columns is obtained by comparing the extent of the capillary-like tube formation by ABAE cells
in the presence of various concentrations of VEGI, as indicated, to that when VEGI is absent
from the culture media.
Figure 22. Graph showing the inhibition of angiogenesis in collagen gels placed on chick
embryonic chorioallantoic membrane (CAM) by VEGI. Growth of new capillary vessels into
collagen gel pellets (0.05 ml) placed on the CAM is induced by either FGF-2 (100 ng) or VEGF
(250 ng), embedded in the gels. The extent of angiogenesis in the gels is determined by
evaluation of the fluorescence intensity of FTIC-dextran injected into the CAM circulation and
retained in the gel. Inhibition of the capillary vessel growth by VEGI, indicated by a value lower
than 100, is shown. The inhibitor is also embedded in the gels. Error bars represent the standard
deviation of triplicate experimental values.
Figure 23. Graph showing the inhibition of the growth of human breast cancer xenograft tumors
in athymic nude mice by VEGI. Mixtures of VEGI-overexpressing or vector-transfected CHO
cells (5 x 106 cells per injection) and human breast cancer cells (1 x 106 cells per injection) were
injected into the mammary fat pads of female nude mice. Tumor sizes were monitored following
injection. Panel A: Plot of the sizes of the MDA-MB-231 xenograft tumors (mm2) as a function
of time post-inoculation (days). Panel B: Plot of the sizes of the MDA-MB-435 xenograft
tumors (mm2) as a function of time post-inoculation (days). Open circles, co-inoculated with
vector-transfected CHO cells. Closed circles, co-inoculated with the secreted VEGI transfected
CHO cells.
Figure 24. Graph showing effect of VEGI-192a on the proliferation of endothelial cells.
Inhibition of the growth of ABAE cells by properly refolded VEGI-192a, but not improperly
refolded VEGI-192a or buffer, is shown. ABAE cells are seeded at 8000 cells/well, respectively,
in triplicate in 24-well plates. The culture media contained IMEM (Gibco) and 10% FCS.
FGF-2 (1 ng/ml) was added to the media for ABAE cells. The cultures were maintained at 37°C,
5% CO2, for 6 days. The cells were then trypsinized, and the number of cells determined by
using a Coulter counter. One fifth of the total number of recovered ABAE cells was shown in
order to normalize the comparison with the cancer cells.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides novel isoforms of VEGI polynucleotides and
polypeptides, which inhibit vascular endothelial cell growth and methods for the treatment of
diseases and processes that are mediated by or associated with angiogenesis via administering
these polynucleotides, polypeptides, and other agents. The VEGI polynucleotides or
polypeptides of the invention can be isolated from body fluids including, but not limited to,
serum, urine, and ascites, or synthesized by chemical or biological methods (for example, cell
culture, recombinant gene expression).
Recombinant techniques include gene amplification from DNA sources using the
polymerase chain reaction (PCR), and gene amplification from RNA sources using reverse
transcriptase/PCR. These methods are well known in the art. VEGI inhibits the growth of blood
vessels into tissues such as unvascularized or vascularized tumors. The present invention
includes a protein that has a molecular weight of approximately 22 kD and any modified form of
the protein, including, but not limited to, a truncation or a post-translational modification such as
a glycosylated form of the protein that is capable of overcoming the angiogenic activity of
endogenous growth factors.
Definitions
As described herein, a "mutant" or "variant" VEGI polynucleotide or polypeptide is a
polynucleotide or polypeptide sequence that comprises one or more deletions, addition,
transversion, or alteration in nucleic acid or amino acid sequence. As described further herein, a
mutant VEGI sequence may result in a truncated or altered VEGI polynucleotide or polypeptide,
increased or decreased expression of a VEGI polynucleotide or polypeptide, or any combination
thereof. The mutation may be in coding, non-coding, 5' or 3' flanking, genomic or coding
nucleotides.
A "functionally preserved" variant of a VEGI isoform (i.e. VEGI-192a, VEGI-192b, or
VEGI-251) polynucleotide or VEGI isoform polypeptide is a VEGI sequence which retains at
least one aspect of VEGI isoform function. Functionally preserved variants can be due to
differences in linear sequence, arising from, for example, single base mutation(s), addition(s),
deletion(s), and/or modifications) of the bases. The difference can also arise from changes in
the sugar(s) and/or linkage(s) between the bases. Regarding polypeptides, functionally preserved
variants may arise, for example, by conservative and/or non-conservative amino acid
substitutions, amino acid analogs, and deletions. The function that is preserved depends upon
the relevant function being considered. For example, if a VEGI isoform polynucleotide is
considered for a probe, then the ability of a variant polynucleotide sequence to hybridize to the
target is the relevant function. If a polynucleotide is considered for its ability to encode a VEGI
isoform polypeptide (or fragment thereof), then the ability of a variant sequence to encode the
same polypeptide is the relevant function. If a VEGI isoform polypeptide is considered for its
ability to bind to a particular entity (such as an antibody or another protein), then the ability of a
variant sequence to encode a polypeptide with equivalent binding characteristics that is relevant.
A VEGI isoform polypeptide may be considered for its biological activity of the encoded gene
product (e.g., a biological activity ascribed to a gene product corresponded to the VEGI isoform
polynucleotides as a result of the assignment of the gene product to a protein family(ies) and/or
identification of a functional domain present in the gene product). By a polypeptide
demonstrating "functional activity" is meant, a polypeptide capable of displaying one or more
known functional activities associated with a complete or mature VEGI isoform polypeptide.
Such functional activities include, but are not limited to, biological activity (for example,
inhibition of angiogenesis, inhibition of vascular endothelial cell proliferation, induction of cell
adhesion, antigenicity (ability, to bind or compete with one or more VEGI isoform polypeptide
for binding to an anti-VEGI isoform antibody), immunogenicity (ability to generate antibody
which binds to one or more VEGI isoform polypeptides), the ability to form polymers with other
VEGI polypeptides. and ability to bind to a receptor or ligand for a VEGI polypeptide (for
example, DIG).
As used herein, "expression" includes transcription and/or translation.
"Heterologous" means derived from (i.e., obtained from) a genotypically distinct entity
from the rest of the entity to which it is being compared. For example, a polynucleotide may be
placed by genetic engineering techniques into a plasmid or vector derived from a different
source, thus becoming a heterologous polynucleotide. A promoter which is linked to a coding
sequence with which it is not naturally linked is a heterologous promoter.
A "reagent" polynucleotide, polypeptide, or antibody, is a substance provided for a
reaction, the substance having some known and desirable parameters for the reaction. A reaction
mixture may also contain a "target", such as a polynucleotide, antibody, polypeptide, or
assembly of polypeptides that the reagent is capable of reacting with. For example, in some
types of diagnostic tests, the presence and/or amount of the target in a sample is determined by
adding a reagent, allowing the reagent and target to react, and measuring the amount of reaction
product (if any). In the context of clinical management, a "target" may also be a cell, collection
of cells, tissue, or organ that is the object of an administered substance, such as a pharmaceutical
compound.
A "stable duplex" of polynucleotides, or a "stable complex" formed between any two or
more components in a biochemical reaction, refers to a duplex or complex that is sufficiently
long-lasting to persist between formation of the duplex or complex and subsequent detection,
including any optional washing steps or other manipulation that may take place in the interim.
A gene or polynucleotide is "differentially expressed" in a test sample when the
polynucleotide is detected at a higher or lower level compared with a control sample of the same
type. Typically, a differentially expressed polynucleotide includes polynucleotides that are
expressed such that, for example, mRNA is found at levels at least about 25%, at least about 50%
to 75%, at least about 90%, at least about 2-fold, at least about 4-fold, at least about 5-fold, and
at least about 10-fold or more, higher (e.g. overexpressed) or lower (e.g., underexpressed). The
comparison can be made between two tissue, for example, if one is using in situ hybridization or
another assay method that allows some degree of discrimination among cell types in the tissue.
The comparison may also be made between cells removed from their tissue source.
An "effective amount" of drug, compound, or pharmaceutical composition is an amount
sufficient to effect beneficial or desired results including clinical results such as inhibiting
vascular endothelial cell growth, inhibiting angiogenesis, promoting angiogenesis, shrinking the
size of the tumor, retardation of cancerous cell growth, decreasing one or more symptoms
resulting from the disease, increasing the quality of life of those suffering from the disease,
decreasing the dose of other medications required to treat the disease, enhancing effect of
another medication, delaying the progression of the disease, and/or prolonging survival of
patients, either directly or indirectly. An effective amount can be administered in one or more
administrations. As is understood in the angiogenesis-associated disease clinical context, an
effective amount of a drug, compound, or pharmaceutical composition may or may not be
achieved in conjunction with another drug, compound, or pharmaceutical composition. Thus, an
"effective amount" may be considered in the context of administering one or more therapeutic
agents, and a single agent may be considered to be given in an effective amount if, in
conjunction with one or more other agents, a desirable result may be or is achieved.
As used herein, "treatment" or "treating" is an approach for obtaining beneficial or
desired results including and preferably clinical results. For purposes of this invention,
beneficial or desired clinical results include, but are not limited to, one or more of the following:
reducing the proliferation of vascular endothelial cells, inhibiting angiogenesis, promoting
angiogenesis, reducing the size of the tumor, decreasing symptoms resulting from the disease,
increasing the quality of life of those suffering from the disease, decreasing the dose of other
medications required to treat the disease, delaying the progression of the disease, and/or
prolonging survival of patients.
"Development" or "progression" of angiogenesis-associated disease herein means initial
manifestations and/or ensuing progression of the disorder. Development of angiogenesis-
associated disease can be detectable and assessed using standard clinical techniques. However,
development also refers to disease progression that may be undetectable. For purposes of this
invention, development or progression refers to the biological course of the disease state.
"Development" includes occurrence, recurrence, and onset. As used herein "onset" or
"occurrence" of angiogenesis-associated disease includes initial onset and/or recurrence.
As used herein, "delaying development" of angiogenesis-associated disease means to
defer, hinder, slow, retard, stabilize, and/or postpone development of the disease. This delay can
be of varying lengths of time, depending on the history of the disorder and/or the medical profile
of the individual being treated. As is evident to one skilled in the art, a sufficient or significant
delay can, in effect, encompass prevention, in that the individual does not develop detectable
disease. A method that "delays" development of disease is a method that reduces the extent of
the disease in a given time frame, when compared to not using the method. Such comparisons
are typically based on clinical studies, using a statistically significant number of subjects,
although this knowledge can be based upon anecdotal evidence. "Delaying development" can
mean that the extent and/or undesirable clinical manifestations are lessened and/or time course of
the progression is slowed or lengthened, as compared to not administering the agent. Thus the
term also includes, but is not limited to, alleviation of symptoms, diminishment of extent of
disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression,
and remission (whether partial or total) whether detectable or undetectable.
As used herein and in the appended claims, the singular forms "a", "and", and "the"
include plural referents unless the context clearly dictates otherwise. Thus, for example,
reference to "a polynucleotide" includes a plurality of such polynucleotides and reference to "the
agent" includes reference to one or more agents and equivalents thereof known to those skilled in
the art, and so forth.
General Techniques
The practice of the present invention will employ, unless otherwise indicated,
conventional techniques of molecular biology (including recombinant techniques), microbiology,
cell biology, biochemistry and immunology, which are within the skill of the art. Such
techniques are explained fully in the literature, such as: "Molecular Cloning: A Laboratory
Manual", second edition (Sambrook et al., 1989); "Oligonucleotide Synthesis" (M.J. Gait, ed.,
1984); "Animal Cell Culture" (R.I. Freshney, ed., 1987); "Methods in Enzymology" (Academic
Press, Inc.); "Handbook of Experimental Immunology" (D.M. Wei & C.C. Blackwell, eds.);
"Gene Transfer Vectors for Mammalian Cells" (J.M. Miller & M.P. Calos, eds., 1987); "Current
Protocols in Molecular Biology" (F.M. Ausubel et al., eds., 1987); "PCR: The Polymerase
Chain Reaction", (Mullis et al., eds., 1994); "Current Protocols in Immunology" (J.E. Coligan et
al., eds., 1991).
Polynucleotides of the invention
The present invention provides polynucleotides of VEGI isoforms, including
polynucleotides encoding VEGI-192a, VEGI-192b, and VEGI-251. The nucleotide sequences
corresponding to the novel isoforms are given in Tables 1,2, and 3 (SEQ ID NO:1, SEQ ID
NO:2, and SEQ ID NO:3), and their respective polypeptide sequences are given in Tables 4, 5,
and 6 (SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6).
Table 1. Polynucleotide sequence encoding VEGI-192a (SEQ ID NO:1)
CTCCTATCAT AGGCGCCATG CAACTCACAA AGGGCCGTCT TCATTTCAGT CACCCTTTGT
CTCATACAAA GCACATTTCT CCTTTTGTTA CAGATGCACC TCTTAGAGCA GACGGAGATA
AGCCAAGGGC ACACCTGACA GTTGTGAGAC AAACTCCCAC ACAGCACTTT AAAAATCAGT
TCCCAGCTCT GCACTGGGAA CATGAACTAG GCCTGGCCTT CACCAAGAAC CGAATGAACT
ATACCAACAA ATTCCTGCTG ATCCCAGAGT CGGGAGACTA CTTCATTTAC TCCCAGGTCA
CATTCCGTGG GATGACCTCT GAGTGCAGTG AAATCAGACA AGCAGGCCGA CCAAACAAGC
CAGACTCCAT CACTGTGGTC ATCACCAAGG TAACAGACAG CTACCCTGAG CCAACCCAGC
TCCTCATGGG GACCAAGTCT GTATGCGAAG TAGGTAGCAA CTGGTTCCAG CCCATCTACC
TCGGAGCCAT GTTCTCCTTG CAAGAAGGGG ACAAGCTAAT GGTGAACGTC AGTGACATCT
CTTTGGTGGA TTACACAAAA GAAGATAAAA CCTTCTTTGG AGCCTTCTTA CTATAG
Table 2. Polynucleotide sequence encoding VEGI-192b (SEQ ID NO:2)
TTAAACGGGC CCTCTAGACT CGAGCGGCCG CCACTGTGCT GGATATCTGC AGAATTCGGC
TTAGCGCGTG AATCAGATCG GGGGGGGGGG TTAAGCAAAG CCATAAAACT GTCAGTTTAA
TATACCATCA TTTCACTAAC ATGAAGTGTG CCGGCTCTGT CCCCCCCTTT CTTTTCCTCC
TTCCAACTCT TTTAAAAAAG AACAGCTCTA CTTACGCCAA GGTGGAATTT TGGCTCTACT
AGCCACTATT CTGCGACAGA GTGGCTTTGT TGACGTGAGA AAGGCTCTCT TTGCTTTGCC
AGAATTAGTC ATGGAAACTT CACAGGAACA CCAGGGCCCC TCAGATATAC ACAGAATACC
ATGGAGCTGG GGACAAAGGA ATTCACATGC ACCTCTTAGA GCAGACGGAG ATAAGCCAAG
GGCACACCTG ACAGTTGTGA GACAAACTCC CACACAGCAC TTTAAAAATC AGTTCCCAGC
TCTGCACTGG GAACATGAAC TAGGCCTGGC CTTCACCAAG AACCGAATGA ACTATACCAA
CAAATTCCTG CTGATCCCAG AGTCGGGAGA CTACTTCATT TACTCCCAGG TCACATTCCG
TGGGATGACC TCTGAGTGCA GTGAAATCAG ACAAGCAGGC CGACCAAACA AGCCAGACTC
CATCACTGTG GTCATCACCA AGGTAACAGA CAGCTACCCT GAGCCAACCC AGCTCCTCAT
GGGGACCAAG TCTGTATGCG AAGTAGGTAG CAACTGGTTC CAGCCCATCT ACCTCGGAGC
CATGTTCTCC TTGCAAGAAG GGGACAAGCT AATGGTGAAC GTCAGTGACA TCTCTTTGGT
GGATTACACA AAAGAAGATA AAACCTTCTT TGGAGCCTTC TTACTATAGG ATCCGGAGCC
GAATTCCACC ACACTGGACT AAGTGGATTC GAGCTCGGTA CCAAAGCTTA AGTTTAAACG
CTAGCCAGCT TGGGTCCCCC TATAGTGAGT CNTATTAATT TCGATAAGCC AGTAAGCAGT
GGGTT
Table 3. Polynucleotide sequence encoding VEGI-251 (SEQ ID NO:3)
TTGTAATACG ACTCACTATA GGGCGGCCGC GAATTCGGCA CGAGATTTAA TGGCCGAGGA
TCTGGGACTG AGCTTTGGGG AAACAGCCAG TGTGGAAATG CTGCCAGAGC ACGGCAGCTG
CAGGCCCAAG GCCAGGAGCA GCAGCGCACG CTGGGCTCTC ACCTGCTGCC TGGTGTTGCT
CCCCTTCCTT GCAGGACTCA CCACATACCT GCTTGTCAGC CAGCTCCGGG CCCAGGGAGA
GGCCTGTGTG CAGTTCCAGG CTCTAAAAGG ACAGGAGTTT GCACCTTCAC ATCAGCAAGT
TTATGCACCT CTTAGAGCAG ACGGAGATAA GCCAAGGGCA CACCTGACAG TTGTGAGACA
AACTCCCACA CAGCACTTTA AAAATCAGTT CCCAGCTCTG CACTGGGAAC ATGAACTAGG
CCTGGCCTTC ACCAAGAACC GAATGAACTA TACCAACAAA TTCCTGCTGA TCCCAGAGTC
GGGAGACTAC TTCATTTACT CCCAGGTCAC ATTCCGTGGG ATGACCTCTG AGTGCAGTGA
AATCAGACAA GCAGGCCGAC CAAACAAGCC AGACTCCATC ACTGTGGTCA TCACCAAGGT
AACAGACAGC TACCCTGAGC CAACCCAGCT CCTCATGGGG ACCAAGTCTG TATGCGAAGT
AGGTAGCAAC TGGTTCCAGC CCATCTACCT CGGAGCCATG TTCTCCTTGC AAGAAGGGGA
CAAGCTAATG GTGAACGTCA GTGACATCTC TTTGGTGGAT TACACAAAAG AAGATAAAAC
CTTCTTTGGA GCCTTCTTAC TATAGGAGGA GAGCAAATAT CATTATATGA AAGTCCTCTG
CCACCGAGTT CCTAATTTTT TTGTTCAAAT GTAATTATAA CCAGGGGTTT TCTTGGGGCC
GGGAGTAGGG GGCATTCCAC AGGGACAACG GTTTAGCTAT GAAATTTGGG GCCCAAAATT
TCACACTTCA TGTGCCTTAC TGATGAGAGT ACTAACTGGA AAAAGGCTGA AGAGAGCAAA
TATATTATTA AGATGGGTTG GAGGATTGGC GAGTTTCTAA ATATTAAGAC ACTGATCACT
AAATGAATGG ATGATCTACT CGGGTCANGA TTGAAAGAGA AATATTTCAA CACCTTCCTG
CTATACAATG GTCACCAGTG GTCCAGTTAT TGTTCAATTT GATCATAAAT TGCTTCAATT
CANGAGCTTT GAAGGAAGTC CAAGGAAAGC TCTAGAAAAC AGTATAAACT TTCAGAGGCA
AAATCCTTCA CCAAATTTTC CACATACTTT CATGCCCTGC CTAAAAAAAA TGAAAAAGAA
AAGTTGGTAT GTCTCATGAA TGTTCACACA NAAAGAGTTG GGTTCATGTC ATCCNCAACA
TATGAGAAAA ANCTACCTTC TTTTGNTTAT GTCACAGATT C
Table 4. Amino acid sequence of VEGI-192a (SEQ ID NO:4)
MQLTKGRLHFSHPLSHTKHISPFVTDAPLRADGDKPRAHLTVVRQTPTQHFKNQFPALHW
EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV
VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT
KEDKTFFGAFLL
Table 5. Amino acid sequence of VEGI-192b (SEQ ID NO:5)
METSQEHQGPSDIHRIPWSWGQRNSHAPLRADGDKPRAHLTWRQTPTQHFKNQFPALHW
EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV
VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT
KEDKTFFGAFLL
Table 6. Amino acid sequence of VEGI-251 (SEQ ID NO:6)
MAEDLGLSFGETASVEMLPEHGSCRPKARSSSARWALTCCLVLLPFLAGLTTYLLVSQL
RAQGEACVQFQALKGQEFAPSHQQVYAPLRADGDKPRAHLTVVRQTPTQHFKNQFPALHW
EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV
VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT
KEDKTFFGAFLL
Referring to the sequence alignment comparing the deduced amino acid sequences for
SEQ ID NOS: 4, 5, and 6 (Table 7), the C-terminal region of the polypeptides encoded by these
SEQ ID's is identical from Val-24 of VEGI-174 to the C-terminus of the protein. However, the
N-termini of the four isoforms are different. It is shown in the Examples that VEGI-174 does not
inhibit angiogenesis because it is not efficiently exported from the cell upon expression. In
contrast, VEGI-251 is efficiently trafficked to the extracellular medium upon expression, and is
thereby effective, at inhibiting angiogenesis. Export of VEGI-251 results in cleavage of the
presequence; the location for proteolysis is believed to be at position 61 or 96 of VEGI-2si;but
may also be located at another site located approximately between Glu-20 and Ser-57 of VEGI-
251. Possible sites include, but are not limited to, E64, K73, E77, S81, R90, and K95. Purified
VEGI-192a polypeptides is also effective at inhibiting vascular endothelial cell growth.
Table 7. Alignment of the amino acid sequences of the four VEGI isoforms *: (SEQ ID
NOS:6,4,5,7)
VEGI-251 MAEDLGLSFGETASVEMLPEHGSCRPKARSSSARWALTCCLVLLPFLAGLTTYLLVSQL 59
VEGI-251 RAQGEACVQFQALKGQEFAPSHQQVYAPLRADGDKPRAHLTWRQTPTQHFKNQFPALHW 119
VEGI-192a MQLTKGRLHFSHPLSHTKHISPFVTDAPLRADGDKPRAHLTWRQTPTQHFKNQFPALHW 60
VEGI-192b METSQEHQGPSDIHRIPWSWGQRNSHAPLRADGDKPRAHLTVVRQTPTQHFKNQFPALHW 60
VEGI-174 MRRFLSKVYSFPMRKLILFLVFPWRQTPTQHFKNQFPALHW 42
VEGI-251 EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV 17 9
VEGI-192a EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV 120
VEGI-192b EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV 120
VEGI-174 EHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEIRQAGRPNKPDSITV 102
VEGI-251 VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT 239
VEGI-192a VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT 180
VEGI-192b VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT 180
VEGI-174 VITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGDKLMVNVSDISLVDYT 162
VEGI-251 KEDKTFFGAFLL 251
VEGI-192a KEDKTFFGAFLL 192
VEGI-192b KEDKTFFGAFLL 192
VEGI-174 KEDKTFFGAFLL 174
* VEGI-174 (SEQ ID NO: 7) is referred to previously as VEGI (GenBank accession number
AF039390)
** Homologous sequence in all isoforms begins at V24 of VEGI-174 (SEQ ID NO:7), V101 of VEGI-
251(SEQ ID NO: 6), V42 of VEGI-192a (SEQ ID NO:4), and V42 of VEGI-192b (SEQ ID NO:5).
Accordingly, the present invention provides isolated nucleic acid molecules comprising
sequences corresponding to novel isoforms of VEGI shown in Table 1,2, and 3 (SEQ ID NO:1,
SEQ ID NO:2, and SEQ ID NO:3). The polynucleotides of this invention, including fragments
of polynucleotides of this invention, are useful as probes, primers, in expression systems
(including in vivo and in vitro expression systems, as described herein, which may also be a
basis of gene therapy), and in screening systems. Especially useful applications of the
polynucleotides will be discussed below.
By "isolated" nucleic acid molecule is intended a nucleic acid molecule, DNA or RNA,
that has been removed from its native environment. In some embodiments, at least 50%,
preferably at least 70%, more preferably at least 80%, and even more preferably at least 90% free
of the materials with which it is associated in nature have been removed. For example,
recombinant DNA molecules contained in a vector are considered isolated for the purposes of the
present invention. Further examples of isolated DNA molecules include recombinant DNA
molecules maintained in heterologous host cells or purified (partially or substantially) DNA
molecules in solution. Isolated RNA molecules include in vivo or in vitro RNA transcripts of the
DNA molecules of the present invention. Isolated nucleic acid molecules further includes such
molecules produced synthetically. Accordingly, an "isolated" polynucleotide or polypeptide also
refers to recombinant or other non-naturally occurring forms polynucleotides or polypeptides,
which, by virtue of origin or manipulation: (1) are not associated with all or a portion of a
polynucleotide or polypeptide with which it is associated in nature, (2) are linked to a
polynucleotide or polypeptide other than that to which it is linked in nature, or (3) does not occur
in nature, or (4) in the case of polypeptides arise from expression of recombinant
polynucleotides.
The present invention also provides nucleic acid molecules (including, as is well
understood by one in the art and described herein, isolated and/or recombinant forms) encoding a
mature form of the polypeptide proteins described herein. The amino acid sequence of the
complete VEGI isoform polypeptide includes a leader sequence and a mature protein. According
to the signal hypothesis, once export of the growing protein chain across the rough endoplasmic
reticulum has been initiated, proteins secreted by mammalian cells have a signal or secretory
leader sequence which is cleaved from the complete polypeptide to produce a secreted "mature"
form of the protein. Most mammalian cells and even insect cells cleave secreted proteins with the
same specificity. However, in some cases, cleavage of a secreted protein is not entirely uniform,
which results in two or more mature species of the protein. Further, it has long been known that
the cleavage specificity of a secreted protein is ultimately determined by the primary structure of
the complete protein, that is, it is inherent in the amino acid sequence of the polypeptide.
The present invention also provides polynucleotides encoding a fusion protein. As is
well known in the art, a fusion protein or polypeptide is a polypeptide comprising regions in a
