CA2518912A1 - Polypeptide compounds for inhibiting angiogenesis and tumor growth - Google Patents

Abstract

In certain embodiments, this present invention provides polypeptide compositions, and methods for inhibiting Ephrin B2 or EphB4 activity. In other embodiments, the present invention provides methods and compositions for treating cancer or for treating angiogenesis-associated diseases.

Description

POLYPEPTIDE COMPOUNDS FOR INHIBITING tllV GIOGENESIS AND TUMOR GROWTH
RELATED APPLICATIONS
This application claims the benefit of priority of U.S. Provisional Application number 60/454,300 filed March 12, 2003 and U.S. Provisional Application number 601454,432 filed March 12, 2003. The entire teachings of the referenced Provisional Applications are incorporated herein by reference in their entirety.
BACKGROUND OF THE INVENTION
Angiogenesis, the development of new blood vessels from the endothelimn of a preexisting vasculature, is a critical process in the growth, progression, and metastasis of solid tumors within the host. During physiologically normal angiogenesis, the autocrine, paracrine, and amphicrine interactions of the vascular endothelium with its surrounding stromal components are tightly regulated both spatially and temporally.
Additionally, the levels and activities of proangiogenic and angiostatic cytol~ines and growth factors are maintained in balance. In contrast, the pathological angi~genesis necessary for active tumor growth is sustained and persistent, representing a dysregulation of the normal angiogenic system. Solid and hematopoietic tumor types are particularly associated with a high level of abnormal angiogenesis.
It is generally thought that the development of tumor consists ~f sequential, and interrelated steps that lead to the generation of an autonomous clone with aggressive growth potential. These steps include sustained gr~wth and unlimited self renewal.
Cell populations in a tumor are generally characterized by growth signal self sufficiency, decreased sensitivity to growth suppressive signals, and resistance to apoptosis. Genetic or cytogenetic events that initiate aberrant growth sustain cells in a prolonged "ready" state by preventing apoptosis.
It is a goal of the present disclosure to provide agents and therapeutic treatments for inhibiting angiogenesis and tumor growth.
SUMMARY OF THE INVENTION

hl certain aspects, the disclosure provides polypeptide agents that inhibit EphB4 or EphrinB2 mediated functions, including monomeric ligand binding portions of the EphB4 and EphrinB2 proteins and antibodies that bind to and affect EphB4 or EphrinB2 in particular ways. As demonstrated herein, EphB4 and EphrinB2 participate in various disease states, including cancers and diseases related to unwanted or excessive angiogenesis.
Accordingly, certain polypeptide agents disclosed herein may be used to treat such diseases. In further aspects, the disclosure relates to the discovery that EphB4 and/or EphrinB2 are expressed, often at high levels, in a variety of tumors. Therefore, polypeptide agents that downregulate EphB4 or EphrinB2 function may affect tumors by a direct effect on the tumor cells as well as an indirect effect on the angiogenic processes recruited by the tumor. h1 certain embodiments, the disclosure provides the identity of tumor types particularly suited to treatment with an agent that downregulates EphB4 or EphrinB2 function.
In certain aspects, the disclosure provides soluble EphB4 polypeptides comprising an amino acid sequence of an extracellular domain of an EphB4 protein. The soluble EphB4 polypeptides bind specifically to an EphrinB2 polypeptide. The term "soluble"
is used merely to indicate that these polypeptides do not contain a transmembraaze domain or a portion of a transmembrane domain sufficient to compromise the solubility of the polypeptide in a physiological salt solution. Soluble polypeptides are preferably prepared as monomers that compete with EphB4 for binding to ligand such as EphrinB2 and inhibit the signaling that results from EphB4. activation. ~ptionally, a soluble polypeptide may be prepared in a multimeric form, by, for example, expressing as an Fc fusion protein or fusion with another multimeri~ation domain. Such multimeric forms may have complex activities, having agonistic or antagonistic effects depending on the context. In certain embodiments the soluble EphB4 polypeptide comprises a globular domain of an EphB4 protein. A
soluble EphB4 polypeptide may comprise a sequence at least 90% identical to residues 1-522 of the amino acid sequence defined by Figure 65. A soluble EphB4 polypeptide may comprise a sequence at least 90% identical to residues 1-412 of the amino acid sequence defined by Figure 65. A soluble EphB4 polypeptide may comprise a sequence at least 90%
identical to residues 1-312 of the amino acid sequence defined by Figure 65. A soluble EphB4 polypeptide may comprise a sequence as set forth in Figure 1 or 2. In certain embodiments, the soluble EphB4 polypeptide may inhibit the interaction between Ephrin B2 and EphB4.
The soluble EphB4 polypeptide may inhibit clustering of or phosphorylation of Ephrin B2 or EphB4. Phosphorylation of EphrinB2 or EphB4 is generally considered to be one of the initial events in triggering intracellular signaling pathways regulated by these proteins. As noted above, the soluble EphB4 polypeptide may be prepared as a monomeric or multimeric fusion protein. The soluble polypeptide may include one or more modified amino acids.
Such amino acids may contribute to desirable properties, such as increased resistance to protease digestion.
In certain aspects, the disclosure provides soluble EphrinB2 polypeptides comprising an amino acid sequence of an extracellular domain of an EphrinB2 protein. The soluble EphrinB2 polypeptides bind specifically to an EphB4 polypeptide. The term "soluble" is used merely to indicate that these polypeptides do not contain a transmembrane domain or a portion of a transmembrane domain sufficient to compromise the solubility of the polypeptide in a physiological salt solution. Soluble polypeptides are preferably prepared as monomers that compete with EphrinB2 for binding to ligand such as Ep11B4 and inhibit the signaling that results from EphrinB2 activation. Optionally, a soluble polypeptide may be prepared in a multimeric form, by, for example, expressing as an Fc fusion protein or fusion with another multimerization domain. Such multimeric forms may have complex activities, having agonistic or antagonistic effects depending on the context. A soluble EphrinB2 polypeptide rnay comprise residues 1-225 of the amino acid sequence defined by Figure 66.
A soluble EphrinB2 polypeptide may comprise a sequence defined by Figure 3. In certain embodiments, the soluble EphrinB2 polypeptide may inhibit the interaction between Ephrin B2 and EphB4. The soluble EphrinB2 polypeptide may inhibit clustering of or phosphorylation of EphrinB2 or EphB~. As noted above, the soluble EphrinB2 polypeptide may be prepared as a monomeric or multimeric fusion protein. The soluble polypeptide may include one or more modified amino acids. Such amino acids may contribute to desirable properties, such as increased resistance to protease digestion.
In certain aspects, the disclosure provides antagonist antibodies for EphB4 and EphrinB2. An antibody may be designed to bind to an extracellular domain of an EphB4 protein and inhibit an activity of the EphB4. An antibody may be designed to bind to an extracellular domain of an Ephrin B2 protein and inhibit an activity of the Ephrin B2. An antibody may be designed to inhibit the interaction between Ephrin B2 and EphB4. An antagonist antibody will generally affect Eph and/or Ephrin signaling. For example, an antibody may inhibit clustering or phosphorylation of Ephrin B2 or EphB4. An antagonist antibody may be essentially any polypeptide comprising a variable portion of an antibody, including, for example, monoclonal and polyclonal antibodies, single chain antibodies, diabodies, minibodies, etc.
In certain aspects, the disclosure provides pharmaceutical formulations comprising a polypeptide reagent and a pharmaceutically acceptable carrier. The polypeptide reagent may be any disclosed herein, including, for example, soluble EphB4 or EphrinB2 polypeptides and antagonist antibodies. Additional formulations include cosmetic compositions and diagnostic kits.
In certain aspects the disclosure provides methods of inhibiting signaling through Ephrin B2/EphB4 pathway in a cell. A method may comprise contacting the cell with an effective amount of a polypeptide agent, such as (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4. protein and inhibits an activity of the EphB4.; or (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.
In certain aspects the disclosure provides methods for reducing the growth rate of a tumor, comprising administering an amount of a polypeptide agent sufficient to reduce the growth rate of the tumor9 v~herein the polypeptide agent is selected from the group consisting o~ (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide; (b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2. Optionally, the tumor comprises cells expressing a higher level of EphB4 and/or EphrinB2 than noncancerous cells of a comparable tissue.
In certain aspects, the disclosure provides methods for treating a patient suffering from a cancer. A method may comprise administering to the patient a polypeptide agent selected from the group consisting of (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide; (b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.
Optionally, the cancer comprises cancer cells expressing EphrinB2 and/or EphB4 at a higher level than noncancerous cells of a comparable tissue. The cancer may be a metastatic cancer.
The cancer may be selected from the group consisting of colon carcinoma, breast honor, mesothelioma, prostate tumor, squamous cell carcinoma, Kaposi sarcoma, and leul~emia.
Optionally, the cancer is an angiogenesis-dependent cancer or an angiogenesis independent cancer. The polypeptide agent employed may inhibit clustering or phosphorylation of Ephrin B2 or EphB4. A polypeptide agent may be co-administered with one or more additional anti-cancer chemotherapeutic agents that inhibit cancer cells in an additive or synergistic mamler with the polypeptide agent.
hl certain aspects, the disclosure provides methods of inhibiting angiogenesis. A
method may comprise contacting a cell with an amount of a polypeptide agent sufficient to inhibit angiogenesis, wherein the polypeptide agent is selected from the group consisting of:
(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4~ protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide; (b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B~ protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.
In certain aspects, the disclosure provides methods for treating a patient suffering from an angiogenesis-associated disease, comprising administering to the patient a polypeptide agent selected from the group consisting of (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2. The soluble polypeptide may be formulated with a pharmaceutically acceptable carrier. An angiogenesis related disease or unwanted angiogenesis related process may be selected from the group consisting of angiogenesis-dependent cancer, benign tumors, inflammatory disorders, chronic articular rheumatism and psoriasis, ocular a~igiogenic diseases, Osler-Webber Syndrome, myocardial angiogenesis, plaque neovascularization, telangiectasia, hemophiliac joints, angiofibroma, wound granulation, wound healing, telangiectasia psoriasis scleroderma, pyogenic granuloma, cororany collaterals, ischemic limb angiogenesis, rubeosis, arthritis, diabetic neovascularization, fractures, vasculogenesis, and hematopoiesis.
An polypeptide agent may be co-administered with at least one additional anti-angiogenesis agent that inhibits angiogenesis in an additive or synergistic manner with the soluble polypeptide.
In ceutain aspects, the disclosure provides for the use of a polypeptide agent in the manufacture of medicament for the treatment of cancer or an angiogenesis related disorder, wherein the polypeptide agent is selected from the group consisting of (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B~
polypeptide; (b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) a~.z antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.
In certain aspects, the disclosure provides methods for for treating a patient suffering from a cancer, comprising: (a) identifying in the patient a tumor having a plurality of cancer cells that express EphB4 and/or EphrinB2; and (b) administering to the patient a polypeptide agent selected from the group consisting of (i) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide; (ii) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide; (iii) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (iv) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.
Optionally, a method may comprise identifying in the patient a tumor having a plurality of cancer cells having a gene amplification of the EphB4 and/or EphrinB2 gene.
In certain aspects, the disclosure provides methods for identifying a tumor that is suitable for treatment with an EphrinB2 or EphB4 antagonist. A method may comprise detecting in the tumor cell one or more of the following characteristics: (a) expression of EphB4 protein and/or mRNA; (b) expression of EphrinB2 protein andlor mRNA; (c) gene amplification of the EphB4 gene; or (d) gene amplification of the EphrinB2 gene. A tumor cell having one or more of characteristics (a)-(d) may be suitable for treatment with an EphrinB2 or EphB4 antagonist, such as a polypeptide agent described herein.
BRIEF DESCRIPTION OF THE I~IZAW1NC1S
Figure 1 shows amino acid sequence of the B4.ECv3 protein (predicted sequence of the precursor including uncleaved Eph B4 leader peptide is shown).
Figure 2 shows amino acid sequence of the B4ECv3NT protein (predicted sequence of the precursor including uncleaved Eph B4. leader peptide is shown).
Figure 3 shows amino acid sequence of the B2EC protein (predicted sequence of the precursor including uncleaved Ephrin B2 leader peptide is shown).
Figure 4 shows amino acid sequence of the B4ECv3-FC protein (predicted sequence of the precursor including uncleaved Eph B4 leader peptide is shown).
Figure 5 shows amino acid sequence of the B2EC-FC protein (predicted sequence of the precursor including uncleaved Ephrin B2 leader peptide is shown).
Figure 6 shows B4EC-FC binding assay (Protein A-agarose based).
Figure 7 shows B4EC-FC inhibition assay (Inhibition in solution).
Figure 8 shows B2EC-FC binding assay (Protein-A-agarose based assay).
Figure 9 shows chemotaxis of HUAEC in response to B4Ecv3.
Figure 10 shows chemotaxis of HHEC in response to B2EC-FC.
_7_ Figure 11 shows chemotaxis of HHAEC in response to B2EC.
Figure 12 shows effect of B4Ecv3 on HUAEC tubule formation.
Figure 13 shows effect of B2EC-FC on HUAEC tubule formation.
Figure 14 is a schematic representation of human Ephrin B2 constructs.
Figure 15 is a schematic representation of human EphB4 constructs.
Figure 16 shows the domain structure of the recombinant soluble EphB4EC
proteins.
Designation of the domains are as follows: L - leader peptide, G - globular (ligand-binding domain), C - Cys-rich domain, F1, F2 - fibronectin type III repeats, H - 6 x His-tag.
Figure 17 shows purification and ligand binding properties of the EphB4EC
proteins.
A. SDS-PAAG gel electrophoresis of purified EphB4-derived recombinant soluble proteins (Coomassie-stained). B. Binding of Ephrin B2-AP fusion to EphB4-derived recombinant proteins immobilized on Ni-NTA-agarose beads. Results of three independent experiments are shown for each protein. Vertical axis - optical density at 420 nm.
Figure 18 shows that EphB4v3 inhibits chemotaxis.
Figure 19 shows that EphB4v3 inhibits tubule formation on Matrigel. A displays the strong inhibition of tubule formation by B4.v3 in a representative experiment.
B shows a quantitation of the reduction of tube-length obtained with B4v3 at increasing concentrations as well as a reduction in the number of junctions, in comparison to cells with no protein.
Results are displayed as mean values - S.D. obtained from three independent experiments performed with duplicate wells.
Figure 20 shows that soluble EphB4 has no detectable cytotoxic effect as assessed by MTS assay.
Fig~.me 21 shows that B4v3 inhibits invasion and tubule formation by endothelial cells in the Matrigel assay. (A) to detect total invading cells, photographed at 20X
magnification or with Masson's Trichrome Top left of A B displays section of a Matrigel plug with no GF , top right of A displays section with B4IgG containing GF and lowef°
left section contains GF, and lower right shows GF in the presence of B4v3. Significant invasion of endothelial cells is only seenin GF containing Matrigel. Top right displays an area with a high number of invaded cells induced by B4IgG, which signifies the dimeric form of B4v3. The left upper pats of the pictures correspond to the cell layers formed around the Matrigel plug from which cells invade toward the center of the plug located in the direction of the right lower _g_ co~rzef°. Total cells in sections of the Matrigel plugs were quantitated with Scion Image software. Results obtained from two experiments with duplicate plugs are displayed as mean values S.D.
Figure 22 shows tyrosine phosphorylation of EphB4 receptor in PC3 cells in response to stimulation with EphrinB2-Fc fusion in presence or absence of EphB4-derived recombinant soluble proteins.
Figure 23 shows effects of soluble EphB4ECD on viability and cell cycle. A) 3-day cell viability assay of two HNSCC cell lines. B) FAGS analysis of cell cycle in HNSCC-15 cells treated as in A. Treatment of these cells resulted in accumulation in subGO/G1 and S/G2 phases as indicated by the arrows.
Figure 24 shows that B4v3 inhibitis neovascular response in a marine corneal hydron micropocket assay.
Figure 25 shows that that SCC15, B16, and MCF-7 co-injected with sB4v3 in the presence of matrigel and growth factors, inhibits the in vivo tumor growth of these cells.
Figure 26 shows that soluble EphB4 causes apoptosis, necrosis and decreased angiogenesis in threes tumor types, B16 melanoma, SCC15, head and neck carcinoma, and MCF-7 Breast carcinoma. Tumors were injected premixed with Matrigel plus growth factors and soluble EphB4 subcutaneously. After 10 to 14 days, the mice were inj ected intravenously with fits-lectin (green) to assess blood vessel perfusion.
Tumors treated with control PBS displayed abundant tumor density and a robust angiogenic response Tumors treated with sEphB4. displayed a decrease in tumor cell density and a marked inhibition of tumor angiogenesis in regions with viable tumor cells, as well as tumor necrosis and apoptosis.
Figure 27 shows expression of EphB4 in prostate cell lines. A) Western blot of total cell lysates of various prostate cancer cell lines, normal prostate gland derived cell line (MLC) and acute myeloblastic lymphoma cells (AML) probed with EphB4 monoclonal antibody. B) Phosphorylation of EphB4 in PC-3 cells determined by Western blot.
Figure 28 shows expression of EphB4 in prostate cancer tissue. Representative prostate cancer frozen section stained with EphB4 monoclonal antibody (top left) or isotype specific control (bottom left). Adjacent BPH tissue stained with EphB4 monoclonal antibody (top right). Positive signal is brown color in the tumor cells. Stroma and the normal epithelia are negative. Note membrane localization of stain in the tumor tissue, consistent with trans-membrane localization of EphB4. Representative QRT-PCR of RNA extracted from cancer specimens and adj acent BPH tissues (lower right).
Figure 29 shows downregulation of EphB4 in prostate cancer cells by tmnor suppressors and RXR expression. A) PC3 cells were co-transfected with truncated CD4 and p53 or PTEN or vector only. 24 h later CD4-sorted cells were collected, lysed and analyzed sequentially by Western blot for the expression of EphB4 and (3-actin, as a normalizer protein. B) Western blot as in (A) of various stable cell lines. LNCaP-FGF is a stable transfection clone of FGF-8, while CWR22R-RXR stably expresses the RXR
receptor. BPH-1 was established from benign hypertrophic prostatic epithelium.
Figure 30 shows downregulation of EphB4 in prostate cancer cells by EGFR and IGFR-1. A) Western blot of PC3 cells treated with or without EGFR specific inhibitor AG1478 (1 nM) for 36 hours. Decreased EphB4 signal is observed after AG 1478 treatment.
The membrane was stripped and reprobed with (3-actin, which was unaffected. B) Western Blot of triplicate samples of PC3 cells treated with or without IGFR-1 specific neutralizing antibody MAB391 (2 ~,g/ml; overnight). The membrane was sequentially probed with EphB4, IGFR-1 and ~i-actin antibodies. IGFR-1 signal shows the expected repression of signal with MAB391 treatment.
Figure 31 shows effect of specific EphB4 AS-ODNs and siRNA on expression and prostate cell functions. A) 293 cells stably expressing full-length construct of EphB4 was used to evaluate the abilit~~ of siRNA 4.72 to inhibit EphB4. expression.
Cells were tra~isfected with 50 nM RNAi using Lipofectamine 2000. Western blot of cell lysates 40 h post transfection with control siRNA (green fluorescence protein; GFP siRNA) or EphB4 siRNA
472, probed with EphB4 monoclonal antibody, stripped and reprobed with [3-actin monoclonal antibody. B) Effect of EphB4 AS-10 on expression in 293 transiently expressing full-length EphB4. Cells were exposed to AS-10 or sense ODN for 6 hours and analyzed by Western blot as in (A). C) 48 h viability assay of PC3 cells treated with siRNA as described in the Methods section. Shown is mean + s.e.m. of triplicate samples. D) 5-day viability assay of PC3 cells treated with ODNs as described in the Methods. Shown is mean +
s.e.m. of triplicate samples. E) Scrape assay of migration of PC3 cells in the presence of 50 nM
siRNAs transfected as in (A). Shown are photomicrographs of representative 20x fields taken immediately after the scrape was made in the monolayer (0 h) and after 20h continued culture. A large number of cells have filled in the scrape after 20 h with control siRNA, but not with EphB4 siRNA 472. F) Shown is a similar assay for cells treated with AS-10 or sense - to -ODN (both 10 ~,M). G) Matrigel invasion assay of PC3 cells transfected with siRNA or control siRNA as described in the methods. Cells migrating to the underside of the Matrigel coated insert in response to 5 mg/ml fibronectin in the lower chamber were fixed and stained with Giemsa. Shown are representative photomicrographs of control siRNA and siRNA 472 treated cells. Cell numbers were counted in 5 individual high-powered fields and the average ~ s.e.m. is shown in the graph (bottom right).
Figure 32 shows effect of EphB4 siRNA 472 on cell cycle and apoptosis. A) PC3 cells transfected with siRNAs as indicated were analyzed 24 h post transfection for cell cycle status by flow cytometry as described in the Methods. Shown are the plots of cell number vs.
propidium iodide fluorescence intensity. 7.9% of the cell population is apoptotic (in the Sub GO peak) when treated with siRNA 472 compared to 1 % with control siRNA. B) Apoptosis of PC3 cells detected by Cell Death Detection ELISApI°S kit as described in the Methods.
Absorbance at 405 nm increases in proportion to the amount of histone and DNA-POD in the nuclei-free cell fraction. Shown is the mean + s.e.m. of triplicate samples at the indicated concentrations of siI~NA 472 and GFP siI2NA (control).
Figure 33 shows that EphB4 and EphrinB2 are expressed in mesothelioma cell lines as shown by RT-PCR (A) and Western Blot (B).
Figure 34 shows expression of ephrin B2 and EphB4 by in situ hybridization in mesothelioma cells. NCI H28 mesothelioma cell lines cultured in chamber slides hybridized ~Tith sntisense probe to ephrin B2 or EphB4. (top row). Control for each hybridization was sense (bottom row). Positive reaction is dark blue cytoplasmic stain.
Figure 35 shows cellular expression of EphB4 and ephrin B2 in mesothelioma cultures. Immunofluorescence staining of primary cell isolate derived from pleural effusion of a patient with malignant mesothelioma and cell lines NCI H28, NCI H2373, and NCI
H2052 for ephrin B2 and EphB4. Green color is positive signal for FITC labeled secondary antibody. Specificity of immunofluorescence staining was demonstrated by laclc of signal with no primary antibody (first row). Cell nuclei were counterstained with DAPI (blue color) to reveal location of all cells. Shown are merged images of DAPI and FITC
fluorescence.
Original magnification 200X.
Figure 36 shows expression of ephrin B2 and EphB4 in mesothelioma tumor.
Immunohistochemistry of malignant mesothelioma biopsy. H&E stained section to reveals tumor architecture; bottom left panel is background control with no primary antibody. EphB4 and ephrin B2 specific staining is brown color. Original magnification 200X.
Figure 37 shows effects of EPHB4 antisense probes (A) and EPHB4 siRNAs (B) on the growth of H28 cells.
Figure 38 shows effects of EPHB4 antisense probes (A) and EPHB4 siRNAs (B) on cell migration.
Figure 39 shows that EphB4 is expressed in HNSCC primary tissues and metastases.
A) Top: hnmunohistochemistry of a representative archival section stained with EplzB4 monoclonal antibody as described in the methods and visualized with DAB (brown color) localized to tumor cells. Bottom: Hematoxylin and Eosin (H&E) stain of an adjacent section.
Dense purple staining indicates the presence of tumor cells. The right hand column are frozen sections of lymph node metastasis stained with EphB4 polyclonal antibody (top right) and visualized with DAB. Control (middle) was incubation with goat serum and H&E
(bottom) reveals the location of the metastatic foci surrounded by stroma which does not stain. B) In situ hybridization of serial frozen sections of a HNSCC case probed with EphB4 (left colurm) and ephrin B2 (right column) DIG labeled antisense or sense probes generated by run-off transcription. Hybridization signal (dark blue) was detected using alkaline-phosphatase-conjugated anti-DIG antibodies and sections were counterstained with Nuclear Fast Red. A serial section stained with H&E is shown (bottom left) to illustrate tumor architecture. C) W astern blot of protein extract of patient samples consisting of tumor (T), uninvolved normal tissue (N) and lymph node biopsies (LN). Samples were fractionated by polyacrylamide gel electrophoresis in 4-20°J° Tris-glycine gels and subsequently electroblotted onto nylon membranes. Membranes were sequentially probed with EphB4 monoclonal antibody and (3-actin lVIoAb. Chemiluminescent signal was detected on autoradiography film. Shown is the EphB4 specific band which migrated at 120 l~ and (3-actin which migrated at 40 kD. The (3-actin signal was used to control for loading and transfer of each sample.
Figure 40 shows that EphB4 is expressed in HNSCC cell lines and is regulated by EGF: A) Survey of EphB4 expression in SCC cell lines. Western blot of total cell lysates sequentially probed with EphB4 monoclonal antibody, stripped and reprobed with [3-actin monoclonal antibody as described for Fig. 39C. B) Effect of the specific EGFR
inhibitor AG1478 on EphB4 expression: Western blot of crude cell lysates of SCC15 treated with 0-1000 nM AG 1478 for 24 h in media supplemented with 10% FCS (left) or with 1 mM AG
1478 for 4, 8, 12 or 24 h (right). Shown are membranes sequentially probed for EphB4 and (3-actin. C) Effect of inhibition of EGFR signaling on EphB4 expression in SCC
cell lines: Cells maintained in growth media containng 10% FCS were treated for 24 hr with 1 ~,M
AG 1478, after which crude cell lysates were analyzed by Western blots of cell lysates sequentially probed with for EGFR, EphB4, ephrin B2 and [3-actin antibodies. Specific signal for EGFR
was detected at 170 l~D and ephrin B2 at 37 kD in addition to EphB4 and (3-actin as described in Fig. 1 C. (3-actin serves as loading and transfer control.
Figure 41 shows mechanism of regulation of EphB4 by EGF: A) Schematic of the EGFR signaling pathways, showing in red the sites of action and names of specific lcinase inhibitors used. B) SCC15 cells were serum-starved for 24 h prior to an additional 24 incubation as indicated with or without EGF (10 ng/ml), 3 p,M U73122, or 5 ~.M
SH-5, 5 ~,M
SP600125, 25 nM LY294002, -- ~M PD098095 or 5 ~,M SB203.580. N/A indicates cultures that received equal volume of diluent (DMSO) only. Cell lysates were subjected to Western Blot with EphB4~ monoclonal antibody. (3-actin signal serves as control of protein loading and transfer.
Figure 4.2 shows that specific EphB4 siRNAs inhibit EphB4 expression, cell viability and cause cell cycle arrest. A) 293 cells stably expressing full length EphB4 were transfected with 50 nM RNAi using LipofectamineTM2000. 40 h post-transfection cells were harvested, lysed and processed for Western blot. I~sTembranes vrere probed v~ith EphB4 monoclonal antibody, stripped and reprobed with (3-actin monoclonal antibody as control for protein loading and transfer. Negative reagent control was RNAi to scrambled green fluorescence protein (GFP) sequence and control is transfection with LipofectamineTM2000 alone. B) MTT cell viability assays of SCC cell lines treated with siRNAs for 4.8 h as described in the Methods section. Shown is mean + s.e.m. of triplicate samples. C) SCC15 cells transfected with siRNAs as indicated were analyzed 24 h post transfection for cell cycle status by flow cytometry as described in the Methods. Shown are the plots of cell number vs.
propidium iodide fluorescence intensity. Top and middle row show plots for cells 16 h after siRNA
transfection, bottom row shows plots for cells 36 h post transfection.
Specific siRNA and concentration are indicated for each plot. Lipo = LipofectamineTM200 mock transfection.
Figure 43 shows in vitro effects of specific EphB4 AS-ODNs on SCC cells. A) cells transiently transfected with EphB4 full-length expression plasmid were treated 6 h post transfection with antisense ODNs as indicated. Cell lysates were collected 24 h after AS-ODN treatment and subjected to Western Blot. B) SCC25 cells were seeded on 48 well plates at equal densities and treated with EphB4 AS-ODNs at 1, 5, and 10 ~,M on days 2 and 4. Cell viability was measured by MTT assay on day 5. Shown is the mean + s.e.m. of triplicate samples. Note that AS-ODNs that were active in inhibiting EphB4 protein levels were also effective inhibitors of SCC15 cell viability. C) Cell cycle analysis of SCC15 cells treated for 36 h with AS-10 (bottom) compared to cells that were not treated (top). D) Confluent cultures of SCC15 cells scraped with a plastic Pasteur pipette to produce 3 mm wide breaks in the monolayer. The ability of the cells to migrate and close the wound in the presence of inhibiting EphB4 AS-ODN (AS-10) and non-inhibiting AS-ODN (AS-1) was assessed after 48 h. Scrambled ODN is included as a negative control ODN. Culture labeled no treatment was not exposed to ODN. At initiation of the experiment, all cultures showed scrapes of equal width and similar to that seen in 1 ~.M EphB4 AS-10 after 48 h. The red brackets indicate the width of the original scrape. E) Migration of SCC15 cells in response to 20 mg/ml EGF in two-chamber assay as described in the Methods. Shown are representative photomicrographs of non-treated (NT), AS-6 and AS-10 treated cells and 10 nghnl Taxol as positive control of migration inhibition. F) Cell numbers were counted in 5 individual high-powered fields and the average + s.e.m. is shown in the graph.
Figure 44. shows that EphB4 AS-ODN inhibits tLllTlor growth in vivo. Growth curves for SCC15 subcutaneous tumor xenografts in Balb/C nude mice treated with EphB4 AS-10 or scrambled ODN at 20 mg/kg/day starting the day following implantation of 5 x 106 cells.
Control mice received and equal volume of diluent (PBS). Shown are the mean +
s.e.m. of 6 mice/group. ~° P = 0.0001 by Student's t-test compared to scraanbled ODN treated group.
Figure 45 shows that Ephrin B2, but not EphB4 is expressed in KS biopsy tissue. (A) In situ hybridization with antisense probes for ephrin B2 and EphB4 with corresponding HB~E stained section to show tumor architecture. Dark blue color in the ISH
indicates positive reaction for ephrin B2. No signal for EphB4 was detected in the Kaposi's sarcoma biopsy. For contrast, ISH signal for EphB4 is strong in squamous cell carcinoma tumor cells.
Ephrin B2 was also detected in KS using EphB4-AP fusion protein (bottom left).
(B) Detection of ephrin B2 with EphB4lFc fusion protein. Adjacent sections were stained with H&E (left) to show tumor architecture, black rectangle indicates the area shown in the EphB4/Fc treated section (middle) detected with FITC-labeled anti-human Fc antibody as described in the methods section. As a control an adjacent section was treated with human Fc fragment (right). Specific signal arising from EphB4/Fc binding to the section is seen only in areas of tumor cells. (C) Co-expression of ephrin B2 and the HHV8 latency protein LANA1.
Double-label confocal immunofluorescence microscopy with antibodies to ephrin B2 (red) LANAI (green), or EphB4 (red) of frozen KS biopsy material directly demonstrates co-expression of LANA1 and ephrin B2 in KS biopsy. Coexpression is seen as yellow color.
Double label confocal image of biopsy with antibodies to PECAM-1 (green) in cells with nuclear propidium iodide stain (red), demonstrating the vascular nature of the tumor.
Figure 46 shows that HHV-8 induces arterial marker expression in venous endothelial cells. (A) Immunofluorescence of cultures of HUVEC and HWEC/BC-1 for artery/vein markers and viral proteins. Cultures were grown on chamber slides and processed for immunofluorescence detection of ephrin B2 (a, e, i), EphB4 (m, q, u), CD148 (j, v), and the HHV-8 proteins LANA1 (b, f, m) or ORF59 (r) as described in the Materials and Methods. Yellow color in the merged images of the same field demonstrate co-expression of ephrin B2 and LANA or ephrin B2 and CD148. The positions of viable cells were revealed by nuclear staining with DAPI (blue) in the third column (c, g, k, o, s, w).
Photomicrographs are of representative fields. (B) RT-PCR of HUVEC and two HHV-8 infected cultures (HIJVEC/BC-1 and HUVEC/BC-3) for ephrin B2 and EphB4. Ephrin B2 product (200 bp) is seen in HLTVEC/BC-l, HUVEC/BC-3 and EphB4 product (4.00 bp) is seen in HUVEC.
Shown also is ~3-actin RT-PCR as a control for amount and integrity of input RNA.
Figure 47 shows that HHV-8 induces arterial marker expression in Kaposi's sarcoma cells. (A) western blot for ephrin B2 on various cell lysates. SLh-vGPCR is a stable clone of SLK expressing the HHV-8 vGPCR, and SLK-pCEFL is control stable clone transfected with empty expression vector. SLK cells transfected with LANA or LANA~440 are SLK-LANA
and SLK-X440 respectively. Quantity of protein loading and transfer was determined by reprobing the membranes with (3-actin monoclonal antibody. (B) Transient transfection of KS-SLK cells with expression vector pvGPCR-CEFL resulted in the expression of ephrin B2 as shown by immunofluorescence staining with FITC (green), whereas the control vector pCEFL had no effect. KS-SLK cells (0.8 x 105/well) were transfected with 0.8 ~,g DNA
using Lipofectamine 2000. 24 hr later cells were fixed and stained with ephrin B2 polyclonal antibody and FITC conjugated secondary antibody as described in the methods.
(C) Transient transfection of HUVEC with vGPCR induces transcription from ephrin B2 luciferase constructs. 8 x 103 HUVEC in 24 well plates were transfected using Superfect with 0.8 p,g/well ephrin B2 promoter constructs containing sequences from -2941 to -11 with respect to the translation start site, or two 5'-deletions as indicated, together with 80 ng/well pCEFL

or pvGPCR-CEFL. Luciferase was determined 48 h post transfection and induction ratios are shown to the right of the graph. pGL3Basic is promoterless luciferase control vector.
Luciferase was normalized to protein since GPCR induced expression of the cotransfected [3-galactosidase. Graphed is mean + SEM of 6 replicates. Shown is one of three similar experiments.
Figure 48 shows that VEGF and VEGF-C regulate ephrin B2 expression. A) Inhibition of ephrin B2 by neutralizing antibodies. Cells were cultured in full growth medium and exposed to antibody (100 ng/ml) for 36 hr before collection and lysis for Western blot. B) For induction of ephrin B2 expression cells were cultured in EBM growth medium containing 5% serum lacking growth factors. Individual growth factors were added as indicated and the cells harvested after 36 h. Quantity of protein loading and transfer was determined by reprobing the membranes (3-actin monoclonal antibody.
Figure 49 shows that Ephrin B2 knock-down with specific siRNA inhibits viability in KS cells a~.zd HLTVEC grown in the presence of VEGF but not IGF, EGF or bFGF.
A) KS-SLK cells were transfected with various siRNA to ephrin B2 and controls. After 48 hr the cells were harvested and crude cell lysates fractionated on 4-20% SDS-PAGE.
V~estern blot was performed with monoclonal antibody to ephrin B2 generated in-house. The membrane was stripped and reprobed with (3-actin monoclonal antibody (Sigma) to illustrate equivalent loading and transfer. B) 3 day cell viability assay of KS-SLK cultures in the presence of ephrin B2 and EphB4 siRNAs. 1 x 105 cells/well in 24-well plates were treated with 0, 10 and 100 nghnl siRNAs as indicated on the graph. Viability of cultures was determined by MTT
assay as described in the methods section. Shown are the mean + standard deviation of duplicate samples. C) HUVE cells were seeded on eight wells chamber slides coated with fibronectin. The HITVE cells were grown overnight in EGM-2 media, which contains all growth supplements. ~n the following day, the media was replaced with media containing VEGF (lOng/ml) or EGF, FGF and IGF as indicated. After 2 hrs of incubation at 37 °C, the cells were transfected using Lipofectamine 2000 (Invitrogen) in Opti-MEM
medium containing 10 nM of siRNA to ephrin B2, Eph B4 or green fluorescence protein (GFP) as control. The cells were incubated for 2 hr and then the fresh media containing growth factors or VEGF alone was added to their respective wells. After 48 hrs, the cells were stained with crystal violet and the pictures were taken immediately by digital camera at lOX
magnification.

Figure 50 shows that soluble EphB4 inhibits KS and EC cord formation and in vivo angiogenesis. Cord formation assay of HWEC in MatrigelTM (upper row). Cells in exponential growth phase were treated oveniight with the indicated concentrations of EphB4 extracellular domain (ECD) prior to plating on MatrigelTM. Cells were trypsinized and plated (1 x 105 cells/well) in a 24-well plate containing 0.5 ml MatrigelTM.
Shown are representative 20X phase contrast fields of cord formation after 8 hr plating on MatrigelTM
in the continued presence of the test compounds as shown. Original magnification 200 X.
KS-SLK cells treated in a similar manner (middle row) in a cord formation assay on MatrigelTM. Bottom row shows in vivo MatrigelTM assay: MatrigelTM plugs containing growth factors and EphB4 ECD or FBS were implanted subcutaneously in the mid-ventral region of mice. After 7 days the plugs were removed, sectioned and stained with HOE to visualize cells migrating into the matrix. Intact vessels with large lumens are observed in the control, whereas EphB4 ECD almost completely inhibited migration of cells into the Matrigel.
Figure 51 shows expression of EPHB4 in bladder cancer cell lines (A), and regulation of EPHB4 expression by EGFR signaling pathway (B).
Figure 52 shows that transfection of p53 inhibit the expression of EPHB4 in cell.
Figure 53 shows growth inhibition of bladder cancer cell line (5637) upon treatment with EPHB4 si~TA 4.72.
Figure 54. shows results on apoptosis study of 5637 cells transfected with siRNA 472.
Figure 55 shows effects of EfHB4 antisense probes on cell migration. 5637 cells were treated with EPHB4AS 10 ( 10 ~,M).
Figure 56 shows effects of EFHB4 siRNA on cell invasion. 5637 cells were transfected with. siRNA 472 or control siRNA.
Figure 57 shows comparison of EphB4 monoclonal antibodies by 6250 and in pull-down assay.
Figure 58 shows that EphB4 antibodies inhibit the growth of SCC15 xenograft tumors.

Figure 59 shows that EphB4 antibodies cause apoptosis, necrosis and decreased angiogenesis in SCC15, head and neck carcinoma tumor type.
Figure 60 shows that systemic administration of EphB4 antibodies leads to tumor regression.
Figure 61 shows a genomic nucleotide sequence of hiunan EphB4.
Figure 62 shows a cDNA nucleotide sequence of human EphB4.
Figure 63 shows a genomic nucleotide sequence of human Ephrin B2.
Figure 64 shows a cDNA nucleotide sequence of human Ephrin B2.
Figure 65 shows an amino acid sequence of human EphB4.
Figure 66 shows an amino acid sequence of human Ephrin B2.
DETAILED DESCRIPTION OF THE INVENTI~N
I. ~veiwiew The current invention is based in part on the discovery that signaling through the ephrin/ephrin receptor pathway contributes to tumorigenesis. Applicants detected expression of ephrin B2 and EphB4 in tumor tissues and developed anti-tumor therapeutic agents for blocking signaling through the ephrin/ephrin receptor. In addition, the disclosure provides pol-ypeptide therapeutic agents and methods for polypeptide-based inhibition of the function of EphB4. and/or Ephrin >32. Accordingly, in certain aspects, the disclosure provides numerous polypeptide compounds (agents) that may be used to treat cancer as well as angiogenesis related disorders and unwanted angiogenesis related processes.
As used herein, the terms Ephrin and Eph are used to refer, respectively, to ligands and receptors. They can be from any of a variety of animals (e.g., mammals/non-mammals, vertebrates/non-vertebrates, including humans). The nomenclature in this area has changed rapidly and the terminology used herein is that proposed as a result of work by the Eph Nomenclature Committee, which can be accessed, along with previously-used names at web site http:J/www.eph-nomenclature.com.
The work described herein, particularly in the examples, refers to Ephrin B2 and EphB4. However, the present invention contemplates any ephrin ligand and/or Eph receptor within their respective family, which is expressed in a tumor. The ephrins (ligands) are of two structural types, which can be further subdivided on the basis of sequence relationships and, functionally, on the basis of the preferential binding they exhibit for two corresponding receptor subgroups. Stuucturally, there are two types of ephrins: those which are membrane-anchored by a glycerophosphatidylinositol (GPI) linkage and those anchored through a transmembrane domain. Conventionally, the ligands are divided into the Ephrin-A subclass, which are GPI-linlced proteins which bind preferentially to EphA receptors, and the Ephrin-B
subclass, which are transmembrane proteins which generally bind preferentially to EphB
receptors.
The Eph family receptors are a family of receptor protein-tyrosine kinases which are related to Eph, a receptor named for its expression in an erythropoietin-producing human hepatocellular carcinoma cell line. They are divided into two subgroups on the basis of the relatedness of their extracellular domain sequences and their ability to bind preferentially to Ephrin-A proteins or Ephrin-B proteins. Receptors which interact preferentially with Ephrin-A proteins axe EphA receptors and those which interact preferentially with Ephrin-B proteins are EphB receptors.
Eph receptors have an extracellular domain composed of the ligand-binding globular domain, a cysteine rich region followed by a pair of fibronectin type III
repeats (e.g., see Figure 16). The cytoplasmic domain consists of a juxtamembrane region containing two conserved tyrosine residues; a protein tyrosine kinase domain; a sterile a-motif (SAM) and a PDZ-domain binding motif. EphB4 is specific for the membrane-b~und ligand Ephrin B2 (Sakano, S. et al 1996; Brambilla R. et al 1995). Ephrin B2 belongs to the class of Eph ligands that have a transmembrane domain and cytoplasmic region with five conserved tyrosine residues and PDZ domain. Eph receptors are activated by binding of clustered, membrane attached ephrins (Davis S et al, 1994), indicating that contact between cells expressing the receptors and cells expressing the ligands is required for Eph activation.
Upon ligand binding, an Eph receptor dimerizes and autophosphorylate the juxtamembrane tyrosine residues to acquire full activation (Kalo MS et al, 1999, Binns KS, 2000). In addition to forward signaling through the Eph receptor, reverse signaling can occur through the ephrin Bs. Eph engagement of ephrins results in rapid phosphorylation of the conserved intracellular tyrosines (Bruckner K, 1997) and somewhat slower recniitment of PDZ binding proteins (Palmer A 2002). Recently, several studies have shown that high expression of Eph/ephrins may be associated with increased potentials for tumor growth, tumorigenicity, and metastasis (Easty DJ, 1999; Kiyokawa E, 1994; Tang XX, 1999; Vogt T, 1998; Liu W, 2002; Stephenson SA, 2001; Steube KG 1999; Berclaz G, 1996).
In certain embodiments, the present invention provides polypeptide therapeutic agents that inhibit activity of Ephrin B2, EphB4, or both. As used herein, the term "polypeptide therapeutic agent" or "polypeptide agent" is a generic term which includes any polypeptide that blocks signaling through the Ephrin B2/EphB4 pathway. A preferred polypeptide therapeutic agent of the invention is a soluble polypeptide of Ephrin B2 or EphB4. Another preferred polypeptide therapeutic agent of the invention is an antagonist antibody that binds to Ephrin B2 or EphB4. For example, such polypeptide therapeutic agent can inhibit function of Ephrin B2 or EphB4, inhibit the interaction between Ephrin B2 and EphB4, inhibit the phosphorylation of Ephrin B2 or EphB4, or inhibit any of the downstream signaling events upon binding of Ephrin B2 to EphB4.
II. Soluble P~lypeptides In certain aspects, the invention relates to a soluble polypeptide comprising an extracellular domain of an Ephrin B2 protein (referred to herein as an Ephrin B2 soluble polypeptide) or comprising an extracellular domain of an EphB4 protein (referred to herein as an EphB4 soluble polypeptide). Preferably, the subject soluble polypeptide is a monomer and is capable of binding with high affinity to Ephrin B2 or EphB4. In a specific embodiment, the EphB4 soluble polypeptide of the invention comprises a globular domain of an EphB4 protein. Specific examples EphB4. soluble polypeptides are provided in Figures 1, 2, and 15. Specific examples of Ephrin B2 soluble polypeptides are provided in Figures 3 and 14.
As used herein, the subject soluble polypeptides include fragments, functional variants, and modified forms of EphB4 soluble polypeptide or an Ephrin B2 soluble polypeptide. These fragments, functional variants, and modified forms of the subject soluble polypeptides antagonize function of EphB4, Ephrin B2 or both.
h1 certain embodiments, isolated fragments of the subject soluble polypeptides can be obtained by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding an EphB4 or Ephrin B2 soluble polypeptides. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f Moc or t-Boc chemistry. The fragments can be produced (recombinantly or by chemical synthesis) and tested to identify those peptidyl fragments that can function to inhibit function of EphB4 or Ephrin B2, for example, by testing the ability of the fragments to inhibit angiogenesis or tmnor growth.
In certain embodiments, a functional variant of an EphB4 soluble polypeptide has an amino acid sequence that is at least 90%, 95%, 97%, 99% or 100% identical to residues 1-522, residues 1-412, or residues 1-312 of the amino acid sequence defined by Figure 65. In other embodiments, a functional variant of an Ephrin B2 soluble polypeptide has a sequence at least 90%, 95%, 97%, 99% or 100% identical to residues 1-225 of the amino acid sequence defined by Figure 66.
In certain embodiments, the present invention contemplates malting functional variants by modifying the structure of the subject soluble polypeptide for such purposes as enhancing therapeutic or prophylactic efficacy, or stability (e.g., ex vivo shelf life and resistance to proteolytic degradation in vivo). Such modified soluble polypeptide are considered functional equivalents of the naturally-occurring EphB4 or Ephrin B2 soluble polypeptide. Modified soluble polypeptides can be produced, for instance, by amino acid substitution, deletion, or addition. For instance, it is reasonable to expect, for example, that an isolated replacement of a leucine with an isoleucine or valine, an aspartate with a glutamate, a threonine with a serine, or a similar replacement of an amino acid with a structurally related amino acid (e.g., conservative mutations) will not have a major effect on the biological activity of the resulting molecule. Conservative replacements are those that take place vrithin a family of amino acids that are related in their side chains.
This invention further contemplates a method of generating sets of combinatorial mutants of the EphB4 or Ephrin B2 soluble polypeptides, as well as truncation mutants, and is especially useful for identifying functional variant sequences. The purpose of screening such combinatorial libraries may be to generate, for example, soluble polypeptide variants which can act as antagonists of EphB4, EphB2, or both. Combinatorially-derived variants can be generated which have a selective potency relative to a naturally occurring soluble polypeptide. Such variant proteins, when expressed from recombinant DNA
constructs, can be used in gene therapy protocols. Likewise, mutagenesis can give rise to variants which have intracellular half lives dramatically different than the corresponding wild-type soluble polypeptide. For example, the altered protein can be rendered either more stable or less stable to proteolytic degradation or other cellular process which result in destruction of, or otherwise inactivation of the protein of interest (e.g., a soluble polypeptide). Such variants, and the genes which encode them, can be utilized to alter the subject soluble polypeptide levels by modulating their half life. For instance, a short half life can give rise to more transient biological effects and, when part of an inducible expression system, can allow tighter control of recombinant soluble polypeptide levels within the cell. As above, such proteins, and particularly their recombinant nucleic acid constructs, can be used in gene therapy protocols.
There are many ways by which the library of potential homologs can be generated from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be carried out in an automatic DNA synthesizer, and the synthetic genes then be ligated into an appropriate gene for expression. The purpose of a degenerate set of genes is to provide, in one mixture, all of the sequences encoding the desired set of potential soluble polypeptide sequences. The synthesis of degenerate oligonucleotides is well known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al., (1981) Recombinant DNA, Proc. 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam:
Elsevier pp273-289; Itakura et al., (1984) Annu. Rev. Biochem. 53:323; Itakura et al., (1984) Science 198:1056; ll~e et al., (1983) Nucleic Acid Res. 11:477). Such techniques have been employed in the directed evolution of other proteins (see, for example, Scott et al., (1990) Science 249:386-390; Roberts et al., (1992) PNAS USA 89:2429-2433; Devlin et al., (1990) Science 249: 404-406; Cwirla et al., (1990) PNAS USA 87: 6378-6382; as well as U.S.
Patent Nos:
5,223,409, 5,198,346, and 5,096,815).
Alternatively, other forms of mutagenesis can be utilized to generate a combinatorial library. For example, soluble polypeptide variants (e.g., the antagonist fornls) can be generated and isolated from a library by screening using, for example, alanine scanning mutagenesis and the like (Ruf et al., (1994) Biochemistry 33:1565-1572; Wang et al., (1994) J. Biol. Chem. 269:3095-3099; Balint et al., (1993) Gene 137:109-118; Grodberg et al., (1993) Eur. J. Biochem. 218:597-601; Nagashima et al., (1993) J. Biol. Chem.
268:2888-2892; Lowman et al., (1991) Biochemistry 30:10832-10838; and Cunningham et al., (1989) Science 244:1081-1085), by linker scanning mutagenesis (Gustin et al., (1993) Virology 193:653-660; Brown et al., (1992) Mol. Cell Biol. 12:2644-2652; McKnight et al., (1982) Science 232:316); by saturation mutagenesis (Meyers et al., (1986) Science 232:613); by PCR mutagenesis (Leung et al., ( 1989) Method Cell Mol Biol 1:11-19); or by random mutagenesis, including chemical mutagenesis, etc. (Miller et al., (1992) A
Short Course in Bacterial Genetics, CSHL Press, Cold Spring Harbor, NY; and Greener et al., (1994) Strategies in Mol Biol 7:32-34). Linker scanning mutagenesis, particularly in a combinatorial setting, is an attractive method for identifying truncated (bioactive) forms of the subject soluble polypeptide.
A wide range of techniques are known in the art for screening gene products of combinatorial libraries made by point mutations and truncations, and, for that matter, for screening cDNA libraries for gene products having a certain property. Such techniques will be generally adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of the subject soluble polypeptides. The most widely used techniques for screening large gene libraries typically comprises cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the illustrative assays described below are amenable to high through-put analysis as necessary to screen large numbers of degenerate sequences created by combinatorial mutagenesis techniques.
In certain embodiments, the subject soluble polypeptides of the invention include a a small molecule such as a peptide and a peptidomimetic. As used herein, the term "peptidomimetic" includes chemically modified peptides and peptide-like molecules that contain non-naturally occurring amino acids, peptoids, and the like.
Peptidomimetics provide various advantages over a peptide, including enhanced stability when administered to a subjects Methods for identifying a peptidomimetic are well known in the art and include the screening of databases that contain libraries of potential peptidomimetics.
For example, the Cambridge Structural Database contains a collection of greater than 300,000 compounds that have known crystal structures (Allen et al., Acta Crystallogr. Section B, 35:2331 (1979)).
Where no crystal structure of a target molecule is available, a structure can be generated using, for example, the program C~NCORD (l~usinko et al., J. Chem. Inf.
Comput. Sci.
29:251 (199)). Another database, the Available Chemicals Directory (Molecular Design Limited, Informations Systems; San Leandro Calif.), contains about 100,000 compounds that are commercially available and also can be searched to identify potential peptidomimetics of the EphB4 or Ephrin B2 soluble polypeptides.
To illustrate, by employing scanning mutagenesis to map the amino acid residues of a soluble polypeptidewhich are involved in binding to another protein, peptidomimetic compounds can be generated which mimic those residues involved in binding. For instance, non-hydrolyzable peptide analogs of such residues can be generated using benzodiazepine - 23 =

(e.g., see Freidinger et al., in Peptides: Chemistry and Biology, G.R.
Marshall ed., ESCOM
Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al., in Peptides:
Chemistry and Biology, G.R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gamma lactam rings, (Garvey et al., in Peptides: Chemistry and Biology, G.R.
Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto-methylene pseudopeptides (Ewenson et al., (1986) J. Med. Chem. 29:295; and Ewenson et al., in Peptides:
Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co.
Roclcland, IL, 1985), b-turn dipeptide cores (Nagai et al., (1985) Tetrahedron Lett 26:647;
and Sato et al., (1986) J Chem Soc Perkin Trans 1:1231), and b-aminoalcohols (Gordon et al., (1985) Biochem Biophys Res Commun 126:419; and Dann et al., (1986) Biochem Biophys Res Commun 134:71).
In certain embodiments, the soluble polypeptides of the invention may further comprise post-translational modifications. Such modifications include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. As a result, the modified soluble polypeptides may contain non-amino acid elements, such as polyethylene glycols, lipids, poly- or mono-saccharide, and phosphates.
Effects of such non-amino acid elements on the functionality of a soluble polypeptide may be tested for its antagozing role in EphB4 or Ephrin B2 function, e.g, it inhibitory effect on angiogenesis or on tumor growth.
In certain aspects, functional variants or modified forms of the subject soluble polypeptides in elude fusion proteins having at least a portion of the soluble polypeptide and one or more fusion domains. Well known examples of such fusion domains include, but are not limited to, polyhistidine, Glu-Glu, glutathione S transferase (GST), thioredoxin, protein A, protein G, and an immunoglobulin heavy chain constant region (Fc), maltose binding protein (MBP), which are particularly useful for isolation of the fusion proteins by affinity chromatography. For the purpose of affinity purification, relevant matrices for affinity chromatography, such as glutathione-, amylase-, and nickel- or cobalt-conjugated resins are used. Another fusion domain well known in the art is green fluorescent protein (GFP).
Fusion domains also include "epitope tags," which are usually short peptide sequences for which a specific antibody is available. Well known epitope tags for which specific monoclonal antibodies are readily available include FLAG, influenza virus haemagglutinin (HA), and c-myc tags. In some cases, the fusion domains have a protease cleavage site, such as for Factor Xa or Thrombin, which allows the relevant protease to partially digest the fusion proteins and thereby liberate the recombinant proteins therefrom. The liberated proteins can then be isolated from the fusion domain by subsequent chromatographic separation. In certain embodiments, the soluble polypeptides of the present invention contain one or more modifications that are capable of stabilizing the soluble polypeptides. For example, such modifications enhance the in vitro half life of the soluble polypeptides, enhance circulatory half life of the soluble polypeptides or reducing proteolytic degradation of the soluble polypeptides.
In certain embodiments, soluble polypeptides (unmodified or modified) of the invention can be produced by a variety of art-known techniques. For example, such soluble polypeptides can be synthesized using standard protein chemistry techniques such as those described in Bodansky, M. Principles of Peptide Synthesis, Springer Verlag, Berlin (1993) and Grant G. A. (ed.), Synthetic Peptides: A User's Guide, W. H. Freeman and Company, New York (1992). In addition, automated peptide synthesizers are commercially available (e.g., Advanced ChemTech Model 396; Milligen/Biosearch 9600). Alternatively, the soluble polypeptides, fragments or variants thereof may be recombinantly produced using various expression systems as is well known in the art (also see below).
III. Nzrcleie ezeids eyz.c~dihg solublelaol~ peptides In certain aspects, the invention relates to isolated and/or recombinant nucleic acids encoding an EphB4 or Ephrin B2 soluble polypeptide. The subject nucleic acids may be single-stranded or double-stranded9 DNA or I~NA molecules. These nucleic acids are useful as therapeutic agents. For example, these nucleic acids are useful in making recombinant soluble polypeptides which are administered to a cell or an individual as therapeutics.
Alternative, these nucleic acids can be directly administered to a cell or an individual as therapeutics such as in gene therapy.
In certain embodiments, the invention provides isolated or recombinant nucleic acid sequences that are at least 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100°/~
identical to a region of the nucleotide sequence depicted in Figure 62 or 63. One of ordinary skill in the art will appreciate that nucleic acid sequences complementary to the subject nucleic acids, and variants of the subject nucleic acids are also within the scope of this invention. In further embodiments, the nucleic acid sequences of the invention can be isolated, recombinant, and/or fused with a heterologous nucleotide sequence, or in a DNA library.