different position than occurs in nature. The regions may normally exist in separate proteins and
are brought together in the fusion polypeptide, or they may normally exist in the same protein
but are placed in a new arrangement in the fusion polypeptide. Accordingly, the invention
provides polynucleotides, wherein the coding sequence for the mature polypeptide may be fused
in the same reading frame to a polynucleotide sequence which aids in expression and secretion of
a polypeptide from a host cell, for example, a leader sequence which functions as a secretory
sequence for controlling transport of a polypeptide from the cell. The polypeptide having a
leader sequence is a preprotein and may have the leader sequence cleaved by the host cell to
form the mature form of the polypeptide. The polynucleotides may also encode for a proprotein
which is the mature protein plus additional 5' amino acid residues. A mature protein having a
prosequence is a proprotein and is an inactive form of the protein. Once the prosequence is
cleaved an active mature protein remains. Thus, for example, the polynucleotide of the present
invention may encode for a mature protein, or for a protein having a prosequence and a
presequence (leader sequence).
The polynucleotides of the present invention provides coding sequence fused in frame to
a marker sequence allows for purification or detection of the polypeptide of the present
invention. The marker sequence may be a hexa-histidine tag supplied by a pQE-9 vector to
provide for purification of the mature polypeptide fused to the marker in the case of a bacterial
host, or, for example, the marker sequence may be a hemagglutinin (HA) tag when a mammalian
host, e.g., COS-7 cells, is used. The HA tag, corresponds to an epitope derived from the
influenza hemagglutinin protein (Wilson. I., et al., Cell, 37:767 (1984)).
. Thus, the term "polynucleotide encoding a polypeptide" encompasses a polynucleotide
which includes only coding sequence for the polypeptide as well as a polynucleotide which
includes additional coding and/or non-coding sequence. For purposes of this invention, and to
avoid cumbersome referrals to complementary strands, the anti-sense (or complementary) strand
of such a polynucleotide is also said to encode the sequence; that is, a polynucleotide sequence
that "encodes" a polypeptide includes both the conventional coding strand and the
complementary sequence (or strand).
A mutant or a variant of the polynucleotide may be a naturally occurring allelic variant of
the polynucleotide or a non-naturally occurring variant of the polynucleotide. Such nucleotide
mutants or variants include deletion variants, substitution variants and addition or insertion
variants. A variant sequence may result in a truncated or altered polynucleotide or polypeptide,
increased or decreased expression of a polynucleotide or polypeptide, or any combination
thereof. The variant may be in coding, non-coding, 5' or 3' flanking, genomic or coding
nucleotides.
In some embodiments, the polynucleotide sequence comprises a sequence different from
those shown Tables 1,2, or 3 (SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3) due to the
degeneracy of the genetic code. Genetic code is well known in the art. It would be routine for
one skilled in the art to generate such degenerate variants. Accordingly, in some embodiments,
the present invention provides a polynucleotide encoding the polypeptide of SEQ ID NO:4, SEQ
ID NO:5,or SEQ ID NO:6.
The present invention is further provides fragments or truncated form of the isolated
nucleic acid molecules described herein. By a fragment of an isolated nucleic acid molecule
having the nucleotide sequence of the nucleotide sequences herein, or the complementary strand
thereto, is intended fragments at least 5 nt, at least 10 nt, at least 15 nt, at least 20 nt, at least 30
nt, at least 40,50,100,150,200,250,300,400, or 500 nt in length (contiguous nucleotides).
These fragments have numerous uses which include, but are not limited to, diagnostic probes and
primers as discussed herein. As is well understood in the art, generally a probe is used for
detection on a target by hybridization. In some embodiments, a probe may comprise a label or a
means by which a label can be attached, either before or subsequent to the hybridization reaction.
Suitable labels include, but are not limited to radioisotopes, fluorochromes, chemiluminescent
compounds, dyes, and enzymes. Further, those skilled in the art understand that a primer is
generally extended by polymerization after hybridizing to a target sequence. Of course, larger
fragments 50-1500 nt in length are also useful according to the present invention. By a fragment
at least 20 nt in length, for example, is intended fragments which include 20 or more contiguous
bases from the nucleotide sequence. In some embodiments, these fragments comprises
nucleotides 93 and 94 of the sequence shown in Table 1 (SEQ ID NO:1) or nucleotides 386 and
387 of the sequence shown in Table 2 (SEQ ID NO:2). Alternatively, fragments may be less
than 1500, 1250, 1000, 750, 500,250,200,150,100, 50, 40 nt in length and comprise
nucleotides 93 and 94 of the sequence shown in Table 1 (SEQ ID NO:1) or nucleotides 386 and
387 of the sequence shown in Table 2 (SEQ ID NO:2).
The present invention also provides polynucleotides comprising the sequence of VEGI-
192a (nucleotides 1 to 93 of the sequence shown in Table 1 (SEQ ID NO:1)), or VEGI-192b
(nucleotides 1 to 386 of the sequence shown in Table 2 (SEQ ID NO:2)).
In some embodiments, the invention provides a polynucleotide comprising at least 10, at
least 15, at least 18, at least 20, at least 25, at least 30, at least 50, and at least 100 or more
contiguous nucleotides of SEQ ID NO: 1 (which generally may also be referred to as regions),
said contiguous nucleotides are within nucleotides 1 to 93 of the sequence shown in Table 1
(SEQ ID NO:1). In some embodiments, the invention provides a polynucleotide comprising at
least 10, at least 15, at least 18, at least 20, at least 25, at least 30, at least 50, and at least 100 or
more contiguous nucleotides of SEQ ID NO:1, said contiguous nucleotides comprise nucleotides
93 and 94 of SEQ ID NO: 1.
In some embodiments, the invention provides a polynucleotide comprising at least 10, at
least 15, at least 18, at least 20, at least 25, at least 30, at least 50, at least 100, at least 150, at
least 175, at least 200, at least 250, at least 275, at least 300, at least 350, at least 375, at least 400
or more contiguous nucleotides of SEQ ID NO:2, said contiguous nucleotides are within
nucleotides 1 to 386 of the sequence shown in Table 2 (SEQ ID NO:2). In some embodiments,
the invention provides a polynucleotide comprising at least 10, at least 15, at least 18, at least 20,
at least 25, at least 30, at least 50, at least 100, at least 150, at least 175, at least 200, at least 250,
at least 275, at least 300, at least 350, at least 375, at least 400 or more contiguous nucleotides of
SEQ ID NO:2, said contiguous nucleotides comprise nucleotides 386 and 387 of SEQ ID NO:2.
The invention provides an isolated polynucleotide comprising a sequence encoding the
polypeptide of SEQ ID NO:4. The invention also provides an isolated polynucleotide
comprising a sequence encoding at least 5, at least 8, at least 10, at least 15, at least 20, at least
25, or more contiguous amino acids of SEQ ID NO:4, said contiguous amino acids are within
amino acid residues 1-26 shown in Table 4 (SEQ ID NO:4). The invention also provides an
isolated polynucleotide comprising a sequence encoding at least 5, at least 8, at least 10, at least
15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:4, said contiguous
amino acids comprise amino acids 26 and 27 of the sequence shown in Table 4 (SEQ ID NO:4).
The invention also provides an isolated polynucleotide comprising a sequence encoding amino
acid residues 5-192,10-192,15-192,25-192 of the sequence shown in Table 4 (SEQ ID NO:4).
The invention provides an isolated polynucleotide comprising a sequence encoding the
polypeptide of SEQ ID NO:5. The invention also provides an isolated polynucleotide
comprising a sequence encoding at least 5, at least 8, at least 10, at least 15, at least 20, at least
25, or more contiguous amino acids of SEQ ID NO:5, said contiguous amino acids are within
amino acid residues 1 -26 shown in Table 5 (SEQ ID NO:5). The invention also provides an
isolated polynucleotide comprising a sequence encoding at least 5, at least 8, at least 10, at least
15, at least 20, at least 25, or more contiguous amino acids of SEQ ID NO:5, said contiguous
amino acids comprise amino acids 26 and 27 of the sequence shown in Table 5 (SEQ ID NO:5).
The invention also provides an isolated polynucleotide comprising a sequence encoding amino
acid residues 5-192,10-192,15-192,25-192 of the sequence shown in Table 5 (SEQ ID NO:5).
It is understood that, a region of contiguous amino acids or nucleotides that are within a
given pair of amino acids or nucleotides can, but not necessarily, include either member of the
specified pair. For example, contiguous nucleotides within nucleotides 1-93 of SEQ ID NO:1
can include nucleotide 1 and/or nucleotide 93 of SEQ ID NO:1.
The embodiments of the present invention excludes polynucleotides encoding a
polypeptide consisting of amino acids 27-192 of SEQ ID NO:4 or SEQ ID NO:5 or any truncated
form of such polynucleotides.
The invention also provides polynucleotides comprising the sequence encoding any of
VEGI polypeptides described herein.
In specific embodiments, the polynucleotide fragments of the invention encode a
polypeptide which demonstrates a functional activity. By a polypeptide demonstrating
"functional activity" is meant, a polypeptide capable of displaying one or more known functional
activities associated with a complete or mature VEGI polypeptide. Such functional activities
include, but are not limited to, biological activity (for example, inhibition of angiogenesis,
inhibition of vascular endothelial cell proliferation, induction of cell adhesion, antigenicity
(ability, to bind or compete with a VEGI-192a and/or VEGI-192b polypeptide for binding to an
anti-VEGI-192a and/or ami-VEGI-192b antibody), immunogenicity (ability to generate antibody
which binds to a VEGI-192a and/or VEGI-192b polypeptide), the ability to form polymers with
other VEGI polypeptides. and ability to bind to a receptor or ligand for a VEGI polypeptide (for
example, DR3).
Similarly, the VEGI polypeptides encoded by any of the polynucleotides described herein
may have one or more functional activities of VEGI as described above and herein.
Another embodiment of the invention provides an isolated polynucleotide having at least
85%, at least 88%, at least 90%, at least 92%, at least 94%, at least 96 %, at least 98%, or at least
99% sequence identity with the polynucleotides of the invention as described herein. One
embodiment provides an isolated polynucleotide having at least 85%, at least 88%, at least 90%,
at least 92%, at least 94%, at least 96 %, at least 98%, or at least 99% sequence identity with the
VEGI-192a or VEGI-192b sequence shown in Table 1 or Table 2 (SEQ ID NO: 1 or SEQ ID NO:2).
In other embodiments, isolated polynucleotides additionally have less than 85%, 83%, 80%,
75%, 70 % sequence identity with the above VEGI-192a or VEGI-192b sequence. The invention
also includes isolated polynucleotides having at least 85%, at least 88%, at least 90%, at least
92%, at least 94%, at least 96 %, at least 98%, or at least 99% sequence identity to fragments of
at least 10 contiguous nucleotides (or more, such as 15,18,20,25,35,40,45, 50,60,75, or 100
contiguous nucleotides) of the sequence shown in Table 1 (SEQ ID NO:1) or 2 (SEQ ID NO:2),
wherein the contiguous nucleotides comprise nucleotides 93 and 94 of SEQ ID NO:1, or
nucleotides 386 and 387 of SEQ ID NO:2. In some embodiments, the polynucleotides having at
least 85%, at least 88%, at least 90%, at least 92%, at least 94%, at least 96 %, at least 98%, or at
least 99% sequence identity to fragments of at least 10 contiguous nucleotides (or more, such as
15,18,20,25, 35,40,45, 50, 60,75, or 100 contiguous nucleotides) of the sequence shown in
Table 1 (SEQ ID NO: 1) or of the sequence shown in Table 2 (SEQ ID NO:2), wherein the
contiguous nucleotides are within nucleotides 1-93 of SEQ ID NO:1 or nucleotides 1-386 of
SEQ ID NO:2.
A polynucleotide or polynucleotide region has a certain percentage (for example, 80%,
85%, 90%, or 95%) of "sequence identity" to another sequence means that, when aligned, that
percentage of bases are the same in comparing the two sequences. This alignment and the
percent homology or sequence identity can be determined using software programs known in the
art, for example those described in Current Protocols in Molecule Biology (F.M. Ausubel et al,
eds., 1987) Supplement 30, section 7.718, Table 4.7.1. Percent identity can be determined
electronically, e.g., by using the MegAlign.TM. program (DNASTAR, Inc., Madison Wiss.). Th MegAlign.TM. program can create alignments between two or more sequences according to
different methods, e.g., the clustal method. (See, e.g., Higgins, D. G. and P. M. Sharp (1988)
Gene 73:237-244.) The clustal algorithm groups sequences into clusters by examining the
distances between all pairs. The clusters are aligned pairwise and then in groups. The
percentage similarity between two amino acid sequences, e.g., sequence A and sequence B, is
calculated by dividing the length of sequence A, minus the number of gap residues in sequence
A, minus the number of gap residues in sequence B, into the sum of the residue matches between
sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the tw amino acid sequences are not included in determining percentage similarity. Percent identity
between nucleic acid sequences can also be counted or calculated by other methods known in the
art, e.g., the Jotun Hein method. (See, e.g., Hein, J. (1990) Methods Enzymol. 183:626-645.)
The invention also provides an isolated nucleic acid that hybridizes under high stringenc)
conditions to a nucleic acid having a sequence complementary to the nucleotide sequence
selected from the group consisting of SEQ ID NO:1, and SEQ ID NO:2, or to the nucleic acid
having a sequence complementary to a nucleotide encoding polypeptide of SEQ ID NO:4 or
SEQ ID NO:5, or their complement thereof.
hi terms of hybridization conditions, the higher the sequence identity required, the more
stringent are the hybridization conditions if such sequences are determined by their ability to
hybridize to a polynucleotide sequence of the invention. Accordingly, the invention also
includes polynucleotides that are able to hybridize to a sequence comprising a polynucleotide of
the invention as discussed herein. An example of stringent hybridization conditions is overnight
incubation at 42°C in a solution: 50% formamide, 1xSSC (150 mM sodium chloride, 15 mM
sodium citrate), 50 mM sodium phosphate (pH 7.6), 5 X denhardt's solution, 10% dextran
sulfate, and 20 µg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in
0.1 x SSC at about 65°C. For discussion regarding hybridization reactions, see below.
In one embodiment, the invention provides an isolated polynucleotide comprising a
sequence of at least 10 contiguous nucleotides (or more, such as 15,18,20,25,35,40,45, 50,
60, 75, or 100 (or more) contiguous nucleotides) that hybridizes with a polynucleotide (such as
DNA or RNA) comprising the sequence depicted in Table 1 (SEQ ID NO:1) or Table 2 (SEQ ID
NO:2), or fragments thereof, as described above, under conditions where it does not hybridize
with other polynucleotides from a mammalian cell, preferably a human cell, or under conditions
in which hybridization to the polynucleotide having the sequence depicted in Table 1 (SEQ ID
NO:1) or Table 2 (SEQ ID NO:2) is enriched relative to hybridization with other polynucleotides
from a mammalian cell. In some embodiments, the fragments comprise nucleotides 93 and 94 of
SEQ ID NO: 1 or nucleotides 386 and 387 of SEQ ID NO:2. In some embodiments, the
fragments are within nucleotides 1-93 of SEQ ID NO:1 or nucleotides 1-386 of SEQ ID NO:2.
These embodiments are particularly useful in the diagnostic (detection) context.
In another embodiment, the invention includes a polynucleotide sequence comprising at
least 10, preferably 15, preferably 18, preferably 20, more preferably 25, more preferably 35,
more preferably 50, still more preferably 75,100,125,150,200,250 contiguous nucleotides of
the non-coding (i.e., flanking) shown in Table 1 (SEQ ID NO:1) or Table 2 (SEQ ID NO:2).
These embodiments may be particularly useful as diagnostic probes, or as primers for
amplification of noncoding portions of the VEGI-192a or VEGI-192b gene.
It is understood that (unless otherwise specified or required), any embodiment of the
invention described herein that is a polynucleotide encompasses both the double-stranded form
and each of two complementary single-stranded forms known or predicted to make up the double
stranded form.
Hybridization reactions can be performed under conditions of different "stringency".
Conditions that increase stringency of a hybridization reaction of widely known and published in
the art. See, for example, Sambrook et al. (1989). Examples of relevant conditions include (in
order of increasing stringency): incubation temperatures of 25°C, 37°C, 50°C and 68°C; buffer
concentrations of 10 X SSC, 6 X SSC, 1 X SSC, 0.1 X SSC (where SSC is 0.15 M NaCl and 15
mM citrate buffer) and their equivalents using other buffer systems; formamide concentrations of
0%, 25%, 50%, and 75%; incubation times from 5 minutes to 24 hours; 1,2, or more washing
steps; wash incubation times of 1,2, or 15 minutes; and wash solutions of 6 X SSC, 1 X SSC,
0.1 X SSC, or deionized water. An example of stringent hybridization conditions is
hybridization at 50°C or higher and O.lxSSC (15 mM sodium chloride/1.5 mM sodium citrate).
Another example of stringent hybridization conditions is overnight incubation at 42°C in a
solution: 50% formamide, lxSSC (150 mM sodium chloride, 15 mM sodium citrate), 50 mM
sodium phosphate (pH 7.6), 5 X denhardt's solution, 10% dextran sulfate, and 20 ug/ml
denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1 x SSC at about
65°C. Stringent hybridization conditions are hybridization conditions that are at least as
stringent as the above representative conditions. Other stringent hybridization conditions are
known in the art and may also be employed to identify nucleic acids of this particular
embodiment of the invention.
The invention also provides primers and probes comprising a region of SEQ ID NO:1 or
SEQ ID NO:2, wherein the region is within nucleotides 1-93 of SEQ ID NO: 1 or nucleotides 1-
386 of SEQ ID NO:2. The invention also provides primers and probes comprising a region of
SEQ ID NO:1 or SEQ ID NO:2, wherein the region comprises nucleotides 93 and 94 of SEQ ID
NO:1 or nucleotides 386 and 387 of SEQ ID NO:2.
Probes from more than one polynucleotide sequence provided herein can hybridize with
the same nucleic acid if the cDNA from which they were derived corresponds to one mRNA. By
using probes, particularly labeled probes of DNA sequences, one can isolate homologous or
related genes. The source of homologous genes can be any species, e.g. primate species,
canines, felines, bovines, ovines, equines, yeast, nematodes. Probes of more than 10 nucleotides
("nt") can be used, e.g. probes of a size within a range of about 15 nt, 18 nt, 20, nt, 25nt, 75 nt, or
100 nt, but in general about 15 nt represents sufficient sequence for unique identification.
"Tm" is the temperature in degrees Centigrade at which 50% of a polynucleotide duplex
made of complementary strands hydrogen bonded in anti-parallel direction by Watson-Crick
base pairing dissociates into single strands under conditions of the experiment. Tm may be
predicted according to a standard formula, such as:
Tm = 81.5 + 16.6 log[X+] + 0.41 (%G/C) - 0.61 (%F) - 600/L
where [X+] is the cation concentration (usually sodium ion, Na+) in mol/L; (%G/C) is the
number of G and C residues as a percentage of total residues in the duplex; (%F) is the percent
formamide in solution (wt/vol); and L is the number of nucleotides in each strand of the duplex.
As described above, the invention includes variants or modifications to the VEGl-192a and
VEGI-192b polynucleotides such as deletions, substitutions, additions, or changes in the nature of
any nucleic acid moieties. A variant or modification is any difference in nucleotide sequence as
compared to a polynucleotide shown herein to encode a VEGI-192a or a VEGI-192b polypeptide,
and/or any difference in terms of the nucleic acid moieties of the polynucleotide(s). Such
changes can be useful to facilitate cloning and modifying expression of VEGI-192a or VEGI-192b
polynucleotides. Such changes also can be useful for conferring desirable properties to the
polynucleotide(s), such as stability. The definition of polynucleotide provided herein gives
examples of these modifications. Hence, the invention also includes functionally-preserved
variants of the nucleic acid sequences disclosed herein, which include nucleic acid substitutions,
additions, and/or deletions. Variants include naturally occurring variants of the polynucleotide
sequence (e.g. degenerate variants, allelic variants, etc. In general, allelic variants contain 15-
25% base pair (bp) mismatches and can contain as little as 5-15%, or 2-5%, or 1-2% bp
mismatch, as well as a single bp mismatch.
As described above, the invention encompasses VEGI-192a or VEGI-192b polynucleotides
including full-length (unprocessed), processed, coding, non-coding or portions thereof. A partial
map of the VEGI-192a genomic region is shown in Figure 6, including predicted intron-exon
boundaries. The invention can further include the 3' and 5' untranslated regions found in the
mature mRNA, specific transcriptional and translational regulatory sequences, such as
promoters, enhancers, etc., including about 1 kb, and possibly more of flanking genomic DNA at
either the 5' or 3' end of the transcribed region. The genomic DNA can be isolated as a fragment
of 100 kbp or smaller, and substantially free of flanking chromosomal sequence. The genomic
DNA flanking the coding region, either 3' or 5', or internal regulatory sequences as sometime
found in introns, contains sequences required for proper tissue, stage-specific or disease-state
specific expression. Also embodied are the mRNA and cDNA sequences and fragments thereof,
including fragments that include a portion of a VEGI-192a or VEGI-192b encoding segment.
Normally, mRNA species have contiguous exons, with the intervening introns, when present,
being removed by nuclear RNA splicing, to create a continuous open reading frame encoding a
polypeptide. mRNA species can also exist with both exons and introns, where the introns may
be removed by alternative splicing. Furthermore, different species of mRNAs encoded by the
same genomic species can exist at varying levels in a cell, and detection of these various levels
of mRNA species can be indicative of differential expression of the encoded gene product in the
cell.
The invention also encompasses polynucleotides encoding for functionally equivalent
variants and derivatives of full-length VEGI-192a or VEGI-192b and functionally equivalent
fragments (such as deletion of amino acids from N-terminal and/or from C-terminal of VEGI-
192a, or VEGI-192b) thereof which may enhance, decrease or not significantly affect properties of
the polypeptides encoded thereby. For instance, changes in a DNA sequence that do not change
the encoded amino acid sequence, as well as those that result in conservative substitutions of
amino acid residues, non-deleterious non-conservative substitutions, one or a few amino acid
deletions or additions, and substitution of amino acid residues by amino acid analogs are those
which will not significantly affect properties of the encoded polypeptide. Nucleotide
substitutions that do not alter the amino acid residues encoded can be useful for optimizing gene
expression in different systems. Suitable substitutions are known to those of skill in the art and
are made, for instance, to reflect preferred codon usage in the particular expression systems. In
another example, alternatively spliced polynucleotides can give rise to a functionally equivalent
fragment or variant of VEGI. Alternatively processed polynucleotide sequence variants are
defined as polynucleotide sequences corresponding to mRNAs that differ in sequence for one
another but are derived from the same genomic region, for example, mRNAs that result from: 1)
the use of alternative promoters; 2) the use of alternative polyadenylation sites; or 3) the use of
alternative splice sites.
This invention also provides a DNA insert comprising a nucleic acid having a nucleotide
sequence of SEQ ID NO: 1 or a complement thereof. In other embodiment, the invention
provides a DNA insert comprising a nucleic acid having a nucleotide sequence of SEQ ID NO:2
or a complement thereof.
As well understood in the art, a "polynucleotide" refers to a polymeric form of
nucleotides of any length, which contain deoxyribonucleotides, ribonucleotides, and/or their
analogs. The terms "polynucleotide" and "nucleic acid" as used herein are used interchangeably,
and as is well known in the art. Polynucleotides may have any three-dimensional structure. The
term "polynucleotide" includes double-, single-stranded, and triple-helical molecules. Unless
otherwise specified or required, any embodiment of the invention described herein that is a
polynucleotide encompasses both the double-stranded form and each of two complementary
single-stranded forms known or predicted to make up the double stranded form. Not all linkages
in a polynucleotide need be identical.
In some embodiments, a polynucleotide may comprise modified nucleotides, such as
methylated nucleotides and nucleotide analogs. The use of uracil as a substitute for thymine in a
deoxyribonucleic acid is also considered an analogous form of pyrimidine.
As is widely known in the art, if present, modification to the nucleotide structure may be
imparted before or after assembly of the polymer. In some embodiments, the sequence of
nucleotides may be interrupted by non-nucleotide components. As described herein, a
polynucleotide may be further modified after polymerization, such as by conjugation with a
labeling component. Other types of modifications are, for example, "caps", substitution of one
or more of the naturally occurring nucleotides with an analog, internucleotide modifications such
as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters,
phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates,
phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins
(e.g., nucleases, toxins, antibodies, signal peptides, ploy-L-lysine, etc.), those with intercalators
(e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron,
oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha
anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide(s). All of these
modifications are well known in the art.
Further, any of the hydroxyl groups ordinarily present in the sugars may be replaced by
phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to
prepare additional linkages to additional nucleotides, or may be conjugated to solid supports.
The 5' and 3' terminal OH groups can be phosphorylated or substituted with amines or organic
capping group moieties of from 1 to 20 carbon atoms. Other hydroxyls may also be derivatized
to standard protecting groups.
Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are
generally known in the art, including, but not limited to, 2'-O-methyl-, 2'-O-allyl, 2'-fiuoro- or
2'-azido-ribose, carbocyclic sugar analogs, a-anomeric sugars, epimeric sugars such as
arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs
and abasic nucleoside analogs such as methyl riboside.
Although conventional sugars and bases are generally used, substitution of analogous
forms of sugars, purines and pyrimidines can be advantageous in designing a final product, as
can alternative backbone structures like a polyamide backbone or phosphorothioate backbone.
This invention encompasses compositions, including pharmaceutical compositions,
comprising polynucleotides described herein. These compositions may further comprise suitable
excipients, such as pharmaceutically acceptable excipients including buffers, which are well
known in the art.
This invention also provides kits comprising any of the polynucleotides described herein.
In some embodiments, the kits comprise polynucleotides of SEQ ID NO:1 and/or SEQ ID NO:2.
In some embodiments, the kits comprise polynucleotides encoding a polypeptide of SEQ ID
NO:4 and/or SEQ ID NO:5. In some embodiments, the kits comprise probes and primers
comprising at least 15 contiguous, at least 20, at least 25, at least 30, or at least 50 nucleotides of
SEQ ID NO:1 or SEQ ID NO:2, said contiguous nucleotides are within nucleotides 1-93 of SEQ
ID NO:1 or nucleotides 1-386 SEQ ID NO:2. These kits may further include reagents and
instructions for detecting the presence or absence or the level of expression of VEGI-192a and/or
VEGI-192b- The kits of this invention are in suitable packaging, and may optionally provide
additional components such as, buffers and instructions.
This invention also provides polynucleotides described herein attached to a solid support.
Methods of attaching polynucleotides to a solid support, for example surface of arrays, are well
known in the art. The solid support is of any suitable material, including polystyrene based
beads and glass chips, such as a GeneChip.RTM. product (Affymetrix, Inc., Santa Clara, Calif.).
See International Publication Nos. WO 97/10365, WO 97/29212, WO 97/27317, WO 95/11995,
WO 90/15070, and U.S. Pat. Nos. 5,744,305 and 5,445,934.
This invention also provides arrays comprising VEGI-192a and/or VEGI-192b
polynucleotides. Polynucleotide arrays provide a high throughput technique that can assay a
large number of polynucleotides or polypeptides in a sample. This technology can be used as a
tool to test for differential expression. A variety of methods of producing arrays, as well as
variations of these methods, are known in the art and contemplated for use in the invention. For
example, arrays can be created by spotting polynucleotide probes onto a substrate (e.g., glass,
nitrocellulose, etc.) in a two-dimensional matrix or array having bound probes. The probes can
be bound to the substrate by either covalent bonds or by non-specific interactions, such as
hydrophobic interactions. Samples of polynucleotides can be detectably labeled (e.g., using
radioactive or fluorescent labels) and then hybridized to the probes. Double stranded
polynucleotides, comprising the labeled sample polynucleotides bound to probe polynucleotides,
can be detected once the unbound portion of the sample is washed away. Alternatively, the
polynucleotides of the test sample can be immobilized on the array, and the probes detectably
labeled. Techniques for constructing arrays and methods of using these arrays are described in,
for example, Schena et al. (1996) Proc Natl Acad Sci USA. 93 (20): 10614-9; Schena et al.
(1995) Science 270(5235):467-70; Shalon et al. (1996) Genome Res. 6(7):639-45, USPN
5,807,522, EP 799 897; WO 97/29212; WO 97/27317; EP 785 280; WO 97/02357; USPN
5,593,839; USPN 5,578,832; EP 728 520; USPN 5,599,695; EP 721 016; USPN 5,556,752; WO
95/22058; and USPN 5,631,734.
Arrays can be used to examine differential expression of genes and can be used to
determine gene function. For example, arrays can be used to detect differential expression of a
VEGI isoform corresponding to a polynucleotide described herein, where expression is
compared between a test cell and control cell. For example, high expression of a particular
VEGI isoform message in an cell from a subject who has a disease, which is not observed in a
corresponding normal cell, can indicate an association of this VEGI isoform with such disease.
Exemplary uses of arrays are further described in, for example, Pappalarado et al., Sem.
Radiation Oncol. (1998) 8:217; and Ramsay Nature Biotechnol. (1998) 16:40. Furthermore,
many variations on methods of detection using arrays are well within the skill in the art and
within the scope of the present invention. For example, rather than immobilizing the probe to a
solid support, the test sample can be immobilized on a solid support which is then contacted with
the probe.
A VEGI isoform polynucleotide that is differentially expressed in a cell from an
individual having a disease would be of clinical significance with respect to this disease. A
VEGI isoform polynucleotide is differentially expressed in a cell when the polynucleotide is
detected at higher or lower levels in a cell of an individual having a disease compared to a cell of
the same cell type that is from an individual who does not having the disease. Typically,
screening for polynucleotides differentially expressed focuses on a polynucleotide that is
expressed such that, for example, mRNA is found at levels at least about 25%, at least about 50%
to about 75%, at least about 90%, at least about 2-fold, at least about 4-fold; at least about 5-fold,
at least about 10-fold, or at least about 50-fold or more, higher (e.g. overexpressed) or lower
(e.g., underexpressed) in a cell from an individual who has the disease when compared with a
cell of the same cell type that is not from such an individual. The comparison can be made
between two tissues, for example, if one is using in situ hybridization or another assay method
that allows some degree of discrimination among cell types in the tissue. The comparison may
also be made between cells removed from their tissue source.
Thus, the invention provides an array comprising a VEGI isoform polynucleotides as
described herein. In some embodiments, the invention provides an array comprising a
polynucleotide sequence shown is Table 1 (SEQ ID NO:1), or a region of polynucleotide of the
sequence shown in Table 1 (SEQ ID NO:1), wherein said region is at least 10 contiguous
nucleotides (or more, such as at least 15,18,20, 25,35,40,45, 50,60,75 or 100 contiguous
nucleotides). In other embodiments, the region further comprises nucleotides 93 and 94 of the
sequence shown in Table 1 (SEQ ID NO:1). In other embodiments, the region is within
nucleotides 1-93 of the sequence shown in Table 1 (SEQ ID NO:1).
In some embodiments, the invention provides an array comprising a polynucleotide
sequence shown in Table 2 (SEQ ID NO:2), or a region of polynucleotide of the sequence shown
in Table 2 (SEQ ID NO:2), wherein said region is at least 10 contiguous nucleotides (or more,
such as at least 15,18,20,25,35,40,45, 50,60,75 or 100 contiguous nucleotides). In other
embodiments, the region further comprises nucleotides 386 and 387 of the sequence shown in
Table 2 (SEQ ID NO:2). In other embodiments, the region is within nucleotides 1-386 of the
sequence shown in Table 1 (SEQ ID NO:1).
Arrays are also useful for detecting mutant VEGI isoform polynucleotides. Mutant VEGI
isoform polynucleotides can be detected in genomic DNA, e.g., genomic DNA isolated from the
blood of an individual or from another tissue sample. Mutant VEGI isoform polynucleotides can
also be detected using cDNA or mRNA from an individual possessing an altered VEGI isoform
polynucleotide, if the mutant VEGI isoform polynucleotide results in an mRNA that is altered in
size (for example). A mutant VEGI isoform gene may also result in the differential expression
(increased or decreased) of a VEGI isoform mRNA, which can be detected as described herein.
The present invention also provides an array comprising one or more isolated
polynucleotides that specifically hybridize to the polynucleotide described herein. In some
embodiments, the invention provides an array comprising one or more isolated polynucleotides
that specifically hybridize to the polynucleotide shown in Table 1 (SEQ ID NO:1), or a region of
polynucleotide of the sequence shown in Table 1 (SEQ ID NO:1), wherein said region is at least
10 contiguous nucleotides (or more, such as at least 15,18,20,25,35,40,45, 50,60,75 or 100
contiguous nucleotides). In other embodiments, the region further comprises nucleotides 93 and
94 of the sequence shown in Table 1 (SEQ ID NO:1). In other embodiments, the region is within
nucleotides 1-93 of the sequence shown in Table 1 (SEQ ID NO:1).
In other embodiments, the invention provides an array comprising one or more isolated
polynucleotides that specifically hybridize to a polynucleotide sequence shown in Table 2 (SEQ
ID NO:2), or a region of polynucleotide of the sequence shown in Table 2 (SEQ ID NO:2),
wherein said region is at least 10 contiguous nucleotides (or more, such as at least 15,18,20,25,
35,40,45, 50,60,75 or 100 contiguous nucleotides). In other embodiments, the region further
comprises nucleotides 386 and 387 of the sequence shown in Table 2 (SEQ ID NO.2). In other
embodiments, the region is within nucleotides 1-386 of the sequence shown in Table 1 (SEQ ID
NO:1).
Polypeptides of the invention
The present invention encompasses human VEGI-192a, VEGI-192b, and VEGI-251
polypeptide sequences shown in Tables 4 (SEQ ID NO: 4), 5 (SEQ ID NO:5), and 6 (SEQ ID
NO:6). The VEGI polypeptides can be recovered and purified from recombinant cell cultures by
methods including ammonium sulfate or ethanol precipitation., acid extraction, anion or cation
exchange chromatography, phosphocellulose chromatography, hydrophobic interaction
chromatography, affinity chromatography, hydroxylapatite chromatography and lectin
chromatography. Protein refolding steps can be used as necessary in completing configuration of
the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed
for final purification steps. Examples of protein refolding and purification methods are described
in U.S. Pat. Appl. 20010044521 and WO 01/55174.
The polypeptides of the present invention may be a naturally purified product or a
product of chemical synthetic procedures, or produced by recombinant techniques from a
prokaryotic (such as E.coli) or eukaryotic host (such as CHO cells). Depending upon the host
employed in a recombinant production procedure, the polypeptides of the present invention may
be glycosylated or may be non-glycosylated. Polypeptides of the invention may also include an
initial methionine amino acid residue.
The VEGI-192a, VEGI-192b, and VEGI-251 polypeptides of the invention (which, as described
herein, include various embodiments, such as full-length, nurture, fusion, fragments, etc.) have a
variety of uses, as described herein. The polypeptides are of particular interest as genetic or
biochemical markers (e.g., in blood or tissues) that indicate angiogenesis related disease, and/or
to monitor the efficacy of various therapies and preventative interventions. Diagnostic (i.e.,
detection) and screening methods are described in more detail below. The polypeptides of the
invention also are of use in making antibodies that bind to these polypeptides, their use as an
agent to screen pharmaceutical candidates (both in vitro and in vivo), their use in rational (i.e.,
structure-based) drug design, as well as other uses include therapeutic uses which are described
herein (for example, if full-length VEGI-192a or VEGI-192b exerts its action by binding to another
protein, a polypeptide that binds competitively to VEGI-192a or \HEGI-192b could compromise
VEGI-192a or VEGI-192b function as a competitive inhibitor and thus exert therapeutic activity).
The VEGI-192a or VEGI-192b polypeptides may also be used to identifying proteins especially
those from humans that bind (or interact physically) with VEGI-192a or VEGI-192b which could
thus themselves be drug targets.
The invention provides polypeptide, truncated forms, or fragments, of VEGI-192a and
VEGI-192b. The VEGI polypeptides of the invention have one or more functions, as described in
the previous section. In some embodiments, the VEGI polypeptide serves to bind a specific
antibody. In other embodiments a VEGI polypeptide is an immunogen. In yet other
embodiments a VEGI polypeptide inhibits vascular endothelial cell growth and/or angiogenesis.
Methods for testing the activity of a VEGI polypeptide (including a truncated form of VEGI) is
well known in the art and are described in the Examples in detail, such as assay for testing effect
on vascular endothelial cell growth, capillary-like tube formation, capillary growth in collagen
gels placed on chick embryo chorioallantoic membrane, xenograft tumor growth.
The size of the polypeptide fragments may vary widely. Thus, the invention includes
polypeptide fragments of full-length VEGI-192a or VEGI-192b comprising a portion of the amino acid
sequence depicted in Table 4 (SEQ ID NO.4) or Table 5 (SEQ ID NO:5) in which the VEGI-192a or
VEGI-192b polypeptide is at least about 5, about 10, about 15,25,50,75,100,150, or more
contiguous amino acids of a sequence shown in Table 4 (SEQ ID NO:4) or Table 5 (SEQ ID NO:5).
It is understood that the fragments comprising at least one amino acids within amino acids 1-26
of SEQ ID NO:4 or SEQ ID NO:5, preferably a region, within amino acids 1-26 of SEQ ID
NO:4 or SEQ ID NO:5. In some embodiments, the portion of the amino acid sequence comprises
amino acids 26 and 27 shown in Table 4 (SEQ ID NO:4) or Table 5 (SEQ ID NO:5). In some
embodiments, the portion of the amino acid sequence are within amino acids 1-26 of SEQ ID NO:4
or SEQ ID NO:5. As is evident to one skilled in the art, these polypeptides, regardless of their size,
may also be associated with, or conjugated with, other substances or agents to facilitate, enhance, or
modulate function and/or specificity of a VEGI-192a or a VEGI-192b polypeptide. These fragments
may be used for a variety of purposes, including as an immunogen (either alone or in conjunction
with a suitable agent), or as an agent to inhibit angiogenesis. The fragments (as with polypeptides)
should have one or more of the biological functions described above for a VEGI polypeptide. In
some embodiments, the fragments inhibit angiogenesis. The truncated forms may be less than
about any of the following: 185,170,160,150,125,100,80,50,40,25,20,15, or 10 amino acids.
It is understood that, a region of contiguous amino acids or nucleotides that are within a
given pair of amino acids or nucleotides can, but not necessarily, include either member of the
specified pair. For example, the contiguous amino acids within amino acids 1-26 of SEQ ED NO:4
can include amino acid 1 and/or amino acid 26 of SEQ ID NO:4.
In some embodiments of the invention, the polypeptides of the invention comprise at least
5, at least 8, at least 10, at least 15, at least 20, at least 25, or more contiguous amino acids within
amino acid residues 1-26 shown in Table 4 (SEQ ID NO:4) or Table 5 (SEQ ID NO:5) (which
generally may also be referred to as regions). The invention also provides polypeptides
comprising amino acid residues about 5-192,10-192,15-192,20-192, 25-192 of the sequence
shown in Table 4 (SEQ ID NO:4) or Table 5 (SEQ ID NO:5).
The embodiments of the present invention excludes any polypeptides consisting of amino
acids 27-192 of SEQ ID NO:4 or SEQ ID NO:5 or a truncated form of such polypeptides.
The present invention further include polypeptides which have at least 90% similarity,
more preferably at least 95% similarity, and still more preferably at least 96%, 97%, 98% or 99%
similarity to those described above. The polypeptides of the invention also comprise those,
which are at least 80% identical, more preferably at least 90%, or 95% identical, still more
preferably at least 96%, 97%, 98% or 99% identical to the polypeptides described herein and
also include portions of such polypeptides with at least 30 amino acids and more preferably at
least 50 amino acids. In some embodiments, the invention provides polypeptides which have at
least 90% similarity, more preferably at least 95% similarity, and still more preferably at least
96%, 97%, 98% or 99% similarity to the polypeptide of SEQ ID NO:4 or the polypeptide of SEQ
ID NO:5. The polypeptides of the invention also comprise those, which are at least 80%
identical, more preferably at least 90%; or 95% identical, still more preferably at least 96%,
97%, 98% or 99% identical to the polypeptide of SEQ ID NO:4 or the polypeptide of SEQ ID
NO:5.
This invention also provides fusion proteins comprising polypeptides described herein.
The polypeptides described herein can be fused with sequences, such as sequences that enhance
immunological reactivity, facilitate the coupling of the polypeptide to a support or a carrier, or
facilitate purification (e.g., sequences encoding epitopes such as Myc, HA derived from
influenza virus hemagglutinin, His-6, or FLAG). In addition, the protein or polynucleotide can
be fused to other or polypeptides which increase its function, or specify its localization in the
cell, such as a secretion sequence is discloses herein. For Methods for producing the
recombinant fusion protein described above are common in the art. The recombinant or fusion
protein can be isolated by methods well known in the art. Tile transformed host cells can be
used to analyze the effectiveness of drugs and agents which inhibit or activate VEGI function,
such as host proteins or chemically derived agents or other proteins which interact with VEGI
polynucleotides to down-regulate or alter the expression of VEGI polypeptides or affect its
ability to inhibit angiogenesis. A method for testing the effectiveness of an anti-VEGI or anti-
angiogenesis drug or agent can for example, be the blockage of the endothelial cell growth
inhibitor.
This invention encompasses compositions, including pharmaceutical compositions,
comprising polypeptides described herein. In some embodiments, the composition comprises
polypeptide of SEQ ID NO:4. This composition is useful for inhibiting angiogenesis. These
compositions may further comprise suitable excipients, such as pharmaceutically acceptable
excipients including buffers, which are well known in the art.
This invention also provides kits comprising polypeptides described herein. In some
embodiments, the composition comprises polypeptide of SEQ ID NO:4. In some aspects, the
kits may be used for treating pathological angiogenesis, inhibiting angiogenesis, or treating
cancer such as reducing tumor size. The kits of this invention are in suitable packaging, and
may optionally provide additional components such as, buffers and instructions.
This invention also provides polypeptides described herein attached to a solid support.
Methods of making such attachment, for example attaching to an array surface, are well known
in the art. The polypeptides of the invention attached to a solid support, such as, particles of
agarose, SEPHADEX, or the like, are useful for screening molecules that selectively binding the
polypeptides describe herein.
The invention also encompasses an array comprising VEGI isoform polypeptides of the
invention, as described herein. Therefore, in one aspect, the invention provides an array
comprising VEGI isoform polypeptides encoded by a polynucleotide of the invention as described
herein. In other aspect, the invention provides an array comprising a polypeptide comprising the
sequence shown in Table 4 (SEQ ID NO:4), or a region thereof, wherein the region is at least 5
contiguous amino acids in length (or more, e.g. at least 10,15,25, 50,75,100,150, or more amino
acids in length). In some embodiments, the region comprises amino acids 26 and 27 of the
sequence shown in Table 4 (SEQ ID NO:4). In other embodiments, the region is within amino
acids 1-26 of the sequence shown in Table 4 (SEQ ID NO:4).
In other aspect, the invention also provides an array comprising a polypeptide comprising
the sequence shown in Table 5 (SEQ ID NO.5), or a region thereof, wherein the region is at least 5
contiguous amino acids in length (or more, e.g. at least 10,15,25,50,75,100,150, or more amino
acids in length)m In some embodiments, the region comprises amino acids 26 and 27 of the
sequence shown in Table 5 (SEQ ID NO.5). In other embodiments, the region is within amino
acids 1-26 of the sequence shown in Table 5 (SEQ ID NO:5).
The terms "polypeptide", and "protein" are used interchangeably herein, and, as is well-
known in the art to refer to polymers of amino acids of any length. In various embodiments, the
polymer may be linear or branched, it may comprise modified amino acids, it may be interrupted
by non-amino acids, and/or it may be assembled into a complex of more than one polypeptide
chain. As is well understood in the art, a polypeptide may be modified naturally or by
intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation,
phosphorylation, or any other manipulation or modification, such as conjugation with a labeling
component. In some embodiments, polypeptides contain one or more analogs of an amino acid
(including, for example, unnatural amino acids, etc.), as well as other modifications known in the
art.
This invention also includes functionally preserved variants of the VEGI polypeptides
described herein. Such variants may be made using methods standard in the art, for example, by
conservative amino acid substitutions. In various embodiments, a functionally preserved variant
comprises preserved variant comprises (or, in some embodiments, consist of) any of one, two, three,
four, five, six, seven, eight, nine, ten conservative amino acid substitutions.
Vectors and host cells