In other embodiments, nucleic acids of the invention also include nucleotide sequences that hybridize under highly stringent conditions to the nucleotide sequence depicted in Figure 62 or 63, or complement sequences thereof. As discussed above, one of ordinary skill in the art will understand readily that appropriate stringency conditions which promote DNA hybridization can be varied. One of ordinary skill in the art will understand readily that appropriate stringency conditions which promote DNA hybridization can be varied. For example, one could perform the hybridization at 6.0 x sodium chloride/sodium citrate (SSC) at about 45 °C, followed by a wash of 2.0 x SSC at 50 °C. For example, the salt concentration in the wash step can be selected from a low stringency of about 2.0 x SSC at 50 °C to a high stringency of about 0.2 x SSC at 50 °C. In addition, the temperature in the wash step can be increased from low stringency conditions at room temperature, about 22 °C, to high stringency conditions at about 65 °C. Both temperature and salt may be varied, or temperature or salt concentration may be held constant while the other variable is changed.
In one embodiment, the invention provides nucleic acids which hybridize under low stringency conditions of 6 x SSC at room temperature followed by a wash at 2 x SSC at room temperature.
Isolated nucleic acids which differ from the subj ect nucleic acids due to degeneracy in the genetic code are also within the scope of the invention. For example, a number of amino acids are designated by more than one triplet. Codons that specify the same amino acid, or synonyms (for example, CALT and CAC are synonyms for histidine) may result in "silently mutations which do not affect the amino acid sequence of the protein. However, it is expected that DNA sequence polymorphisms that do lead to changes in the amino acid sequences of the subject proteins will exist among mammalian cells. One skilled in the art will appreciate that these variations in one or more nucleotides (up to about 3-5% of the nucleotides) of the nucleic acids encoding a particular protein may exist among individuals of a given species due to natural allelic variation. Any and all such nucleotide variations and resulting amino acid polymorphisms are within the scope of this invention.
In certain embodiments, the recombinant nucleic acids of the invention may be operably linked to one or more regulatory nucleotide sequences in an expression construct.
Regulatory nucleotide sequences will generally be appropriate for a host cell used for expression. Numerous types of appropriate expression vectors and suitable regulatory sequences are known in the art for a variety of host cells. Typically, said one or more regulatory nucleotide sequences may include, but are not limited to, promoter sequences, leader or signal sequences, ribosomal binding sites, transcriptional start and termination sequences, translational start and termination sequences, and enhancer or activator sequences.
Constitutive or inducible promoters as known in the art are contemplated by the invention.
The promoters may be either naturally occurnng promoters, or hybrid promoters that combine elements of more than one promoter. An expression construct may be present in a cell on an episome, such as a plasmid, or the expression construct may be inserted in a chromosome. In a preferred embodiment, the expression vector contains a selectable marker gene to allow the selection of transformed host cells. Selectable marker genes are well known in the art and will vary with the host cell used.
In certain aspect of the invention, the subject nucleic acid is provided in am expression vector comprising a nucleotide sequence encoding an EphB4 or Ephrin B2 soluble polypeptide and operably linked to at least one regulatory sequence.
Regulatory sequences are art-recognized and are selected to direct expression of the soluble polypeptide.
Accordingly, the term regulatory sequence includes promoters, enhancers, and other expression control elements. Exemplary regulatory sequences are described in Goeddel;
CPerae Ex~aF~essioaa Teclaaz~lo~y: lllethoe~s ira Ehzysn~l~~y, Academic Press, San Diego, CA
(1990). For instance, any of a wide variety of expression control sequences that control the expression of a DNA sequence when operatively linked to it may be used in these vectors to express DNA sequences encoding a soluble polypeptide. Such useful expression control ~0 sequences, include, for example, the early and late promoters of SV40, tet promoter, adenovirus or cytomegalovirus immediate early promoter, the lac system, the trp system, the TAC or TRC system, T7 promoter whose expression is directed by T7 RNA
pol~nnerase, the major operator and promoter regions of phage lambda , the control regions for fd coat protein, the promoter for 3-phosphoglycerate lcinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., PhoS, the promoters of the yeast a-mating factors, the polyhedron promoter of the baculovirus system and other sequences known to control the expression of genes of prokaryotic or eukaryotic cells or their viruses, and various combinations thereof. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to be expressed. Moreover, the vector's copy number, the ability to control that copy number and the expression of any other protein encoded by the vector, such as antibiotic markers, should also be considered.

This invention also pertains to a host cell transfected with a recombinant gene including a coding sequence for one or more of the subject soluble polypeptide. The host cell may be any prokaryotic or eukaryotic cell. For example, a soluble polypeptide of the invention may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art.
Accordingly, the present invention further pertains to methods of producing the subject soluble polypeptides. For example, a host cell transfected with an expression vector encoding an EphB4 soluble polypeptide can be cultured under appropriate conditions to allow expression of the EphB4 soluble polypeptide to occur. The EphB4 soluble polypeptide may be secreted and isolated from a mixture of cells and medium containing the soluble polypeptides. Alternatively, the soluble polypeptides may be retained cytoplasmically or in a membrane fraction and the cells harvested, lysed and the protein isolated. A
cell culture includes host cells, media and other byproducts. Suitable media for cell culture are well known in the art. The soluble polypeptides can be isolated from cell culture medium, host cells, or both using techniques lmown in the art for pw-ifying proteins, including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of the soluble polypeptides. W a preferred embodiment, the soluble polypeptide is a fusion protein containing a domain which facilitates its purification.
A recombinant nucleic acid of the invention can be produced by ligating the cloned gene, or a poution thereof, into a vector suitable for expression in either prokaryotic cells, eukaryotic cells (yeast, avian, insect or mammalian), or both. Expression vehicles for production of a recombinant soluble polypeptide include plasmids and other vectors. For instance, suitable vectors include plasmids of the types: pBR322-derived plasmids, pEMBL-derived plasmids, pEX-derived plasmids, pBTac-derived plasmids and pUC-derived plasmids for expression in prolcaiyotic cells, such as E. coli.
The preferred mammalian expression vectors contain both prokaryotic sequences to facilitate the propagation of the vector in bacteria, and one or more eukaryotic transcription units that are expressed in eukaryotic cells. The pcDNAI/amp, pcDNAI/neo, pRc/CMV, pSV2gpt, pSV2neo, pSV2-dhfr, pTk2, pRSVneo, pMSG, pSVT7, plco-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells. Some of these vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells. Alternatively, derivatives of viruses such as the bovine papilloma virus (BPV-1), or Epstein-Ban virus (pHEBo, PREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells. Examples of other viral (including retroviral) expression systems can be found below in the description of gene therapy delivery systems.
The various methods employed in the preparation of the plasmids and transformation of host organisms are well known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells, as well as general recombinant procedures, see Moleculaf°
Cloning A Labof-atof~y Mayaual, 2nd Ed., ed. by Sambroolc, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press, 1989) Chapters 16 and 17. In some instances, it may be desirable to express the recombinant SLCSA8 polypeptide by the use of a baculovirus expression system. Examples of such baculovirus expression systems include pVL-derived vectors (such as pVL1392, pVL1393 and pVL941), pAcUW-derived vectors (such as pAcUWl), and pBlueBac-derived vectors (such as the 13-gal containing pBlueBac III).
Techniques for making fusion genes are well known. Essentially, the joining of various DIVA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blest-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DATA synthesizers. Alternatively, PCR
amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed to generate a chimeric gene sequence (see, for example, Cuf-Yent Protocols ifa Moleculay~ Biology, eds. Ausubel et al., John Wiley ~ Sons: 1992).
1h Aratibotlies In certain aspects, the the present invention provides antagonist antibodies against Ephrin B2 or EphB4. As described herein, the term "antagonist antibody" refers to an antibody that inhibits function of Ephrin B2 or EphB4. Preferably, the antagonist antibody binds to an extracellular domain of Ephrin B2 or EphB4. It is understood that antibodies of the invention may be polyclonal or monoclonal; intact or truncated, e.g., F(ab')2, Fab, Fv;
xenogeneic, allogeneic, syngeneic, or modified forms thereof, e.g., humanized, chimeric, etc.
For example, by using immunogens derived from an Ephrin B2 or EphB4 polypeptide, anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (see, for example, Antibodies: A Laboratory Manual ed. by Harlow and Lane (Cold Spring Harbor Press: 1988)). A mammal, such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide. (e.g., a polypeptide or an antigenic fragment which is capable of eliciting an antibody response, or a fusion protein).
Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. An immunogenic portion of an Ephrin B2 or EphB4 polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies. In one embodiment, antibodies of the invention are specific for the extracellular portion of the Ephrin B2 or EphB4 protein. In another embodiment, antibodies of the invention are specific for the intracellular portion or the transmembrane portion of the Ephrin B2 or EphB4 protein. In a further embodiment, antibodies of the invention are specific for the extracellular portion of the Ephrin B2 or EphB4 protein.
Following immunization of an animal with an antigenic preparation of an Ephrin or EphB4 polypeptide, antisera can be obtained and, if desired, polyclonal antibodies can be isolated from the serum. To produce monoclonal antibodies, antibody-producing cells (lymphocytes) can be harvested from an immunized animal and fused by standard somatic cell fusion procedures with immortalizing cells such as myeloma cells to yield hybridoma cells. Such techniques are well known in the art, and include, for example, the hybridoma technique (originally developed by I~ohler and Milstein, (1975) Nature, 256:
495-497), the human B cell hybridoma technique (I~ozbar et al., (1983) Immunology Today, 4:
72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96).
Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with an Ephrin B2 or EphB4 polypeptide and monoclonal antibodies isolated from a culture comprising such hybridoma cells.
The term antibody as used herein is intended to include fragments thereof which are also specifically reactive with an Ephrin B2 or EphB4 polypeptides. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab)2 fragments can be generated by treating antibody with pepsin. The resulting F(ab)2 fragment can be treated to reduce disulfide bridges to produce Fab fragments. The antibody of the present invention is further intended to include bispecific, single-chain, and chimeric and humanized molecules having affinity for an Ephrin B2 or EphB4 polypeptide conferred by at least one CDR region of the antibody. Techniques for the production of single chain antibodies (US
Patent No.
4,946,778) can also be adapted to produce single chain antibodies. Also, transgenic mice or other organisms including other mammals, may be used to express humanized antibodies. In preferred embodiments, the antibodies further comprise a label attached thereto and able to be detected (e.g., the label can be a radioisotope, fluorescent compound, enzyme or enzyme co-factor).
In certain preferred embodiments, an antibody of the invention is a monoclonal antibody, and in certain embodiments the invention makes available methods for generating novel antibodies. For example, a method for generating a monoclonal antibody that binds specifically to an Ephrin B'? or EphB4 polypeptide may comprise administering to a mouse an amount of an immunogenic composition comprising the Ephrin B? or EphB4 polypeptide effective to stimulate a detectable immune response, obtaining antibody-producing cells (e.g., cells from the spleen) from the mouse and fusing the antibody-producing cells with myeloma cells to obtain antibody-producing hybridomas, and testing the antibody-producing hybridomas to identify a hybuidoma that produces a monocolonal antibody that binds specifically to the Epln-in B2 or EphB4 polypeptide. ~nce obtained, a hybridoma can be propagated in a cell culture, optionally in culture conditions where the hybridoma-derived cells produce the monoclonal antibody that binds specifically to the Ephrin B2 or EphB4 polypeptide. The monoclonal antibody may be purified from the cell culture.
In addition, the techniques used to screen antibodies in order to identify a desirable antibody may influence the properties of the antibody obtained. For example, an antibody to be used for certain therapeutic purposes will preferably be able to target a particular cell type.
Accordingly, to obtain antibodies of this type, it may be desirable to screen for antibodies that bind to cells that express the antigen of interest (e.g., by fluorescence activated cell sorting).
Likewise, if an antibody is to be used for binding an antigen in solution, it may be desirable to test solution binding. A variety of different techniques are available for testing antibody: antigen interactions to identify particularly desirable antibodies.
Such techniques include ELISAs, surface plasmon resonance binding assays (e.g. the Biacore binding assay, Bia-core AB, Uppsala, Sweden), sandwich assays (e.g. the paramagnetic bead system of IGEN International, Inc., Gaithersburg, Maryland), western blots, immunoprecipitation assays and immunohistochemistry.
Tl D~~ug Screey~ing Assays There are numerous approaches to screening for polypeptide therapeutic agents as antagonists of EphB4, Epllrin B2 or both. For example, high-throughput screening of compounds or molecules can be carried out to identify agents or drugs which inhibit angiogenesis or inhibit tumor growth. Test agents can be any chemical (element, molecule, compound, drug), made synthetically, made by recombinant techniques or isolated from a natural source. For example, test agents can be peptides, polypeptides, peptoids, sugars, hormones, or nucleic acid molecules. In addition, test agents can be small molecules or molecules of greater complexity made by combinatorial chemistry, for example, and compiled into libraries. These libraries can comprise, for example, alcohols, alkyl halides, amines, amides, esters, aldehydes, ethers and other classes of organic compounds. Test agents can also be natural or genetically engineered products isolated from lysates or growth media of cells -- bacterial, animal or plant -- or can be the cell lysates or growth media themselves. Presentation of test compounds to the test system can be in either an isolated form or as mixtures of compounds, especially in initial screening steps.
For example, an assay can be cat-ried out to screen for compounds that specifically inhibit binding of Ephrin B2 (ligand) to EphB4 (receptor), or vice-versa, e.g., by inhibition of binding of labeled ligand- or receptor-Fc fusion proteins to immortalized cells. Compounds identified through this screening can then be tested in animals to assess their anti-angiogenesis or anti-tumor activity in vivo.
In one embodiment of an assay to identify a substance that interferes with interaction of two cell surface molecules (e.g., Ephrin B2 and EphB4), samples of cells expressing one type of cell surface molecule (e.g., EphB4) are contacted with either labeled ligand (e.g., Ephrin B2, or a soluble portion thereof, or a fusion protein such as a fusion of the extracellular domain and the Fc domain of IgG) or labeled ligand plus a test compound (or group of test compounds). The amount of labeled ligand which has bound to the cells is determined. A lesser amount of label (where the label can be, for example, a radioactive isotope, a fluorescent or colormetric label) in the sample contacted with the test compounds) is an indication that the test compounds) interferes with binding. The reciprocal assay using cells expressing a ligand (e.g., an Ephrin B2 ligand or a soluble form thereof) can be used to test for a substance that interferes with the binding of an Eph receptor or soluble portion thereof.
An assay to identify a substance which interferes with interaction between an Eph receptor and an ephrin can be performed with the component (e.g., cells, purified protein, including fusion proteins and portions having binding activity) which is not to be in competition with a test compound, linked to a solid support. The solid support can be any suitable solid phase or matrix, such as a bead, the wall of a plate or other suitable surface (e.g., a well of a microtiter plate), column pore glass (CPG) or a pin that can be submerged into a solution, such as in a well. Linkage of cells or purified protein to the solid support can be either direct or through one or more linker molecules.
In one embodiment, an isolated or purified protein (e.g., an Eph receptor or an ephrin) can be immobilized on a suitable affinity matrix by standard techniques, such as chemical cross-linking, or via an antibody raised against the isolated or purified protein, and bound to a solid support. The matrix can be packed in a column or other suitable container and is contacted with one or more compounds (e.g., a mixture) to be tested under conditions suitable for binding of the compound to the protein. For example, a solution containing compounds cm be made to flow through the matrix. The matrix can be washed with a suitable wash buffer to remove unbound compounds and non-specifically bound compounds.
Compounds which remain bound can be released by a suitable elution buffer. For example, a change in the ionic strength or pH of the elution buffer can lead to a release of compounds.
Alternatively, the elution buffer can comprise a release component or components designed to disrupt binding of compounds (e.g., one or more ligands or receptors, as appropriate, or analogs thereof which can disrupt binding or competitively inhibit binding of test compound to the protein).
Fusion proteins comprising all, or a portion of, a protein (e.g., an Eph receptor or an ephrin) linked to a second moiety not occurnng in that protein as found in nature can be prepared for use in another embodiment of the method. Suitable fusion proteins for this purpose include those in which the second moiety comprises an affinity ligand (e.g., an enzyme, antigen, epitope). The fusion proteins can be produced by inserting the protein (e.g., an Eph receptor or an ephrin) or a portion thereof into a suitable expression vector which encodes an affinity ligand. The expression vector can be introduced into a suitable host cell for expression. Host cells are disrupted and the cell material, containing fusion protein, can be bound to a suitable affinity matrix by contacting the cell material with an affinity matrix under conditions sufficient for binding of the affinity ligand portion of the fusion protein to the affinity matrix.
In one aspect of this embodiment, a fusion protein can be immobilized on a suitable affinity matrix under conditions sufficient to bind the affinity ligand portion of the fusion protein to the matrix, and is contacted with one or more compounds (e.g., a mixture) to be tested, under conditions suitable for binding of compounds to the receptor or ligand protein portion of the bound fusion protein. Next, the affinity matrix with bound fusion protein can be washed with a suitable wash buffer to remove unbound compounds and non-specifically bound compounds without significantly disrupting binding of specifically bound compounds.
Compounds which remain bound can be released by contacting the affinity matrix having fusion protein bound thereto with a suitable elution buffer (a compound elution buffer). In this aspect, compound elution buffer can be formulated to permit retention of the fusion protein by the affinity matrix, but cam be formulated to interfere with binding of the compounds) tested to the receptor or ligand protein portion of the fusion protein. For example, a change in the ionic strength or pH of the elution buffer can lead to release of compounds, or the elution buffer can comprise a release component or components designed to disrupt binding of compounds to the receptor or ligand protein portion of the fusion protein (e.g., one or more ligaaids or receptors or analogs thereof which can disrupt binding of compounds to the receptor or ligand protein portion of the fusion protein).
Immobilization can be performed prior to, simultaneous with, or after contacting the fusion protein with compound, as appropriate. Various permutations of the method are possible, depending upon factors such as the compounds tested, the affinity matrix selected, and elution buffer formulation. For example, after the wash step, fusion protein with compound bound thereto can be eluted from the affinity matrix with a suitable elution buffer (a matrix elution buffer).
Where the fusion protein comprises a cleavable linl~er, such as a thrombin cleavage site, cleavage from the affinity ligand can release a portion of the fusion with compound bound thereto. Bound compound can then be released from the fusion protein or its cleavage product by an appropriate method, such as extraction.
YI. Methods of Ti°eatfnefat In certain embodiments, the present invention provides methods of inhibiting angiogenesis and methods of treating angiogenesis-associated diseases. In other embodiments, the present invention provides methods of inhibiting or reducing tumor growth and methods of treating an individual suffering from cancer. These methods involve administering to the individual a therapeutically effective amount of one or more polypeptide therapeutic agents as described above. These methods are particularly aimed at therapeutic and prophylactic treatments of animals, and more particularly, humans.
As described herein, angiogenesis-associated diseases include, but are not limited to, angiogenesis-dependent cancer, including, for example, solid tumors, blood born tumors such as leukemias, and tumor metastases; benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas; inflammatory disorders such as immune and non-immune inflarmnation; chronic articular rheumatism and psoriasis; ocular angiogenic diseases, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, retrolental fibroplasia, rubeosis;
~sler-Webber Syndrome; myocardial angiogenesis; plaque neovascularization;
telangiectasia; hemophiliac joints; angiofibroma; and wound granulation and wound healing;
telangiectasia psoriasis scleroderma, pyogenic granuloma, cororany collaterals, ischemic limb angiogenesis, corneal diseases, rubeosis, arthritis, diabetic neovasculas-ization, fractures, vasculogenesis, hematopoiesis.
It is understood that methods and compositions of the invention are also useful for treating any angiogenesis-independent cancers (tmnors). As used herein, the term "angiogenesis-independent cancer" refers to a cancer (tumor) where there is no or little neovascularization in the tumor tissue.
W particular, polypeptide therapeutic agents of the present invention are useful for treating or preventing a cancer (tumor), including, but not limited to, colon carcinoma, breast cancer, mesothelioma, prostate cancer, bladder cancer, squamous cell carcinoma of the head and neck (HNSCC), Kaposi sarcoma, and leukemia.
In certain embodiments of such methods, one or more polypeptide therapeutic agents can be administered, together (simultaneously) or at different times (sequentially). In addition, polypeptide therapeutic agents can be administered with another type of compounds for treating cancer or for inhibiting angiogenesis.

In certain embodiments, the subject methods of the invention can be used alone.
Alternatively, the subject methods may be used in combination with other conventional anti-cancer therapeutic approaches directed to treatment or prevention of proliferative disorders (e.g., tumor). For example, such methods can be used in prophylactic cancer prevention, prevention of cancer recurrence and metastases after surgery, and as an adjuvant of other conventional cancer therapy. The present invention recognizes that the effectiveness of conventional cancer therapies (e.g., chemotherapy, radiation therapy, phototherapy, immunotherapy, and surgery) can be enhanced through the use of a subject polypeptide therapeutic agent.
A wide array of conventional compounds have been shown to have anti-neoplastic activities. These compounds have been used as pharmaceutical agents in chemotherapy to shrink solid tumors, prevent metastases and further growth, or decrease the number of malignant cells in leukemic or bone marrow malignancies. Although chemotherapy has been effective in treating various types of malignancies, many anti-neoplastic compounds induce undesirable side effects. It has been shown that when two or more different treatments are combined, the treatments may work synergistically and allow reduction of dosage of each of the treatments, thereby reducing the detrimental side effects exerted by each compound at higher dosages. In other instances, malignancies that are refractory to a treatment may respond to a combination therapy of two or more different treatments.
'?0 then a polypeptide therapeutic agent of the present invention is administered in combination with another conventional anti-neoplastic agent, either concomitantly or sequentially, such therapeutic agent is shown to enhance the therapeutic effect of the anti-neoplastic agent or overcome cellular resistance to such anti-neoplastic agent. This allows decrease of dosage of an anti-neoplastic agent, thereby reducing the undesirable side effects, or restores the effectiveness of an anti-neoplastic agent in resistant cells.
Pharmaceutical compounds that may be used for combinatory anti-tumor therapy include, merely to illustrate: aminoglutethimide, amsacrine, anastrozole, asparaginase, bcg, bicalutamide, bleomycin, buserelin, busulfan, campothecin, capecitabine, carboplatin, cannustine, chlorambucil, cisplatin, cladribine, clodronate, colchicine, cyclophosphamide, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, dienestrol, diethylstilbestrol, docetaxel, doxorubicin, epirubicin, estradiol, estramustine, etoposide, exemestane, filgrastim, fludarabine, fludrocortisone, fluorouracil, fluoxymesterone, flutamide, gemcitabine, genistein, goserelin, hydroxyurea, idarubicin, ifosfamide, imatinib, interferon, irinotecan, ironotecan, letrozole, leucovorin, leuprolide, levamisole, lomustine, mechlorethamine, medroxyprogesterone, megestrol, melphalan, mercaptopurine, mesna, methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide, nocodazole, octreotide, oxaliplatin, paclitaxel, pamidronate, pentostatin, plicamycin, porfimer, procarbazine, raltitrexed, rituximab, streptozocin, suramin, tamoxifen, temozolomide, teniposide, testosterone, thioguanine, thiotepa, titanocene dichloride, topotecan, trastuzumab, tretinoin, vinblastine, vincristine, vindesine, and vinorelbine.
These chemotherapeutic anti-tumor compounds may be categorized by their mechanism of action into, for example, following groups: anti-metabolites/anti-cancer agents, such as pyrimidine analogs (5-fluorouracil, floxuridine, capecitabine, gemcitabine and cytarabine) and purine analogs, folate antagonists and related inhibitors (mercaptopurine, thioguanine, pentostatin and 2-chlorodeoxyadenosine (cladribine));
antiproliferative/antimitotic agents including natural products such as vinca all~aloids (vinblastine, vincristine, and vinorelbine)~ microtubule disnuptors such as taxane (paclitaxel, docetaxel), vincristin, vinblastin, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracyclines, bleomycin, busulfan, camptothecin, carboplatin, chlorambucil, cisplatin, cyclophosphamide, cytoxan, dactinomycin, daunorubicin, doxorubicin, epirubicin, he~~amethyhnelamineoxaliplatin, iphosphamide, melphalan, merchlorehtamine, mitomycin, mit~xantrone, nitrosourea, plicamycin, procarbazine, taxol, ta~~otere, teniposide, triethylenethiophosphoramide and etoposide (VP16)); antibiotics such as dactinomycin (actinomycin D), daunorubicin, doxorubicin (adriamycin), idarubicin, anthracyclines, mitoxantrone, bleomycins, plicamycin (mithramycin) and mitomycin; enzymes (L-asparaginase which systemically metabolizes L-asparagine and deprives cells which do not have the capacity to synthesize their own asparagine); antiplatelet agents;
antiproliferative/antimitotic alkylating agents such as nitrogen mustards (mechlorethamine, cyclophosphamide and analogs, melphalan, chlorambucil), ethylenimines and methylmelamines (hexamethylmelamine and thiotepa), allcyl sulfonates-busulfan, nitrosoureas (carmustine (BCNLI) and analogs, streptozocin), trazenes -dacarbazinine (DTIC); antiproliferative/antimitotic antimetabolites such as folic acid analogs (methotrexate); platinum coordination complexes (cisplatin, carboplatin), procarbazine, hydroxyurea, mitotane, aminoglutethimide; hormones, hormone analogs (estrogen, tamoxifen, goserelin, bicalutamide, nilutamide) and aromatase inhibitors (letrozole, anastrozole); anticoagulants (heparin, synthetic heparin salts and other inhibitors of thrombin); flbrinolytic agents (such as tissue plasminogen activator, streptokinase and urokinase), aspirin, dipyridamole, ticlopidine, clopidogrel, abciximab;
antimigratory agents;
antisecretory agents (breveldin); immunosuppressives (cyclosporine, tacrolimus (FIB-506), sirolimus (rapamycin), azathioprine, mycophenolate mofetil); anti-angiogenic compounds (TNP-470, genistein) and growth factor inhibitors (vascular endothelial growth factor (VEGF) inhibitors, fibroblast growth factor (FGF) inhibitors); angiotensin receptor blocker;
nitric oxide donors; anti-sense oligonucleotides; antibodies (trastuzumab);
cell cycle inhibitors and differentiation inducers (tretinoin); mTOR inhibitors, topoisomerase inhibitors (doxorubicin (adriamycin), amsacrine, camptothecin, daunorubicin, dactinomycin, eniposide, epirubicin, etoposide, idarubicin and mitoxantrone, topotecan, irinotecan), corticosteroids (cortisone, dexamethasone, hydrocortisone, methylpednisolone, prednisone, and prenisolone); growth factor signal transduction kinase inhibitors;
mitochondrial dysfunction inducers and caspase activators; and chromatin disruptors.
In certain embodiments, pharmaceutical compounds that may be used for combinatory anti-angiogenesis therapy include: (1) inhibitors of release of "angiogenic molecules," such as bFGF (basic fibroblast growth factor); (2) neutralizers of angiogenic molecules, such as an anti-(3bFGF antibodies; and (3) inhibitors of endothelial cell response to angiogenic stimuli, including collagenase inhibitor, basement membrane turnover inhibitors, angiostatic steroids, fungal-derived angloge11eS1S 111111b1tol'S, platelet factor 4, thrombospondin, arthritis drugs such as D-penicillamine and gold thiomalate, vitamin D3 analogs, alpha-interferon, and the like. For additional proposed inhibitors of angiogenesis, see Blood et al., Bioch. Biophys. Acta., 1032:89-118 (1990), Moses et al., Science, 248:1408-1410 (1990), Ingber et al., Lab. Invest., 59:44-51 (1988), and U.S. Pat. Nos.
5,092,885, 5,112,946, 5,192,744, 5,202,352, and 6573256. In addition, there are a wide variety of compounds that can be used to inhibit angiogenesis, for example, peptides or agents that block the VEGF-mediated angiogenesis pathway, endostatin protein or derivatives, lysine binding fragments of angiostatin, melanin or melanin-promoting compounds, plasminogen fragments (e.g., Kringles 1-3 of plasminogen), tropoin subunits, antagonists of vitronectin a,~(i3, peptides derived from Saposin B, antibiotics or analogs (e.g., tetracycline, or neomycin), dienogest-containing compositions, compounds comprising a MetAP-2 inhibitory core coupled to a peptide, the compound EM-138, chalcone and its analogs, and naaladase inhibitors. See, for example, U.S. Pat. Nos. 6,395,718, 6,462,075, 6,465,431, 6,475,784, 6,482,802, 6,482,810, 6,500,431, 6,500,924, 6,518,298, 6,521,439, 6,525,019, 6,538,103, 6,544,758, 6,544,947, 6,548,477, 6,559,126, and 6,569,845.
Depending on the nature of the combinatory therapy, administration of the polypeptide therapeutic agents of the invention may be continued while the other therapy is being administered and/or thereafter. Administration of the polypeptide therapeutic agents may be made in a single dose, or in multiple doses. In some instances, administration of the polypeptide therapeutic agents is commenced at least several days prior to the conventional therapy, while in other instances, administration is begun either immediately before or at the time of the administration of the conventional therapy.
TiII. Met~t~ds ofAd~rtinistt~ation and Phat~maceutical Compositions In certain embodiments, the subject polypeptide therapeutic agents (e.g., soluble polypeptides or antibodies) of the present invention are formulated with a pharmaceutically acceptable carrier. Such therapeutic agents can be administered alone or as a component of a pharmaceutical formulation (composition). The compounds may be formulated for administration in any convenient way for use in human or veterinary medicine.
Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions.
Formulations of the subject polypeptide therapeutic agents include those suitable for oral/ nasal, topical, parenteral, rectal, and/or intravaginal administration.
The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient which can be combined with a Garner material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect.
In certain embodiments, methods of preparing these formulations or compositions include combining another type of anti-tumor or anti-angiogenesis therapeutic agent and a carrier and, optionally, one or more accessory ingredients. In general, the formulations can be prepared with a liquid carrier, or a finely divided solid carrier, or both, and then, if necessary, shaping the product.
Formulations for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a subject polypeptide therapeutic agent as an active ingredient.
In solid dosage forms for oral administration (capsules, tablets, pills, dragees, powders, granules, and the like), one or more polypeptide therapeutic agents of the present invention may be mixed with one or more pharmaceutically acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mamiitol, and/or silicic acid;
(2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose, and/or acacia; (3) humectants, such as glycerol; (4.) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodimn carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; (8) absorbents, such as kaolin and bentonite clay;
(9) lubricants, such a talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof; and (10) coloring agents. In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents.
Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols a.nd the like.
Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs. W
addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (in particular, cottonseed, groundnut, corn, germ olive, castor, and sesame oils), glycerol, tetrahydrofwyl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming, and preservative agents.
Suspensions, in addition to the active compounds, may contain suspending agents such as ethoxylated isostearyl alcohols, polyoxyethylene sorbitol, and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
In particular, methods of the invention can be administered topically, either to skin or to mucosal membranes such as those on the cervix and vagina. This offers the greatest opportunity for direct delivery to tumor with the lowest chance of inducing side effects. The topical formulations may further include one or more of the wide variety of agents known to be effective as skin or stratum corneum penetration enhancers. Examples of these are 2-pyrrolidone, N-methyl-2-pyrrolidone, dimethylacetamide, dimethylformamide, propylene glycol, methyl or isopropyl alcohol, dimethyl sulfoxide, and atone. Additional agents may further be included to make the formulation cosmetically acceptable. Examples of these are fats, waxes, oils, dyes, fragrances, preservatives, stabilizers, and surface active agents.
I~eratolytic agents such as those known in the art may also be included.
Examples are salicylic acid and sulfur.
Dosage forms for the topical or transdermal administration include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches, and inhalants.
The subject polypeptide therapeutic agents may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants which may be required. The ointments, pastes, creams and gels may contain, in addition to a subject polypeptide agent, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
Powders and sprays can contain, in addition to a subject polypeptide therapeutic agent, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates, and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.

Pharmaceutical compositions suitable for parenteral administration may comprise one or more polypeptide therapeutic agents in combination with one or more pharmaceutically acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents. Examples of suitable aqueous and nonaqueous earners which may be employed in the pharmaceutical compositions of the invention include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the lilce), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate.
Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
These compositions may also contain adjuvants, such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, amd the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the life into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption, sash as aluminum monostearate and gelatin.
W jectable depot forms are made by forming microencapsule matrices of one or more polypeptide therapeutic agents in biodegradable polymers such as polylactide-polyglycolide.
Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) amd poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.
Formulations for intravaginal or rectally administration may be presented as a suppository, which may be prepared by mixing one or more compounds of the invention with one or more suitable nonirntating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound.
In other embodiments, the polypeptide therapeutic agents of the instant invention can be expressed within cells from eul~aryotic promoters. For example, a soluble polypeptide of EphB4 or Ephrin B2 can be expressed in eukaryotic cells from an appropriate vector. The vectors are preferably DNA plasmids or viral vectors. Viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus.
Preferably, the vectors stably introduced in and persist in target cells.
Alternatively, viral vectors can be used that provide for transient expression. Such vectors can be repeatedly administered as necessary. Delivery of vectors encoding the subj ect polypeptide therapeutic agent can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from the patient followed by reintroduction into the patient, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al., 1996, TIG., 12, 510).
E~EMPLIFICATI~N
The invention now being generally described, it will be more readily understood by reference to the following examples, which are included merely for purposes of illustration of certain aspects and embodiments of the present invention, and are not intended to limit the invention.
Example 1. Soluble derivatives of the extracellular domains of human Ephrin B2 and EphB4 rots teins Soluble derivatives of the extracellular domains of human Ephrin B2 and EphB4 proteins represent either tn2ncated full-length predicted extracellular domains of Ephrin B2 (B4ECv3, B2EC) or translational fusions of the domains with constant region of human irnmunoglobulins (IgGl Fc fragment), such as B2EC-FC, B4ECv2-FC and B4ECv3-FC.
Representative human Ephrin B2 constructs and human EphB4 constructs are shown Figures 14 and 15.
The cDNA fragments encoding these recombinant proteins were subcloned into mammalian expression vectors, expressed in transiently or stably transfected mammalian cell lines and purified to homogeneity as described in detail in Materials and Methods section (see below). Predicted amino acid sequences of the proteins are shown in Figures 1-5. High purity of the isolated proteins and their recognition by the corresponding anti-Ephrin B2 and anti-EphB4 monoclonal or polyclonal antibodies were confirmed. The recombinant proteins exhibit the expected high-affinity binding, binding competition and specificity properties with their corresponding binding partners as corroborated by the biochemical assays (see e.g., Figures 6-8).
Such soluble derivative proteins human Ephrin B2 and EphB4 exhibit potent biological activity in several cell-based assays and ifz vivo assays which measure angiogenesis or anti-cancer activities, and are therefore perspective drug candidates for anti-angiogenic and anti-cancer therapy. B4ECv3 as well as B2EC and B2EC-FC proteins blocked chemotaxis of human endothelial cells (as tested with umbilical cord and hepatic AECs or VECs), with a decrease in degradation of the extracellular matrix, Matrigel, and a decrease in migration in response to growth factor stimuli (Figures 9-11). B4ECv3 and BZEC-FC proteins have potent anti-angiogenic effect as demonstrated by their inhibition of endothelial cell tube formation (Figures 1?-13).
Materials and Methods 1) Mammalian expression vectors for producing recombinant soluble derivatives of Ephrin B2 and Eph B4 Plasmids vectors for expressing recombinant soluble derivatives of Ephrin B~
and EphB4 were based on pEF6/VS-His-TOPO vector (Invitrogen), pIG (IVovagen) or pRI~S.
pEF6/VS-His-TOPO contains hmnan elongation factor 1 a enhancer/promoter and blasticidin resistance marker. pIG vector is designed for high-level expression of protein fusions with Fc portion of human IgGlunder CMV promoter control and pRI~S is a general purpose CMV
promoter-containing mammalian expression vector. To generate plasmid construct pEF6-B4EC-NT, cDNA fragment of human EphB4 was amplified by PCR using oligo primers 5'-GGATCCGCC ATGGAGCTC CGGGTGCTGCT-3' and 5'-TGGATCCCT GCTCCCGC
CAGCCCTCG CTCTCATCCA-3', and TOPO-cloned into pEF6/VS-His-TOPO vector.
pEF6-hB4ECv3 was derived from pEF6-B4ECNT by digesting the plasmid DNA with EcoRV and BstBI, filling-in the ends with I~lenow enzyme and religating the vector.
Recombinant EphB4 derivative encoded by pEF6-B4EC-NT does not contain epitope-or purification tags, while the similar B4ECv3 protein encoded by pEF6-hB4ECv3 contains VS
epitope tag and 6xHis tag on its C-terminus to facilitate purification from conditioned media.

Plasmid construct pEF6-hB2EC was created by PCR amplification of Ephrin B2 cDNA using oligo primers 5'- TGGATCCAC CATGGCTGT GAGAAGGGAC-3' plus 5'-ATTAATGGTGATGGT GAT GATGACTAC CCACTTCGG AACCGAGGATGTTGTTC-3' and TOPO-cloning into pEF6/VS-His-TOPO vector. Plasmid construct pIG-hB2EC-FC
was created by PCR amplification of Ephrin B2 cDNA with oligo primers 5'-TAAAGCTTCCGCCATGG CTGTGAGAAGGGAC-3' and 5'-TAGGATCCACTTCGGA
ACCGAGGATGTTGTT CCC-3' , followed liy TOPO-cloning and sequencing the resulting PCR fragment with consecutive subcloning in pIG hIgG1 Fc fusion expression vector cut with Bam HI and Hind III. Similarly, pIG-hB2EC and pIG-hB4ECv3 were generated by PCR
amplifying portions of EphB4 ECD cDNA using oligo primers 5'-ATAAGCTTCC
GCCATGGAGC TCCGGGTGCTG-3' plus 5'-TTGGATCCTGCTCCCG CCAGCCCTCGC
TCTCATC-3' with consecutive subcloning into pIG hIgGl Fc fusion expression vector cut with Bam HI and Hind III. Predicted sequences of the proteins encoded by the vectors described above are shown in Figures 1-5.
2) Mammalian cell culture and transfections HEI~293T (human embryonic kidney line) cells were maintained in DMEM with 10%
dialyzed fetal calf serum aald 1 % penicillin/streptomycin/neomycin antibiotics. Cells were maintained at 37 °C in a humidified atmosphere of 5% 002/95% air.
Transfections were performed using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer's protocol. One day before transfections, 293T cells v~ere seeded at a high density to reach 80%
confluence at the time of transfection. Plasmid DNA and Lipofectamine reagent at 1:3 ratio were diluted in Opti-MEM I reduced sentm medium (Invitrogen) for 5 min and mixed together to fomn DNA:Lipofectamine complex. For each 10 cm culture dish, 10 p,g of plasmid DNA was used. After 20 min, above complex was added directly to cells in culture medium. After 16 hours of transfection, medium was aspirated, washed once with serum free DMEM and replaced with senim free DMEM. Secreted proteins were harvested after hours by collecting conditional medium. Conditional medium was clarified by centrifugation at 10,000 g for 20 min, filtered through 0.2 ~m filter and used for purification.
3) Generating stable cell lines To create stable cell lines producing EphB4ECv3 and EphB4ECnt HEI~293 or HEK293T cells were transfected with either pEF6-B4ECv3 or pEF6-B4EC-NT plasmid constructs as described above and selected using antibiotic Blasticidin. After 24 hours of transfection, cells were seeded at low density. Next day, cells were treated with 10 ~,g/ml of Blasticidin. After two weeks of drug selection, surviving cells were pooled and selected further for single cell clone expansion. After establishing stable cells, they were maintained at 4 ~.g/ml Blasticidin. Conditioned media were tested to confirm expression and secretion of the respective recombinant proteins. Specificity of expression was confirmed by Western blot with anti-B4 mono- or polyclonal ABs and B2EC-AP reagent binding and competition assays.
4) Protein purification HEK293 cells were transiently transfected with a plasmid encoding secreted form of EphB4ectodomain (B4ECv3). Conditional media was harvested and supplemented with 10 mM imidazole, 0.3 M NaCl and centrifuged at 20,OOOg for 30 min to remove cell debris and insoluble particles. 80 ml of obtained supernatant were applied onto the pre-equilibrated column with 1 ml of Ni-NTA-agarose ((~iagen) at the flow rate of 10 ml/h.
After washing the column with 10 ml of 50 mh/I Tris-HCI, 0.3 M NaCI and 10 mM imida2ole, pH 8, remaining proteins were eluted with 3 ml of 0.25 M imida~ole. Eluted proteins were dialysed against 20 mM Tris-HCI, 0.15 M NaCI, pH 8 overnight. Purity and identity of B4ECv3 was verified by PAGE/Coomassie G-250 and Western blot with anti-Eph.B4 antibody. Finally, the concentration of B4ECv3 was measured, and the protein was aliquoted and stored at -70 °C.
B4EC-FC protein and B2EC-FC protein were similarly purified.
5) Biochemical Assays A. binding assay 10 ~ul of Ni-NTA-Agarose were incubated in microcentrifuge tubes with 50 ~.l of indicated amount of B4ECv3 diluted in binding buffer BB (20 mM Tris-HCI, 0.15 M NaCI, 0.1% bovine serum albumin pH 8) After incubation for 30 min on shaking platform, Ni-NTA
beads were washed twice with 1.4 ml of BB, followed by application of 50 ~.l of B2-AP in the final concentration of 50 nM. Binding was performed for 30 min on shaking platform, and then tubes were centrifuged and washed one time with 1.4 ml of BB. Amount of precipitated AP was measured colorimetrically after application of PNPP.

B. Iinhibition assay Inhibition in solution. Different amounts of B4ECv3 diluted in 50 ~,1 of BB
were pre-incubated with 50 ~.l of 5 nM B2EC-AP reagent (protein fusion of Ephrin B2 ectodomain with placental alkaline phosphatase). After incubation for 1 h, unbound B2EC-AP was precipitated with 5,000 HEK293 cells expressing membrane-associated full-length EphB4 for 20 min. Binding reaction was stopped by dilution with 1.2 ml of BB, followed by centrifugation for 10 min. Supernatants were discarded and alkaline phosphatase activities associated with collected cells were measured by adding para-nitrophenyl phosphate (PNPP) substrate.
Cell based inhibition. B4ECv3 was serially diluted in 20 mM Tris-HCl, 0.15 M
NaCI, 0.1% BSA, pH 8 and mixed with 5,000 HEI~293 cells expressing membrane-associated full-length Ephrin B2. After incubation for 1 h, 50 ~,1 of 5 nM B4EC-AP reagent (protein fusion of EphB4 ectodomain with placental alkaline phosphatase were added into each tube for 30 min to detect unoccupied Ephrin B2 binding sites. Binding reactions were stopped by dilution with 1.2 ml of BB and centrifugation. Colorimetric reaction of cell-pr ecipitated AP was developed with PNPP substrate.
C. B4EC-FC binding assay P~oteiya A-agaf~ose based assail. 10 ~l of Protein A-agarose were incubated in Eppendorf tubes with 50 ~.l of indicated amount of B4.EC-FC diluted in binding buffer BB
(20 mM Tris-HCI, 0.15 M NaCI, 0.1 % BSA pH 8). After incubation for 30 min on shaking platform, Protein AAagarose beads were washed twice with 1.4 ml of BB, followed by application of 50 ~.l of B2ECAP reagent at the final concentration of 50 nM.
Binding was performed for 30 min on shaking platform, and then tubes were centrifuged and washed once with 1.4 ml of BB~ Colorimetric reaction of precipitated AP was measured after application of PNPP (Fig. 6).
Nitrocellulose based assay. B4EC-FC was serially diluted in 20 mM Tris-HCI, 0.15 M NaCI, 50 ~,g/ml BSA, pH 8. 2 ~.l of each fraction were applied onto nitrocellulose strip and spots were dried out for 3 min. Nitrocellulose strip was blocked with 5% non-fat milk for 30 min, followed by incubation with 5 nM B2EC-AP reagent. After 45 min incubation for binding, nitrocellulose was washed twice with 20 mM Tris-HCl, 0.15 M NaCI, 50 ~g/ml BSA, pH 8 and color was developed by application of alkaline phosphatase substrate Sigma Fast (Sigma).
D. B4EC-FC inhibition assay If~laibitiora in solutiofa. See above, for B4ECv3. The results were shown in Figure 7.
Cell based inhibition. See above, for B4ECv3.
E. B2EC-FC binding assay Pf~oteiya A-agay~ose based assay. See above, for B4EC-FC. The results were shown in Figure 8.
Nitf°ocellul~se based assay. See above, for B4EC-FC.
6) Cell-Based Assays A. Growth Inhibition Assay Human umbilical cord vein endothelial cells (HIJ~EC) (1.5x103) are plated in a well plate in 100 ~,l of EBM-~ (Clonetic # CC3162). After 24 hours (day 0), the test recombinant protein (100 g,1) is added to each well at 2X the desired concentration (5-7 concentration levels) in EBM-2 medium. ~n day 0, one plate is stained with 0.5% crystal violet in 20% methanol for 10 minutes, rinsed ~rith v~~ater, snd air-dried.
The remaining plates are incubated for 72 h at 37 °C. After 72 h, plates are stained with 0.5% crystal violet in 20%
methanol, rinsed with water and airdried. The stain is eluted with 1:1 solution of ethanol: 0.1 M sodium citrate (including day 0 plate), and absorbance is measured at 540 nm with an ELISA reader (Dynatech Laboratories). Day 0 absorbance is subtracted from the 72 h plates and data is plotted as percentage of control proliferation (vehicle treated cells). IC50 (drug concentration causing 50% inhibition) is calculated from the plotted data.
B. Cord Formation Assay (Endothelial Cell Tube Formation Assay) Matrigel (60 ~,l of 10 mg/ml; Collaborative Lab # 35423) is placed in each well of an ice-cold 96-well plate. The plate is allowed to sit at room temperature for 15 minutes then incubated at 37 °C for 30 minutes to permit the matrigel to polymerize.
In the mean time, HUVECs are prepared in EGM-2 (Clonetic # CC3162) at a concentration of 2X105 cells/ml.

The test compound is prepared at 2X the desired concentration (5 concentration levels) in the same medium. Cells (500 ~,1) and 2X drug (500 ~.1) is mixed and 200 ~1 of this suspension are placed in duplicate on the polymerized matrigel. After 24 h incubation, triplicate pictures are tal~en for each concentration using a Bioquant Image Analysis system. Drug effect (IC50) is assessed compared to untreated controls by measuring the length of cords formed and number of junctions.
C. Cell Migration Assay Migration is assessed using the 48-well Boyden chamber and 8 ~,m pore size collagen-coated (10 ~,g/ml rat tail collagen; Collaborative Laboratories) polycarbonate filters (~smonics, Inc.). The bottom chamber wells receive 27-29 ~1 of DMEM medium alone (baseline) or medium containing chemo-attractant (bFGF, VEGF or Swiss 3T3 cell conditioned medium). The top chambers receive 45 ~ul of HCTVEC cell suspension (1X106 cells/ml) prepared in DMEM+1 % BSA with or without test compound. After 5 h incubation at 37 °C, the membrane is rinsed in fBS, fixed and stained in Diff Quiclc solutions. The filter is placed on a glass slide with the migrated cells facing down and cells on top are removed using a I~imwipe. The testing is performed in 4-6 replicates and five fields are counted from each well. Negative unstimulated control values are subtracted from stimulated control and drug treated values and data is plotted as mean migrated cell ~ S.D. IC50 is calculated from the plotted data.
Example 2. Extracellular domain fragments of Ep11B4 receptor inhibit angi~,~;enesis and tumor growth.
A. Globular domain of EphB4 is required for EphriaB2 binding and for the activity of Ep11B4-derived soluble proteins in endothelial tube formation assay.
To identify subdomain(s) of the ectopic part of EphB4 necessary and sufficient for the anti-angiogenic activity of the soluble recombinant derivatives of the receptor, four recombinant deletion variants of EphB4EC were produced and tested (Fig. 16).
Extracellular paxt of EphB4, similarly to the other members of EphB and EphA receptor family, contains N-terminal ligand-binding globular domain followed by cysteine-rich domain and two fibronectin type III repeats (FNIII). In addition to the recombinant B4-GCF2 protein containing the complete ectopic part of EphB4, we constructed three deletion variants of EphB4EC containing globular domain and Cys-rich domain (B4-GC); globular, Cys-rich and the first FNIII domain (GCF1) as well as the ECD version with deleted globular domain (CF2). Our attempts to produce several versions of truncated EphB4EC protein containing the globular domain alone were not successful due to the lack of secretion of proteins expressed from all these constructs and absence of ligand binding by the intracellularly expressed recombinant proteins. In addition, a non-tagged version of B4-GCF2, called GCFZ-F, containing complete extracellular domain of EphB4 with no additional fused amino acids was expressed, purified and used in some of the experiments described here.
All four C-terminally 6xHis tagged recombinant proteins were preparatively expressed in transiently transfected cultured mammalian cells and affinity purified to homogeneity from the conditioned growth media using chromatography on Ni2+-chelate resin (Fig. 17). Apparently due to their glycosylation, the proteins migrate on SDS-PAAG
somewhat higher than suggested by their predicted molecular weights of 34.7 kDa (GC), 41.5 (CF2), 45.6 kDa (GCF1) and 57.8 kDa (GCF2). Sequence of the extracellular domain of human EphB4 contains three predicted N-glycosylation sites (NXS/T) which are located in tlae Cys-rich domain, within the first fibronectin type III repeat and between the first and the second fibronectin repeats.
To confirm ability of the purified recombinant proteins to bind Ephrin B2, they were tested in an iaa vitf~~ binding assay. As expected, GC, GCF1 and GCF2, but not CF2 are binding the cognate ligand Ephrin B2 as confirmed by interaction between Ephrin B2 -allcaline phosphatase (Ephrin B2-AP) fusion protein with the B4 pr~teins immobilised on Ni'+-resin or on nitrocellulose membraale (Fig. 17).
All four proteins were also tested for their ability to block ligand-dependent dimerization and activation of Eph B4 receptor kinase in PC3 cells. The PC3 human prostate cancer cell line is lmown to express elevated levels of human Eph B4.
Stimulation of PC3 cells with Ephrin BZ IgG Fc fusion protein leads to a rapid induction of tyrosine phosphorylation of the receptor. However, preincubation of the ligand with GCF2, GCF1 or GC, but not CF2 proteins suppresses subsequent EphB4 autophosphorylation.
Addition of the proteins alone to the PC3 cells or preincubation of the cells with the proteins followed by changing media and adding the ligand does not affect EphB4 phosphorylation status.
Further, we found that globular domain of EphB4 is required for the activity of EphB4-derived soluble proteins in endothelial tube formation assay.
B. Effects of soluble EphB4 on HUV/AEC in vity-o.