The present invention also relates to vectors which include the isolated polynucleotides of
the present invention, host cells which are genetically engineered with the recombinant vectors,
or which are otherwise engineered to produce the polypeptides of the invention, and the
production of polypeptides of the invention by recombinant techniques.
The term "vector" refers to a plasmid, virus or other vehicle known in the art that has
been manipulated by insertion or incorporation of the VEGI-251, VEGI-192a or VEGI-192b genetic
sequences or fragments thereof. This polynucleotide (generally, DNA) element which renders
the vector suitable for multiplication can be an origin of replication which works in prokaryotic
or eukaryotic cells. An example for an origin of replication which works in prokaryotic cells is
the colEl ori. A recombinant vector needs further a selection marker for control of growth of
these organisms which harbor the vector. Suitable selection markers include genes which protect
organisms from antibiotics (antibioticum resistance), for example, ampicillin, streptomycin,
chloramphenicol or provide growth under compound deprived environmental conditions
(auxotrophic growth conditions) when expressed as proteins in cells. In a preferred embodiment
of the invention for multiplication of the recombinant vector the prokaryotic cells are bacteria. In
special preferred versions of the inventions the bacteria are in particular bacteria of Escherichia
coli or of Bacillus sp. In a further preferred embodiment of the invention for the multiplication
of the recombinant vector the eukaryotic cells are cells of a cell line or yeast cells. In special
preferred versions of the invention the cells of the cell line are cells of a CHO, COS, Hela-, or
3T3 -cell-line and the yeast cells are cells of Saccharomyces cerevisiae.
The present invention includes a variety of vectors (i.e., cloning and/or expression
vectors, as well as vectors for cloning and/or replication) having cloned therein VEGI-192a,
VEGI-192b, or VEGI-251 polynucleotide(s). These vectors can be used for expression of
recombinant polypeptides as well as a source of VEGI-192a, VEGI-192b, or VEGI-251
polynucleotides. Cloning vectors can be used to obtain replicate copies of the VEGI-192a, VEGI-
192b, or VEGI-251 polynucleotides they contain, or as a means of storing the polynucleotides in a
depository for future recovery. Expression vectors (and host cells containing these expression
vectors) can be used to obtain polypeptides produced from the polynucleotides they contain.
They may also be used where it is desirable to express VEGI-192a, VEGI-192b, or VEGI-251
polypeptides in an individual, such as for eliciting an immune response via the polypeptide(s)
encoded in the expression vector(s). Suitable cloning and expression vectors include any known
in the art e.g., those for use in bacterial, mammalian, yeast and insect expression systems.
Specific vectors and suitable host cells are known in the art and need not be described in detail
herein. For example, see Gacesa and Ramji, Vectors, John Wiley & Sons (1994).
Cloning and expression vectors typically contain a selectable marker (for example, a gene
encoding a protein necessary for the survival or growth of a host cell transformed with the
vector), although such a marker gene can be carried on another polynucleotide sequence co-
introduced into the host cell. Only those host cells into which a selectable gene has been
introduced will survive and/or grow under selective conditions. Typical selection genes encode
protein(s) that (a) confer resistance to antibiotics or other toxins substances, e.g., ampicillin,
neomycyin, methotrexate, etc.; (b) complement auxotrophic deficiencies; or (c) supply critical
nutrients not available from complex media. The choice of the proper marker gene will depend
on the host cell, and appropriate genes for different hosts are known in the art. Cloning and
expression vectors also typically contain a replication system recognized by the host.
Suitable cloning vectors may be constructed according to standard techniques, or may be
selected from a large number of cloning vectors available in the art. While the cloning vector
selected may vary according to the host cell intended to be used, useful cloning vectors will
generally have the ability to self-replicate, may possess a single target for a particular restriction
endonuclease, and/or may carry genes for a marker that can be used in selecting clones
containing the vector. Suitable examples include plasmids and bacterial viruses, e.g., pUCl 8,
pUC19, Bluescript (e.g., pBS SK+) and its derivatives, mpl8, mpl9, pBR322, pMB9, ColE1,
pCR1, RP4, phage DNAs, and shuttle vectors such as pSA3 and pAT28. These and many other
cloning vectors are available from commercial vendors such as BioRad, Strategene, and
Invitrogen.
Expression vectors generally are replicable polynucleotide constructs that contain a
polynucleotide encoding a VEGI polypeptide of interest. The polynucleotide encoding the VEGI
polypeptide is operatively linked to suitable transcriptional controlling elements, such as
promoters, enhancers and terminators. For expression (i.e., translation), one or more
translational controlling elements are also usually required, such as ribosome binding sites,
translation initiation sites, and stop codons. These controlling elements (transcriptional and
translational) may be derived from VEGI polynucleotides (i.e., one of the VEGI isoform gene),
or they may be heterologous (i.e., derived from other genes and/or other organisms). A
polynucleotide sequence encoding a signal peptide can also be included to allow a VEGI
polypeptide to cross and/or lodge in cell membranes or be secreted from the cell. A number of
expression vectors suitable for expression in eukaryotic cells including yeast, avian, and
mammalian cells are known in the art.
The vectors containing the polynucleotides of interest can be introduced into the host cell
by any of a number of appropriate means, including electroporation, transfection employing
calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances;
microprojectile bombardment; lipofection; and infection (where the vector is an infectious agent,
such as vaccinia virus). The choice of means of introducing vectors or polynucleotides will often
depend on the host cell.
The invention includes further a host cell and a cell culture comprised of the host cells.
This host cell comprising at least one recombinant polynucleotide (generally, DNA) vector was
mentioned before. "Host cells" are cells in which a vector can be propagated and its DNA
expressed. The cell may be prokaryotic or eukaryotic. The term also includes any progeny of the
subject host cell. It is understood that all progeny may not be identical to the parental cell since
there may be mutations that occur during replication. However, such progeny are included when
the term "host cell" is used. Methods of stable transfer, meaning that the foreign DNA is
continuously maintained in the host, are known in the art. When the host cell is taken from
prokaryotic cells it preferably consists of a cell of a bacterium in particular of Escherichia coli or
Bacillus sp. When this host cell consists of a eukaryotic cell it is preferred a cell of a cell line in
particular a cell of a COS-, a Hela-, or 3T3-cell-line or a cell of a yeast in particular a cell of
Saccharomyces cerevisiae.
The host cells of this invention can be used, inter alia, as repositories of VEGI
polynucleotides and/or vehicles for production of VEGI polynucleotides and/or polypeptides as
described herein. Host cells can also serve as repositories of mutant VEGI-192a, VEGI-192b, or
VEGI-251 polynucleotides, as further described herein. Such hosts cells can be useful for
screening, production of therapeutic protein or polypeptide as further described herein.
Antibodies and their preparation
The invention also provides antibodies that selectively bind to VEGI-192a and/or VEGI-
192b (including fragments) proteins as described herein. The term "antibody" includes, but not
limited to intact molecules, fragments thereof, such as Fab, (Fab'), Fv, which are capable of
binding the epitopic determinant. These antibody fragments retain some ability to selectively
bind with its antigen or receptor and are defined as follows:
(1) Fab, the fragment which contains a monovalent antigen-binding fragment of an
antibody molecule can be produced by digestion of whole antibody with the enzyme papain to
yield an intact light chain and a portion of one heavy chain;
(2) Fab1, the fragment of an antibody molecule can be obtained by treating whole
antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the
heavy chain; two Fab' fragments are obtained per antibody molecule;
(3) (Fab')2, the fragment of the antibody that can be obtained by treating whole antibody
with the enzyme pepsin without subsequent reduction; (Fab')2, is a dimer of two Fab' fragments
held together by two disulfide bonds;
(4) Fv, defined as a genetically engineered fragment containing the variable region of the
light chain and the variable region of the heavy chain expressed as two chains; and
(5) Single chain antibody ("SCA"), defined as a genetically engineered molecule
containing the variable region of the light chain, the variable region of the heavy chain, linked by
a suitable polypeptide linker as a genetically fused single chain molecule.
In some embodiments, the antibodies of the present invention may be any one or more of
the following: polyclonal, monoclonal, single chain (ScFv), mutants of these embodiments,
fusion proteins comprising an antibody portion (such as one or more CDR regions), humanized
antibodies, chimeric antibodies, human antibodies, or any modified configuration of the
immunoglobulin molecule that comprises an antigen recognition site of the required specificity.
As is understood in the art, a "monoclonal antibody" refers to a homogeneous antibody
population wherein the monoclonal antibody is comprised of amino acids (naturally occurring
and non-naturally occurring) that are involved in the selective binding of an antigen.
Monoclonal antibodies are highly specific, being directed against a single antigenic site. The
term "monoclonal antibody" encompasses not only intact monoclonal antibodies and full-length
monoclonal antibodies, but also fragments thereof (such as Fab, Fab', F(ab')2, Fv), single chain
(ScFv), mutants thereof, fusion proteins comprising an antibody portion, humanized monoclonal
antibodies, chimeric monoclonal antibodies, and any other modified configuration of the
immunoglobulin molecule that comprises an antigen recognition site of the required specificity
and the ability to bind to an antigen. It is not intended to be limited as regards to the source of
the antibody or the manner in which it is made (e.g., by hybridoma, phage selection, recombinant
expression, transgenic animals, etc.).
"Humanized" antibodies refer to a molecule having an antigen binding site that is
substantially derived from an immunoglobulin from a non-human species and the remaining
immunoglobulin structure of the molecule based upon the structure and/or sequence of a human
immunoglobulin. The antigen binding site may comprise either complete variable domains fused
onto constant domains or only the complementarity determining regions (CDRs) grafted onto
appropriate framework regions in the variable domains. Antigen binding sites may be wild type
or modified by one or more amino acid substitutions, e.g., modified to resemble human
immunoglobulin more closely. Some forms of humanized antibodies preserve all CDR
sequences (for example, a humanized mouse antibody which contains all six CDRs from the
mouse antibodies). Other forms of humanized antibodies have one or more CDRs (one, two,
three, four, five, six) which are altered with respect to the original antibody, which are also
termed one or more CDRs "derived from" one or more CDRs from the antibody.
Methods of making antibodies and antibody fragments are known in the art. (See for
example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory,
New York, 1988, incorporated herein by reference).
The invention also provides an antibody that selectively binds a polypeptide comprising
SEQ ID NO:4, SEQ ID NO:5 or a fragment thereof, wherein the fragment is within amino acids
1-26 of SEQ ID NO:4 or SEQ ID NO:5, or the fragment comprises amino acids 26 and 27 of
SEQ ID NO:4 or SEQ ID NO:5. The invention also provides antibodies that selectively binds
VEGI-192a and VEGI-192b but not other isoforms of VEGI (does not selectively bind to other
VEGI isoforms, such as VEGI-251). This invention also provides antibodies that selectively
binds VEGI-192a or VEGI-192b.
The present invention further provides an antibody that selectively binds a polypeptide
encoded by SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3 or a fragment thereof.
In some embodiments, the invention provides an antibody that selectively binds to a
polypeptide comprising a region of at least 5, at least 10, at least 15, at least 20, at least 25, or
more contiguous amino acids of SEQ ID NO:4 or SEQ ID NO:5, wherein the region is within
amino acid residues 1-26 shown in Table 4 (SEQ ID NO:4) or Table 5 (SEQ ID NO:5). In other
embodiments, the invention provides an antibody that selectively binds to a polypeptide
comprising a region of at least 5, at least 10, at least 15, at least 20, at least 25, or more
contiguous amino acids of SEQ ID NO:4 or SEQ ID NO:5, wherein the region comprises amino
acids 26 and 27 of SEQ ID NO:4 or SEQ ID NO:5.
In some embodiments, an antibody of the invention inhibits VEGI activity; for example,
such an antibody could promote angiogenesis. Methods of screening such antibody are
described below.
In some embodiments, an antibody of the invention can be an agonist antibody in that it
promotes VEGI activity. Methods of screening such antibody are described below.
It is understood that, in this context, in which there are various isoforms of VEGI,
selective binding indicates binding preferentially (or even exclusively) to a given isoform as
compared to another isoform (unless already indicated otherwise). In some embodiments, the
antibody selectively binds a VEGI polypeptide of the invention as compared to a non-human
VEGI isoform. As an example, an antibody of the invention could selectively bind human
VEGI-192a but not mouse (non-human) VEGI-192a.
The antibodies of this invention can be linked (i.e., conjugated) to a detectable agent or a
hapten. The complex is useful to detect the polypeptide(s) (or polypeptide fragments) to which
the antibody specifically binds in a sample, using standard immunochemical techniques such as
immunohistochemistry as described by Harlow and Lane (1988), supra. Examples of types of
immunoassays which can utilize monoclonal antibodies of the invention are competitive and
non-competitive immunoassays in either a direct or indirect format. Examples of such
hnmunoassays are the enzyme linked immunoassay (ELIS A) radioimmunoassay (RIA) and the
sandwich (immunometric) assay. Detection of using the monoclonal antibodies of the invention
can be done by utilizing immunoassays which are run in either the forward, reverse, or
simultaneous modes, including immunohistochemical assays on physiological samples. Those of
skill in the art will know, or can readily discern, other immunoassay formats without undue
experimentation.
Another technique which may also result in greater sensitivity consists of coupling the
antibodies to low molecular weight haptens. These haptens can then be specifically detected by
means of a second reaction. For example, it is common to use such haptens as biotin, which
reacts avidin, or dinitropherryl, pyridoxal, and fluorescein, which can react with specific anti-
hapten antibodies. See Harlow and Lane (1988) supra.
The antibodies of the invention can be bound to many different carriers. Thus, this
invention also provides compositions containing antibodies and a carrier. Carriers can be active
and/or inert. Examples of well-known carriers include glass, polystyrene, polypropylene,
polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides,
agaroses and magnetite. The nature of the carrier can be either soluble or insoluble for purposes
of the invention. Those skilled in the art will know of other suitable carriers for binding
monoclonal antibodies, or will be able to ascertain such, using routine experimentation.
There are many different labels and methods of labeling known to those of ordinary skill
in the art. Examples of the types of labels which can be used in the present invention include
enzymes, radioisotopes, fluorescent compounds, colloidal metals, chemiluminescent compounds,
and bioluminescent compounds. Those of ordinary skill in the art will know of other suitable
labels for binding to the monoclonal antibody, or will be able to ascertain such, using routine
experimentation. Furthermore, the binding of these labels to the monoclonal antibody of the
invention can be done using standard techniques common to those of ordinary skill in the art.
For purposes of the invention, polypeptides of this invention may be detected by the
antibodies of the invention when present in samples, such as fluids and tissues. This use of
antibodies is discussed in more detail below.
Compositions containing the antibodies, fragments thereof or cell lines which produce the
antibodies, are encompassed by this invention. When these compositions are to be used
pharmaceutically, they are combined with a pharmaceutically acceptable excipient. Arrays
comprising the antibodies or fragments thereof are encompassed by this invention. Antibodies
may be immobilized on a surface, e.g., an array for use in detection and diagnostic assays as
described in more detail below. Antibodies may also be immobilized on a support for
purification of the polypeptides or fragments described herein.
Compositions
The present invention further provides compositions, including pharmaceutical
compositions, comprising the polypeptides, polynucleotides, antibodies, recombinant vectors,
and host cells of the invention. These compositions may include a buffer, which is selected
according to the desired use of the polypeptide, antibody, polynucleotide, recombinant vector, or
host cell, and may also include other substances appropriate to the intended use. Those skilled in
the art can readily select an appropriate buffer, a wide variety of which are known in the art,
suitable for an intended use. In some instances, the composition is a pharmaceutical composition
and can comprise a pharmaceutical acceptable excipient, a variety of which are known in the art
and need not be discussed in detail herein. Pharmaceutical acceptable excipients have been
amply described in a variety of publications, including, for example, A. Gennaro (2000)
"Remington: The Science and Practice of Pharmacy", 20th edition, Lippincott, Williams, &
Wilkins.
Kits comprising polynucleotides, polypeptides, and/or antibodies of the invention
As described herein, the present invention also encompasses kits containing
polynucleotide(s), polypeptide(s), and/or antibodies of this invention, such as kits for diagnosis,
for therapy. Kits embodied by this invention include those that allow someone to conduct an
assay for the presence of VEGI polynucleotides, polypeptides, and/or anti-VEGI antibodies, such
as any of those describe herein, thus detecting and/or quantitating those molecules. Accordingly,
the invention includes (a) a kit for detection or quantification of a VEGI polynucleotide in a
sample comprising any of the VEGI polynucleotide described herein; (b) a kit comprising any of
the antibodies described herein for detection or quantification of a VEGI polypeptide in a
sample; (c) a kit comprising any of the polypeptides described herein for detection or
quantification of anti-VEGI antibody in a sample. The invention also provides kits comprising
polynucleotides or polypeptides of the invention for use in therapy.
The kits of this invention are in suitable packaging, and may optionally provide
additional components that are useful in the procedure. These optional components include, but
are not limited to, buffers, capture reagents, developing reagents, labels, reacting surfaces, means
for detection, control samples, instructions, and interpretive information.
Methods of using polynucleotides, polypeptides and antibodies: Detection systems
The invention also provides methods using the VEGI-192a and VEGI-192b polynucleotides,
polypeptides, and/or antibodies of the invention to detect suitable targets in a sample. As this
disclosure makes clear, detection methods refer to any of detecting presence, absence, as well as
quantitation. Procedures for conducting diagnostic (i.e., detection) tests using polynucleotides,
polypeptides or antibodies are extensively known in the art and are routine for a practitioner or
ordinary skill. Generally, to perform a diagnostic method of this invention, one of the
compositions of this invention is provided as a reagent to detect a target with which it reacts in a
sample. The target is supplied by obtaining a suitable sample from an individual for whom the
diagnostic parameter is to be measured. Many types of samples are suitable for this purpose. If
desired, the target may be partially purified from the sample or amplified before the assay is
conducted.
The present invention relates to a method of detecting the presence or absence or level of
VEGI-192a or VEGI-192b polypeptides in a sample comprising contacting a sample from a human
or animal with antibodies which selectively binds to the polypeptide described herein, and
detecting the presence or absence or the amount of a complex formed between the polypeptide
and the antibodies. Such detecting is useful for the purpose of diagnosis, prognosis, and/or
monitoring of an angiogenic-associated disease. In some embodiments, the invention provides a
method for the diagnosis of pathological angiogenesis comprising the steps of contacting a
sample from a human or animal suspected of having pathological angiogenesis with antibodies
which recognize the polypeptide described herein, and detecting the presence or absence of a
complex formed between the polypeptide and the antibodies.
A competition assay can be employed wherein antibodies that selectively bind to VEGI-
192a and/or VEGI-192b polypeptides are attached to a solid support and labeled VEGI-192a and/or
VEGI-192b and a sample derived from the host are passed over the solid support and the amount
of label detected, for example, by liquid scintillation chromatography, can be correlated to a
quantity of VEGI-192a and/or VEGI-192b in the sample.
A "sandwich" assay is similar to an ELISA assay. In a "sandwich" assay VEGI-192a
and/or VEGI-192b is passed over a solid support and binds to antibody attached to a solid support.
A second antibody is then bound to the VEGI-192a and/or VEGI-192b. A third antibody which is
labeled and specific to the second antibody is then passed over the solid support and binds to the
second antibody and an amount can then be quantitated.
Using standard methodology well known in the art, a diagnostic assay can be constructed
by coating on a surface (i.e., a solid support), for example, a microtitration plate or a membrane
(e.g. nitrocellulose membrane), antibodies specific for or which selectively bind to, VEGI-192a or
VEGI-192b polypeptides or both, and contacting the coated surface with serum, tissue or other
biological or chemical sample obtained from a person suspected of having an angiogenic-
associated disease. The presence or absence of a resulting complex formed between VEGI-192a or
VEGI-192b polypeptide in the sample and antibodies specific therefor can be detected by any of
the known methods common in the art, such as fluorescent antibody spectroscopy or colorimetry.
This method of detection can be used, for example, for the diagnosis or prognosis of cancer.
Assaying VEGI-192a and/or VEGI-192b polypeptide levels in a sample can use any
antibody-based techniques that are well known in the art. For example, VEGI-192a and/or VEGI-
192b polypeptide expression in tissues can be studied with classical immunohistological methods
(Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985); Jalkanen, M., et al., J. Cell. Biol.
105:3087-3096 (1987)). Other antibody-based methods useful for detecting VEGI-192a and/or
VEGI-192b polypeptide gene expression include immunoassays, such as the enzyme linked
immunosorbent assay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assay labels
are known in the art and include enzyme labels, such as, glucose oxidase, and radioisotopes, such
as iodine (125I, 121I), carbon (14C), sulfur (35S), tritium (3H), indium (112In), and technetium
(99mTc), and fluorescent labels, such as fluorescein and rhodamine, and biotin.
In addition to assaying VEGI-192a and/or VEGI-192b polypeptide levels in a sample
obtained from an individual, VEGI-192a and/or VEGI-192b polypeptide can also be detected in
vivo by imaging. Antibody labels or markers for in vivo imaging of VEGI-192a and/or VEGI-192b
polypeptide include those detectable by X-radiography, NMR or ESR. For X-radiography,
suitable labels include radioisotopes such as barium or cesium, which emit detectable radiation
but are not overtly harmful to the subject. Suitable markers for NMR and ESR include those with
a detectable characteristic spin, such as deuterium, which may be incorporated into the antibody
by labeling of nutrients for the relevant hybridoma.
An antibody or antibody fragment that selectively binds to VEGI-192a and/or VEGI-192b
polypeptide which has been labeled with an appropriate detectable imaging moiety, such as a
radioisotope (for example, 1311,112In, 99mTc), a radio-opaque substance, or a material detectable
by nuclear magnetic resonance, is introduced (for example, parenterally, subcutaneously or
intraperitoneally) into the mammal to be examined for immune system disorder. It will be
understood in the art that the size of the subject and the imaging system used will determine the
quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope
moiety, for a human subject, the quantity of radioactivity injected will normally range from
about 5 to 20 millicuries of "mTc. The labeled antibody or antibody fragment will then
preferentially accumulate at the location of cells which contain VEGI-192a and/or VEGI-192b
polypeptide. In vivo tumor imaging is described by Burchiel and coworkers (Chapter 13 in
Tumor Imaging: The Radiochemical Detection of Cancer, Burchiel, S. W. and Rhodes, B. A.,
eds., Masson Publishing Inc. (1982)).
As is understood in the art, VEGI-192a and/or VEGI-192b polypeptides may be detected
using any agent which selectively binds to the polypeptides.
In another embodiment, the present invention relates to a diagnostic kit comprising
antibodies that selectively binds to the polypeptides of the present invention, for example,
antibodies that selectively binds VEGI-192a or VEGI-192b or both polypeptides, and ancillary
reagents suitable for use in detecting the presence of the polypeptide in a sample. These reagents
are well known in the art and that are suitable for use in detecting the presence or absence of
VEGI polypeptides in a serum, tissue or other sample. Tissue samples contemplated can be
obtained from monkey or human, or other mammals. The kit may further include instructions
for use, controls, and interpretative information.
This invention also provides a method for detecting the presence or absence or the level
of the polynucleotides described herein comprising contacting a sample from an individual such
as a human or an animal with a polynucleotide (in some embodiments, an oligonucleotide) which
selectively binds to the polynucleotide described herein, and detecting the presence or absence or
the amount of a duplex formed between the polynucleotide used and a polynucleotide in the
sample. In some embodiments, the method of the invention, which is useful for the diagnosis of
pathological angiogenesis comprising the steps of contacting a sample from a human or animal
suspected of having pathological angiogenesis with a polynucleotide (such as an oligonucleotide)
which binds to the polynucleotide described herein, and detecting the presence or absence of a
duplex formed between the polynucleotide used and a polynucleotide in the sample, hi another
embodiment, the present invention relates to RNA, DNA or other nucleotide sequences for use in
detecting the presence or absence of VEGI polynucleotides using the polymerase chain reaction
(PCR) or reverse transcription PCR (RT-PCR). Other primer-based amplification methods may
be used. The DNA sequence of the present invention shown in Table 1 (SEQ ID NO:1 or Table
2 (SEQ ID NO:2) can be used to design primers which specifically bind to the VEGI-192a or
VEGI-192b polynucleotide sequence in the case of PCR, or to a VEGI-192a or a VEGI-192b cDNA
produced from reverse transcription of an RNA encoding a VEGI-192a or VEGI-192b polypeptide,
for the purpose of detecting the presence, absence, or quantitating the amount of VEGI-192a or
VEGI-192b polynucleotide by comparison to a standard. The primers can be any length ranging,
for example, from 7-40 nucleotides, preferably 10-15 nucleotides, most preferably 18-25
nucleotides. Reagents and controls necessary for PCR or RT-PCR reactions are well known in
the art. The amplified products can then be analyzed for the presence or absence of VEGI-192a or
VEGI-192b polynucleotide sequences, for example by gel fractionation, with or without
hybridization, by radiochemistry, and immunochemical techniques. This method is advantageous
since only a small sample size is required to generate a sufficient amount of template DNA with
which to perform PCR or RT-PCR.
In some embodiments, the detection methods entail using one or more primers to amplify
the VEGI-192a and/or VEGI-192b sequence of interest. In other embodiments, detection is
accomplished using specific probes (such as labeled probes) which detect presence or absence of
(or can quantitate) a VEGI-192a and/or VEGI-192b sequence of interest. In some embodiments, the
probe comprises a label.
In some embodiments, the method is used for detecting level of VEGI-192a or VEGI-192b
by detecting the presence or absence or the amount of cellular RNA encoding VEGI-192a or
VEGI-192b or a fragment described herein. Total cellular RNA can be isolated from a sample
using any suitable technique such as the single-step guanidinium-thiocyanate-ph- enol-
chloroform method described by Chomczynski and Sacchi (Anal. Biochem. 162:156-159
(1987)). Levels of mRNA encoding the VEGI-192a and/or VEGI-192b polypeptide are then assayed
using any appropriate method. These include Northern blot analysis, SI nuclease mapping, the
polymerase chain reaction (PCR), reverse transcription in combination with the polymerase
chain reaction (RT-PCR), and reverse transcription in combination with the ligase chain reaction
(RT-LCR).
In another embodiment, the present invention relates to a diagnostic kit which contains
PCR or RT-PCR primers, one or more primers, such as specific for VEGI-192a or VEGI-192b
polynucleotides, and/or primers specific for other isoforms of VEGI, such VEGI-251, VEGI-174,
and ancillary reagents that are well known in the art and that are suitable for use in detecting the
presence or absence of VEGI isoform polynucleotides, or quantitating the amount of an RNA
which encodes a VEGI isoform polypeptide in a sample using PCR or RT-PCR, or one or more
other amplification methods. Samples contemplated can be obtained from humans or animals.
In another embodiment, the present invention relates to a diagnostic kit which contains
probes, one or more probes, such as specific for VEGI-192a or VEGI-192b polynucleotides, and/or
probes specific for other isoforms of VEGI, such VEGI-251, VEGI-174, and ancillary reagents that
are well known in the art and that are suitable for use in detecting the presence or absence of
VEGI isoform polynucleotides, or quantitating the amount of an RNA which encodes a VEGI
isoform polypeptide in a sample using methods, such as Northern blotting, or one or more other
methods. Samples contemplated can be obtained from humans or animals.
As is understood in the art a "sample" can be any sample obtained from an individual
(often referred to as a "biological sample"), body fluid, cell line, tissue culture, or other source
which contains or may contain VEGI-192a and/or VEGI-192b polypeptide or mRNA. As indicated,
biological samples include body fluids (such as sera, plasma, urine, synovial fluid and spinal
fluid) which contain free VEGI-192a and/or VEGI-192b polypeptide, immune and circulatory
systems tissue, and other tissue sources found to express complete or mature VEGI-192a and/or
VEGI-192b polypeptides or a VEGI-192a and/or VEGI-192b receptor. Methods for obtaining tissue
biopsies and body fluids from mammals are well known in the art. Where the biological sample
is to include mRNA, a tissue biopsy is the preferred source.
By "assaying the expression level of the gene encoding the VEGI-192a aad/or VEGI-192b
protein" is intended qualitatively or quantitatively measuring or estimating the level of the
VEGI-192a and/or VEGI-192b polypeptide or the level of the mRNA encoding the VEGI-192a and/or
VEGI-192b polypeptide in a first sample either directly (e.g., by determining or estimating
absolute polypeptide level or mRNA level) or relatively (e.g., by comparing to the VEGI-192a
and/or VEGI-192b polypeptide level or mRNA level in a second sample). Preferably, the VEGI-
192a and/or VEGI-192b polypeptide level or mRNA level in the first sample is measured or
estimated and compared to a standard VEGI-192a and/or VEGI-192b polypeptide level or mRNA
level, the standard being taken from a second sample obtained from an individual not having the
disorder or being determined by averaging levels from a population of individuals not having a
disorder of the immune and circulatory systems. As will be appreciated in the art, once a
standard VEGI-192a and/or VEGI-192b polypeptide level or mRNA level is known, it can be used
repeatedly as a standard for comparison.
As noted above, VEGI-192a and/or VEGI-192b polynucleotides and polypeptides are useful
for diagnosis of conditions involving abnormally high or low expression of VEGI-192a and/or
VEGI-192b activities. Given the cells and tissues where VEGI-192a and/or VEGI-192b is expressed
as well as the activities modulated by VEGI-192a and/or VEGI-192b, it is readily apparent that a
substantially altered (increased or decreased) level of expression of VEGI-192a and/or VEGI-192b
in an individual compared to the standard or "normal" level produces pathological conditions
related to the bodily system(s) in which VEGI-192a and/or VEGI-192b is expressed and/or is active.
The invention also provides methods of aiding diagnosis of a VEGI associated disorder
or condition. These methods assist in making a clinical determination regarding the
classification, or nature, of pathological angiogenesis or prognosis of cancer, and may or may not
be conclusive with respect to the definitive diagnosis. Accordingly, a method of aiding diagnosis
of pathological angiogenesis or prognosis of cancer, or a related disease, can comprise the step of
detecting the level of VEGI isoforms (i.e. VEGI-192a, VEGI-192b) expression in a sample from the
individual. A method of aiding diagnosis of angiogenesis-associated disease can also comprise
the step of detecting altered levels of a VEGI isoform polynucleotide and/or polypeptide in a
sample from the individual and/or detecting increased or decreased levels of a VEGI isoform
polynucleotide and/or polypeptide in a sample from the individual.
The invention also provides method of detecting an individual at risk who may or may
not have detectable angiogenesis associated disease, and/or a condition associated with an
abnormal level of VEGI-192a or VEGI-192b, and may or may not have displayed detectable disease
prior to the treatment methods described therein. "At risk" denotes that an individual who is
determined to be more likely to develop a symptom based on conventional risk assessment
methods or has one or more risk factors that correlate with development of angiogenesis-
associated disease. An individual having one or more of these risk factors has a higher
probability of developing angiogenesis-associated disease than an individual without these risk
factors. Examples (i.e., categories) of risk groups are well known in the art and discussed herein.
The VEGI-192a and/or VEGI-192b polynucleotide can also be used as probes for the
detection of the presence or absence of mutantions or polymorphisms in VEGI-192a and/or VEGI-
192b gene, as well as any VEGI-192a or VEGI-192b sequence of interest, whether or not a mutation.
A mutant VEGI-192a and/or VEGI-192b may be associated with angiogenesis or various immune
and circulatory system-related disorders. Methods for detecting mutant polynucleotide
sequences are well known in the art, and include, e.g., single strand conformational
polymorphism (SSCP), and various sequence amplification based methods for detecting
sequence mutations including point mutations, e.g., LCR, NASBA, PCR, limited primer
extension, etc. Methods for detecting altered protein sequences include Western blot analysis,
capillary electrophoresis, mass spectroscopy, and WAVE. Generally, a detection experiment
will be performed in parallel with a control VEGI-192a and/or VEGI-192b polynucleotide or,
polypeptide, or, in the case when altered expression levels are being assessed, with a control
sample possessing normal levels of a VEGI-192a and/or VEGI-192b polynucleotide or polypeptide.
The sequences of the present invention are valuable for chromosome identification. The
sequence is specifically targeted to and can hybridize with a particular location on an individual
human chromosome. Moreover, there is a current need for identifying particular sites on the
chromosome. The mapping of DNAs to chromosomes according to the present invention is an
important first step in correlating those sequences.
Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably
15-25 bp) from the cDNA. Computer analysis of the 3' untranslated region of the sequence is
used to rapidly select primers that do not span more than one exon in the genomic DNA, thus
complicating the amplification process. These primers are then used for PCR screening of
somatic cell hybrids containing individual human chromosomes. Only those hybrids containing
the human gene corresponding to the primer will yield an amplified fragment.
PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular DNA
to a particular chromosome. Using the present invention with the same oligonucleotide primers,
sublocalization can be achieved with panels of fragments from specific chromosomes or pools of
large genomic clones in an analogous manner. Other mapping strategies that can similarly be
used to map to its chromosome include in situ hybridization, prescreening with labeled flow-
sorted chromosomes and preselection by hybridization to construct chromosome specific-cDNA
libraries.
Fluorescence in situ hybridization (FISH) of a cDNA clone to a metaphase chromosomal
spread can be used to provide a precise chromosomal location in one step. This technique can be
used with cDNA as short as 50 or 60 bases. For a review of this technique, see Verma et ah,
Human Chromosomes: a Manual of Basic Techniques, Pergamon Press, New York (1988).
Once a sequence is mapped to a precise chromosomal location, the physical position of
the sequence on the chromosome can be correlated with genetic map data. Such data are found,
for example, in V. McKusick, Mendelian Inheritance in Man. The relationship between genes
and diseases that have been mapped to the same chromosomal region are then identified through
linkage analysis (coinheritance of physically adjacent genes).
Next, it is necessary to determine the differences in the cDNA or genomic sequence
between affected and unaffected subject. If a mutation is observed in some or all of the affected
individuals but not in any normal subjects, then the mutation is likely to be the causative agent of
the disease; a gene localized to a chromosomal region associated with the disease could be one of
between 50 and 500 potential causative genes. This assumes I megabase mapping resolution and
one gene per 20 kb. Utilizing the techniques described above, the chromosomal location of
VEGI was detemined with very high confidence to be 9q32. Previous chromosomal mapping
studies have linked several developmental defects to loci in this area of chromosome 9.
The present invention is also useful for diagnosis or treatment of various immune and
circulatory system-related disorders in mammals, preferably humans. Such disorders include
infections by bacteria, viruses, and other parasites, immunodeficiencies, inflammatory diseases,
lymphadenopathy, autoimmune diseases, graft versus host disease, and any disregulation of
immune and circulatory systems cell function including, but not limited to, autoimmunity,
leukemias, lymphomas, immunosuppression, immunity, humoral immunity, inflammatory bowel
disease, myelo suppression, and the like.
For a number of disorders, substantially altered (increased or decreased) levels of VEGI-
192a and/or VEGI-192b gene expression can be detected in various tissue (such as circulatory
tissue) or other cells or bodily fluids (e.g., sera, plasma, urine, synovial fluid or spinal fluid)
taken from an individual having such a disorder, relative to a "standard" VEQI-192a and/or VEGI-
192b gene expression level, that is, the VEGI-192a and/or VEGI-192b expression level from an
individual not having the disorder. Thus, the invention provides a diagnostic method useful
during diagnosis of a VEGI associated disorder, which involves measuring the expression level
of the gene encoding the VEGI-192a and/or VEGI-192b protein in a sample from an individual and
comparing the measured gene expression level with a standard VEGI-192a and/or VEGI-192b gene
expression level, whereby an increase or decrease in the gene expression level compared to the
standard is indicative of the disorder.
Thus, the invention provides a diagnostic method useful during diagnosis of a VEGI-
associated disorder which involves measuring the expression level of the gene encoding the
VEGI-192a and/or VEGI-192b protein in a sample from an individual and comparing the measured
gene expression level with a standard VEGI-192a and/or VEGI-192b gene expression level,
whereby an increase or decrease in the gene expression level compared to the standard is
indicative of the disorder.
Where a diagnosis of a disorder has already been made according to conventional
methods, the present invention is useful as a prognostic and/or monitoring indicator, whereby
patients exhibiting depressed VEGI-192a and/or VEGI-192b gene expression will experience a
worse clinical outcome relative to patients expressing the gene at a level nearer the standard
level.
Methods of using polynucleotides, polypeptides and antibodies: Screening assays
The polynucleotides and polypeptides of the present invention may be employed as
research reagents and materials for discovery of treatments and diagnostics to human disease.
This invention provides a method for identifying agents which modulate an activity of
VEGI-192a and/or VEGI-192b; methods for identifying agents which modulate the expression of
VEGI-192a and/or VEGI-192b in a cell. In some embodiments, the assay is a cell-free assay. In
other embodiments, the assay is a cell-based assay,
As used herein, the term "modulate" encompasses "increase" and "decrease". In some
embodiments, of particular interest are agents, which inhibit an activity VEGI-192a and/or VEGI-
i92b- Such agents are useful for promoting angiogenesis. In other embodiments, agents of
interest are those that increase an activity of VEGI-192a and/or VEGI-192b- Such agents are of
interest for inhibiting angiogenesis and treating angiogenesis associated disease.
Generally, the screening or testing methods employ agents or drugs from any variety of
sources. An agent or drug may be, for example, a biological or chemical compound such as a
simple or complex organic or inorganic molecule, a peptide, a protein, oligonucleotide,
polynucleotide, carbohydrate, or lipoprotein. A vast array of compounds can be synthesized, for
example oligomers, such as oligopeptides and oligonucleotides, and synthetic organic
compounds based on various core structures, and these are also included in the term "agent". In
addition, various natural sources can provide compounds for screening, such as plant or animal
extracts, and the like. Compounds can be tested singly or in combination with one another.
The invention provides methods for identifying agents that modulates an activity of
VEGI-192a and/or VEGI-192b after binding to VEGI-192a and/or VEGI-192b. The method generally
comprises contacting a testing agent that selectively binds to VEGI-192a and/or VEGI-192b with a
sample containing a VEGI-192a and/or VEGI-192b; and assaying an activity of VEGI-192a and/or
VEGI-192b in the presence or absence of the agents. An increase or a decrease in an activity of
VEGI-192a and/or VEGI-192b in the presence of the agent compared to in the absence of the agent
indicates that the agent increase (agonist) or decrease (antagonist) the activity of VEGI-192a
and/or VEGI-192b- Potential agonists or antagonist include small organic molecules, peptides,
polypeptides and antibodies that bind to a polypeptide of the invention and thereby increase or
decrease its activity.
Assays for testing the ability of an agent for selectively binding to a polypeptide of the
invention is known in the art. For example, the polypeptides of the invention can be attached to
a solid support and the agent that selectively binds to the polypeptide can be identified using
methods known in the art. Alternatively, VEGI-192a and/or VEGI-192b agonist and/or antagonists
may be detected by combining VEGI-192a or VEGI-192b and a potential agonist and/or antagonist
with membrane-bound VEGI-192a or VEGI-192b receptors (if such receptors are identified) or
recombinant receptors under appropriate conditions for a competitive inhibition assay. VEGI-
192a or VEGI-192b can be labeled, such as by radioactivity, such that the number of VEGI-192a or
VEGI-192b molecules bound to the receptor can determine the effectiveness of the potential
agonist and/or antagonist.
Assays for testing activity of VEGI are known in the art. Examples of such cell-based
assays are described in the Examples in further detail, such as testing effect on vascular
endothelial cell growth, formation and organization of endothelial cells into capillary-like tubular
structures, or organization of endothelial cells into capillary vessels in chicken embryo
chorioallantoic membrane.
Antibodies that selectively bind to VEGI-192a and/or VEGI-192b polypeptides may be used
as antagonists by binding to VEGI-192a and/or VEGI-192b and preventing it from performing its
activity.
This invention also provides methods for identifying agents that modulates the activity of
VEGI isoform described herein without binding to the VEGI isoform. Such agents include, but
not limited to, agents that regulate upstream or downstream of activity VEGI. These methods
comprise assaying the activity of VEGI in the presence or absence of an agent to be tested.
This invention also provides methods for identifying agents that modulates a level of
VEGI mRNA and/or polypeptide described herein.
Accordingly, the present invention provides a method for identifying an agent that
modulates a level of VEGI expression in a cell, the method comprising: contacting a candidate
agent to be tested with a cell comprising a nucleic acid which encodes a VEGI polypeptide
described herein, and determining the effect of said agent on VEGI polypeptide expression. In
some embodiments, the effect is measured by detecting the level of mRNA encoding the VEGI
polypeptide using the VEGI polynucleotides described herein. In other embodiments, the effect
is measured by detecting the level of the VEGI polypeptide using antibodies described herein.
Other potential antagonists include antisense molecules. Antisense technology can be
used to control gene expression through antisense DNA or RNA or through triple-helix
formation. Antisense techniques are discussed in a number of studies (for example, Okano, J.
Neurochem. 56:560 (1991); "Oligodeoxynucleotides as Antisense Inhibitors of Gene
Expression." CRC Press, Boca Raton, Fla. (1988)). Triple helix formation is discussed in a
number of studies, as well (for instance, Lee, et al., Nucleic Acids Research 6:3073 (1979);
Cooney, et al., Science 241:456 (1988); Dervan, et al., Science 251:1360 (1991)). The methods
are based on binding of a polynucleotide to a complementary DNA or RNA. For example, the 5'
coding portion of a polynucleotide that encodes the mature polypeptide of the present invention
may be used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in
length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved
in transcription thereby preventing transcription and the production of VEGI-192a and/or VEGI-
192b. The antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation
of the mRNA molecule into VEGI-192a and/or VEGI-192b polypeptide. The oligonucleotides
described above can also be delivered to cells such that the antisense RNA or DNA may be
expressed in vivo to inhibit production of VEGI-192a and/or VEGI-192b polypeptide.
This invention also provides methods for identifying agents such as mutants or variants
of VEGI-192a and/or VEGI-192b which may compete for binding with the targets which VEGI-192a
and/or VEGI-192b bind to and prevents VEGI-192a and/or VEGI-192b from interacting with their
targets. Such mutants or variants may be agonist or antagonist of VEGI-192a and/or VEGI-192b.
This invention provides a method for identifying agents that bind to VEGI-192a and/or
VEGI- 192b comprising contacting the agents with VEGI-192a and/or VEGI-192b and then detecting
agents' binding to VEGI-192a and/or VEGI-192b.
Methods of using polynucleotides, polypeptides and antibodies: treating disease
The invention provides methods for inhibiting vascular endothelial cell growth, inhibiting
angiogenesis, for the treatment or amelioration of diseases and processes that are mediated by
uncontrolled angiogenesis, treating cancer, such as suppressing tumor growth. Contrary to the
teachings that VEGI-251 is a membrane bound protein, the Examples show that VEGHsi is a
secreted protein, inhibits vascular endothelial cell growth, and has anti-angiogenesis effect upon
expression. In addition, the Example also shows that VEGI-192a inhibits vascular endothelial cell
growth.
Accordingly, the compositions that can be used for the method of the invention include,
but not limited to, polynucleotides described herein, such as polynucleotides encoding
polypeptides of SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6; polypeptides described herein,
such as polypeptides of SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, or a truncated form
which comprises at least one or more amino acids from the region of amino acids 1-26 of SEQ
ID NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of SEQ ID NO:6; and agonist
or antagonist of VEGI polypeptides described herein, such as an antibody that blocks the activity
of VEGI polypeptide.
The invention also includes methods of delaying development of an angiogenesis-
associated disease in an individual.
VEGI isoform polypeptides of the present invention (and polynucleotides encoding VEGI
isoform polypeptides) can be used to reduce the formation of capillary-like tubular structures
formed by endothelial cells in vitro. VEGI isoform polypeptides of the present invention can be
used to inhibit the formation of endothelial cells organized into capillary-like tubular structures
in response to angiogenic factors such as FGF-2. Furthermore, isolated VEGI isoform
polypeptides described herein of the present invention can also be used to inhibit the growth and
organization of endothelial cells into capillary vessels in a modified chicken embryo
chorioallantoic membrane (CAM). As a result, VEGI isoform polypeptides of the present
invention can be used to inhibit the formation of capillaries or capillary-like structures from
endothelial cells in vitro.
It will be appreciated that conditions caused by a decrease in the standard or normal level
of VEGI isoform polypeptides activities in an individual, particularly disorders of the immune
and circulatory systems, can be treated by administration of VEGI isoform polypeptides
described herein (or polynucleotides encoding the VEGI isoform polypeptides). Thus, the
invention also provides a method of treatment of an individual in need of an increased level of a
VEGI isoform activity comprising administering to such an individual a pharmaceutical
composition comprising an amount of an isolated VEGI isoform polypeptide of the invention (or
a polynucleotide), such as a mature form of the VEGI isoform polypeptide of the invention,
effective to increase the VEGI isoform polypeptide activity level in such an individual. The
invention also provides a method of treatment of an individual in need of a decreased level of a
VEGI isoform activity comprising administering to such an individual a pharmaceutical
composition comprising an amount of antagonist of the VEGI isoform, such as an antibody
specific for the VEGI isoform that blocks the activity of the VEGI isoform, effective to decrease
the VEGI isoform polypeptide activity level in such an individual.
Polynucleotide-based delivery
In some embodiments, the invention includes a method of inhibiting angiogenesis in a
tissue or cell comprising causing an effective amount of a polypeptide having an amino acid
sequence of SEQ ID NO:4 or SEQ ID NO:5, or SEQ ID NO:6, or a truncated form which
comprises at least one or more amino acids from the region of amino acids 1-26 of SEQ ID
NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of SEQ ID NO:6 to come into
contact with, or be expressed in the proximity of, the tissue or the cell, such that angiogenesis is
inhibited. In some embodiments, the invention includes a method of inhibiting angiogenesis
comprising administering to an individual, such as a human or animal, a composition comprising
the nucleic acid molecule encoding polypeptide of SEQ ID NO:4, SEQ ID NO:5, or SEQ ID
NO:6, or a truncated form which comprises at least one or more amino acids from the region of
amino acids 1-26 of SEQ ID NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of
SEQ ID NO:6, in a dosage sufficient to inhibit angiogenesis. In some embodiments, the nucleic
acid molecule is operably associated with a regulatory sequence that controls gene expression.
Such regulatory sequences are known in the art.
As an individual is an animal, in some embodiments, an individual may be a mammal.
The invention also provides a method for the treatment or amelioration of disease and
processes that are mediated by uncontrolled angiogenesis, comprising the step of administering
to an individual, such as a human or animal, a composition comprising a nucleic acid molecule
encoding SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, or a truncated form which comprises
at least one or more amino acids from the region of amino acids 1-26 of SEQ ID NO:4, amino
acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of SEQ ID NO:6, in a dosage sufficient to
control angiogenesis. In some embodiments, the nucleic acid molecule is operably associated
with a regulatory sequence that controls gene expression.
This invention also provides a method for treating cancer or suppressing tumor growth
comprising the step of administering to an individual, such as a human or animal, a composition
comprising the nucleic acid molecule encoding SEQ ID NO:4, or a SEQ ID NO:5, or a SEQ ID
NO:6, or a truncated form which comprises at least one or more amino acids from the region of
amino acids 1-26 of SEQ ID NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of
SEQ ID NO:6, in a dosage sufficient to suppress tumor growth. In some embodiments, the
nucleic acid molecule is operably associated with a regulatory sequence that controls gene
expression.
It is understood, if a truncated form of VEGI is used and the truncation occurs at the
secretory signal sequence, the truncated form includes a secretory signal sequence, either
homologous or heterologous, for directing secretion of the protein. Heterologous secretory
signal sequences are known in the art.
Methods of delivering polynucleotides for expression in an individual (both ex vivo and
in vivo) are known in the art. Generally, an appropriate polynucleotide vector construct is
prepared and administered.
Targeted delivery of therapeutic compositions containing polynucleotides, expression
vector, or subgenomic polynucleotides can be used. Receptor-mediated DNA delivery
techniques are described in, for example, Findeis et al., Trends Biotechnol (1993) 11:202; Chiou
et ah, Gene Therapeutics: Methods And Applications Of Direct Gene Transfer (J.A. Wolff, ed.)
(1994); Wu et al.,J. Biol Chem. (1988) 263:621; Wu et ah, J. Biol. Chem. (1994) 269:542;
Zenke et ah, Proc. Natl. Acad. Sci. USA (1990) 87:3655; Wu et ah, J- Biol. Chem. (1991)
266:338. Therapeutic compositions containing a polynucleotide may be administered in a range
of about 100 ng to about 200 mg of DNA for local administration in a gene therapy protocol.
Concentration ranges of about 500 ng to about 50 mg, about 1 |xg to about 2 mg, about 5 µg to
about 500 µg, and about 20 µg to about 100 µg of DNA can also be used during a gene therapy
protocol. The therapeutic polynucleotides of the present invention can be delivered using gene
delivery vehicles. The gene delivery vehicle can be of viral or non-viral origin {see generally,
Jolly, Cancer Gene Therapy (1994) 1:51; Kimura, Human Gene Therapy (1994) 5:845;
Connelly, Human Gene Therapy (1995) 1:185; and Kaplitt, Nature Genetics (1994) 6:148).
Expression of such coding sequences can be induced using endogenous mammalian or
heterologous promoters. Expression of the coding sequence can be either constitutive or
regulated.
Viral-based vectors for delivery of a desired polynucleotide and expression in a desired
cell are well known in the art. Exemplary viral-based vehicles include, but are not limited to,
recombinant retroviruses {see, e.g., PCT Publication Nos. WO 90/07936; WO 94/03622; WO
93/25698; WO 93/25234; WO 93/11230; WO 93/10218; WO 91/02805; U.S. Patent Nos. 5,
219,740 and 4,777,127; GB Patent No. 2,200,651; and EP 0 345 242), alphavirus-based vectors
(e.g., Sindbis virus vectors, Semliki forest virus (ATCC VR-67; ATCC VR-1247), Ross River
virus (ATCC VR-373; ATCC VR-1246) and Venezuelan equine encephalitis virus (ATCC VR-
923; ATCC VR-1250; ATCC VR 1249; ATCC VR-532)), and adeno-associated virus (AAV)
vectors {see, e.g., PCT Publication Nos. WO 94/12649, WO 93/03769; WO 93/19191; WO
94/28938; WO 95/11984 and WO 95/00655). Administration of DNA linked to killed
adenovirus as described in Curiel, Hum. Gene Ther. (1992) 3:147 can also be employed.
Non-viral delivery vehicles and methods can also be employed, including, but not limited
to, polycationic condensed DNA linked or unlinked to killed adenovirus alone {see, e.g., Curiel,
Hum. Gene Ther. (1992) 3:147); ligand-linked DNA(see, e.g., Wu, J. Biol. Chem. (1989)
264:16985); eukaryotic cell delivery vehicles cells (see, e.g., U.S. Patent No. 5,814,482; PCT
Publication Nos. WO 95/07994; WO 96/17072; WO 95/30763; and WO 97/42338) and nucleic
charge neutralization or fusion with cell membranes. Naked DNA can also be employed.
Exemplary naked DNA introduction methods are described in PCT Publication No. WO
90/11092 and U.S. Patent No. 5,580,859. Liposomes that can act as gene delivery vehicles are
described in U.S. Patent No. 5,422,120; PCT Publication Nos. WO 95/13796; WO 94/23697;
WO 91/14445; and EP 0524968. Additional approaches are described in Philip, Mol. Cell Biol.
(1994) 14:2411, and in Woffendin, Proc. Natl. Acad. Sci. (1994) 91:1581.
Thus, for example, cells from a patient may be engineered with a polynucleotide (DNA
or RNA) encoding a polypeptide, such as VEGI-251, ex vivo, with the engineered cells then being
provided to a patient to be treated with the polypeptide. Such methods are well-known in the art
and are apparent from the teachings herein. For example, cells may be engineered by the use of a
viral or a retroviral particle containing DNA or RNA encoding a polypeptide of the present
invention.
Similarly, cells may be engineered in vivo for expression of a polypeptide in vivo by, for
example, procedures known in the art. For example, a producer cell for producing a retroviral
particle containing RNA encoding a polypeptide of the present invention may be administered to
a patient for engineering cells in vivo and expression of the polypeptide in vivo. These and other
methods for administering a polypeptide of the present invention by such method should be
apparent to those skilled in the art from the teachings of the present invention. For example, the
expression vehicle for engineering cells may be other than a retrovirus, for example, an
adenovirus which may be used to engineer cells in vivo after combination with a suitable
delivery vehicle.
Retroviruses from which the retroviral plasmid vectors mentioned above may be derived
include, but are not limited to, Moloney Murine Leukemia Virus, spleen necrosis virus,
retroviruses such as Rous Sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, gibbon
ape leukemia virus, human immunodeficiency virus, adenovirus, Myeloproliferative Sarcoma