Initial experiments were performed to determine whether soluble EphB4 affected the three main stages in the angiogenesis pathway. These were carried out by establishing the effects of soluble EphB4 on migration / invasion, proliferation and tubule formation by HLJV/AEC in vitro. Exposure to soluble EphB4 significantly inhibited both bFGF
and VEGF-induced migration in the Boyden chamber assay in a dose-dependent manner, achieving significance at nM (Fig. 18). Tubule formation by HUV/AECS on wells coated with Matrigel was significantly inhibited by soluble Ep11B4 in a dose-dependent manner in both the absence and presence of bFGF and VEGF (Fig. 19). We also assessed iJZ
vitro, whether nM of soluble EphB4 was cytotoxic for HCTVECS. Soluble EphB4 was found to have no detectable cytotoxic effect at these doses, as assessed by MTS assay (Fig. 20).
C. Soluble EphB4 receptor Inhibits Vascularization of Matrigel Plugs, in vivo To demonstrate that soluble Ep11B4 can directly inhibit angiogenesis in vivo, we performed a murine matrigel plug experiment. Matrigel supplemented with bFGF
and VEGF
with and without soluble EphB4 was injected s.c. into Balb/C nu/numice, forming semi-solid plugs, for six days. Plugs without growth factors had virtuallyno vascularization or vessel structures after 6 days (Fig. 21). In contrast, plugs supplemented with bFGF
and VEGF lead extensive vascularization and vessels throughout the plug. Plugs taken from mice treated with ~ g of soluble EphB4 had markedly reduced vascularization of plugs, comparable to plugs without growth factor (Fig. 21). Furthermore, histological examination of plugs showed decreased vessel staining (Fig. 21). Treatment at 0 ~.g/dose significantly lrlhlblted the andoullt of infiltration in Matrigel plugs compared to control (Fig. 21).
We examined EphB4 receptor phosphorylation in HUVECs by performing Western blot analyses with lysates from soluble Ep11B4-treated cells and antibodies against phosphor-tyrosine. We found that soluble EphB4 treatment of serum-starved HUVECs stimulated a rapid and transient decrease in the level of phosphorylated EphB4, in the presence of EphrinB2Fc, EphB4 ligand dimer. Ephrin B2Fc without the soluble EphB4 protein induced phosphorylation of EphB4 receptor (Fig. 22).
D. Effects of soluble EphB4 on tumor growth, in vitro.
We found that soluble Ep11B4 inhibits the growth of SCC15 tumors grown in Balb/C
Nu/Nu mice (Fig. 23).
E. Soluble EphB4 inhibited corneal neovascularization To further investigate the antiangiogenic activity of soluble EphB4 in vivo, we studied the inhibitory effect of administration of soluble EphB4 on neovascularization in the mouse cornea induced by bFGF. Hydron Pellets implanted into corneal micropocket could induce angiogenesis, in the presence of growth factors, in a typically avascular area. The angiogenesis response in mice cornea was moderate, the appearance of vascular buds was delayed and the new capillaries were sparse and grew slowly. Compared with the control group, on day 7 of implantation, the neovascularization induced by bFGF in mice cornea was markedly inhibited in soluble EphB4-treated group (Fig. 24).
F. Effects of soluble EphB4 on tumor growth, in vivo.
The same model was used to determine the effects of soluble EphB4 in viv~.

tumors implanted subcutaneously, pre-incubated with matrigel and with or w/o growth factors, as well as implanted sc alone, and mice treated sc or ip daily with 1-Sug of soluble EphB4 were carried out.
Tumors in the control group continued to grow steadily over the treatment period, reaching a final tumor volume of mm3. However, animals inj ected with soluble Eph~4 exhibited a significantly (p<0.0/) reduced growth rate, reaching a final tumor volume of only mm3 (Fig. 25). Similar results were obtained in two further cohorts of such tumor-bearing mice. Soluble EphB4 administration appeared to be well tolerated ifa viv~, with no sigluficant effect on body weight or the general well-being of the animals (as determined by the absence of lethargy, intermittent hunclalng, tremors or disturbed breathing patterns).
G. Effects of soluble Eph~4 on tumor histology.
Histological analysis revealed the presence of a central area of necrosis in all SCC15 tumors, which was usually surrounded by a viable rim of tumor cells um in width. The central necrotic areas were frequently large and confluent and showed loss of cellular detail.
Necrosis, assessed as a percentage of tumor section area, was significantly (p<0.02) more extensive in the soluble EphB4-treated group (% necrosis in treated vs.
control). To determine whether the reduced volume of soluble EphB4 treated tumors was due to an effect of this protein on the tumor vascular supply, endothelial cells in blood vessels were identified in tumor sections using immunostaining with an anti-platelet cell adhesion molecule (PECAM-1; CD31) antibody (Fig. 26) and the density of microvessels was assessed.
Microvessel density was similar in the outer viable rim of tumor cells (the uniform layer of cells adjacent to the tumor periphery with well defined nuclei) in control and soluble EphB4-treated tumors. Microvessel density was significantly in the inner, less viable region of tumor cells abutting the necrotic central areas in soluble EphB4-treated than control tumors. Fibrin deposition, as identified by Masson's Trichrome staining, was increased in and around blood vessels in the inner viable rim and the central necrotic core of soluble EphB4 treated than control tumors. In the outer viable rim of soluble EphB4 treated tumors, although the vessel lumen remained patent and contained red blood cells, fibrin deposition was evident around many vessels. Soluble EphB4 was found to have no such effects on the endothelium in the normal tissues examined (lungs, liver and kidneys).
H. Materials and Methods 1) Expression constructs To construct expression vectors for producing soluble, 6xHis-tagged EphB4-ECD
variants, cloned full-length human EphB4 cDNA was amplified by PCR using the following oligo primers: TACTAGTCCGCCATGGAGCTCCGGGTGCTGCT (common EphB4 N-terminal primer) and GCGGCCGCTTAATGGTGATGGTGA TGATGAGCCGAAGGA
GGGGTGGTGCA (B4-GC), AGCGGCCGCTTAATGGTGATGGTGAT
GATGGACATTGA CAGGCTCAAATGGGA (B4-GCF1) or TGCGGCCGCTTAATGGTGATGGTGATGAT
GCTGCTCCCGCCAGCCCTCGCTCTCAT (B4-GCF2). The resulting PCR fragments were TA-cloned into mammalian expression vector pEF6/VS-His-T~P~ (Invitrogen) under EF-lc~
promoter control. The expressed recombinant proteins encode the following fragments of the mature extracellular part of human EphB4: amino acid positions 1-522 (GCF2), 1-(GCF1) and 1-312 (GC). To generate the B4-CF2 deletion (& amino acids 13-183) PCR
fragment for pEF6 cloning, EphB4 cDNA was amplified by two-step overlap PCR
using oligo primers TACTAGTCCGCCATGGAGCTCCGGGTGCTGCT, CAGCTGAGTTTCCAATTTTGTGTTC, GAACACAAAATTGGAAACTCAGCTGACTGTGAACCTGACandGCGGCCGCCCTG
CTCCCGCCAGCCCTCGCT.
Vector for producing secreted human EphrinB2-alkaline phosphatase (B2-AP) reagent was constructed by PCR amplification of human Ephrin B2 cDNA using primers TAAAGCTTCCGCCATGGCTGTGAGAAGGGACandTAGGATCCTTCGGAACCG
AGGATGTTGTTCCC and cloning the resulting fragment, digested with Hind III and Bam HI, into Hind III-Bgl II digested pAPTag2 vector (GenHunter, Inc.). In each case, inserts in expression vectors were verified by complete sequencing.
2) Antibodies and other reagents Anti-Eph B4 monoclonal antibodies mAB79 and mAB23 were raised in mice against the GCF2 protein containing amino acids 1-522 of mature human EphB4 and purified from hybridoma supernatants by Protein A chromatography. The anti-phosphotyrosine antibody 4610 was from UBI (Lake Placid, NY). Protein G-HRP conjugate was purchased from Bio-Rad.
3) Expression and purification of EphB4-derived recombinant proteins To produce the EplzB4-ECD soluble proteins, cultured human embryonic kidney cells HEK293T were transfected with the corresponding plasmid constructs using standard calcium phosphate or Lipofectamin 2000 reagent (Invitrogen) protocols. Twelve to sixteen hours post-transfection, the growth medium (DMEM+10% fetal bovine serum) was aspirated, cells washed once with serum free DMEM and replaced with serum free DMEM.
Conditioned media containing the secreted proteins were harvested 72-96 hours later, clarified by centrifugation and used for purification of His-tagged proteins using Ni-NTA
Agarose (Qiagen). The purity and quantity of the recombinant proteins was tested by SDS-PAAG electrophoresis with Coomassie Blue or silver staining, Western blotting and UV
spectroscopy. Purified proteins were dialysed against 20 mlVl Tris-HCI, 0.15 M
NaCI, pH 8 and stored at -~0 ~C.
To test ligand binding properties of the proteins, 10 ~,1 of Ni-NTA-Agarose (Qiagen) were incubated in microcentrifuge tubes with 10-S00 ng sample of a B4-ECD
protein diluted in 0.5 ml of binding buffer BB (20 mM Tris-HCI, 0.1 S M NaCl, 0.1 % bovine serum albumin, pH ~). After incubation for 30 min on shaking platform, Ni-NTA beads were washed twice with 1.4 ml of BB, followed by addition of B2-AP fusion protein at concentration of 50 nM.
Binding was performed for 30 min on a shaking platform. Tubes were centrifuged and washed once with 1.4 ml of BB. Amount of precipitated AP was measured colorimetrically at 420 nm after application of p-nitrophenyl phosphate (PNPP) and incubation for 5-30 min.
4) Immunoprecipitation All lysates were processed at 4 °C. Cells were lysed in 1 ml of buffer containing 20 mM Hepes at pH 7.4, 100 mM sodium chloride, 50 mM sodium fluoride, 2 mM EDTA, mM EGTA, 1 mM sodium orthovanadate, 1%(v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1 mM phenyl methylsulphonyl fluoride (added freshly) and 100U Trasylol.
Lysates were scraped into Epperidorf tubes and 50 ~.1 of boiled, formalin-fixed Stczplaylococcus aureus was added (Calbiochem, San Diego). After 30 min of mixing, the lysates were centrifuged for 5 min at 25,OOOg in a minifuge and the supernatants transferred to new tubes containing the appropriate antibody. Lysates were mixed with antibodies for 1 h, after which time 50 ~1 of protein A-Sepharose beads were added and the contents of the tubes mixed for 1 h to collect the immunoprecipitates. Protein A beads were collected by centrifugation at 25,OOOg for 30 s.
The supernatants were discarded and the beads washed three times with 1 ml lysis buffer minus deoxycholate.
5) Cell-based EphB4 tyrosine lcinase assay The human prostate carcinoma cell line PC3 cells were maintained in RPMI
medium with 10% dialyzed fetal calf serum and 1% penicillin/streptomycin/neomycin antibiotics mix.
Cells were maintained at 37 °C in a humidified atmosphere of 5°/~ C~Z/95% air. Typically, cells were grown in 60 mm dishes until confluency and were either treated with mouse Eplv-in E2-Fc fusion at 1 ~,g/ml in I~PMI for 10 min to activate EphE4 receptor or plain medium as a control. To study the effect of different derivatives of soluble EphE4 ECD
proteins on EphB4 receptor activation, three sets of cells were used. In the first set, cells were treated with various proteins (5 proteins; GC, GCF1, GCF2, GCF2-F, CF2) at 5 ~.g/ml for 20 min. W the second set of cells, prior to application, proteins were premixed with ephrir~2-Fc at 1:5 (EphB4 protein: E2-Fc) molar ratio, incubated for 20 rnin and applied on cells for 10 min. In the third set of cells, cells were first treated with the proteins for 20 min at 5 ~,g/ml, media was replaced with fresh media containing 1 ~,ghnl of EphrinB2-Fc and incubated for another 10 min.
After the stimulation, cells were immediately harvested with protein extraction buffer containing 20 mM Tris-HCI, pH 7.4, 150 mM NaCl, 1% (v/v) Triton X100, 1 mM
EDTA, 1 mM PMSF, 1 mM Sodium vanadate. Protein extracts were clarified by centrifugation at 14,000 rpm for 20 min at 4 °C. Clarified protein samples were incubated overnight with protein A/G coupled agarose beads pre-coated with anti-EphB4 monoclonal antibodies. The IP complexes were washed twice with the same extraction buffer containing 0.1%
Triton X100. The immunoprecipitated proteins were solubilized in 1X SDS-PAGE sample loading buffer and separated on 10% SDS-PAGE. For EphB4 receptor activation studies, electroblotted membrane was probed with anti-pTyr specific antibody 4610 at 1:1000 dilution followed by Protein G-HRP conjugate at 1:5000 dilutions.
6) Cell Culture Normal HUVECs were obtained from Cambrex (BioWhittaker) and maintained in EBM2 medium supplemented with 0.1 mg/ml endothelial growth supplement (crude extract from bovine brain), penicillin (50 U/ml), streptomycin (50 U/ml), 2 mrnol/1 glutamine and 0.1 mg/ml sodium heparin. Aliquots of cells were preserved frozen between passages 1 and 3.
For all experiments, HUVECs were used at passages 4 or below and collected from a confluent dish.

7) Endothelial Cell Tube Formation Assay Matrigel (60 q1 of lOmg/ml; Collaborative Lab, Cat. No. 35423) was placed in each well of an ice-cold 96-well plate. The plate was allowed to sit at room temperature for 15 minutes then incubated at 37 °C for 30 minutes to permit Matrigel to polymerize. In the mean time, human umbilical vein endothelial cells were prepared in EGM-2 (Clonetic, Cat. No.
CC3162) at a concentration of 2x105 cells/ml. The test protein was prepared at 2x the desired concentration (5 concentration levels) in the same medium. Cells (500 ~,1) and 2x protein (500 p,1) were mixed and 200 ~,1 of this suspension were placed in duplicate on the polymerized Matrigel. After 24 h incubation, triplicate pictures were taken for each concentration using a Bioquant Image Analysis system. Protein addition effect (ICSO) was assessed compared to untreated controls by measuring the length of cords formed and number of junctions.
~) Cell Migration Assay Chemotaxis of PnJVECs to VEGF was assessed using a modified Boyden chamber, transwell membrane filter inserts in 24 well plates, 6.5 rmn diam, 8 ~m pore size, 10 ~.m thick matrigel coated, polycarbonate membranes (BD Biosciences). The cell suspensions of HUVECs (2x 105 cells/ml) in 200 ~1 of EBM were seeded in the upper chamber and the soluble EphB4 protein were added simultaneously with stimulant (VEGF or bFGF) to the lower compartment of the chamber and their migration across a polycarbonate filter in response tol0- 20 ng/ml of VEGF with or without 100 nM-1 ~M test compound was investigated. After incubation for 4-24 h at 37 °C, the upper surface of the filter was scraped with swab and filters were fixed and stained with Diff Quick. Ten random fields at 200x mag were counted and the results expressed as mean # per field. Negative unstimulated control values were subtracted from stimulated control and protein treated sample values and the data was plotted as mean migrated cell ~ S.D. ICSn was calculated from the plotted data.
9) Growth Inhibition Assay HUVEC (1.5x103 cells) were plated in a 96-well plate in 100 ~1 of EBM-2 (Clonetic, Cat. No. CC3162). After 24 hours (day 0), the test recombinant protein (100 ~,l) is added to each well at 2x the desired concentration (5-7 concentration levels) in EBM-2 medium. On day 0, one plate was stained with 0.5% crystal violet in 20% methanol for 10 minutes, rinsed with water, and air-dried. The remaining plates were incubated for 72 h at 37 °C. After 72 h, plates were stained with 0.5% crystal violet in 20% methanol, rinsed with water and air-dried.
The stain was eluted with 1:1 solution of ethanol: O.1M sodium citrate (including day 0 plate), and absorbance measured at 540 nm with an ELISA reader (Dynatech Laboratories).
Day 0 absorbance was subtracted from the 72 h plates and data is plotted as percentage of control proliferation (vehicle treated cells). ICSO value was calculated from the plotted data.
10) Murine Matrigel Plug Angiogenesis Assay In vivo angiogenesis was assayed in mice as growth of blood vessels from subcutaneous tissue into a Matrigel plug containing the test sample. Matrigel rapidly forms a solid gel at body temperature, trapping the factors to allow slow release and prolonged exposure to surrounding tissues. Matrigel (8.13 mg/ml, 0.5 ml) in liquid form at 4 °C was mixed with Endothelial Cell Growth Supplement (EGGS), test proteins plus ECGS
or Matrigel plus vehicle alone (PBS containing 0.25°/~ BSA). hJlatnigel (O.SmI) was injected into the abdominal subcutaneous tissue of female nu/nu mice (6 wks old) along the peritoneal rnid line. There were 3 mice in each group. The animals were cared for in accordance with institutional and NIH guidelines. At day 6, mice were sacrificed and plugs were recovered and processed for histology. Typically the overlying skin was removed, and gels were cut out by retaining the peritoneal lining for support, fixed in 10% buffered formalin in PBS and embedded in paraffin. Sections of 3 ~.m were cut and stained with Hc~E or Masson's trichrome stain and examined under light microscope 11) Mouse Corneal Micropoclcet assay Mouse corneal micropocket assay was performed according to that detailed by Kenyon et al., 1996. Briefly, hydron pellets (polyhydroxyethyhnethacrylate [polyHEMA], W terferon Sciences, New Brunswick, NJ, U.S.A.) containing either 90 ng of bFGF (RED) or 180 ng of VEGF (R&D Systems, Minneapolis, MN, U.S.A.) and 40 ~.g of sucrose aluminium sulfate (Sigma) were prepared. Using an operating microscope, a stromal linear keratotomy was made with a surgical blade (Bard-Parker no. 15) parallel to the insertion of the lateral rectus muscle in an anesthetized animal. An intrastromal micropocket was dissected using a modified von Graefe knife (2"30 mm). A single pellet was implanted and advanced toward the temporal corneal limbus (within 0~7~1~0 mm for bFGF pellets and 0~5 mm for VEGF
pellets). The difference in pellet location for each growth factor was determined to be necessary given the relatively weaker angiogenic stimulation of VEGF in this model.
Antibiotic ointment (erythromycin.) was then applied to the operated eye to prevent infection and to decrease surface irregularities. The subsequent vascular response was measured extending from the limbal vasculature toward the pellet and the contiguous circumferential zone of neovascularization Data and clinical photos presented here were obtained on day 6 after pellet implantation, which was found to be the day of maximal angiogenic response.
12) In vitro invasion assay "Matrigel" matrix-coated 9-mm cell culture inserts (pore size, 8 ~,m; Becton Dickinson, Fran~lin Lakes, IVJ) were set in a 24-well plate. The I~UUVEC cells were seeded at a density of 5x103 cells per well into the upper layer of the culture insect and cultured with serum-free EBM in the presence of EphB4 ECD for 24 h. The control group was cultured in the same media without EphB4. Then 0.5 ml of the human SCC15 cell line, conditioned medium was filled into the lower layer of the culture insert as a chemo-attractant. The cells were incubated for 24 h, then the remaining cells in the upper layer were swabbed with cotton and penetrating cells in the lower layer were fixed with 5°J°
glutaraldehyde and stained with Diff Quick. The total number of cells passing through the Matrigel matrix and each 8 ~m pore of the culture insert wascounted using optical microscopy and designated as an invasion index (cell number/area).
13) SCC15 tumor growth in mice Subcutaneously inject logarithmically growing SCC15, head and neclc squamous cell carcinoma cell line, at SX10G cell density; with or without EphB4 ECD in the presence or absence of human bFGF, into athymic Balb/c nude mice, along with Matrigel (BD
Bioscience) synthetic basement membrane (1:1 v/v), and examine tumors within 2 weeks.
Tumor volumes in the EphB4 ECD group, in the presence and absence of growth factor after implantation were three-fold smaller than those in the vehicle groups. There was no difference in body weight between the groups. Immunohistochemical examination of cross-sections of resected tumors and TUNEL-positive apoptosis or necrosis, CD34 immunostaining, and BrdU proliferation rate will be performed, after deparaffinized, rehydrated, and quenched for endogenous peroxidase activity, and after 10 min permeabilization with proteinase K. Quantitative assessment of vascular densities will also be performed. Local intratumoral delivery or IV delivery of EphB4 ECD will also be performed twice a week.
30 athymic nude mice, BALB/c (nu/nu), were each injected with 1 x 106 B16 melanoma cells with 0.1 ml PBS mixed with 0.1 ml matrigel or 1.5 x 106 SCC15 cells resuspended in 200 ~,1 of DMEM serum-free medium and injected subcutaneously on day 0 on the right shoulder region of mice. Proteins were injected intravenously or subcutaneously, around the tumor begimung on day 1 at a loading dose of 4 ~g/mg, with weekly injections of 2ug/mg. (10 ~,g/g, 50 ~,g/kg/day), and at 2 weeks post-inoculation. Mice are sacrificed on Day 14. Control mice received PBS 50 ~1 each day.
14) Tumor formation in nude mice All animals were treated under protocols approved by the institutional animal care committees. Cancer cells (5x106) were subcutaneously inoculated into the dorsal skin of nude mice. When the tumor had grown to a size of about 100 rmn3 (usually it took 12 days), sEphB4 was either intraperitoneally or subcutaneously injected once/day, and tumorigenesis was monitored for 2 weeks. Tumor volmne was calculated according to the formula ezZxb, where ca and b are the smallest and largest diameters, respectively. A
Student's t test was used to compare tumor volwnes, with 1'~.OS being considered significant.
15) Quantification of microvessel density Tumors were fixed in 4% formaldehyde, embedded in paraffin, sectioned by 5 Vim, and stained with hematoxylineosin. Vessel density was semi-quantitated using a computer-based image analyzer (five fields per section from three mice in each group).
Example 3. EphB4 Is Upregulated and Imparts Growth Advantage in Prostate Cancer A. Expression of EphB4 in prostate cancer cell lines We first examined the expression of EphB4 protein in a variety of prostate cancer cell lines by Western blot. We found that prostate cancer cell lines show marked variation in the abundance of the 120 kD EphB4. The levels were relatively high in PC3 and even higher in PC3M, a metastatic clone of PC3, while normal prostate gland derived cell lines (MLC) showed low or no expression of EphB4 (Fig. 27A). We next checlced the activation status of EphB4 in PC3 cells by phosphorylation study. We found that even under normal culW re conditions, EphB4 is phosphorylated though it can be further induced by its ligand, ephrin B2 (Fig. 27B).
B. Expression of EphB4 in clinical prostate cancer samples To determine whether EphB4 is expressed in clinical prostate samples, tumor tissues and adjacent normal tissue from prostate cancer surgical specimens were examined. The histological distribution of EphB4 in the prostate specimens was determined by immunohistochemistry. Clearly, EphB4 expression is confined to the neoplastic epithelium (Fig. 28, top left), and is absent in stromal and normal prostate epithelium (Fig. 28, top right).
In prostate tissue array, 24 of the 32 prostate cancers examined were positive. We found EphB4 mRNA is expressed both in the normal and tumor tissues of clinical samples by quantitative RT-PCR. However, tumor EphB4 mRNA levels were at least 3 times higher than in the normal in this case (Fig. 28, lower right).
C. p53 and PTEN iWibited the expression of EphB4 in PC3 cells PC3 cells are known to lack PTEN expression (Davis, et al., 1994, Science.
266:816-819) and wild-type p53 function (Gale, et al., 1997, Cell Tissue Res. 290:227-241). We investigated whether the relatively high expression of EphB4 is related to p53 and/or PTEN
by re-introducing wild-type p53 and/or PTEN into PC3 cells. To compensate for the transfection efficiency and the dilution effect, transfected cells were souted for the cotransfected truncated CI~4 marker. We found that the expression of EphB4 in PC3 cells was reduced by the re-introduction of either wild-type p53 or PTEN. The co-transfection of p53 and PTEN did not further inhibit the expression of EphB4 (Fig. 29A).
D. Retinoid X receptor (RXR a ) regulates the expression of EphB4 We previously found that RXRa was down-regulated in prostate cancer cell lines (thong, et al., 2003, Cancer Biol Ther. 2:179-184) and here we found EphB4 expression has the reverse expression pattern when we looked at "normal" prostate (MLC), prostate cancer (PC3), and metastatic prostate cancer (PC3M) (Fig. 27A), we considered whether RXRa regulates the expression of Ep11B4. To confirm the relationship, the expression of EphB4 was compared between CWR22R and CWR22R-RXRa, which constitutively expresses RXRa.
We found a modest decrease in EphB4 expression in the RXRa overexpressing cell line, while FGF8 has no effect on EphB4 expression. Consistent with initial results, EphB4 was not found in "normal" benign prostate hypertrophic cell line BPH-1 (Fig. 29B).
E. Growth factor signaling pathway of EGFR and IGF-1R regulates EphB4 expression EGFR and IGF-1R have both been shown to have autocrine and paracrine action on PC3 cell growth. Because we found that EphB4 expression is higher in the more aggressive cell lines, we postulated that EphB4 expression might correlate with these pro-survival growth factors. We tested the relationship by independently blocking EGFR and signaling. EphB4 was down-regulated after blocking the EGFR signaling using EGFR kinase inhibitor AG 1478 (Fig. 30A) or upon blockade of the IGF-1R signaling pathway using IGF-1R neutralizing antibody (Fig. 30B).
F. EphB4 siRNA and antiasnsa ODNs inhibit PC3 cell viability To define the significance of this EphB4 overexpression in our prostate cancer model, we concentrated our study on PC3 cells, which have a relatively high expression of EphB4.
The two approaches to decreasing EphB4 expression were siRNA and AS-~DNs. A
number of different phosphorothioate-modified AS-~DNs complementary to different segments of the EphB4 coding region were tested for specificity and efficacy of EphB4.
inhibition. Using 293 cells transiently transfected with full-length EphB4. expression vector AS-10 was found to be the most effective (Fig. 31B). A Similar approach was applied to the selection of specific siRNA. EphB4 siRNA 472 effectively knocks down EphB4 protein expression (Fig.
31A). Both siRNA 472 and antiasnsa AS-10 ~DN reduced the viability of PC3 cells in a dose dependent masmer (Fig. 31 C, D). TJnrelated siRNA or sense oligonucleotide had no effect on viability.
G. EphB4 siRNA and antiasnsa ~DNs inhibit the mobility of PC3 Cells PC3 cells can grow aggressively locally and can form lymph node metastases when injected orthotopically into mice. In an effort to study the role of EphB4 on migration of PC3 cells ifa vita~, we performed a wound-healing assay. When a wound was introduced into a monolayer of PC3 cells, over the course of the next 20 hours cells progressively migrated into the cleared area. However, when cells were transfected with siRNA 472 and the wound was introduced, this migration was significantly inhibited (Fig. 31E).
Pretreatment of PC3 cells with 10 p,M EphB4 AS-10 for 12 hours generated the same effect (Fig. 31F). W
addition, lcnoclc-down of EphB4 expression in PC3 cells with siRNA 472 severely reduced the ability of these cells to invade Matrigel as assessed by a double-chamber invasion assay (Fig. 31 G), compared to the control siRNA.
H. EphB4 siRNA induces cell cycle arrest and apoptosis in PC3 cells Since knock-down of EphB4 resulted in decreased cell viability (Fig. 31 C) we sought to determine whether this was due to effects on the cell cycle. In comparison to control siRNA transfected cells, siRNA 472 resulted in an accumulation of cells in the sub GO and S
phase fractions compared to cells treated with control siRNA. The sub GO
fraction increased from 1 % to 7.9%, and the S phase fraction from 14.9 % to 20.8 % in siRNA 472 treated cells compared to control siRNA treated cells (Fig. 32A). Cell cycle arrest at sub GO and G2 is indicative of apoptosis. Apoptosis as a result of EphB4 knock-down was confirmed by ELISA assay. A dose-dependent increase in apoptosis was observed when PC3 cells were transfected with siRNA 472, but not with control siRNA (Fig. 32B). At 100 nM
there was 15 times more apoptosis in siRNA 472 transfected than control siRNA transfected PC3 cells.
I. Materials and Methods 1) P~eagents Neutralizing IGF-1P~ antibody was from RED Systems (Minneapolis MN). Anti-IGF-11((3), -EGFI~, -EphB4.(C-16) were from Santa Cruz Biotech (Santa Cruz, CA).
(3-actin monoclonal antibody was purchased from Sigma Chemical Co. (St Louis, MO).
Media and fetal bovine serum (FBS) were from Invitrogen (Carlsbad, CA). AG 14.78(4.-(3'-Chloroanilino)-6,7-dimethoxy-quinazoline) was from Calbiochem (San Diego, CA).
2) Antisense oligodeoxynucleotides and EphB4 siRNAs EphB4 specific antisense phosphorothioate-modified oligodeoxynucleotide (~DN) and sense ~DN were synthesized and purified by Qiagen (Alameda CA). The sequences are:
Sense, 5'-TCC-TGC-AAG-GAG-ACC-TTC-AC-3 ; AS1: 5'-GTG-CAG-GGA-TAG-CAG-GGC-CAT-3'; AS10: 5'-ATG-GAG-GCC-TCG-CTC-AGA-AA-3'. siRNAs were synthesized at the USC/Norris Comprehensive Cancer Center Microchemical Core laboratory. Sequences of EphB4 siRNAs are siRNA 472 5'-GGU-GAA-UGU-CAA-GAC-GCU-GUU-3' and siRNA 2303 5'-cuc-uuc-cga-ucc-cac-cue-cuu-3'. Negative control siRNA
to scrambled GAPDH was from Ambion (Austin, TX) 3) Cell lines and culture The prostate cancer cell lines, PC3, PC3M, DU145, ALVA31, LAPC-4, LNCaP, CWR22R and adult human normal prostate epithelial cell line MLC SV40, and BPH-1 were obtained and cultured as described previously (7). Stable cell line CWR22R-RXR, LNCaP-FGFB were established and cultured as described before (7, 33).
4) Generation of EphB4 monoclonal antibody The extracellular domain (ECD) of EphB4 was cloned into pGEX-4T-1 to generate GST-fused ECD (GST-ECD). EphB4ECD expressed as a GST fusion protein in BL21 E.
coli was purified by affinity chromatography and the GST domain was cleaved by thrombin.
Monoclonal antibody was generated and the sensitivity and specificity of the antibody was reconfirmed by Western blot with whole cell lysate of 293 cells stably transfected with EphB4.
5) One-Step RT-PCR and Quantitative RT-PCR
Total RNA was extracted using RNA STAT-60 (Tel-Test, lizc. Friendswood TX) from prostate cancer specimens and adjacent normal specimens. For duantitative RT-PCR
first strand cDNA was synthesized from 5 p.g of total RNA using Superscript III (Invitrogen, Carlsbad CA). Quantitative RT-PCR was performed on the Stratagene MX3000P
system (Stratagene, La Jolla CA) using S~'BR Green I Brilliant Mastemlix (Stragene) according to the manufacture's instructions. Optimized reactions for EphB4 and [3-actin (used as the normalizes gene) were 150 nM each of the forward primer ((3-actin, 5'-GGA-CCT-GAC-TGA-CTA-CCT-A-3'; EphB4., 5'-AAG-GAG-ACC-TTC-ACC-GTC-TT-3') and reverse primer ((3-actin 5'-TTG-AAG-GTA-GTT-TCG-TGG-AT-3'; EphB4, 5'-TCG-AGT-CAG-GTT-CAC-AGT-CA-3') with DNA denaturation/activation of polyrnssese at 95 °C for 10 min followed by 40 cycles of 95 °C for 30s, 60 °C for lmin, 72 °C for lmin. The specificity of the gene-specific amplification was confirmed by the presence of a single dissociation peals. All reactions were performed in triplicate with RT and no template negative controls.
6) Irnmunohistochemistry OCT-embedded tissues were sectioned at 5 ~,m and fixed in phosphate-buffered 4%
paraformaldehyde. Sections were washed for 3 x 5 min in PBS and endogenous peroxidase was blocked by incubation in 0.3% H202 in PBS for 10 min at room temperature.
Sections were incubated with Eph4 (C-16) antibody (1:50) for 1 h at room temperature followed by three washes in PBS and incubation with dou~ey anti-goat secondary antibody (Santa Cruz Biotech.) for 1 h at room temperature. Afterthree washes in PBS, peroxidase activity was localized by incubation in DAB substrate solution (Vector Laboratories, Inc.
Burlingame CA) for 10 min at room temperature. Sections were counterstained with Hematoxylin for 20 s, dehydrated and mounted. Negative control for staining was substitution of normal goat serum for primary antibody. Immunohistochemical staining on prostate array (BioMeda, Foster City, CA) was done using goat ABC Staining System (Santa Cruz Biotech.) according to the manufacturer's instructions.
7) Western blot Whole cell lysates were prepared using Cell Lysis Buffer (GeneHunter, Basgvukke TN) supplemented with protease inhibitor cocktail (Pierce, Rockford IL), unless otherwise noted. Total protein was detennined using the DC reagent system (Bio-Rad, Hercules CA).
Typically, 20 p,g whole cell lysate was run on 4-20% Tris-Glycine gradient gel. The samples were electro-transferred to PVDF membrane and the non-specific binding was blocked in TBST buffer (0.5 mM Tris-HCI, 45 mM NaCI, 0.05% Tween-20, pH 7.4) containing 5% non-fat milk. Membranes were first probed with primary antibody overnight, stripped with Restores Western Blot stripping buffer (Pierce, Rockford IL) and reprobed with (3-actin to confirm equivalent loading and transfer of protein. Signal was detected using SuperSignal West Femto Maximum Sensitivity Substrate (Pierce).