Virus, and mammary tumor virus. In one embodiment, the retroviral plasmid vector is derived
from Moloney Murine Leukemia Virus.
The vector generally includes one or more promoters. Suitable promoters which may be
employed include, but are not limited to, the retroviral LTR; the SV40 promoter; and the human
cytomegalovirus (CMV) promoter described by Miller and colleagues (Biotechniques 7:980-990
(1989)), or any other promoter (e.g., cellular promoters such as eukaryotic cellular promoters
including, but not limited to, the histone, pol III, and b-actin promoters). Other viral promoters
which may be employed include, but are not limited to, adenovirus promoters, thymidine kinase
(TK) promoters, and B 19 parvovirus promoters. The selection of a suitable promoter will be
apparent to those skilled in the art from the teachings contained herein.
The nucleic acid sequence encoding the polypeptide of the present invention is under the
control of a suitable promoter. Suitable promoters which may be employed include, but are not
limited to, adenoviral promoters, such as the adenoviral major late promoter; or hetorologous
promoters, such as the cytomegalovirus (CMV) promoter; the respiratory syncytial virus (RSV)
promoter; inducible promoters, such as the MMT promoter, the metallothionein promoter; heat
shock promoters; the albumin promoter; the ApoAI promoter; human globin promoters; viral
thymidine kinase promoters, such as the Herpes Simplex thymidine kinase promoter; retroviral
LTRs (including the modified retroviral LTRs hereinabove described); the b-actin promoter; and
human growth hormone promoters. The promoter also may be the native promoter which
controls the gene encoding the polypeptide.
If a retroviral vector system is chosen, the retroviral plasmid vector is employed to
transduce packaging cell lines to form producer cell lines. Examples of packaging cells which
may be transfected include, but are not limited to, the PE501, PA317, b-2, b-AM, PA12, T19-
14X, VT-19-17-H2, CRE, .beta.-CRIP, GP+E-86, GP+envAml2, and DAN cell lines as
described by Miller (Human Gene Therapy 1:5-14 (1990)), which is incorporated herein by
reference in its entirety. The vector may transduce the packaging cells through any means known
in the art. Such means include, but are not limited to, electroporation, the use of Hposomes, and
CaPO4 precipitation. In one alternative, the retroviral plasmid vector may be encapsulated into a
liposome, or coupled to a lipid, and then administered to a host.
The producer cell line generates infectious retroviral vector particles which include the
nucleic acid sequence(s) encoding the polypeptides. Such retroviral vector particles then may be
employed, to transduce eukaryotic cells, either in vitro or in vivo. The transduced eukaryotic
cells will express the nucleic acid sequence(s) encoding the polypeptide. Eukaryotic cells which
may be transduced include, but are not limited to, embryonic stem cells, embryonic carcinoma
cells, as well as hematopoietic stem cells, hepatocytes, fibroblasts, myoblasts, keratinocytes,
endothelial cells, and bronchial epithelial cells.
These general principles apply to other viral based delivery systems, such as AAV.
Polypeptide delivery
The invention also provides a method of inhibiting angiogenesis comprising
administering to an individual, such a human or animal a polypeptide described herein, such as
the polypeptide of SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, or a truncated form which
comprises at least one or more amino acids from the region of amino acids 1-26 of SEQ ID
NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of SEQ ID NO:6, in a dosage
sufficient to inhibit angiogenesis.
The invention also provides a method for the treatment or amelioration of disease and
processes that are mediated by uncontrolled angiogenesis, comprising the step of administering
to an individual, such as a human or animal, a composition comprising the polypeptide of SEQ
ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, or a truncated form which comprises at least one or
more amino acids from the region of amino acids 1-26 of SEQ ID NO:4, amino acids 1-26 of
SEQ ID NO.5, or amino acids 1-85 of SEQ ID NO:6, in a dosage sufficient to control
angiogenesis.
This invention also provides a method for treating cancer or suppressing tumor growth
comprising the step of administering to an individual, such as a human or animal, a composition
comprising the polypeptide of SEQ ID NO:4, SEQ ID NO:5, or SEQ ID NO:6, or a truncated
form which comprises at least one or more amino acids from the region of amino acids 1-26 of
SEQ ID NO:4, amino acids 1-26 of SEQ ID NO:5, or amino acids 1-85 of SEQ ID NO:6, in a
dosage sufficient to suppress tumor growth.
Methods for testing the activity of a VEGI polypeptide (including a truncated form of
VEGI) is well known in the art and are described in the Examples in detail, such as assay for
testing effect on vascular endothelial cell growth, capillary-like tube formation, capillary growth
in collagen gels placed on chick embryo chorioallantoic membrane, xenograft tumor growth.
As used herein, "angiogenesis associated disease" a disease or condition that is associated
with undesired and/or unregulated angiogenesis, or a disease or condition for which it is
advantageous to inhibit angiogenesis. It includes disease or processes mediated by undesired
and/or uncontrolled angiogenesis. Examples of such angiogenesis associated diseases, such as
tumor growth, are described herein.
VEGI isoform polypeptides described herein may be used to inhibit the proliferation of
endothelial cells, for example, aortic endothelial cells. As a result, VEGI-192a, VEGI-192b and/or
VEGI-152 polypeptide can be used to treat diseases and disorders in which inhibition of
endothelial cell growth is advantageous.
The VEGI isoform polypeptide composition will be formulated and dosed in a fashion
consistent with good medical practice, taking into account the clinical condition of the individual
patient (especially the side effects of treatment with VEGI isoform polypeptides alone), the site
of delivery of the VEGI isoform polypeptide composition, the method of administration, the
scheduling of administration, and other factors known to practitioners. The "effective amount" of
VEGI isoform polypeptide for purposes herein is thus determined by such considerations.
The VEGI isoform polypeptides and agonists and antagonists of the present invention
may be employed in combination with a suitable pharmaceutical carrier. Such compositions
comprise a therapeutically effective amount of the compound, and a pharmaceutically acceptable
carrier or excipient. Such a carrier includes but is not limited to saline, buffered saline, dextrose,
water, glycerol, ethanol, and combinations thereof. The formulation should suit the mode of
administration.
The invention also provides a pharmaceutical pack or kit comprising one or more
containers filled with one or more of the ingredients of the pharmaceutical compositions of the
invention. Associated with such container(s) can be a notice in the form prescribed by a
governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological
products, which notice reflects approval by the agency of manufacture, use or sale for human
administration. In addition, the pharmaceutical compositions of the present invention may be
employed in conjunction with other therapeutic compounds.
The pharmaceutical compositions may be administered in a convenient manner such as
by the topical, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or
intradermal routes. The pharmaceutical compositions are administered in an amount which is
effective for treating and/or prophylaxis of the specific indication. In general, they are
administered in an amount of at least about 10 g/kg body weight and in most cases they will be
administered in an amount not in excess of about 8 mg/Kg body weight per day. In most cases,
the dosage is from about 10 g/kg to about 1 mg/kg body weight daily, taking into account the
routes of administration, symptoms, etc.
Various delivery systems are known and can be used to administer VEGI isoform
polypeptides of the present invention, e.g., encapsulation in liposomes, microparticles,
microcapsules, receptor-mediated endocytosis (see, e.g., Wu and Wu 1987, J. Biol. Chem.
262:4429-4432). Methods of introduction include, but are not limited to, topical, intradermal,
intramuscular, intraperitoneal, intravenous, subcutaneous, intranasal, epidural, ophthahnic, and
oral routes. The compounds may be administered by any convenient route, for example, by
infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral
mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other
biologically active agents.
In a specific embodiment, it may be desirable to administer the pharmaceutical
compositions of the invention locally to the area in need of treatment. This may be achieved by,
for example, and not in limitation of, local infusion during surgery, topical application, e.g., in
conduction with a wound dressing, by Injection, by means of a catheter, by means of a
suppository, or by means of an implant, said implant being of a porous, non-porous, or
gelatinous material, including membranes, such as sialastic membranes or fibers.
Assessment of disease is performed using standard methods in the art, such as imaging
methods and monitoring appropriate markers.
It will also be appreciated by one of ordinary skill that, since the VEGI isoform
polypeptides of the invention are members of the TNF family the mature secreted form of the
protein may be released in soluble form from the cells which express VEGI isoform polypeptides
described herein by proteolytic cleavage. Therefore, when the mature form or soluble
extracellular domain of VEGI isoform polypeptides is added from an exogenous source to cells,
tissues or the body of an individual, the polypeptide will exert its physiological activities on its
target cells of that individual. Also, cells expressing this type II transmembrane polypeptide may
be added to cells, tissues or the body of an individual and these added cells will bind to cells
expressing receptor for VEGI isoform polypeptides described herein, whereby the cells
expressing VEGI isoform polypeptides can cause actions (e.g. regulation of endothelial cell
growth and regulation) on the receptor-bearing target cells.
As stated above, VEGI is shown to have strong anti-proliferation effects on endothelial
cell growth. Accordingly, VEGI may also be employed to regulate the development of
endothelial cells from hematopietic and circulating endothelial precursor cells.
Accordingly, the invention provides methods of enhancing angiogenesis comprising
administering an inhibitor of VEGI-192a or VEGI-192b, such that angiogenesis is enhanced. Such
enhancement may be desirable, for example, in the context of conditions associate with an
obstruction of a blood vessel, such as ischemic conditions or heart attack. The formulations may
be administered locally or systemically using methods known in the art.
The antibody of the present invention that blocks or suppress the activity the VEGI
polypeptide may be used for promoting or enhancing angiogenesis.
EXAMPLES:
Described below are examples of the present invention which are provided only for
illustrative purposes, and not to limit the scope of the present invention. In light of the present
disclosure, numerous embodiments within the scope of the claims will be apparent to those of
ordinary skill in the art.
The present invention will be further described with reference to the following examples,
however, it is to be understood that the present invention is not limited to such examples.
The discovery of an endothelial cell-specific gene product, vascular endothelial cell
growth inhibitor (VEGI) has recently been reported (Zhai Y, et al, FASEB J., 13:181-189,
1999; Zhai, Y, et al, Int. J. Cancer, 82:131-136,1999). The protein consists of 174-amino
acids, i.e., VEGI-m, with a 20-30% sequence homology to members of the TNF superfamily.
Northern blotting analysis of a wide variety of cell lines and primary cell cultures indicates that
the VEGI-174 gene is expressed predominantly in endothelial cells. Additionally, the VEGI-174
mRNA is detectable in many adult human organs, suggesting a physiological role of the gene in
a normal vasculature. The function of VEGI-174 was examined in a number of cellular and
animal models. Recombinant truncated form of VEGI-174 inhibited endothelial cell proliferation
with a remarkable potency, but had no effect on the growth of any other types of cells examined.
The truncated form of the protein also inhibited the formation of capillary-like structures by
endothelial cells in collagen gels, and the growth of capillaries into collagen gels placed on the
chick chorioallantoic membrane. Overexpression of a secreted form of VEGI-174 in murine colon
cancer cells (MC-38) nearly completely prevented these cells from growing tumors in syngenic
C57/BL mice. Moreover, co-inoculation of human breast cancer cells with Chinese hamster
ovary cells overexpressing secreted form of VEGI-174 led to marked inhibition of the growth of
the breast cancer xenograft tumors in nude mice.
Example 1. ELISA analysis of human sera:
Normal human sera of normal male and female adult individuals are obtained from the
Lombardi Cancer Center serum bank. Sandwich ELISA was used to measure serum VEGI
content. Serum samples (100 µl) or varying amounts of recombinant VEGI protein in 3% BSA
were added to 96-well plates coated with a polyclonal anti-VEGI antibody and blocked with 3%
BSA. A monoclonal antibody (100µl, 2 µg/ml) against VEGI (3-12D) was added. Biotinylated
anti-mouse IgG antibody (2µg/ml, Vector laboratories, Burlingame, CA) was added, followed by
avidin-horseradish peroxidase, with 3,3',5,5'-tetramethylbenzidine (Vector laboratories) as
substrate. The samples were incubated at room temperature for 10 min, the reaction terminated
with 50 µl 1M H2SO4, then analyzed at 450 nm with a spectrophotometric plate reader, using the
standard curve y= -0.72 + 0.409*log(x). Standard protein range used was 0.32 - 1000 ng/ml.
Example 2. Northern blotting:
Multi-tissue Northern blots and multi-tissue dot-blot panels (Clontech, Palo Alto, CA)
were hybridised in ExpressHyb solution (Clontech) with double-stranded cDNA probes. The full
length VEGI-174 probe used was a Hind III- BamHI cDNA fragment (GenBank Accession
#AF03990) in pCDNA3.1 (Invtrogen, Carlsbad, CA). For isoform-specific probes, a 297-bp
VEGI-251 template encoding its N-terminal 99 amino acids was made by PCR amplification, and
labeled wth 32P-dCTP by random priming (Life Technologies.Invitrogen, CA). The VEGI-174
specific probe corresponding to its N-terminal 22 amino acids was made by end-labeling a 66-bp
PCR product. The blots were hybridized at 42 °C overnight and washed in wash buffer 1 (2 X
SSC, 0.1% Sodium lauryl sulfate) and wash buffer 2 (1 X SSC, 1% SDS) at 42° C followed by
autoradiography at -70 °C with an intensifying screen.
Example 3. 5'RACE and VEGI isoform cloning:
5' VEGI sequences were amplified from a multi-tissue RACE panel (ORIgene,
Rockville, MD) according to the manufacturer's instructions. This panel contains cDNA samples
prepared from 24 individual human tissues, with an adapter ligated to the 5' ends of the cDNAs.
Two rounds of nested PCR were performed using two pairs of oligonucleotide primers. In the
first round of PCR, an adapter primer ADP1, 5' CGGAATTCGT CACTCAGCG 3' (SEQ ID
NO:8) and a VEGI gene-specific primer GSP1, 5'CCCGGATCCT ATAGTAAGAA GGCTCC
3' (SEQ ID NO:9) were used. The reaction products were then diluted 1:10 with water. The
diluted PCR samples were then used for the second round of PCR with another adapter primer,
ADP2,5' AGCGCGTGAA TCAGATCG3' (SEQ ID NO:10), and a VEGI gene-specific primer,
GSP2,5' CGGTGGATCC CGAGTTTGTC TCACAACTG3' (SEQ ID NO:11). The PCR
products were resolved on an agarose gel, purified, and sequenced on an ABI automatic
sequencer.
Example 4. Isolation of VEGI 251 and VEGI-192a:
Gene-specific primers designed according to sequencing results of the RACE products
were used to repeat the second round PCR to confirm their sequence identities. The gel-purified
RACE products were then cloned into plasmid pCR3.1 (Invitrogen, Frederick, MD) and
sequenced. Based on these sequences, isoform-specific primers were designed. The shared
reverse primer, Vgl61 (161), 5'GTGTAATCCA CCAAAGAG3' (SEQ ID NO:12) was used
with forward primers listed in Table 8.
Example 5. Cell Culture and TNFa Treatment:
Human umbilical vein endothelial cells (HUVE), and fetal bovine heart endothelial
(FBHE) cells were obtained from Clonetics (Walkersville, MD) and grown in EGM-2
(Clonetics). Human dermal microvascular endothelial (HMVE), human coronary artery
endothelial (HCAE) cells and NIH3T3 cells were obtained from the American Type Culture
Collection and grown in EGM2-MV (Clonetics). Adult bovine aortic endothelial (ABAE) cells,
and mouse brain endothelioma bEND.3 were gifts from Dr Peter Bohlen of ImClone Inc, New
York, NY. Human coronary artery smooth muscle cells (HCASM) (Clonetics) and ABAE cells
were cultured in IMEM (Bioftuids, Biosource International, Camarillo, CA), 10% FBS, 1 ng/ml
fibroblast growth factor-2 (Promega, Madison,WI). EA.Hy926, a human endothelial-derived cell
line, was a gift from Dr Cora-Jean Edgell, University of North Carolina. These cells, together
with mouse brain bEND.3 and heart H5V endothelioma cell lines, were maintained in IMEM
with 10% FBS. Subconfiuent cells grown in 100-mm dishes were treated with various doses of
tumor necrosis factor a (TNFa) (Biosource International, Camarillo, CA) prior to RNA analysis.
Example 6. Ribonuclease protection assays:
For isoform-specific probes, cDNA fragments from human VEGI-174 (862-1062bp),
VEGI-251 (1-160 bp), VEGI-192a (277-656 bp), were generated by PCR and inserted between the
EcoRI and NotI sites of pcDNA3 (Invitrogen) in the antisense direction. A mouse ß-actin probe
(824-942) was cloned into pSP72 (Promega) between the HindIII and BamIII sites. The VEGI
and ß-actin templates were linearized with Hindlll and EcoRI, respectively. Antisense run-off
probes were synthesized with SP6 RNA polymerase using the Maxiscript transcription kit
(Ambion, Woodward TX). For nuclease protection with the RPAIII kit (Ambion, TX), 15-20 µg
of total RNA was hybridised overnight with 1-3 x 105 cpm of each probe at 52 °C. RNase
digestion was performed with 1:100 dilution of RNase A/T1 mix (Ambion) for 30 min at 37 °C.
The products of digestion were precipitated, resolved on a 6% polyacrylamide gel, and subjected
to autoradiography at -70 °C.
Example 7. Gene structure analysis:
The organization of the human VEGI gene was analyzed by PCR using a bacterial
artificial chromosome (BAC) clone (Genome Systems, Inc, St Louis, MO). PCR primers from
exonic sequences were designed which generated overlapping PCR products. These PCR
products were sequenced to determine their relative positions. Primers for the intronic region
were designed based the GenBank entry for Chromsome 9 Contig NT_017568, which
correspond to sequences between bases 2,643,881 and 2,694,724. These are listed in Table 9.
With human placenta DNA as a template, extra long PCR was performed using an rTth XL PCR
kit from Perkin Elmer (Foster City, CA) and the following extra long PCR conditions: 95°C, 1
min, 97°C, 15 sec, 60.5°C, 10 min, 17 cycles; 97°C, 15 sec, 60.5°C, 10 min plus 15 sec
extension, 13 cycles, followed by final extension at 72°C for 11 min. The PCR fragments were
generated with the primer pairs shown in Table 9. The PCR products were sequenced.
Example 8. Expression plasmids and transient transfections:
The open reading frames of VEGI-174 and VEGI-251 were inserted into pcDNA3.1-myc
(Invitrogen, MD) to generate peptides bearing a C-terminal myc tag. The resultant plasmids were
transfected into ABAE and HUVE cells for cellular localization studies. For cell transfections, 3
x 104 cells were seeded on Lab-Tek chambered coverglass (Nalge, Naperville, IL) overnight.
Plasmid DNA (400 ng) in 25 µl serum-free IMEM was mixed with PLUS reagent (4 ul)
(GIBCO-BRL). LipofectAMINE (GIBCO) reagent (1 ul) was 200-fold and mixed with the DNA
solution for 15 mins. The DNA-lipofectAMINE complex was then added to cells with 200 µl
IMEM and incubated at 37 °C for 3 h. The cells were allowed to recover in serum-containing
growth medium for 36 h prior to immuno-staining and subsequent fluorescence microscopy. The
full length coding region of VEGI-174 or VEGI-251 was also inserted between the EcoR1 and
BamH1 sites of pEGFP-C2 (Clontech) to make GFP-VEGI fusion proteins. The GFP-VEGI
fusion constructs were transfected into ABAE cells as described above. At 48 h post-
transfection, the cellular localization of the fusion protein were examined by fluorescence
microscopy.
Example 9. Immunostaining for subcellular localization:
Transfected adult bovine aortic (ABAE) and HUVE cells were washed with PBS and
fixed with 3.7% paraformaldehyde/0.1% Triton X-100 in PBS for 10 min, permeabilized with
0.5% Triton X-l 00 in PBS for 5 mins, then incubated with a 1:300 dilution of an anti-myc
monoclonal antibody 9-10E (Sigma) for 1 h. The cells were washed with PBS and incubated
with anti-mouse IgG, Texas Red-conjugated monoclonal antibody at a 1:60 dilution (Jackson
ImmunoResearch Labs, Inc West Grove, PA), then washed thrice with PBS. The cells were
visualized by confocal fluorescence microscopy (Olympus IX70-SIF).
Example 10. Production of monoclonal antibodies:
Six-week-old female BALB/c mice (Charles River Laboratories, Wilmington, MA )
were injected subcutaneously with purified recombinant VEGI protein (residues 29-174) at 50 µg
per mouse in 0.1 ml of a complete Freud's adjuvant ( Life Technologies). Following
intraperitoneal boosters, mice with higher titers received a final intraperitoneal antigen injection
of 30 µg/mouse. Spleen cells were isolated and fused with mouse myeloma SP2/O cells, using
polyethylene glycol 1500 (Boehringer Mannheim). Hybridomas were selected by HAT medium
and screened by ELISA. Positive hybridomas were cloned and the subclass of monoclonal
antibodies was determined using the mouse isotype kit (SIGMA, MO). Hybridomas were
cultured on an INTEGRA CL 350 (INTEGRA Biosciences, Inc., Iiamsville, MD), the
supematants collected, and monoclonal antibodies were purified by AffiGel protein A agarose
(Bio-Rad).
Example 11. Production of polyclonal antibodies:
Four to six-month-old SPF New Zealand White rabbits (Charles River) were inoculated
subcutaneously with 100 µg of E. coli expressed recombinant VEGI (as above) mixed with
complete Freud's adjuvant (Life Technologies). Following intramuscular boosters, serum was
collected from rabbits showing substantial immune response. Sera was purified by absorption
with E. coli (transformed with an empty expression vector) cell lysate, then with human coronary
artery smooth muscle cell lysate.
Example 12. Analysis of VEGI in mammalian cells and conditioned media:
The full-length VEGI-251 coding region was inserted between the Hind III and BamHI
sites of pcDNA3 (Invitrogen). These pcDNA3 plasmids, including vector, were transfected into
MDA-MB231 breast cancer cells by electroporation. Stable transfectants were selected in 2
mg/ml G418 sulfate (GIBCO). Conditioned media were concentrated with Centricon columns
(MW cutoff 10,000). Both cell lysates and conditioned media were immunoprecipitated with
protein A/G agarose (Oncogene, Boston, MA) and the polyclonal antibody against VEGI. The
samples were analyzed by Western blotting. Detection was effected with a 1:1000 dilution of
mouse monoclonal antibodies 1-8F, and visualized with anti-mouse IgG antibody conjugated
with horseradish peroxidase (ECL kit, Amersham).
Example 13. Lentiviral gene transfer:
The lentiviral vectors containing VEGI-174, sVEGI and VEGI-251 were prepared using
previously described methods (Dull, et al. J Virol 72, 8463-8471,1998; Naldini, et al Proc Natl
AcadSci (USA) 93,11382-11388,1996; Naldini, et al. Science 272,263-267,1996; Stewart, et
al. Proc Natl AcadSci (USA) 96,12039-12043. 1999). Briefly, the lentiviral vector was
generated in 293T cells with 3 plasmids : the transducing plasmid pHR'CMV-VEGI, the
packaging plasmid pCMV AR8.2 Avpr and the envelope plasmid pCMV-VSV-G. Viral
supernatants were collected every 24 h from two days post-transfection, purified by 0.45 urn
filtration and titrated by p24 assay (Dull, et al. J Virol 72, 8463-8471,1998; Naldini, et al. Proc
Natl Acad Sci (USA) 93,11382-11388,1996; Naldini, et al. Science 272,263-267,1996;
Stewart, et al. Proc Natl Acad Sci (USA) 96,12039-12043.1999). One pg of p24 count was
defined as one tissue culture infective dose (TCID). For cell toxicity assays, HUVE cells were
plated at a density of 2 x 104 per well in a 24-well plate 20 h before infection with viral
supernatant. The cell number was expected to double 20 h after plating. Increasing doses of viral
vector were added to HUVE cells. The multiplicity of infection (MOI) was estimated as TCID
per cell at the time of infection. The number of adherent cells remaining in culture 24 h after
viral infection were determined by Coulter Counter.
Example 14. In vivo tumorigenicity assay:
Stably transfected MDA-MB-231 cells containing empty pcDNA3 vector, VEGI-174,
VEGI-251 or sVEGI were injected into mammary fat pads of female athymic nude mice (1x106
cells/injection). There were 2 injection sites per animal and 15 animals in each group which
received the VEGI-174, VEGI-251 and sVEGI transfectants. A group of 5 animals injected with
pcDNA3 vector transfectants was used as control. The sizes of the resultant xenograft tumors
monitored in a blinded manner. Determination of microvessel density was carried out as
described (Weidner, et al N Engl J Med 324,1-8,1991). Briefly, intratumor microvessels were
immunostained with rat anti-mouse CD31 (PECAM-1) monoclonal antibody (clone MEC13.3,
Pharmingen International, San Diego, CA). The antibody was diluted 1:100 in PBS, incubated
overnight with 5 µm paraffin-fixed tumor sections, and visualized with a biotinylated anti-rat
IgG antibody (Vector Laboratories) by the Vectastain ABC method (Vector Laboratories). Each
sample was examined under low power (x10 objective lens and xlO ocular lens) to identify the
most vascular areas of the tumor ("hot spots", see reference (Weidner, et al. N Engl J Med 324,
1-8, 1991)). Within these areas, a maximum of 10 fields at x 400 magnification (x40 objective
and xlO ocular lens; 0.16 mm2 per field) were examined, and the mean values calculated. Large
vessels with muscular walls were excluded. The lumen was not required to identify a vessel. Any
positively stained endothelial cells or cell clusters, clearly separate from adjacent microvessel,
tumor cells and connective tissue elements, were regarded as distinct countable microvessels. All
measurements were performed in a blinded manner. The results were analyzed by one-way
analysis of variance (ANOVA). The apriori level of significance was set at P-value of less than
0.05.
Example 15. Detection of VEGI protein in human sera
As an initial screen to determine whether VEGI exists in a soluble form, we analyzed a
human serum bank of healthy adults with monoclonal antibodies. We were able to detect, by
ELISA with an antibody against the C-terminus, VEGI concentrations ranging between 1 and 10
ng/ml (Figure 1). This indicated that, in addition to the previously characterized VEGI which
was believed to be membrane-bound, a soluble form of VEGI would also be of significant
physiological relevance. Since previous studies had shown apoptotic activity of a recombinant C-
terminal peptide, and overexpression of the full length VEGI-174 was ineffective on xenograft
tumors formed by transfected cancer cells, we thus reasoned that the C-terminus-containing
soluble peptide found in human sera was not likely to have been derived from VEGI-174. This
observation then prompted us to propose that the VEGI gene might express alternate forms in
human tissue.
Example 16. Detection of multiple VEGI transcripts and cloning of novel VEGI isoforms
With a full length cDNA of the originally discovered human VEGI as a probe, Northern
blots of normal human tissues consistently revealed multiple bands of the following sizes: 7.5kb,
2.0 kb and 1.5 kb (Figure 2). These multiple transcripts for VEGI showed somewhat overlapping
tissue distribution and demonstrated the existence of a VEGI family. In order to elucidate the
structure of the VEGI-related transcripts, we undertook the isolation of VEGI isoforms by PCR.
With VEGI-specific 3' primers, 5' RACE was employed to amplify 5' ends of VEGI messages
from a number of human tissues. The RACE products were then cloned into pCR3.1 and
sequenced (Figure 3). Sequence analysis revealed two novel VEGI sequences, VEGI-251 and
VEGI-192a (Table 8 and Figure 3). Based on these 5' sequences, isofoim-specific primers were
designed, and full-length cDNA clones isolated from arrayed cDNA panels. Three VEGI
isoforms were thus isolated from fetal brain, adult uterus and lung (Figures 3A and B). The novel
cDNAs contain open reading frames of 251 and 192 amino acids (Figure 3B), with calculated
molecular weights of 28 086 and 21 952 Daltons respectively. The two novel VEGI peptides,
VEGI-2S1 and VEGI-192a, share the carboxyl 151 amino acid residues with the original VEGI
(Zhai, etal. IntJ Cancer 82,131-136,1999), now referred to as VEGI-174. The hydropathic
profile of the proteins indicated a hydrophobic region of 20 amino acid residues in VEGI-251 near
its N-terminus (Figure 3B) which is absent from VEGI-174 and VEGI-192a- This sequence was
predicted to comprise a signal peptide. Another highly hydrophobic, possibly transmembrane
region, was previously identified at the N-terminus of VEGI-174 (Figure 3B).
Example 17. Expression of VEGI isoforms
The individual expression patterns of the isoforms was further examined by Northern
analysis with multi-tissue blots. A 7.5 kb VEGI-251 transcript was detected in placenta, kidney,
lung and liver while the 2 kb VEGI-174 transcript was observed in liver, kidney, skeletal muscle
and heart (Figure 4). When these same probes were used on a multi-tissue RNA dot blot, it was
observed that, in addition to overlapping expression between VEGI 251 and 174 in prostate,
salivary gland and placenta, VEGI-251 was more abundant than VEGI-174 in fetal kidney and fetal
lung, while VEGI-174 is more abundant in heart, skeletal muscle, pancreas, adrenal gland, and
liver (Table 10). The significance of such expression patterns is at present not readily apparent to
us. VEGI-192a mRNA could not be readily detected by Northern blotting because of its low
abundance.
VEGI expression in vitro was also examined by RNase protection assay. In agreement
with previous observations for VEGI-174, VEGI-251 and VEGI-192a were detected in the same cell