8) Phosphorylation analysis Cells growing in 60 mm dishes were either serum starved (1% FBS supplemented RPMI 164.0, 24~ hours) or cultured in normal conditions (10% FBS) a.nd then treated with or without 1 ~,g/ml mouse ephrin B2/F° for 10 min to activate EphB4 receptor Cleared cell lysates were incubated with EphB4 monoclonal antibody overnight at 4 °C. Antigen-antibody complex was immunoprecipitated by the addition of 100 q.1 of Protein G-Sepharose in 20 mM
sodium phosphate, pH 7.0 with incubation overnight at 4 °C.
Imrnunoprecipitates were analyzed by Western blot with pTyr specific antibody (Upstate, clone 4610) at 1:1000 dilution followed by incubation with protein G-HRP (Bio-Rad) at 1:5000 dilution. To monitor immunoprecipitation efficiency, a duplicate membrane was probed with EphB4 specific monoclonal antibody.

9) Transient transfection and sorting of transfected cells PC3 cells were cotransfected with pMACS 4.1 coding for CD4 and wild type p53 (pC53-SN3) or PTEN vector or both using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. The molar ratio of CD4 to p53 or PTEN or vector was 1:3 and total plasmid was 24 ~g for a 10 cm2 dish of 90% confluent cells using 60 ~1 of Lipofectamine 2000. 24 hours after transfection, a single cell suspension was made and sorted using truncated CD4 as a surface marker according to the manufacturer's protocol (Miltenyi Biotec, Germany). Sorted cells were lysed in 1 x SDS sampling buffer and analyzed by Western blot.

10) Study of IGF and EGF signaling pathway on the expression of EphB4 PC3 cells were seeded into 6-well plates and cultured until 80% confluent and treated with 2 ~,g/ml neutralizing IGF-1R monoclonal antibody, MAB391 (Hailey, et al., 2002, Mol Cancer Ther. 1:1349-1353), or with 1 nM AG 1478, a strong EGFR inhibitor (Liu, et al., 1999, J Cell Sci. 112 (Pt 14):2409-2417) for 24 h. Crude cell lysates were analyzed by Western blot. Band density was quantified with the Bio-Rad QuantityOne System software.

11) Cell viability assay PC3 cells were seeded on 48-well plates at a density of approximately 1 ~ 104 cells/well in a total volume of 200 ml. Media was changed after the cells were attached and the cells were treated with various concentrations (1-10 ~M) of EphB4 antiasnsa ~DN or sense ~DN as control. After three days media was changed and fresh ~DNs added.
Following a further 48 h incubation, cell viability was assessed by MTT as described previously (36). EphB4 siRNAs (10-100 nM) were introduced into 2 x 104 PC3 cells/well of a 48-well plate using 2 ~,1 of LipofectamineTM 2000 according to the manufacturer's instructions. 4. h post-transfection the cells were returned to growth media (RPMI 164.0 supplemented with 10 % FBS). liability was assayed by MTT 4.8 h following transfection.

12) Wound healing migration assay PC3 cells were seeded into 6-well plates and cultured until confluent. 10 ~M

or sense ~DN as control were introduced to the wells as described for the viability assay 12 hours before wounding the monolayer by scraping it with a sterile pipette tip.
Medium was changed to RPMI 1640 supplemented with 5% FBS and fresh ~DNs. Confluent cultures transfected with 50 nM siRNA 472 or GAPDH negative control siRNA 12 hours prior to wounding were also examined. The healing process was examined dynamically and recorded with a Nilcon Coolpix 5000 digital camera with microscope adapter.

13) Invasion assay PC3 cells were transfected with siRNA 472 or control siRNA using LipofectamineTM
2000 and 6 hours later 0.5 x 105 cells were transferred into ~ ~,m Matrigel-precoated inserts (BD Bioscience, Palo Alto, CA). The inserts were placed in companion wells containing RPMI supplemented with 5 % FBS and 5 ~,g/ml fibronectin as a chemoattractant.
Following 22 h incubation the inserts were removed and the noninvading cells on the upper surface were removed by with a cotton swab. The cells on the lower surface of the membrane were fixed in 100% methanol for 15 min, air dried and stained with Giemsa stain for 2 min.
The cells were counted in five individual high-powered fields for each membrane under a light microscope.
Assays were performed in triplicate for each treatment group.

14) Cell cycle analysis 80% confluent cultures of PC3 cells in 6-well plates were transfected with siRNA472 (100 nM) using LipofectamineTM 2000. 24 hours after transfection, cells were trypsinized, washed in PBS and incubated for 1 h at 4oC in 1 ml of hypotonic solution containing 50 ~g/ml propidium iodide, 0.1% sodium citrate, 0.1 Triton X-100 and 20 ~g/ml Dnase-free rnaseA. Cells were analyzed in linear mode at the USC Flow cytometry facility.
results were expressed as percentages of elements detected in the different phases of the cell cycle, namely Sub GO peak (apoptosis), GO/G1 (no DNA synthesis), S (active DNA
synthesis), G2 (premitosis) and M (mitosis).

15) Apoptosis ELISA
Apoptosis was studied using the Cell Death Detection ELISApIus I~it (ruche, Piscataway, N~ according to the manufacturers instructions. Briefly, PC3 SO%
confluent cultures in 24-well plates were transfected using LipofectamineT~ 2000 with various concentrations (0-100 nM) of sirNA 472 or 100 nM control siRNA. 16 hours later, cells were detached and 1 x 104 cells were incubated in 200 w1 lysis buffer. Nuclei were pelleted by centrifugation and 20 ~,l of supernatant containing the mono- or oligonucleosomes was taken for ELISA analysis. Briefly, the supernatant was incubated with anti-histone-biotin and anti-DNA-POD in streptavidin-coated 96-well plate for 2 hours at room temperature.
The color was developed with ABST and absorbance at 405 nm was read in a microplate reader (Molecular Devices, Sunnyvale, CA).
Example 4. Expression of EPHB4 in Mesothelioma~ a candidate target for therapy Malignant mesothelioma (MM) is a rare neoplasm that most often arises from the pleural and peritoneal cavity serous surface. The pleural cavity is by far the most frequent site affected (> 90%), followed by the peritoneum (6-10%) (Carbone et al., 2002, Semin Oncol.
29:2-17). There is a strong association with asbestos exposure, about 80% of malignant mesothelioma cases occur in individuals who have ingested or inhaled asbestos.
This tumor is particularly resistant to the current therapies and, up to now, the prognosis of these patients is dramatically poor (Lee et al., 2000, Curr Opin Puhn Med. 6:267-74).
Several clinical problems regarding the diagnosis and treatment of malignant mesothelioma remain unsolved. Malting a diagnosis of mesothelioma from pleural or abdominal fluid is notoriously difficult and often requires a thoracoscopic or laproscopic or open biopsy and hnmunohistochemical staining for certain markers such as meosthelin expressed preferentially in this tumor. Until now, no intervention has proven to be curative, despite aggressive chemotherapeutic regimens and prolonged radiotherapy. The median survival in most cases is only 12-18 months after diagnosis.
In order to identify new diagnostic markers and targets to be used for novel diagnostic and therapeutic approaches, we assessed the expression of EPHB4 and its ligand EphrinB2 in mesothelioma cell lines and clinical samples.
A. EPHB4 and EphrinB2 is expressed in mesothelioma cell lines The expression of Ephrin B2 and EphB4 in malignant mesothelioma cell lines was determined at the T~TA and protein level by a variety of methods. l~T-PCI~
showed that all of the four cell lines express EphrinB2 and EPHB4 (fig. 33A). Protein expression was determined by Western blot in these cell lines. Specific bands for EphB4 were seen at 120 kI). In addition, Ephrin B2 was detected in all cell lines tested as a 37 kD
band on Western blot (fig. 33B). No specific band for Epln-in B2 was observed in 293 human embryonic kidney cells, which were included as a negative control.
To confirm the presence of EpliB4 transcription in mesothelioma cells, ifZ
situ hybridization was carried out on NCI H28 cell lines cultured on chamber slides. Specific signal for EphB4 was detected using antisense probe Ephrin B2 transcripts were also detected in the same cell line. Sense probes for both EphB4 and Ephrin B2 served as negative controls and did not hybridize to the cells (figure 34). Expression of EphB4 and Ephrin B2 proteins was confirmed in the cell lines by immunofluorescence analysis (fig. 35).
Three cell lines showed strong expression of Ep11B4, whereas expression of Ephrin B2 was present in H28 and H2052, and wealely detectable in H2373.
B. Evidence of Expression of EPHB4 and EphrinB2 in clinical samples Tumor cells cultured from the pleural effusion of a patient diagnosed with pleural malignant mesothelioma were isolated and showed positive staining for both EphB4 and Ephrin B2 at passage 1 (figure 35, bottom row). These results confirm co-expression of EphB4 and Ephrin B2 in mesothelioma cell lines. To determine whether these results seen in tumor cell lines were a real reflection of expression in the disease state, tumor biopsy samples were subjected to immunohistochemical staining for EphB4 and Ephrin B2.
Antibodies to both proteins revealed positive stain in the tumor cells. Representative data is shown in figure 36.
C. EPHB4 is involved in the cell growth and migration of mesothelioma The role of EphB4 in cell proliferation was tested using EPHB4 specific antisepses oligonucleotides and siRNA. The treatment of cultured H28 with EPHB4 antisense reduced cell viability. One of the most active inhibitor of EphB4 expression is EPHB4AS-10 (fig.
37A). Transfection of EPHB4 siRNA 472 generated the same effect (fig. 37B).
MM is a locally advancing disease with frequent extension and growth into adjacent vital structures such as the chest wall, heart, and esophagus. In an effort to study this process in vitro, we perform wound healing assay using previously descuibed techniques (3:36).
When a wound was introduced into sub confluent H28 cells, over the course of the next 28 hours cells would progressively migrate into the area of the wound. However, when cells were pretreated with EPHB4AS-10 for 24 hours, and the wound was introduced, this migration was virtually completely prevented (fig. 38A). The migration study with Boyden Chamber assay with EPHB4 siRNA showed that cell migration was greatly inhibited with the inhibition of EPHB4 expression (Fig. 38B).
D. Materials and Methods 1) Cell lines and reagents NCI H28, NCI H2052, NCI H2373, MSTO 211H mesothelioma cell lines and 293 human embryonic kidney cells were obtained from the ATCC (Manassas, VA). Cells were maintained in RPMI 1640 media supplemented with 10 % heat-inactivated fetal bovine senim (FBS; Life Technologies, Gaithersburg, MD) and antibiotics. Primary cells were obtained from pleural effusion of patients with mesothelioma. A large number of EPHB4 phosphorothioate modified antisense oligonucleotides were synthesized.
Similarly a number of EphB4 specific siRNAs were generated. Monoclonal antibody produced against was used for western blot. Polyclonal antibody against EphrinB2 and EPHB4 (C-16) (for immunohistochemical staining) was from Santa Cruz.
2) RT-PCR
Total RNA was reversed transcribed by use of random hexamers (Invitrogen).
Primers for EphB4 and EphrinB2 were designed with Primer 3 software. The sequences for all primers are as follows: EPHB4 forward primer and EPHB4 reverse primer (see, e.g., in Example 2); EphrinB2 forward primer and EphrinB2 reverse primer (see, e.g., in Example 6);
G3PDH forward primer, 5'-GGAGCCAAAAGGGTCATCAT-3'; G3PDH reverse primer, S'-GGCATTGCTGCAAAGAAAGAG-3'; Clonetics kit was used for PCR. PCRs were performed with the ABI PCR System 2700 (Applied Biosystem). The PCR conditions were 95 °C for 5 min, followed by 35 cycles of 95 °C for 30 seconds, 60 °C for 30 seconds and 72 °C for 1 min.
3) Preparation of digoxigenin-labeled RNA probes Ephrin-B2 and EphB4 PCR products were cloned using the pGEM-T Easy System (Promega, Madison WI~ according to the manufacturer's description. The primers and PCR
products were 5'-tccgtgtggaagtactgctg-3' (forward), 5'-tctggtttggcacagttgag-3' (reverse), for ephrin-B2 that yielded a 296-by product and 5'-ctttggaagagaccctgctg-3' (forward), 5~-agacggtgaaggtctccttg-3', for EphB4 that yielded a 297-by product. 'The authenticity and insert orientation were confirmed by DNA sequencing.
The pGEM-T Easy plasmids containing the PCR product of the human ephrin-B2 or EphB4 gene were linearized with Spe I or Nco I. Antisense or sense digoxigenin (DIG)-labeled RNA probes were transcribed from T7 or SP6 promoters by nm-off transcription using a DIG RNA labeling kit (Roche, hldianapolis IN). RNA probes were quantitated by spot assay as described in the DIG RNA labeling kit instructions.
4) Ira situ hybridization Cells were cultured in Labtech II 4-well chamber slides (Nalge Nunc International, Naperville, IL). Cells were washed in PBS (37 °C), then fixed for 30 min at 25 °C in a solution of 4% (w/v) formaldehyde, 5% (v/v) acetic acid, and 0.9% (w/v) NaCl.
After fixation, slides were rinsed with PBS and stored in 70% ethanol at 4 °C
until further use.

Before ira situ hybridization, cells were dehydrated, washed in 100% xylene to remove residual lipid and then rehydrated, finally in PBS. Cells were permeabilized by incubating at 37 °C with 0.1 % (w/v) pepsin in 0.1 N HCl for 20 min and post-fixed in 1 % formaldehyde for min. Prehybridization was performed for 30 min at 37 °C in a solution of 4 X SSC
5 containing 50%(v/v) deionized formamide. Slides were hybridized overnight at 42 °C with 25 ng antisense or sense RNA probes in 40% deionized formamide, 10% dextran sulfate, 1X
Denhardt's solution, 4 X SSC, 10 mM DTT, 1 mg/ml yeast t-RNA and lmg/ml denatured and sheared salmon sperm DNA in a total volume of 40 ~1. Slides were then washed at 37 °C as follows: 2 X 15 min with 2 X SSC, 2 X l5min with 1 X SSC, 2 X 15 min with 0.5 X SSC
10 and 2 X 30 min with 0.2 X SSC. Hybridization signal was detected using alkaline-phosphatase-conjugated anti-DIG antibodies (Roche) according to the manufacturer's instructions. Color development was stopped by two washes in 0.1 M Tris-HCl, 1mM EDTA, pH 8.0 for 10 min. Cells were visualized by counterstaining of nucleic acids with Nuclear Fast Red (Vector Laboratories, Burlingame, CA) and the slides were mounted with IMMU
M~UNT (Shandon, Astmoor UI~).
5) Western Blot Crude cell lysates were prepared by incubation in cell lysis buffer (10 mM
Tris, pH
7.5, 1 mM EDTA, 150 mM NaCl, 1 % Triton' X-100, 1 mM DTT, 10 % glycerol).
Lysates were cleared by centrifugation at 10,000 x g~ for 10 min. Total protein was determined by Bradford assay (Bio-Rad). Samples (20 ~g protein) were fractionated on a 4-20 % Tris-glycine polyacrylamide gel and transferred to polyvinylidene difluoride (PVDT) membrane (Bio-Rad) by electroblotting. Membranes were blocked with 5 % non-fat milk prior to incubation with antibody to EphB4 (1:5000 dilution) at 4° C, for 16 h.
Secondary antibody (1:100,000 dilution) conjugated with horseradish peroxidase was applied for 1 h at 25 °C. The membranes were developed using the SuperSignal West Femto Maximum sensitivity chemiluminescent substrate (Pierce, Roclcford, IL) according to the manufacturer's instructions.
6) Immunohistochemistry Fonnalin-fixed tissue sections were deparaffinized and incubated with 10% goat serum at -70 °C for 10 minutes and incubated with the primary rabbit antibodies against either Ephrin B2 or EphB4 (Santa Cruz Biotechnologies; 1:100) at 4 °C
overnight. Isotype-specific rabbit IgG was used as control. The immunoreactivity for these receptors was revealed using an avidin-biotin kit from Vector Laboratories. Peroxidase activity was revealed by the diaminobenzidine (Sigma) cytochemical reaction. The slides were then counterstained with H&E.
7) Immunofluorescence studies Cells were cultured on Labtech II 4-well chamber slides and fixed in 4%
paraformaldehyde in Dulbecco's phosphate buffered saline pH 7.4 (PBS) for 30 min. The slides were rinsed twice in PBS and preincubated with blocking buffer (0.2%
Triton-X100, 1% BSA in PBS) for 20 min. The slides were then incubated with antibodies to EphB4 or ephrin B2 (1:100 dilution in PBS) in blocking buffer at 4 °C for 16 hr.
After washing three times, the slides were incubated with the appropriate fluorescein-conjugated secondary antibodies (Sigma-Aldrich, St. Louis, MO). Nuclei were counterstained with 4',6-diamidino-2-phenylindole dihydrochloride hydrate (DAPI), washed extensively with PBS and mounted with Vectasheild antifade mounting solution (Vector Laboratories). Images were obtained using an Olympus AX70 fluorescence microscope and Spot v2.2.2 (Diagnostic hzstruments Inc., Sterling heights, MI) digital imaging system.
8) Cell viability assay Cells were seeded at a density of 5 x 10a per well in 4~-well plates on day 0 in appropriate growth media containing 2% fetal calf serum (FCS). On the following day, the media was changed and cells were treated with various conceniTations (1-10 ~,M) of EphB4 Antisense. On day 4, viability was assessed using 3-(4.,5-dimethylthia~ol-2-yl)-2,5 diphenyltetra~olium bromide (MTT) at a final concentration of 0.5 mg/ml. Cells were incubated for 2 hr, medium was aspirated, and the cells were dissolved in acidic isopropanol (90% isopropanol, 0.5% SDS and 40 mM HCl). Optical density was read in an ELISA reader at 490 nm using isopropanol as blank (Molecular Devices, CA).
9) Cell migration In vitro wound healing assay was adopted. Briefly, cells were seeded onto 6-cm plates in full culture media for 24 hours, and then switched to medium containing 5%
FBS. EPHB4 antisense 10 (10 ~M) was also added to treated well. 24 hours later, wounds were made using the tip of a p-200 pipette man; a line was drawn through the middle of the plates. The plate was photographed at 0, 12, 24 hours. The experiment was repeated three times.

Example 5. EphB4 Is Expressed in Squamous Cell Carcinoma of The Head and Neck' Regulation by Epidermal Growth Factor Si alin~ Pathwa~and Growth Advantage Squamous cell carcinoma of the head and neck (HNSCC) is the sixth most frequent cancer worldwide, with estimated 900,000 cases diagnosed each year. It comprises almost 50% of all malignancies in some developing nations. In the United States, 50,000 new cases and 8,000 deaths are reported each year. Tobacco carcinogens are believed to be the primary etiologic agents of the disease, with alcohol consumption, age, gender, and ethnic background as contributing factors.
The differences between normal epithelium of the upper aerodigestive tract and cancer cells arising from that tissue are the result of mutations in specific genes and alteration of their expression. These genes control DNA repair, proliferation, immortalization, apoptosis, invasion, and angiogenesis. For head and neck cancer, alterations of three signaling pathways occur with sufficient frequency and produce such dramatic phenotypic changes as to be considered the critical transforming events of the disease.
These changes include mutation of the p53 tumor suppressor, overexpression of epidermal growth factor receptor (EGFR), and inactivation of the cyclin dependent kinase inhibitor p16. ~ther changes such as Rb mutation, ras activation, cyclin D amplification, and mye overexpression are less frequent in HNSCC.
Although high expression of EphB4. has been reported in hematologic malignancies, breast carcinoma, endometrial carcinoma, aald colon carcinoma, there is limited data on the protein levels of EphB4, and complete lack of data on the biological significance of this protein in tumor biology such as HNSCC.
A. HNSCC tumors express EphB4 We studied the expression of EphB4 in human tumor tissues by immunohistochemistry, in situ hybridization, and Western blot. Twenty prospectively collected himor tissues following IRB approval have been evaluated with specific EphB4 monoclonal antibody that does not react with other members of the EphB and EphA family.
EphB4 expression is observed in all cases, with varying intensity of staining.
Figure 39A (top left) illustrates a representative case, showing that EphB4 is expressed in the tumor regions only, as revealed by the H&E tumor architecture (Fig. 39A bottom left). Note the absence of _7a_ staining for EphB4 in the stroma. Secondly, a metastatic tumor site in the lymph node shows positive staining while the remainder of the lymph node is negative (Fig. 39A, top right).
In situ hybridization was carried out to determine the presence and location of EphB4 transcripts in the tumor tissue. Strong signal for EphB4 specific antisense probe was detected indicating the presence of transcripts (Figure 39 B, top left). Comparison with the H&E stain (Fig. 39B, bottom left) to illustrate tumor architecture reveals that the signal was localized to the tumor cells, and was absent from the stromal areas. Ephrin B2 transcripts were also detected in tumor sample, and as with EphB4, the signal was localized to the tumor cells (Fig.
39B, top right). Neither EphB4 nor ephrin B2 sense probes hybridized to the sections, proving specificity of the signals.
B. High expression of EphB4 in primary and metastatic sites of HNSCC
Western blots of tissue from primary tumor, lymph node metastases and uninvolved tissue were carried out to determine the relative levels of EphB4 expression in these sites.
Tumor and normal adjacent tissues were collected on 20 cases, while lymph nodes positive for tumor were harvested in 9 of these 20 cases. Representative cases are shown in figure 39C. EphB4 expression is observed in each of the tumor samples. Similarly, all tumor positive lymph nodes show EphB4 expression that was equal to or greater than the primary tumor. No or minimal expression is observed in the normal adjacent tissue.
C. EphB4 expression and regulation by EGFR activity in HNSCC cell lines Having demonstrated the expression of EphB4~ limited to tumor cells, we next sought to determine whether there was an in vitro model of EphB4 expression in HNSCC.
Six HN
SCC cell lines were surveyed for EphB4 protein expression by Western Blot (Fig. 40A). A
majority of these showed strong EphB4 expression and thus established the basis for subsequent studies. Since EGFR is strongly implicated in HNSCC we asl~ed whether EphB4 expression is associated with the activation of EGFR. Pilot experiments in SCC-15, which is an EGFR positive cell line, established an optimal time of 24 h and concentration of 1 mM of the specific EGFR l~inase inhibitor AG 1478 (Figure 40B) to inhibit expression of EphB4.
When all the cell lines were studied, we noted robust EGFR expression in all but SCC-4, where it is detectable but not strong (Fig. 40C, top row). In response to EGFR
inhibitor AG1478 marled loss in the total amount of EphB4 was observed in certain cell lines (SCC-15, and SCC-25) while no effect was observed in others (SCC-9, -12, -13 and -71). Thus SCC-15 and -25 serve as models for EphB4 being regulated by EGFR activity, while SCC-9, -12, -13 and -71 are models for regulation of EphB4 in HNSCC independent of EGFR
activity, where there may be input from other factors such as p53, PTEN, IL-6 etc. We also noted expression of the ligand of EphB4, namely ephrin B2, in all of the cell lines tested. As with EphB4 in some lines ephrin B2 expression appears regulated by EGFR
activity, while it is independent in other cell lines.
Clearly, inhibition of constitutive EGFR signaling repressed EphB4 levels in cells. We next studied whether EGF could induce EphB4. We found that EphB4 levels were induced in SCC15 cells that had been serum starved for 24 h prior to 24 h treatment with 10 ng/ml EGF as shovm in figure 41B (lanes 1 and 2). The downstream signaling pathways known for EGFR activation shown in figure'41A, (for review see Yarden &
Slikowski 2001) were then investigated for their input into EGF mediated induction of EphB4.
Blocking PLCg, AKT and JNK phosphorylation with the specific kinase inhibitors U73122, SH-5 and SP600125 respectively reduced basal levels and blocked EGF stimulated induction of EphB4 (Fig. 41B, lanes 3-8). In contrast, inhibition of ERKl/2 with PD09S095 and PI3-I~ with LY294002 or Wortmannin had no discernible effect on EGF induction of EphB4 levels.
However, basal levels of EphB4 were reduced when ERI~l/2 phosphorylation was inhibited.
Interestingly, inhibition of p381VIAPI~ activation with SB2035~0 increased basal, but not EGF induced EphB4 levels. Similar results were seen in the SCC25 cell line (data not shown).
I~. Inhibition of EphB4 in high expressing cell lines results in reduced viability and causes cell-cycle arrest We next turned to the role of EphB4 expression in HNSCC by investigating the effect of ablating expression using siRNA or AS-~I~N methods. Several siRNAs to EphB4 sequence were developed (Table 1) which knocked-down EphB4 expression to varying degrees as seen in figure 42A. Viability was reduced in SCC-15, -25 and -71 cell lines transfected with siRNAs 50 and 472, which were most effective in bloclcing EphB4 expression (Figure 42B). Little effect on viability was seen with EphB4 siRNA
1562 and 2302 or ephrin B2 siRNA 254. Note that in SCC-4, which does not express EphB4 (see Fig.
40A) there was no reduction in cell viability. The decreased cell viability seen with siRNA 50 and 472 treatment was attributable to accumulation of cells in sub G0, indicative of apoptosis.
This effect was both time and dose-dependant (Figure 42C and Table 2). In contrast, siRNA2302 that was not effective in reducing EphB4 levels and had only minor effects on viability did not produce any changes in the cell cycle when compared with the mock LipofectamineTM2000 transfection.

Table 1: EphB4 siRNAs Name siRNA sequence Eph B4 50: 5'-GAGACCCUGCUGAACACAAUU-3' 3'-UUCUCUGGGACGACUUGUGUU-5' Eph B4 472: 5'-GGUGAAUGUCAAGACGCUGUU-3' 3'-UUCCACUUACAGUUCUGCGAC-5' Eph 841562: 5'-CAUCACAGCCAGACCCAACUU-3' 3'-UUGUAGUGUCGGUCUGGGUUG-5' Eph B4 2302 5'-CUCUUCCGAUCCCACCUACUU-3' 3'-UUGAGAAGGCUAGGGUGGAUG-5' Table 2: Effect of different EphE4 siRNA on Cell Cycle Treatment Sub GO G1 S G2 36hr Lipo alone 1.9 39.7 21.3 31.8 100 nM 2302 2.0 39.3 21.2 31.2 100 nM 50 18.1 31.7 19.7 24.4 100 nM 472 80.2 10.9 5.2 2.1 16hr Lipo alone 7.8 55.7 15.2 18.5 100 nM 2302 8.4 57.3 14.3 17.3 nM 50 10.4 53.2 15.7 17.7 100 nM 50 27.7 31.3 18.1 19.6 10 nM 472 13.3 50.2 15.8 17.5 100 nM 472 30.7 31.9 16.4 18.0 ' -'7s -In addition, over 50 phosphorothioate AS-ODNs complementary to the human EpliB4 coding sequences were synthesized and tested for their ability to inhibit EphB4 expression in 293 cells transiently transfected with full length EphB4 expression plasmid.
Figure 43A
shows a representative sample of the effect of some of these AS-ODNs on EphB4 expression.
Note that expression is totally abrogated with AS-10, while AS-11 has only a minor effect.
The effect on cell viability in SCC15 cells was most marked with AS-ODNs that are most effective in inhibiting EphB4 expression as shown in figure 43B. The ICso for AS-10 was approximately 1 pM, while even 10 ~M AS-11 was not sufficient to attain 50 %
reduction of viability. When the effect that AS-10 had on the cell cycle was investigated, it was found that the sub GO fraction increased from 1.9 % to 10.5 % compared to non-treated cells, indicative of apoptosis (Fig. 43C).
E. EphB4 regulates Cell migration We next wished to determine if EphB4 participates in the migration of HNSCC.
Involvement in migration may have implications for growth and metastasis.
Migration was assessed using the wound-healing/scrape assay. Confluent SCC15 and SCC25 cultures were wounded by a single scrape with a sterile plastic Pasteur pipette, which left a 3 mm band with clearly defined borders. Migration of cells into the cleared area in the presence of test compounds was evaluated and quantitated after 24, 4S and 72 hr. Cell migration was markedly diminished in response to AS-10 that block EphB4 expression while the inactive compounds, AS-1 and scrambled ODN had little to no effect as shown in figure 43D.
Inhibition of migration with AS-10 was also shown using the Boyden double chamber assay (Fig. 43E).
F. EphB4 AS-10 in vivo anti-tumor activity The effect of EphB4 AS-10, which reduces cell viability and motility, was determined in SCC15 tumor xenografts in Balb/C nude mice. Daily treatment of mice with 20 mg/kg AS-10, sense ODN or equal volume of PBS by LP. injection was started the day following tumor cell implantation. Growth of tumors in mice receiving AS-10 was significantly retarded compared to mice receiving either sense ODN or PBS diluent alone (Figure 44).
Non-specific effects attributable to ODN were not observed, as there was no difference between the sense ODN treated and PBS treated groups.
G. Materials and Methods 1) Cell lines and reagents HNSCC-4, -9, 12, -13, -15, -25, and -71 were obtained from and 293 human embryonic kidney cells were obtained from the ATCC (Manassas, VA). Cells were maintained in RPMI 1640 media supplemented with 10% heat-inactivated fetal bovine serum (FBS; Invitrogen, Carlsbad, CA) and antibiotics. EGFR, EphB4(C-16) polyclonal antibodies were from Santa Cruz Biotech (Santa Cruz, CA). (3-actin monoclonal antibody was purchased from Sigma Chemical Co. (St Louis, MO). Ephrin B2 and EphB4 polyclonal antibodies and their corresponding blocking peptides were obtained from Santa Cruz Biotechnology (Santa Cruz, CA). AG 1478 (4-(3'-Chloroanilino)-6,7-dimethoxy-quinazoline) was from Calbiochem (San Diego, CA). Kinase inhibitors SH-5 and SP 600125 were from A.G.
Scientific (San Diego, CA), PD98095, U73122, SB203580, LY294002, and Wortmannin were obtained from Sigma.
2) Preparation of digoxigenin-labeled RNA probes See above, e.g., Example 3.
3) Iaa sitzc hybridization See above, e.g., Example 3.
4) Immunohistochemistry Formalin-fixed tissue sections were deparaffmized and incubated with 10% goat serum at -70 °C for 10 minutes and incubated with the EphB4 monoclonal antibody 4 °C
overnight. Isotype specific rabbit IgG was used as control. The immunoreactivity for these receptors was revealed using an avidin-biotin kit from Vector Laboratories.
Peroxidase activity was revealed by the diaminobenzidine (Sigma) cytochemical reaction.
The slides were then counterstained with 0.12% methylene blue or HOE. For frozen sections, OCT-embedded tissues were sectioned at 5 ~.m and fixed in phosphate-buffered 4%
paraformaldehyde. Sections were washed for 3 x 5 min in PBS and endogenous peroxidase was bloclLed by incubation in 0.3°/~ H2O2 in PBS for 10 min at room temperature. Sections were incubated with Eph4 (C-16) antibody (1:50) for 1 h at room temperature followed by three washes in PBS and incubation with donkey anti-goat secondary antibody (Santa Cruz Biotech.) for 1 h at room temperature. Afterthree washes in PBS, peroxidase activity was localized by incubation in DAB substrate solution (Vector Laboratories, Inc.
Burlingame CA) for 10 min at room temperature. Sections were counterstained with Hematoxylin for 20 s, dehydrated and mounted. Negative control for staining was substitution of normal goat serum for primary antibody. Immunohistochemical staining on prostate array (BioMeda, Foster _77_ City, CA) was done using goat ABC Staining System (Santa Cruz Biotech.) according to the manufacturer's instructions.
5) Western Blot See above, e.g., Example 3.
6) Synthesis of EphB4 siRNA by in vitro transcription The SilencerTM siRNA construction kit (Ambion, Austin TX) was used to s5mthesize siRNA to EphB4. Briefly, 21 by target sequences containing 19 by downstream of 5'-AA
dinucleotides were identified that showed no significant homology to other sequences in the GenBank database. Sense and antisense siRNA 29-mer DNA oligonucleotide templates were synthesized at the USC Norris Microchemical Core Facility. Antisense template corresponded to the target sequence followed by 8 by addition (5'-CCTGTCTC-3') at the 3' end complementary to the T7 promoter primer provided by the SilencerTM siRNA
construction kit. Sense template comprised 5'-AA followed by the complement of the target 19 bp, then the T7 8 by sequence as above.
In separate reactions, the two siI~NA oligonucleotide templates were hybridized to a T7 promoter primer. The 3' ends of the hybridized oligonucleotides were extended by the I~lenow fragment of DNA polymerise to create double-stranded siIZNA
transcription templates. The sense and antisense siRNA templates were transcribed by T7 RNA
polymerise and the resulting RNA transcripts were hybridized to create dsRNA.
The leader sequences were removed by digesting the dsRNA with a single-stranded specific ribonuclease leaving the overhanging UU dinucleotides. The DNA template was removed at the saane time by treatment with RNase free deoxyribonuclease. The resulting siRNA was purified by glass fiber filter binding to remove excess nucleotides, short oligomers, proteins, and salts in the reaction. The end products (shown in Table 3) were double-stranded 21-mer siRNAs with 3' terminal uridine that can effectively reduce the expression of target mRNA
when transfected into cells.
A number of phosphorothioate AS-ODNs were also synthesized (Operon, Valencia CA) to test for inhibition of EphB4 expression (Table 3).
Table 3: EphB4 Antisense ODNs Name Position Sequence (5' -j 3') _78_ Eph B4 AS-1 (552-572) GTG CAG GGA TAG CAG GGC CAT

Eph B4 AS-2 (952-972) AAG GAG GGG TGG TGC ACG GTG

Eph B4 AS-3 (1007-1027) TTC CAG GTG CAG GGA GGA GCC

Eph B4 AS-4 (1263-1285) GTG GTG ACA TTG ACA GGC TCA

Eph B4 AS-5 (1555-1575) TCT GGC TGT GAT GTT CCT GGC

Eph B4 AS-6 (123-140) GCC GCT CAG TTC CTC CCA

Eph B4 AS-7 (316-333) TGA AGG TCT CCT TGC AGG

Eph B4 AS-8 (408-428) CGC GGC CAC CGT GTC CAC CTT

Eph B4 AS-9 (1929-1949) CTT CAG GGT CTT GAT TGC CAC

Eph B4 AS-10 (1980-1999) ATG GAG GCC TCG CTC AGA AA

Eph b4 AS-11 (2138-2158) CAT GCC CAC GAG CTG GAT GAC

?) Cell viability assay Cells were seeded at a density of 5 x 103 per well in 48-well plates on day 0 in appropriate growth media containing 2% fetal calf serum (FCS). Cells were treated with various concentrations (1-10 ~g/ml) of ODNs on days 2 and 4. On day 5, viability was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolimn bromide (MTT) as previously described (Masood et al '03). For viability with siRNA, 2 x 104 cellslwell of SOC-4~, -15, -25 or -71 in a 48-well plate were transfected with siRNAs (10-100 nM) using 2 g1 of LipofectamineTM 2000 according to the manufacturer's instructions. 4 h post-transfection the cells were returned to growth media (RPMI 1640 supplemented with 10 % FBS).
Viability was assayed by MTT 48 h following transfection.
8) Cell cycle analysis 80% confluent cultures of SCC15 cells in 6-well plates were transfected with siRNA472 (100 nM) using LipofectamineTM 2000. Either 16 or 36 hours after transfection, cells were trypsinized, washed in PBS and incubated for 1 h at 4 °C in 1 ml of hypotonic solution containing 50 gg/ml propidium iodide, 0.1% sodium citrate, 0.1 Triton X-100 and 20 ~g/ml DNase-free RNaseA. Cells were analyzed in linear mode at the USC Flow cytometry facility. Results were expressed as percentages of elements detected in the different phases of the cell cycle, namely Sub GO peak (apoptosis), GOIGl (no DNA synthesis), S
(active DNA
_79_ systhesis), G2 (premitosis) and M (mitosis). For AS-ODN experiment the cells were exposed to 5 ~uM ODN for 36 h prior to processing.
9) Wound healing migration assay SCC15 cells were seeded into 6-well plates and cultured until confluent. 10 ~,M AS-1, AS-10, or sense ODN as control were introduced to the wells as described for the viability assay 12 hours before wounding the monolayer by scraping it with a sterile pipette tip.
Medium was changed to RPMI 1640 supplemented with 5% FBS and fresh ODNs. The healing process was examined dynamically and recorded with a Nikon Coolpix 5000 digital camera with microscope adapter.
10) Boyden Chamber assay of migration Cell migration assays were performed as previously described (Masood ANUP
paper '99) except that 1 ~.M AS-10 or AS-6 were added to the upper chamber. EGF (20 ng/ml) was used as chemoattractant in the lower chamber. Taxol at 10 ng/ml was used as a negative control.
11) In vivo studies SCC15 (5 x 106 cells) were injected subcutaneously in the lower back of 5-week old male Balb/C Nu+/nu'~ athymic mice. Treatment consisted of daily intraperitoneal injection of ODN (20 mg/kg in a total volume of 100 ~l) or diluent (PBS) begun the day following tumor cell implantation and continued for two weeks. Tumor growth in mice was measured as previously described (Masood CCR'O1). Mice were sacrificed at the conclusion of the study.
All mice were maintained in accord with the University of Southern California Animal Care and Use Committee guidelines governing the care of laboratory mice.
Example 6. Ephrin B2 Expression in Kaposi's Sarcoma Is Induced by Human Herpesvirus Type ~: Phenotype Switch from Venous to Arterial Endothelium Kaposi's Sarcoma (IBS) manifests as a multifocal angioproliferative disease, most commonly of the skin and mucus membranes, with subsequent spread to visceral organs (1) Hallmarks of the disease are angiogenesis, edema, infiltration of lymphomononuclear cells and growth of spindle-shaped tmnor cells. Pathologically, established lesions exhibit an extensive vascular network of slit-like spaces. The IBS vascular network is distinct from normal vessels in the lack of basement membranes and the abnormal spindle shaped -8o-endothelial cell (tumor cell) lining these vessels. Defective vasculature results in an accumulation of the blood components including albumin, red and mononuclear cells in the lesions (1). The KS tumor is endothelial in origin; the tumor cells express many endothelial markers, including lectin binding sites for Ulex europecrus agglutinin-1 (UEA-1), CD34, EN-4, PAL-E (2) and the endothelial cell specific tyrosine kinase receptors, VEGFR-1 (Flt-1), VEGFR-2 (Flk-1/KDR), VEGFR-3 (Flt-4), Tie-1 and Tie-2 (3, RM & PSG unpublished data). KS cells co-express lymphatic endothelial cell related proteins including LYVE and podoplanin (4).
The herpesvirus HHV-8 is considered the etiologic agent for the disease. In sequences of this new herpes virus were identified in KS tumor tissue (5), and subsequent molecular-epidemiology studies have shown that nearly all KS tumors contain viral genome.
Sero-epidemiology studies show that HIV infected patients with KS have the highest prevalence of HHV-8 and secondly that those with HIV infection but no KS have increased risk of developement of KS over the ensuing years if they are also seropositive for HHV-8 (6). Direct evidence for the role of HHV-8 in KS is the transformation of bone marrow endothelial cells after infection with HHV-8 (7). A number of HHV-8 encoded genes could contribute to cellular transformation (reviewed in 8). However, the most evidence has accumulated for the G-protein coupled receptor (vGPCR) in this role (9).
We investigated whether Ks tumor cells are derived from arterial or venous endothelium. In addition, we investigated whether HHV-8 has an effect on expression of arterial or venous markers in a model of KS. KS tumor cells were found to express the ephrin B2 arterial marker. Further, ephrin B2 expression was induced by HHV-8 vGPCR
in KS and endothelial cell lines. Ephrin B2 is a potential target for treatment of KS
because inhibition of ephrin B2 expression or signaling was detrimental to KS cell viability and function.
A. KS tumors express Ephrin B2, but not EphB4 The highly vascular nature of KS lesions and the probable endothelial cell origin of the tumor cells prompted investigation of expression of EphB4 and ephrin B2 which are markers for venous and arterial endothelial cells, respectively. Ephrin B2, but not EphB4 transcripts were detected in tumor cells of KS biopsies by in situ hybridization (figure 45A).
Comparison of the positive signal with ephrin B2 antisense probe and tumor cells as shown by H&E staining shows that ephrin B2 expression is limited to the areas of the biopsy that contain tumor cells. The lack of signal in KS with EphB4 antisense probe is not due to a defect in the probe, as it detected transcripts in squamous cell carcinoma, which we have shown expresses this protein (18). Additional evidence for the expression of ephrin B2 in KS
tumor tissue is afforded by the localization of EphB4/Fc signal to tumor cells, detected by FITC conjugated anti human Fc antibody. Because ephrin B2 is the only ligand for EphB4 this reagent is specific for the expression of ephrin B2 (figure 45B, left).
An adjacent section treated only with the secondary reagent shows no specific signal. Two-color confocal microscopy demonstrated the presence of the HHV-8 latency protein, LANAI in the ephrin B2 positive cells (Fig. 45C, left), indicating that it is the tumor cells, not tumor vessels, which are expressing this arterial marker. Staining of tumor biopsy with PECAM-1 antibody revealed the highly vascular nature of this tumor (Fig. 45C, right). A pilot study of the prevalence of this pattern of ephrin B2 and EphB4 expression on KS biopsies was conducted by RT-PCR analysis. All six samples were positive for ephrin B2, while only 2 were weakly positive for EphB4 (data not shown).
B. Infection of venous endothelial cells with HHV-8 causes a phenotype switch to arterial markers We next asked whether HHV-8, the presumed etiologic agent for KS, could itself induce expression of ephrin B2 and repress EphB4 expression in endothelial cells. Co-culture of HIJVEC and BC-1 lymphoma cells, which are productively infected with HHV-8, results in effective infection ofthe endothelial cells (16). The attached tnonolayers of endothelial cells remaining after extensive washing were examined for ephrin B2 and EphB4 by RT-PCR
and immunofluorescence. HUVEC express EphB4 venous marker strongly at the RNA
level, but not ephrin B2 (figure 46B). In contrast, HHV-8 infected cultures (HLTVEC/BC-1 and HUVEC/BC-3) express ephrin B2, while EphB4 transcripts are almost absent.
Imrnunofluorescence analysis of cultures of HLTVEC and HWEC/HHV-8 for artery/vein marlcers and viral proteins was undertaken to determine whether changes in protein expression mirrored that seen in the RNA. In addition, cellular localization of the proteins could be determined. Consistent with the RT-PCR data HLTVEC are ephrin B2 negative and EphB4 positive (Fig. 46A(a & m)). As expected they do not express any HHV-8 latency associated nuclear antigen (LANAI) (Fig. 46A(b, n)). Co-culture of BC-1 cells, which are productively infected with HHV-8, resulted in infection of HIJVEC as shown by presence of viral proteins LANAI and ORF59 (Fig. 46A(f, r)). HHV-8 infected HUVEC now express ephrin B2 but not EphB4 (Fig. 46A(e, q, u), respectively). Expression of ephrin B2 and LANAI co-cluster as shown by yellow signal in the merged image (Fig.
46A(h)). HHV-8 infected HUVEC positive for ephrin B2 and negative for Eph B 4 also express the arterial marker CD148 (19) (Fig. 46A (j, v)). Expression of ephrin B2 and CD148 co-cluster as shown by yellow signal in the merged image (Fig. 46A(1)). Uninfected HUVEC
expressing Eph B4 were negative for CD 148 (not shown).
C. HHV-8 vGPCR induces ephrin B2 expression To test whether individual viral proteins could induce the expression of ephrin B2 seen with the whole vines KS-SLK cells were stably transfected with HHV-8 LANA, or LANA~440 or vGPCR. Western Blot of stable clones revealed a five-fold induction of ephrin B2 in KS-SLK transfected with vGPCR compared to SLK-LANA or SLK-LANA0440 (Fig.
47A). SLK transfected with vector alone (pCEFL) was used as a control. SLK-vGPCR and SLK-pCEFL cells were also examined for ephrin B2 and Eph B4 expression by immunofluorescence in transiently transfected KS-SLK cells. Figure 47B shows higher expression of ephrin B2 in the SLK-vGPCR cells compared to SLK-pCEFL. No changes in Eph B4 were observed in SLK-vGPCR compared to SLK-pCEFL. This clearly demonstrates that SLK-vGPCR cells expressed high levels of ephrin B2 compared to SLK-pCEFL
cells.
This suggests that vGPCR of HHV-8 is directly involved in the induction of Ephrin B2 and the arterial phenotype switch in KS. Since we had shown that HHV-8 induced expression of ephrin B2 in HLJVEC, we next asked if this could be mediated by a transcriptional effect.
Ephrin B2 5'-flanking DNA-luciferase reporter plasmids were constructed as described in the Materials and Methods and transiently transfected into HUVECs. Ephrin B2 5'-flanking DNA sequences -2491/-11 have minimal activity in HUVEC cells (figure 47C).
This is consistent with ephrin B2 being an arterial, not venous marker. However, we have noted that HUVEC in culture do express some ephrin B2 at the RNA level. Cotransfection of vGPCR induces ephrin B2 transcription approximately 10-fold compared to the control expression vector pCEFL. Roughly equal induction was seen with ephrin B2 sequences -2491/-1 l, -1242/-11, or -577/-11, which indicates that elements between -577 and -11 are sufficient to mediate the response to vGPCR, although maximal activity is seen with the -1242/-11 luciferase construct.
D. Expression of Ephrin B2 is regulated by VEGF and VEGF-C

We next asked whether known KS growth factors could be involved in the vGPCR-mediated induction of ephrin B2 expression. SLK-vGPCR cells were treated with neutralizing antibodies to oncostatin-M, IL-6, IL-8, VEGF or VEGF-C for 36 hr.
Figure 48A
shows that neutralization of VEGF completely blocked expression of ephrin B2 in SLK-vGPCR cells. A lesser, but significant decrease in ephrin B2 was seen neutralization of VEGF-C and IL-8. No appreciable effect was seen with neutralization of oncostatin-M or IL-6. To verify that VEGF and VEGF-C are integral to the induction of ephrin B2 expression we treated HUVEC with VEGF, VEGF-C or EGF. HWECs were grown in EBM-2 media containing 5 % FBS with two different concentration of individual growth factor (10 ng, 100 ng/ml) for 48 h. Qnly VEGF-A or VEGF-C induced ephrin B2 expression in a dose dependent masuzer (Figure 48B). In contrast, EGF had no effect on expression of ephrin B2.
E. Ephrin B2 siRNA inhibits the expression of Ephrin B2 in KS
Three ephrin B2 siRNA were synthesized as described in the methods section. KS-SLK cells were transfected with siRNA and 48 h later ephrin B2 expression was determined by Western Blot. Ephrin B2 siRNAs 137 or 254. inhibited about 70% of ephrin B2 expression Co111pared to control siRNA SLICK as siRNA Eph B4 50 or siRNA GFP. Ephrin B2 63 siRNA
was less effective than the above two siRNA Ephrin B2 (Figure 49A).
F. Ephrin B2 is necessary for full KS and EC viability, cord formation and in vivo angiogenesis activities The most effective ephrin B2 siRNA (254.) was then used to determine whether inhibiting expression of ephrin B2 has any effect on the growth of KS-SLK or HUVEC cells.
The viability of KS-SLK cells was decreased by the same siRNAs that inhibited ephrin B2 protein levels (figure 49B). KS-SLK express high levels of ephrin B2 and this result shows maintenance of ephrin B2 expression is integral to cell viability in this setting. HUVECs do not express ephrin B2, except when stimulated by VEGF as shown in Fig. 48B.
Ephrin B2 siRNA 264 dramatically reduced growth of HUVECs cultured with VEGF as the sole growth factor. In contrast, no significant effect was seen when HIJVECs were cultured with IGF, EGF and bFGF. As a control, EphB4 siRNA 50 had no detrimental effect on HUVECs in either culture condition (figure 49C).In addition to inhibition of viability of KS and primary endothelial cells, EphB4-ECD inhibits cord formation in HLTVEC and KS-SLK and in vivo angiogenesis in the MatrigelTM plug assay (Figure 50).