types as VEGI-174, being present in human endothelial cells, including coronary artery
endothelial (HCAE), human umbilical vein endothelial (HUVE) and human microvascular
endothelial (HMVE) cells and undetectable in human coronary artery smooth muscle (HCASM),
ABAE and mouse endotheliomas bEND.3 (Figure 5). It should also be noted that more than one
isoform was expressed in the same cell type, with VEGI-251 being the most abundant. This
suggests that the expression of these isoforms plays a regulatory role in VEGI function.
Example 18. Human VEGI gene organization
In order to determine the structural relationship of the three VEGI transcripts, the
organization of the human VEGI gene was analyzed. This was done with a BAC clone as well as
with genomic DNA isolated from human placenta samples. It was found that the human VEGI
gene spans over 17 kb, with 4 exons and 3 introns (Figure 6). The intron-exon junctions conform
to the GT-AG rule. Based on the size of fragment 2, intron 1 was estimated at 13-15 kb, although
sequence information could not be obtained from this PCR product. All three isoforms share a
common 438 bp region encoding residues 29-174 of VEGI-174 (Table 12) encoded by exon IVb
(Figure 6), but their 5' regions are generated from alternative exon usage. Interestingly, VEGI-251
and VEGI-192a utilize exonic splice acceptor sites to generate their respective products (Table
11). Ribonuclease protection and 5' RACE studies using genomic probes and HUVE RNA
indicated that the putative transcription initiation site for VEGI-251 is located about 100 bp
upstream of its ATG (unpublished, Chew LJ) but those for VEGI-174 and VEGI-192a have yet to
be mapped. Due to the very low abundance of VEGI-192a RNA, subsequent studies were focused
on VEGI-251. While it is presently unclear whether all the isoforms initiate at the same promoter,
we nonetheless reasoned that the significance of generating multiple transcripts could lie in
differential regulation of synthesis, which in turn may point toward the relative importance of
one particular VEGI isoform.
Organization of the human VEGI gene, with the size of each exon and approximate sizes of
introns. Exon numbers are given in Figure 6. Uppercase letters indicate exon sequence, and
lower case indicate intron sequence. Consensus splice junctions are underlined. * The extreme 5'
ends of VEGI-192a and VEGI-174 mRNA have not yet been identified, therefore intron-exon
junctions in these regions are unknown.
Table 12. Amino acid sequence of VEGI polypeptide (SEQ ID NO:42)
PTQHFKNQFPALHWEHELGLAFTKNRMNYTNKFLLIPESGDYFIYSQVTFRGMTSECSEI
RQAGRPNKPDSITVVITKVTDSYPEPTQLLMGTKSVCEVGSNWFQPIYLGAMFSLQEGD
KLMVNVSDISLVDYTKEDKTFFGAFLL (SEQ ID NO:42)
Example 19. VEGI isoform transcripts are induced in parallel by TNFa
To test for the possibility of differential regulation in VEGI isoform transcription, VEGI
gene regulation using an anti-angiogenic paradigm of TNFa treatment was analyzed. Although
many studies describe anti-proliferative effects of proinflammatory cytokines like TNFa on
endothelial cells, these cytokines can also be angiogenic depending on dose and system used (see
Discussion). Such modulatory effects on endothelial cells may serve to regulate the levels of an
endothelial cell-specific cytokine such as VEGI. We found that concentrations of 15 ng/ml of
TNFa or higher could induce an increase in VEGI RNA levels in both large vessel (umbilical
vein) and small vessel (dermal microvascular) endothelial cells (Figure 7), and that all isoforms
were induced in both these endothelial cell types. It is also clear that VEGI-251 remains the most
abundant of the isoforms. The parallel upregulation of VEGI transcripts by TNFa not only
indicates that VEGI-mediated activity is potentially a target of TNFa action, but also that the
control of VEGI function through the synthesis of multiple peptides most likely lies at the post-
transcriptional level.
Example 20. Subcellular localization
Since TNF-like peptides are often present as both membrane-bound and soluble forms,
the possibility by using recombinant VEGI-transfected ABAE cells was investigated.
Localization experiments were performed with constructs bearing a myc tag at the C-termini of
VEGI coding regions (Figure 8). Expression constructs of VEGI isoforms in pcDNA3.1-myc
were transfected into ABAE cells and the distribution of the VEGI-myc product analyzed by
immunocytochemistry with an anti-myc antibody. VEGI-174 was detected in the cell with
endoplasmic reticulum/Golgi-like distribution (Figure 8A). However, VEGI-251 showed a more
restricted peri-nuclear granular staining (Figure 8B). In both cases, cell surface localization was
not apparent by confocal fluorescence microscopy. In HUVE cells, the VEGI-251-myc-containing
vesicles were found not to be Weibel-Palade bodies of endothelial cells, because the myc signal
did not colocalize with von Willebrand factor (vWF) staining (Figure 8C). It is therefore possible
that, in contrast with vWF, processing of VEGI-251 does not involve a regulated secretory
pathway in endothelial cells.
To determine whether the isoforms might exhibit N-terminus directed differences in
subcellular localization, chimeric GFP-VEGI expression constructs were made with both full-
length VEGI and their corresponding unique N-terminal sequences. These constructs, with GFP
tags at their N-termini (Figure 8), were transiently transfected into ABAE cells. As shown in
Figures 8E through 8 J, with the exception of 8G, the distribution of GFP-VEGI was distinct from
that of untargeted GFP. Full length VEGI-174 showed localization in ER/Golgi, as previously
seen with myc-tagged VEGI-174 while the first 22 residues of VEGI-174 appeared inadequate for
targeting GFP distribution to a specific intracellular organelle (Figure 8G). In contrast, the first
99 amino acids of VEGI-251 was sufficient to result in GFP localization in vesicles which abutted
the plasma membrane. This distribution was seen as a fluorescent band that outlined the cellular
boundary (Figures 8H through J). Our observations suggested that VEGI-251 might be located in
secretory vesicles which underwent constitutive exocytosis.
Unlike GFP-VEGI-251, the lack of plasma membrane localization of VEGI-251-myc
(Figure 8B) strongly suggested that the C-terminal myc tag was lost from the cell, possibly
because of cleavage of the secretory signal and secretion of the soluble C-terminal fragment. It
was known that true signal sequences that were placed downstream of the N-termini, such as in
GFP-VEGI-251 and GFP-VEGI-1-99, were not cleaved during synthesis in the ER. This
difference in distribution patterns of VEGI-251 with C-terminal and N-terminal tags was in
agreement with a secretory mechanism that involved cleavage of VEGI-251 at or within its N-
terminal sequence prior to release into the extracellular milieu.
Example 21. Demonstration of VEGI in cell-conditioned media
Given the hydrophobic residues in the N-terminus of VEGI-251 and its observed
subcellular distribution, it appears likely that VEGI-251 is a secreted protein. To test this
hypothesis, stable transfectants of VEGI-251 in MDA-MB-231 breast cancer cells were generated.
As a negative control, transfectants of pcDNA3 vector were also made. Expression of the
constructs in MDA-MB-231 was confirmed by RNase protection assay. It should be noted that
the survival and proliferation of these cells in vitro was not affected by either vector or VEGI
transfection. The conditioned media of the MB-231 transfectants was collected, concentrated and
immunoprecipitated with a polyclonal VEGI antibody and subjected to Western analysis with an
anti-VEGI monoclonal antibody 3-12D. Our results revealed a protein of molecular weight of
about 25 kD (Figure 9A). The appearance of the doublet cannot be readily explained, but may be
the result of alternate glycosylation or other post-translational modification of the recombinant
peptide in transfected MB231 cells. No VEGI protein was detected in media from untransfected
cells or cells bearing the empty pcDNA3 vector (Figure 9A). VEGI-174 could not be detected in
conditioned medium under similar experimental conditions (not shown). In a separate
experiment, Western analysis of concentrated HUVE cell-conditioned medium also revealed a
band of similar molecular weight as that obtained with VEGI-251 transfectants, as did HUVE
cell-conditioned medium immunoprecipitated with the polyclonal antibody (Figure 9B). These
observations indicate that VEGI-251 is not membrane-bound but is instead a secreted protein.
Example 22. Overexpression of VEGI-251 in endothelial cells causes cell death
In order to test the biological activity of VEGI-251 on endothelial cells, a lentivirus gene
delivery system was selected to transfect HUVE cells with VEGI expression constructs. The
lentiviral gene delivery was first tested with a GFP construct and confirmed that over 90%
HUVE cells could be transduced (not shown). Our observations with VEGI-174, VEGI-251 and the
secreted form of VEGI with the IL6 signal peptide, sVEGI, showed that only the secreted forms
of VEGI, including VEGI-251 and sVEGI, were cytotoxic to HUVEC (Figure 10 A), while VEGI-
174 was without effect. These results indicate that HUVE cells bear membrane receptors for
VEGI that can become activated via an autocrine mechanism.
Example 23. Anti-tumor activity of VEGI-251
It has been previously shown that a recombinant form of VEGI-174 carrying the IL-6
secretory signal peptide, sVEGI, was effective in inhibiting the growth of MC38 colon
carcinoma tumors in vivo (Zhai, et al. Int J Cancer 82,131-136,1999). Since native VEGI-251 is
a secreted protein, we determined whether it could also inhibit the growth of human xenograft
tumors in vivo. Fifteen lines of stably transfected MDA-MB-231 clones for each construct were
selected, with five lines from vector-transfected controls. Cells from each group were pooled and
injected into mammary fat pads of female athymic nude mice. Tumor volumes were determined
as a function of time after injection. Similarly pooled cell cultures of VEGI-174 and sVEGI-
transfected clones were compared. Pooled vector-transfected clones were used as controls.
Untransfected parental cells were also assayed and were found to be identical with the vector-
transfected clones.
Our results show that overexpression of full length VEGI-174 by cancer cells had little
effect on the growth of the xenograft tumors (Figure 10B). However, overexpression of the intact
VEGI-251 as well as the sVEGI fusion protein retarded tumor growth significantly. These
observations are in complete agreement with the effect of lentiviral transfection in vitro (Figure
10 A), confirming the biological activity of native VEGI-251.
We then determined the effect of full-length VEGI-251 overexpression by cancer cells on
tumor neovascularization. Tumor-associated microvessel density was found to be significantly
reduced with the expression of VEGI-251. The extent of reduction was comparable to that in
sVEGI overexpressing tumors. Since the sVEGI fusion protein consists of the secretion signal
peptide of IL6 and residues 23-174 of VEGI-174, the results indicate that residues 23-174 contained
the biological equivalent of native VEGI-251. Taken together, these findings demonstrate that
secretion of VEGI-251 into the extracellular matrix is necessary for its anti-tumor activity. In
addition, similar to sVEGI, this anti-tumor activity of VEGI-251 is not due to a direct effect on
tumor cells, but rather to interference with the development of tumor-associated vasculature.
Example 24. Identification of potential isoforms of VEGI
It is observed that, when a Northern blot membrane of human tissues was analyzed with a
VEGI cDNA probe, a multiple number of mRNA bands appear in different tissues (Fig. 11).
Since the experimental conditions used in these experiments did not favor non-specific binding
of the probes, and judging from the approximate sizes of the mRNA molecules, there were at
least three isoforms corresponding to 7.5 kb, 2.0 kb, and 1.5 kb, respectively. The different
distribution of these isoforms in various tissues suggested that they play different physiological
roles.
Example 25. Confirmation of the novel VEGI isoforms
Using Rapid Amplification of cDNA End (RACE) (commercially available from
OriGene Technology, Rockville, MD), a panel of cDNA libraries representing various human
tissues was used to search for the VEGI isoforms. This panel contains cDNA samples prepared
from 24 individual human tissues, with an adapter ligated to the 5' end of each cDNA molecule.
A gene-specific oligonucleotide primer (GSP) corresponding to part of VEGI cDNA and an
adapter primer (ADP) were used to carry out polymerase chain reaction (PCR) (Fig 12). Two
rounds of nested PCR were performed using two pairs of oligonucleotide primers. After first
round PCR (94°C 3 min, 4 cycles of 94°C for 30sec, 65°C for 30 sec, 72°C for 2 min; 16 cycles
of 94°C for 30 sec, 60°C for 30 sec, 72°C for 2 min; then 72°C for 6 min) with an adapter primer
(ADP1, 5'-CGGAATTCGT CACTCAGCG-3') (SEQ ID NO:8) and a VEGI gene specific
primer (GSP1,5'-CCCGGATCCT ATAGTAAGAA GGCTCC-3') (SEQ ID NO:9), the
reaction products were diluted 1:10 with water. The diluted PCR samples were used in the
second round PCR (94°C for 3 min; 35 cycles of 94°C for 30 sec; 54°C for 30 sec, 72°C for 2
min; then 72°C for 6 min) with another adapter primer (ADP2, 5'-AGCGCGTGAA
TCAGATCG3') (SEQ ID NO:10) and a VEGI gene specific primer (GSP2, 5'-CGGTGGATCC
CGAGTTTGTC TCACAACTG 3') (SEQ ID NO:11). The PCR products were fractionated on
an agarose gel. Positive DNA fragments were excised from the gel, purified for sequencing
analysis. Four PCR products with different lengths were obtained from different tissues (Fig.
13). These PCR products were subjected to DNA sequencing, confirming that the nucleotide
sequences of these PCR products were different from each other. These isoforms are now named
as VEGI-174, VEGI-192a, VEGI-192b, and VEGI-251, according to the number of amino acid
residues in the proteins encoded by these cDNA molecules.
Example 26. Cloning of full-length cDNA of the isoforms
Gene specific primers designed according to sequencing results of the PCR products
obtained from the RACE experiments described above were used to repeat the second round
PCR to confirm the specificity of their sequences. The purified RACE products were then
cloned into plasmid pCR 3.1 of Invitrogene (San Diego, CA) to prepare high quality DNA
samples for sequencing. Based on the presence of an in-frame stop codon and an initiation codon
in the 5'-sequence of VEGI192a and VEGI192b, the full-length cDNA molecule of VEGI192a was
constructed with two pairs of nested PCR primers: Vg3A: 5 '-AATCTCACCT GTCTCTGCCT
G-3' (SEQ ID NO:43) and Vg-3'-1: 5'-CTAAACCGTT GTCCCTGTGG-3' (SEQ ID NO:44);
Vg3B: 5'-CCTGTAAAAA TGGTTATAGT AG-3' (SEQ ID NO:45) and Vg-3'-2: 5'-
GGTGGCAGAG GACTTTC-3' (SEQ ID NO:46). The full-length cDNA.molecule of VEGI192b
was constructed with primer vg4b 5'-CTCTACTTAC GCCAAGG-3' (SEQ ID NO:47) and
primer JY2 5'-CCCGGATCCT ATAGTAAGAA GGCTCC-3' (SEQ ID NO:48). The cDNA
libraries from which the isoforms were identified was used for the PCR. Both VEGI192a and
VEGI192b were cloned into pCR3.1 of Invitrogen (San Diego, CA). Since no in frame translation
initiation codon could be found in the 5' sequence of VEGI251, a pair of gene specific primers
vg5B: 5'-CACCACATAC CTGCTTG-3' (SEQ ID NO:49) and vgl61: 5'-GTGTAATCCA
CCAAAGAG-3' (SEQ ID NO: 12), were used to isolate a full-length VEGI251 cDNA clone from
Arrayed cDNA Library Panels of OriGene (Rockville, MD). The cDNA sequence of VEGI-192a
is shown in Table 13.
Table 13. cDNA sequence of VEGI-192, (SEQ ID NO:33)
ANCCAAAGGGAANTTTTAGGTTTTCTCAAGAANTAATAGACAAACAGAGGCCCNGAGAGGGAAAGGGATTCNCCCAA
AGTCATATAGCTAAAGANTAGTTCCCACCCACTCTTCATCCCATTTCTTNTGGCCATCTATTCAGTGAATATAGTTA
AAGGGCCCTTGGANGANGGCAAAAAGCCAATTCACTCCTGTGAAAGAATTTTGTGGGAAAGAGCAGTGAGTTGTGCT
TTATTGAGCATTGGCCATGTGCAAAATTCATGNTAAGCACCNCCATNTATACTGTGCCCATCTTAGATGAGATGAGA
AAACAGGGTCTCAGGCAGGNTAGATAAACTTGCCCAAAGCCATGGGGCCAAGATTCATTTGTGTTCAAGACTCTTTC
TTGTGAGTCACCCTGTCCTTGGTGGTGCTTGCTGCGGGTGCCACATTCCAATCCAAAATCCTGCAAGGAGTGGCACT
GGACCAAGCTGGAGGAGATCAAGGTTTCTCTCCTATCATAGGCGCCATGCAACTCACAAAGGGCCGTCTTCATTTCA
GTCACCCTTTGTCTCATACAAAGCACATTTCTCCTTTTGTTACAGATGCACATCTTAGGGCAGACGGAGATAAGCCA
AGGGCACACTTGACAGTTGTGAGACAAACTCCCACACAGCACTTTAAAAATCAGTTCCCAGTTCTGCACTGGGAACA
TGAACTAGGCCTGGCCTTCACCAAGAACCGAATGAACTATACCAACAAATTCCTGCTGATCCCAGAGTCGGGAGACT
ACTTCATTTACTCCCGGGTCACATTCCGTGGGATGACCTCTGAGTGCAGTGAAATCAGACAAGCAGGCCGACCAAAC
AAGCCAGACTCCATCACTGTGGTCATCACCAAGGTAACAGACAGCTACCCTGAGCCAACCCAGCTCCTCATGGGGAC
CAAGTCTGTGTGCGAAGTAGGTAGCAACTGGTTCCAGCCCATCTACCTCGGAGCCATGTTCTCCTTGCAAGAAGGGG
ACAAGCTAATGGTGAACGTCAGTGACATCTCTTTGGTGGATTACACAAAAGAAGATAAAACCTTCTTTGGAGCCTTC
TTACTATAGGAGGAGAGCAAATATCATTATATGAAAGTCCTCTGCCACCAGCC
Example 27. Anti-angiogenic and anticancer activity of VEGI251
A recombinant protein made of a truncated form of VEGI174, consisting of residues 29-
174, is a potent inhibitor of tumorigenesis (Zhai Y, ef al, FASEB J., 13: 181-189,1999; Zhai, Y,
et al., Int. J. Cancer, 82:131-136,1999). It is shown that VEGI has no direct effect on the
growth of the cancer cells, and that the mechanism of action of VEGI in the inhibition of tumor
growth is to inhibit the formation of blood vessels in the tumors. Therefore the full-length
cDNA of VEGI251 was transfected into a human breast cancer cell line MDA-MB-231, then
implanted in the mammary fat pads of female athymic nude mice to show that the gene product
was able to inhibit the growth of tumors by these cells. In order to inhibit the growth of the
endothelial cells in the immediate surroundings of the cancer cells, it is necessary for the VEGI
gene product to be released into the outside of the transfected cells. It was demonstrated that a)
that the gene product could be found in the conditioned media of the transfected cells in culture,
and b) the transfected cells could grow tumors in the nude mice.
The MDA-MB-231 breast cancer cells were transfected with either the empty vector, the
full-length VEGI-174 cDNA, the full-length VEGI-251 cDNA, or with a fusion gene in which the
VEGI protein was linked to a secretion signal peptide derived from interleukin-6 (IL6/VEGI).
When analyzed by Western blotting, using a monoclonal antibody (13-2D) to VEGI, the gene
product of VEGI-251 was found in the conditioned media of the transfected cells (Fig. 14). In
contrast, the gene product of the VEGI-174 was not detectable in the conditioned media.
The stably transfected MDA-MB-231 clones were injected into the mammary fat pads of
athymic female nude mice (1 x 106 cells per injection). The tumor sizes were determined as a
function of time. Microvessel density in the tumor was also analyzed. The overexpression of full
length VEGI-174 by the cancer cells had little effect on the growth of the xenograft tumors, and
over-expression of the secreted form of the putative VEGI extracellular domain and the full
length VEGI-251 markedly inhibited tumor growth (Fig. 15). Furthermore, it was demonstrated
that the VEGI protein was available in the tumors by carrying out immunohistochemical analysis
of the tumor sections using a monoclonal antibody to VEGI. Some of the tumors (G9-1R) had
cancer cells that produced a remarkable amount of VEGI-251, while others had cancer cells that
produced little VEGI-251 (G9-2R), as compared with tumors formed by vector-transfected cells
(G10-2R) (Fig. 16). The more VEGI-251 produced by the tumors, the slower was the growth rate
of the tumors (Fig. 17). These findings show that that VEGI-251 is secreted by the transfected
cancer cells, and that the secreted VEGI-251 is a potent inhibitor of tumor growth by inhibiting
the growth of the endothelial cells in the surroundings. In contrast, VEGI-174 is not secreted by
the cells, and consequently, cannot inhibit the growth of the endothelial cells.
Example 28. Tissue Distribution of VEGI expression
Unlike other members of the TNF family, VEGI-174 is specifically expressed in
endothelial cells. Northern blotting analysis of total RNA preparations from 23 cell lines and
primary cell cultures showed that VEGI was only detected in HUVE and human venous
endothelial cells (Fig. 18). VEGI-174 was also not seen in human artery endothelial cells. Using
multiple tissue Northern blots, the VEGI-174 transcript was found in many adult human tissues,
including placenta, lung, skeletal muscle, kidney, pancreas, spleen, prostate, small intestine, and
colon (Fig. 18), suggesting that the gene product may play a role in the function of a normal
vasculature.
Example 29. Specific inhibition of endothelial cell growth by VEGI
A truncated version of VEGI-174 was generated corresponding to the putative
extracellular domain consisting of residues 39-174. The protein was expressed in E. coli, purified
to apparent homogeneity as judged by SDS-polyacrylamide gel electrophoresis, and examined in
a variety of cellular assays. The truncated protein was able to specifically inhibit the
proliferation of adult bovine aortic endothelial (ABAE) cells (Fig. 19). Nearly complete
inhibition of the growth of the endothelial cells was achieved at 10 µg/ml, with a half-maximum
inhibitory concentration value (IC50) of about 1 µg/ml (about 70 nM). In contrast, the protein
had no effect on the growth of human breast cancer cells (MDA-MB-231 or MDA-MB-435)
under similar experimental conditions (Fig. 19). VEGI also did not inhibit the proliferation of
human T-cell leukemia cells (Jurkat), human Burkitts lymphoma cells (Raji), human monocytic
leukemia cells (THP-1), or human promyelocytic leukemia cells (HL60), cells that are often
responsive to the cytotoxic activity of the TNFs. The potency of VEGI appeared to be lower
than what might be expected from a cytokine; however, it is comparable to that of known protein
inhibitors of angiogenesis such as angiostatin and endostatin, as well as the CD40 ligand,
(another TNF-family member). The relatively low potency of the truncated VEGI observed may
also be partly due to an un-optimized truncation site, or the lack of post-translational
modification, such as glycosylation, since the recombinant protein was expressed in E. coli.
Example 30. Up-regulation of VEGI gene in confluent endothelial cells
The endothelial cell-specific inhibitory activity of VEGI indicates that the protein acts as
a negative regulator of angiogenesis. To show that the VEGI gene is down-regulated in
proliferating endothelial cells but up-regulated when the cells are quiescent, the expression of
VEGI in cultured HUVE cells was examined by Northern blotting (Fig. 20). Low levels of
VEGI mRNA were seen in newly seeded HUVE cells; however, as the cell number increases in
the cultures, the VEGI mRNA level increases accordingly, and reaches a plateau when the cell
cultures become confluent.
Example 31. Inhibition of capillary-like tube formation by endothelial cells cultured on
collagen gels
The anti-angiogenic activity of the truncated VEGI was examined with an in vitro
angiogenesis model (Montesano, R. & Oorci, L., Cell 42:469,1985)). Endothelial cells cultured
on the surface of a three-dimensional collagen gel form a quiescent monolayer when the culture
reached confluence. Upon stimulation of the monolayer cells with an angiogenic factor such as
FGF-2, however, the cells invaded into the gel and form capillary-like tubular structures in the
gel. The tube-formation can be inhibited by anti-angiogenic factors. The extent of the tube
formation can be quantitatively assessed by using computer-assisted image analysis (Li, L. Y.,
Biochemistry 33:10999,1994). The truncated VEGI-m was able to inhibit the formation of
capillary-like tubes by ABAE cells (Fig. 21). The IC50 value for the inhibition was
approximately 1 µg/ml, similar to that observed for the inhibition of endothelial cell growth.
Example 32. Inhibition of capillary growth in collagen gels placed on chick embryo
chorioallantoic membrane
The antiangiogenic activity of VEGI-174 was further demonstrated by using a modified
chick embryo chorioallantoic membrane (CAM) assay (Nguyen, M. et al, Microvasc. Res.
47:31,1994). The method is based on the growth of new capillary vessels into a collagen gel
pellet placed on the CAM. Blood vessels were stimulated to grow vertically into a polymerized
collagen gel in the presence of an angiogenic factor, such as FGF-2 or VEGF, embedded in the
gel. The inhibitor was incorporated into the gels in order to determine its effect on the capillary
growth. The extent of angiogenesis in the gel was assessed by the use of FITC-dextran injected
into the circulation of the CAM. The recombinant VEGI-174 (5.0 µg/ml) inhibited about 50% of
the new capillary growth into the collagen gels induced by FGF-2 (2.0 µg/ml) (Fig. 22).
Example 33. Inhibition of breast cancer xenograft tumor growth by co-injected CHO cells
overexpressing VEGI
The anticancer activity of VEGI is demonstrated with a xenograft tumor model, using
breast cancer cells that are highly tumorigenic when implanted into the mammary fat pads of
female athymic nude mice. A secreted form of VEGI-174 is constructed by replacing the
N-terminal and the putative transmembrane segments of VEGI-174 (residues 1-25) with the
secretion signal peptide derived from human interleukin-6. The secreted VEGI-174 construct was
cloned into an eucaryotic expression vector, which was then transfected into Chinese hamster
ovary (CHO) cells. Expression of the corresponding construct was confirmed by Northern blot
analysis. Secretion of the modified VEGI by the transfected cells was confirmed by the ability
of the conditioned medium to inhibit ABAE cell growth. The transfected CHO cells were then
mixed with human breast cancer cells (MDA-MB-231 or MDA-MB-435), and the cell mixtures
were injected into the mammary fat pads of nude mice. The growth of the xenograft tumors
were monitored following injection. Despite the high tumorigenicity of the breast cancer cell
lines used, a marked inhibition of the growth of the xenograft tumors formed by either the MDA-
MB-231 (Fig. 23A) or the MDA-MB-435 cells (Fig. 23B) was observed. In a repeat of the
experiment using the MDA-MB-435 cells, the co-injection also led to complete inhibition of
tumor formation. The vector-transfected CHO cells had no effect on tumor growth in either
case. Since VEGI did not inhibit the growth of these breast cancer cells in culture, the anticancer
activity of the protein arised from its antiangiogenic activity.
Example 34. Inhibition of ABAE cell proliferation by VEGI-ma
Full length VEGI-192a was expressed in E. coli and refolded and purified using method
described in U.S. Pat. Appl. 20010044521 and PCT WO 01/55174. Specifically, an expression
vector (PET11, Novagen) containing a polynucleotide insert which encodes full length VEGI-192a
polypeptide was constructed. The expression vector was transformed into E. coli and the
transformed E. coli were grown to express the VEGI-192a polypeptide. The cells were harvested
and inclusion bodies were purified from the disrupted cells. The OD280 of the solution
containing the inclusion bodies was adjusted to pH 5.0 with the 8 M urea solution. The final
solution contained the following reducing reagents: 10 mM beta-Mercaptoethanol, 10 mM DTT
(Dithiothreitol), 1 mM reduced glutathion (GSH), 0.1 mM oxidized glutathion (GSSG). The
final pH of the solution was 10.0. The above solution was rapidly diluted into 20 volumes of 20
mM TRIS™ base, the pH was adjusted to 9.0, and then slowly adjusted to 8.0 with 1 M HC1, by
adjusting pH to 8.8 for twenty four hours, then 8.6 for twenty four hours, etc., until the pH was
8.0. Alternatively, the proteins could be refolded using dialysis. The OD280 of the 8 M urea
solution was adjusted to 0.5, and dialyzed against 20 volumes of TRIS™ base. The pH of the
solution was again slowly adjusted to 8.0. The refolded material was then concentrated by
ultrafiltration, and separated by gel filtration, for example, on a SEPHACRYL™ S-300 column
equilibrated with 20 mM TRIS™, HC1,0.4 M urea, pH 8.0. The S-300 fractions could be
checked by running a non-reduced SDS-PAGE. The wrongly refolded protein ran at a very high
molecular weight, while properly refolded proteins ran at a normal molecular weight.
The VEGI-192a proteins from S-300 fractions were tested for its ability to inhibit
endothelia cell growth. Adult bovine aortic endothelial (ABAE) cells were seeded in triplicate at
8,000 cells/well in 24-well plates, in IMEM (GIBCO, Gaithersburg, MD), 10% fetal calf serum.
FGF-2 (1 ng/ml) was added to the media. The cultures were maintained at 37°C, 5%CO2, for 6
days. The cells were then trypsinized, and the number of cells determined by using a Coulter
(Hialeah, FL) counter.
As shown in Figure 24, properly folded VEGI-192a, but not misfolded VEGI-192a, from S-
300 fractions was able to inhibit the growth of ABAE cells. Nearly half-complete inhibition of
the growth of the endothelia cells was achieved at 1000 ng/ml, with a half-maximum inhibitory
concentration value (IC50) at about 10 ng/ml.
WE CLAIM:
1. A pharmaceutical composition for use in inhibiting angiogenesis comprising a
polypeptide comprising the amino acid sequence of SEQ ID NO: 4 and a pharmaceutically
acceptable excipient.
2. A pharmaceutical composition as claimed in claim 1, wherein the polypeptide
consists essentially of the sequence of SEQ ID NO: 4.
3. A pharmaceutical composition as claimed in claim 1, wherein the polypeptide
consists of the sequence of SEQ ID NO: 4.
4. A pharmaceutical composition as claimed in claim 1, wherein the polypeptide
is produced from a bacterial cell.
5. A pharmaceutical composition as claimed in claim 4, wherein the bacterial
cell is E. coli.
6. A pharmaceutical composition as claimed in claim 1, wherein the amino acid
sequence of SEQ ID NO:4 is fused with a heterologous amino acid sequence.
7. A pharmaceutical composition as claimed in claim 1, wherein the
heterologous amino acid sequence is a tag selected from the group consisting of Myc, HA
derived from influenza virus hemagglutinin, His-6, and FLAG.
8. An antibody that selectively binds to the polypeptide of SEQ ID NO: 4 but
does not bind to VEGI-174, VEGI-192b, or VEGI-251.
9. A method of detecting VEGI-192a comprising contacting a sample from an
individual with an antibody as claimed in claim 8, and detecting the presence or absence of a
complex formed between a polypeptide in the sample and the antibody.
This invention discloses two new VEGI isoforms named VEGI-¿192a? and VEGI-192b consisting of 192 amino acid
residues. These isoforms show endothelial cell-specific expression and share a C-terminal 151-residues segment with the previously
described VEGI-174 and VEGI-751. Methods of using these isoforms of VEGI in diagnosing, screening agonist and antagonist of the
isoforms, and treating various angiogenesis-related diseases are also disclosed.

Documents:

704-KOLNP-2004-CORRESPONDENCE.pdf

704-KOLNP-2004-FORM 27.pdf

704-KOLNP-2004-FORM-27.pdf

704-kolnp-2004-granted-abstract.pdf

704-kolnp-2004-granted-assignment.pdf

704-kolnp-2004-granted-claims.pdf

704-kolnp-2004-granted-correspondence.pdf

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

704-kolnp-2004-granted-drawings.pdf

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

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

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

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

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

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

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

704-kolnp-2004-granted-gpa.pdf

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

704-kolnp-2004-granted-specification.pdf


Patent Number 222926
Indian Patent Application Number 704/KOLNP/2004
PG Journal Number 35/2008
Publication Date 29-Aug-2008
Grant Date 27-Aug-2008
Date of Filing 26-May-2004
Name of Patentee GEORGETOWN UNIVERSITY
Applicant Address 37TH & O STREETS, N.W. WASHINGTON, DC
Inventors:
# Inventor's Name Inventor's Address
1 LI LUYUAN 16453 TOMAHAWK DR., GAITHERSBURG, MD 20878
2 PAN HONGGUANG 4554 MACARTHUR BLVD., N.W. WASHINGTON, DC 20007
PCT International Classification Number A61K
PCT International Application Number PCT/US02/37426
PCT International Filing date 2002-11-12
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/331,190 2001-11-09 U.S.A.