G. Methods and Materials 1) Cell lines and reagents Human vascular endothelial cells (HLTVEC) were from Clonetics (San Diego, CA) and were maintained in EGM-2 and EGM-2MV media respectively (Clonetics). T1 human fibroblast line was from Dr. Peter Jones, USC. BC-l and BC-3 human pleural effusion lymphoma cell lines and monoclonal antibodies to LANAI and ORF59 were the kind gift of Dr. Dharam Ablashi (Advanced Biotechnologies Inc., Columbia, MD). KS-SLK was isolated from a Classic Kaposi's sarcoma patient (15). Polyclonal antibodies to EphB4, ephrin B2, CD148, PECAM-1 were obtained from Santa Cruz Biotechnology (Santa Cruz, CA).
Mouse EphB4/F~° and monoclonal antibodies to human vascular endothelial growth factor (VEGF), VEGF-C, interleulcin-(IL)6, IL-8 and oncostatin-M were purchased from R & D
Systems (Minneapolis, MN). Expression vectors pKSvGPCR-CEFL and pCEFL were the kind gift of Dr. Enrique Mesri (Cornell University, New York, NY). Expression vectors for latency associated nuclear antigen (LANA) were kindly provided by Dr Matthew Rettig, Veteran's Administration Greater Los Angeles Healthcare System.
2) Collection and preparation of human tissue Human cutaneous Kaposi's sarcoma biopsy material was obtained under local anesthesia with informed consent from patients at the LAC/LJSC Medical Center, using an IRB approved consent f~rm. Biopsies were processed for either total RNA, paraffin blocks ~r frozen tissue blocks in OCT. Total RNA was extracted by h~mogenization in guanidine isothiocyanate, (RNAzoI: Tel-Test, W c., Friendswoods, TX). cDNAs were synthesized by reverse transcriptase using a random hexamer primer (Superscript II;
Invitrogen, Carlsbad, CA).
3) Preparation of digoxigenin-labeled RNA probes Ephrin B2 and EphB4 PCR products from the primers shown in Table 4 for in situ hybridization were cloned using the pGEM-T Easy system (Promega, Madison WI) according to the manufacturer's description using. The authenticity and insert orientation were confirmed by DNA sequencing. The pGEM-T Easy plasmids containing the PCR
product of the human ephrin-B2 or EphB4 gene were linearized with Spe I or Nco I.
Antisense or sense digoxigenin (DIG)-labeled RNA probes were transcribed from T7 or SP6 _85_ promoters by run-off transcription using a DIG RNA labeling kit (Roche, Indianapolis 1N).
RNA probes were quantitated by spot assay as described in the DIG RNA labeling kit instnictions.
Table 4: Primers for Ephrin B2 and EphB4.
Gene Primer Product Size sequence (bp) ISH Probe Primers ephrin B2 5' -TCCGTG TGGAGT ACT GCTG-3' 296 5' -TCTGGT TTGGCA CAG TTGAG-3' EphB4 5' -CTTTGG AAGAGA CCC TGCTG-3' 297 5' -AGACGG TGAAGG TCT CCTTG-3' RT-PCR Primers ephrin B2 5' -AGACAA GAGCCA TGA AGATC-3' 200 5' -GGATCC CACTTC GGA CCCGAG-3' EphB4 5' -TCAGGT CACTGC ATT GAACGG G-3 400 5' -AACTCG CTCTCA TCC AGTT-3' [3-actin 5' -GTGGGG CGCCCC AGG CACCA-3' 546 5' -CTCCTT AATGTC ACG CACGAT TTC-3' 4) Iaa situ hybridization See above, e.g., Example 3.
5) Co-culture of HUVEC and BC-1 HUVEC cells were grown to SO-70% confluence in EGM-2 on gelatin-coated Labtech II 4-well chamber slides (Nalge Nunc International, Naperville, IL). Co-culture with BC-1 or BC-3 was essentially as described by Sakurada and coworkers (16). Briefly, BC-1 or BC-3 cells were pretreated with TPA (20 ng/ml) to induce virus for 48 hrs and then added to the HUVEC culture at a ratio of 10:1 for cocultivation for two days. The HUVECs were washed extensively with PBS to remove the attached BC-1 or BC-3 cells.

6) Preparation of cDNA and RT-PCR
The TITANII1MTM One-Step RT-PCR kit (Clontech, Palo Alto, CA) was used for RT-PCR from 1 x 105 cells. Primer pairs for amplification of EphB4, ephrin B2 and (i-actin are shown in Table 4. Each PCR cycle consisted of denaturation at 94 °C
for 30 s, primer annealing at 60 °C for 30 s and extension at 72 °C for 30 s. The samples were amplified for 30 cycles. PCR products were separated on 1.5% agarose gels and stained with ethidium bromide.
7) Cell viability assay IBS-SLID cells were seeded at a density of 1 x 104 per well in 48-well plates on day 0 in appropriate growth media containing 2% fetal calf serum (FCS). On the following day, the media was changed and cells were treated with 0, 10 or 100 nM siRNA. On day 3, viability was assessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) as previously described (17).
8) Immunofluorescence studies Cells cultured on Labtech II 4-well chamber slides or frozen sections of IBS
biopsy material were fixed in 4% paraformaldehyde in Dulbecco's phosphate buffered saline pH 7.4 (PBS) for 30 min. The slides were rinsed twice in PBS and preincubated with blocking buffer (0.2°/~ Triton-~~100, 1% BSA in PBS) for 20 min, followed by incubation v,~ith antibodies to EphB4, ephrin B2, CD14.8, LANA1 or ORF59 (1:100 dilution in PBS) in blocking buffer at 4 °C for 16 hr. After washing three times, the slides were incubated with the appropt-iate fluorescein or rhodamine-conjugated secondary antibodies (Sigma-Aldrich, St.
Louis, MO).
Nuclei were counterstained with 4',6-diamidino-2-phenylindole dihydrochloride hydrate (DAPI), washed extensively with PBS and mounted with Vectasheild antifade mounting solution (Vector Laboratories, Burlingame, CA). Images were obtained using a Olympus AX70 fluorescence microscope and Spot v2.2.2 (Diagnostic Instruments Inc., Sterling Heights, MI) digital imaging system.
Immunofluorescence detection of EphrinB2 with EPHB4-Fc was done as follows.
Frozen sections fixed in 4% paraformaldehyde and blocked with 20% FBS were incubated with 5 p,g/ml EphB4/Fc (R&D Systems) for 1 h at RT. Sections were then incubated with 10 ~,g/ml rabbit anti-human IgG-FITC in PBS (Jackson ImmunoResearch Laboratories West _87_ Grove, PA) at RT for 1 hour. Nuclei were counterstained with DAPI and sections mounted as above. Human Fc (Jackson ImmunoResearch) was used as the negative control.
9) Western Blot Crude cell lysates were prepared, quantitated, fractionated and transferred to membranes as described previously (17). Membranes were blocked with 5% non-fat mills prior to incubation with antibody to ephrin B2 (1:5000 dilution) at 4 °C, for 16 h. Secondary antibody (1:100,000 dilution) conjugated with horseradish peroxidase was applied for 1 h at 25 °C. The membranes were developed using the SuperSignal West Femto Maximum sensitivity chemiluminescent substrate (Pierce, Rockford, IL) according to the manufacturer's instructions. Membranes were stripped using RestoreTM Western Blot Stripping Buffer (Pierce) and reprobed with EphB4 or (3-actin.
10) Cord formation assay MatngelTM Basement Membrane Matrix (BD Biosciences Discovery Labware, Bedford, MA) was mixed with growth medium (3:1) on ice and 0.5 ml liquid placed in 24-well plates. Incubation of plates at 37 °C for 15 min caused Matrigel~
polymerization.
HUVEC or KS-SLK in exponential phase growtla were treated with 2 or 8 ~,g/ml EphB4-ECD
or PBS as control for 16 h prior to trypsinizing and plating on the MatrigelTM. Culture on MatrigelT~ was continued in the presence of r ecombinant fusion proteins for 6 h. Cultures were fia~ed in 4% parafoumaldehyde for 30 min and evaluated by invented phase-contrast photornicroscopy.
11) Synthesis of Ephrin B2 and EphB4 siRNA by in vitro transcription The SilencerTM siRNA construction kit (Ambion, Austin TX) was used to synthesize siRNA to ephrin B2 and EphB4. Briefly, three 21 by target sequences comprising 19 by downstream of a 5'-AA dinucleotide were identified in the ephrin B2 cDNA
(Accession number NM 004093) that showed no significant homology to other sequences in the GenBank database. Sense and antisense siRNA 29-mer DNA oligonucleotide templates were synthesized at the USC Norris Microchemical Core Facility. Antisense template corresponded to the target sequence followed by 8 by addition (5'-CCTGTCTC-3') at the 3' end complementary to the T7 promoter primer provided with the Silencer SiRNA
Construction Kit. Sense template comprised 5'-AA followed by the complement of the target _88_ 19 bp, then the T7 8 by sequence as above. In separate reactions, the two siRNA
oligonucleotide templates were hybridized to a T7 promoter primer. The 3' ends of the hybridized oligonucleotides were extended by the I~lenow fragment of DNA
polynerase to create double-stranded siRNA transcription templates. The sense and antisense siRNA
templates were transcribed by T7 RNA polymerase and the resulting RNA
transcripts were hybridized to create dsRNA. The dsRNA consisted of 5' terminal single-stranded leader sequences, a 19 nt target specific dsRNA, and 3' terminal UUs. The leader sequences were removed by digesting the dsRNA with a single-stranded specific ribonuclease.
The DNA
template was removed at the same time by treatment with RNAse free deoxyribonuclease.
The resulting siRNAs were purified by glass fiber filter binding to remove excess nucleotides, short oligomers, proteins, and salts in the reaction. End product double-stranded 2lmer siRNAs are shown in Table 5. Similarly, an EphB4 and green fluorescence protein (GFP) siRNAs were synthesized.
Table 5: siRNAs of ephrin B2 and EphB4.
ephrin ~2 5-GCAGACAGAUGCACUAUUAUU-3' 3' -UUCGUCUGUCUACGUGAUAAU-5' ~phi'lll 5' -CUGCGAUUUCCAAAUCGAUUU-3 ~2 63:

3 -UUGACGCUAAAGGUUUAGCUA-5' ephrin X2137: 5'-GGACUGGUACUAUACCCACUU-3 3 -UUCCUGACCAUGAUAUGGGUG-5' Eph ~4 50: 5-GAGACCCUGCUGAACACAAUU-3 3 -UUCUCUGGGACGACUUGUGUU-5' GFP 5'-CGCUGACCCUGAAGUUCAUUU-3' 3' -UUGCGACUGGGACUUCAAGUA-5' 12) Tra~zsfection of Ephrin B2 or EphB4 siRNA
HUVEC were seeded on eight-well chamber slides coated with fibronectin and grown overnight in EGM-2 (Cambrex, Wall~ersville, MD). 16 h later media was replaced either with EBM-2 supplemented with 5% fetal calf serum (FCS) and EGM-2 BulletI~it supplements bFGF, hEGF and R3-IGF-I at the concentrations provided by the manufacturer, or supplemented with 5% FCS and 10 ng/ml rhVEGF (R&D Systems). After 2 h incubation at 37 °C, the cells were transfected using Lipofectamine 2000 (1 ~,g/ml;
Invitrogen) and 10 nM

specific siRNAs in Opti-MEM-1 serum-free medium (Invitrogen). Following transfection for 2 hr in Opti-MEM-1, media supplemented as above was replaced in the appropriate wells.
After 48 hrs, the cells were stained with crystal violet and immediately photographed at l OX
magnification.
13) Construction of ephrin B2 reporter plasmids Human ephrin B2 5'-flanking DNA from -2491 to -11 with respect to the translation start site was amplified from BACPAC clone RP11-297I6 (BacPac Resources, Children's Hospital, Oakland, CA) using the Advantage GC Genomic PCR kit (Clontech Palo Alto, CA) to overcome the large tracts of CG-rich sequence in the target area. Primers were designed to contain MIuI sites for cloning. Amplified product was digested with MIuI, gel purified and ligated into the MIuI site in the multiple cloning site of pGL3Basic (Promega, Madison, WI).
Orientation of the resulting clones was confirmed by restriction digest analysis. The correct clone was designated pEFNB2_24w-i iluc. Digestion of this clone with either K~f~I or SacI
followed by recircularization yielded pEFNB2_l~4zi-nluc and pEFNB2_5~~~_l lluc, respectively.
Plasmid DNAs used for transient transfections were purified using a Mega Prep kit (QIAGEN, Valencia, CA).
14) Transient transfection HLTVEC cells (0.8 x 104 cells/well in 24. well plates) maintained in EGM-2 media were transiently co-transfected with 0.5 ~,g/well ephrin B2 promoter-luciferase constz-~cts together with 50 ng/well either pCEFL or pI~SvGPCR-CEFL, using Superfect reagent (QIAGEN) according to the manufacturer's instructions. Cells were harvested 48 h post-transfection and lysed with Luciferase cell lysis buffer (Promega). Luciferase activity was assayed using the Luciferase Assay System (Promega) according to the manufacturer's instructions. Luciferase was normalized to protein, because pCEFL-vGPCR
induced the expression of ~3-galactosidase from pCMV-Sport-(3gal (Invitrogen).
15) Construction and purification of EphB4 extra cellular domain (ECD) protein See above, e.g., Example 1.
Example 7. Expression of EphB4 in Bladder cancer: a candidate target for therapy Figure 51 shows expression of EPHB4 in bladder cancer cell lines (A), and regulation of EPHB4 expression by EGFR signaling pathway (B).
Figure 52 shows that transfection of p53 inhibit the expression of EPHB4 in cell.
Figure 53 shows growth inhibition of bladder cancer cell line (5637) upon treatment with EPHB4 siRNA 472.
Figure 54 shows results on apoptosis study of 5637 cells transfected with siRNA 472.
Figure 55 shows effects of EPHB4 antisense probes on cell migration. 5637 cells were treated with EPHB4AS10 (10 ~,M).
Figure 56 shows effects of EPHB4 siRNA on cell invasion. 5637 cells were transfected with siRNA 472 or control siRNA.
Examt~le 8. Inhibition of EphB4 Gene Expression by EphB4 antisense probes and RNAi robes Cell lines expressing Ep11B4 were treated with the synthetic phosphorothioate modified oligonucleotides and harvested after 24 hr. Cell lysates were prepared and probed by western blot analysis for relative amounts of EphB4 compared to untreated control cells.
Studies on inhibition of cell proliferation were done in HNSCC cell lines characterized to express EphB4. Loss of cell viability was shown upon l~nock-down of EphB4 expression. Cells were treated in vitro and cultured in 4.8-well plates, seeded with 10 thousand cells per well. Test compounds were added and the cell viability was tested on day 3. The results on EphB4 antisense probes were summarized below in Table 6. The results on EphB4 RNAi probes were summarized below in Table 7.
Table 6. Inhibition of EphB4 Gene Expression by EphB4 antisense probes Name Sequence ~ position TnhibitionPercent 5' 3' of EphB4 reduction Expressionin viability Eph B4169 TCAGTA CTGCGG GGCCGGTCC (2944-2963)++ 36 Eph B4168 TCCTGT CCCACC CGGGGTTC (2924-2943)++ 51 Eph B4167 CCGGCT TGGCCT GGGACTTC (2904-2923)+++ 66 Eph B4166 ATGTGC TGGACA CTGGCC (2884-2903)++++ 70 AA

Eph B4165 GATTTT CTTCTG GTGTCCCG (2864-2883)++++ 75 Eph B4164 CCAGAG TGACTC CGATTCGG (2844-2863)++ 40 Eph B4163 AGCAGG TCCTCA GCAGAGAT (2824-2843)++++ 66 LEphB4162 CTGGCT GACCAG CTCGAAGG (2804-2823) 25 ~ I

Eph B4 161 AGC CAA CAG CGGCTGCG (2784-2803)+ 33 AGC

Eph B4 160 AAA CTTTCTTCG TATCTTCC (2763-2783)+ 25 Eph B4 159 CAT TTTGATGGC CCG CC (2743-2762)++ 40 AAG

Eph B4 158 ACT CGCCCACAG AGCCAA (2723-2742) 30 AA

Eph B4 157 GCT GAGTAGTGA GGCTGCCG (2703-2722)+ 25 Eph B4 156 CTG GTCCAGGAG AGGGTGTG (2683-2702)++ 30 Eph B4 155 AGG CCCCGCCAT TCTCCCGG (2663-2682) 25 Eph B4 154 GCC ACGATTTTG AGGCTGGC (2643-2662)++ 40 Eph B4 153 GGG GTTCCGGAT CATCTTGT (2623-2642)++ 35 Eph B4 152 CCA GGGCGCTGA CCACCTGG (2603-2622)+ 30 Eph B4 151 GGG CGGGGC CGGGCATT (2583-2602)+ 25 AAG

Eph B4 150 CCG GTCTTTCTG CCAACAGT (2563-2582)++ 25 Eph B4 149 CCA GCATGAGCT GGTGGAGG (2543-2562)++ 20 Eph B4 148 GAG GTGGGACAG TCTGGGGG (2523-2542)+ 30 Eph B4 147 CGG GGGCAGCCG GTAGTCCT (2503-2522)++ 40 Eph B4 146 GTT CAATGGCAT TGATCACG (2483-2502)++++ 70 Eph B4 145 TCC TGATTGCTC ATGTCCCA (2463-2482)++++ 80 Eph B4 144 GTA CGGCCTCTC CCC TG (2443-2462)+++ 60 AAA

Eph B4 143 ACA TCACCTCCC ACATCACA (2423-2442)++++ 80 Eph B4 142 ATC CCGTAACTC CAGGCATC (2403-2422)++ 40 Eph B4 141 ACT GGCGGAAGT GAACTTCC (2383-2402)+++ 50 Eph B4 140 GGA AGGCAATGG CCTCCGGG (2363-2382)++ 45 Eph B4 139 GCA GTCCATCGG ATGGGAAT (2343-2362)++++ 70 Eph B4 138 CTT TCCTCCCAG GGAGCTCG (2323-2342)++++ 70 Eph B4 137 TGT AGGTGGGAT CGG AG (2303-2322)++ 40 AAG

Eph B4 136 TTC TCCTCCAGG CGGGA (2283-2302)++ 35 AAT

Eph B4 135 AAG GCCAAAGTC AGACACTT (2263-2282)++++ 60 Eph B4 134 GCA GACGAGGTT GCTGTTGA (2243-2262)++ 50 Eph B4 133 CTA GGATGTTGC GAGCAGCC (2223-2242)++ 40 Eph B4 132 AGG TCTCGGTGG ACGTAGCT (2203-2222)++ 40 Eph B4 131 CAT CTCGGCAAG GTACCGCA (2183-2202)+++ 50 Eph B4 130 TGC CCGAGGCGA TGCCCCGC (2163-2182)++ 50 Eph B4 129 AGC ATGCCCACG AGCTGGAT (2143-2162)++ 50 Eph B4 128 GAC TGTGAACTG TCCGTCGT (2123-2142)++ 50 Eph B4 127 TTA GCCGCAGGA AGGAGTCC (2103-2122)+++ 60 Eph B4 126 AGG GCGCCGTTC TCCATG (2083-2102)++ 50 Al~

Eph B4 125 CTC TGTGAG CATGACGG (2063-2082)++++ 80 AAT

Eph B4 124 GCA TGCTGTTGG TGACCACG (2043-2062)++++ 70 Eph B4 123 CCC TCCAGGCGG ATGATATT (2023-2042)++ 50 Eph B4 122 GGG GTGCTCGAA CTGGCCCA (2003-2022)++++ 80 Eph B4 121 TGA TGGAGGCCT CGCTCAGA (1983-2002)++ 50 Eph B4 120 AAC TCACGCCGC TGCCGCTC (1963-1982)++ 40 Eph B4 119 CGT GTAGCCACC CTTCAGGG (1943-1962)++++ 75 Eph B4 118 TCT TGATTGCCA CACAGCTC (1923-1942)++++ 80 Eph B4 117 TCC TTCTTCCCT GGGGCCTT (1903-1922)++++ 70 Eph B4 116 GAG CCGCCCCCG GCACACCT (1883-1902)++ 50 Eph B4 115 CGC CAA CAC CTGCACCA (1863-1882)++++ 60 ACT

Eph B4 114 ATC ACCTCTTCA ATCTTGAC (1843-1862)++++ 65 Eph B4 113 GTA GGAGACATC GATCTCTT (1823-1842)++++ 90 Eph B4 112 TTG CAA CCC TCACAGCC (1803-1822)++++ 70 ATT

Eph B4 111 TCA TTAGGGTCT TCATAAGT (1783-1802)++++ 70 Eph B4 110 GAA GTCGAT GTAGACCT (1763-1782)++++ 80 GGG

Eph B4 109 TAG TACCATGTC CGATGAGA (1743-1762)++ 50 Eph B4 108 TAC TGTCCGTGT TTGTCCGA (1723-1742)++ 45 Eph B4 107 ATA TTCTGCTTC TCTCCCAT (1703-1722)++++ 70 Eph B4 106 TGC TCTGCTTCC TGAGGCAG (1683-1702)++++ 70 Eph B4 105 AGA ACTGCGACC ACAATGAC (1663-1682)++ 40 ~EphB4 104 CAC CAGGACCAG GACCACAC (1643-1662)++++ 70 I

-92=

Eph B4 103 CCA CGACTGCCG TGCCCGCA (1623-1642)++ 40 Eph B4 102 ATC AGGGCCAGC TGCTCCCG (1603-1622)+++ 50 Eph B4 101 CCA GCCCTCGCT CTCATCCA (1583-1602)++++ 80 Eph B4 100 GTT GGGTCTGGC TGTGATGT (1563-1582)++++ 80 Eph B4 99 TCC TGGCCG GGCCCGTA (1543-1562)++ 35 AAG

Eph B4 98 GCC GGCCTCAGA GCGCGCCC (1523-1542)++ 50 Eph B4 97 GTA CCTGCACCA GGTAGCTG (1503-1522)++++ 80 Eph B4 96 GCT CCCCGCTTC AGCCCCCG (1483-1502)++ 50 Eph B4 95 CAG CTCTGCCCG GTTTTCTG (1463-1482)++ 50 Eph B4 94 ACG TCTTCAGGA ACCGCACG (1443-1462)++++ 80 Eph B4 93 CTG CTGGGACCC TCGGCGCC (1423-1442)++ 40 Eph B4 92 CTT CTCATGGTA TTTGACCT (1403-1422)++++ 80 Eph B4 91 CGT AGTCCAGCA CAGCCCCA (1383-1402)++++ 85 Eph B4 90 CTG GGTGCCCGG GGAACAGC (1363-1382)+++ 50 Eph B4 89 CCA GGCCAGGCT CAA GC (1343-1462)++++ 70 GCT

Eph B4 88 TGG GTGAGGACC GCGTCACC (1323-1342)++ 40 Eph B4 87 CGG ATGTCAGAC ACTGCAGG (1303-1322)++++ 60 Eph B4 86 AGG TACCTCTCG GTCAGTGG (1283-1302)++ 50 Eph B4 85 TGA CATTGACAG GCTCAA (1263-1282)++++ 80 AT

Eph B4 84 GGG ACGGGCCCC GTGGCTAA (1243-1262)++ 50 Eph B4 83 GGA GGATACCCC GTTCAATG (1223-1242)+++ 60 Eph B4 82 CAG TGACCTCAA AGGTATAG (1203-1222)++++ 70 Eph B4 81 GTG AAGTCAGGA CGTAGCCC (1183-1202)+++ 60 Eph B4 80 TCG CACCAC CCAGGGCT (1163-1182)+++ 50 AAC

Eph B4 79 CCA CCAGGTCCC GGGGGCCG (1143-1162)++ 40 Eph B4 78 GGG TCAAAAGTC AGGTCTCC (1123-1142)++++ 70 Eph B4 77 CCC GCAGGGCGC ACAGGAGC (1103-1122)+++ 60 Eph B4 76 CTC CGGGTCGGC ACTCCCGG (1083-1102)+++ 60 Eph B4 75 CAG CGGAGGGCG TAGGTGAG (1063-1082)++ 40 Eph B4 74 GTC CTCTCGGCC ACCAGACT (1043-1062)++ 50 Eph B4 73 CCA GGGGGGCAC TCCATTCC (1023-1042)++ 50 Eph B4 72 AGG TGCAGGGAG GAGCCGTT (1003-1022)++++ 70 Eph B4 71 CAG GCGGGAAAC CACGCTCC (983-1002) ++ 40 Eph B4 70 GCG GAGCCG GAGGGGTG (963-982) +++ 50 AAG

Eph B4 69 GTG CAGGGTGCA CCCCGGGG (943-962) +++ 50 Eph B4 68 GTC TGTGCGTGC CCGGAAGT (923-942) ++ 40 Eph B4 67 ACC CGACGCGGC ACTGGCAG (903-922) ++ 40 Eph B4 66 ACG GCTGATCCA ATGGTGTT (883-902) ++ 50 Eph B4 65 AGA GTGGCTATT GGCTGGGC (863-882( ++++ 60 Eph B4 64 ATG GCTGGCAGG ACCCTTCT (843-862) ++++ 80 Eph B4 63 CCT GACAGGGGC TTG GT (823-842) ++++ 80 AAG

Eph B4 62 GCC CTGGGCACA GGCTCGGC (803-822) +++ 70 Eph B4 61 ACT TGGTGTTCC CCTCAGCT (783-802) ++++ 80 Eph B4 60 GCC TCGAACCCC GGAGCACA (763-782) +++ 50 Eph B4 59 GCT GCAGCCCGT GACCGGCT (743-762) +++ 50 Eph B4 58 GTT CGGCCCACT GGCCATCC (723-742) ++ 45 Eph B4 57 TCA CGGCAGTAG AGGCTGGG (703-722) +++ 70 Eph B4 56 GCT GGGGCCAGG GGCGGGGA (683-702) ++ 50 Eph B4 55 CGG CATCCACCA CGCAGCTA (663-682) ++ 50 Eph B4 54 CCG GCCACGGGC ACAACCAG (643-662) ++ 50 Eph B4 53 CTC CCGAGGCAC AGTCTCCG (623-642) +++ 50 Eph B4 52 GGA ATCGAGTCA GGTTCACA (603-622) ++++ 90 Eph B4 51 GTC AGCTGGGCG CACTTTTT (583-602) +++ 70 Eph B4 50 GTA GAAGAGGTG CAGGGATA (563-582) ++++ 80 Eph B4 49 GCA GGGCCATGC AGGCACCC (543-562) ++++ 80 Eph B4 48 TGG TCCTGG GCCAGGTA (523-542) ++++ 90 AAG

Eph B4 47 GAA GCCAGCCTT GCTGAGCG (503-522) ++++ 80 Eph B4 46 GTC CCAGACGCA GCGTCTTG (483-502) ++ 40 Eph 45 ACA TTCACCTTCCCG GTGGC (463-482) +++ 50 Eph 44 CTC GGCCCCAGGGCG CTTCC (443-462) ++ 50 Eph 43 GGG TGAGATGCTCCG CGGCC (423-442) +++ 60 Eph 42 ACC GTGTCCACCTTG ATGTA (403-422) ++++ g0 Eph 41 GGG GTTCTCCATCCA GGCTG (383-402) ++++ 80 Eph 40 GCG TGAGGGCCGTGG CCGTG (363-382) ++ 50 Eph 39 TCC GCATCGCTCTCA TAGTA (343-362) +++ 60 Eph 38 GAA GACGGTGAA CTCCT (323-342) ++++ 80 Eph 37 TGC AGGAGCGCCCAG CCCGA (303-322) +++ 50 Eph 36 GGC AGGGACAGGCAC TCGAG (283-302) +++ 45 Eph 35 CAT GGTGAAGCGCAG CGTGG (263-282) ++ 50 Eph 34 CGT ACACGTGGACGG CGCCC (243-262) ++ 40 Eph 33 CGC CGTGGGACCCAA CCTGT (223-242) +++ 60 Eph 32 GCG CCAGTGGGC CTGGC (203-222) ++++ 70 Eph 31 CCG GGGCACGCTGCA CGTCA (183-202) +++ 60 Eph 30 CAC ACTTCGTAGGTG CGCAC (l63-182) +++ 70 Eph 29 GCT GTGCTGTTCCTC ATCCA (143-l62) ++++ 80 Eph 28 GGC CGCTCAGTTCCT CCCAC (123-142) ++ 40 Eph 27 TGC CCGTCCACCTGA GGG (103-l22) ++ 50 Eph 26 TGT CACCCACTTCAG ATCAG (83-102) ++++ 70 Eph 25 CAG TTTCCAATTTTG TGTTC (63-82) ++++ 70 Eph 24 AGC AGGGTCTCTTCC AAA (43-62) ++++ 80 Eph 23 TGC GGCCAACGAAGC CCAGC (23-42) ++ 50 Eph 22 AGA GCAGCACCCGGA GCTCC (3-22) +++ 50 Eph 21 AGC AGCACCCGGAGC TCCAT (1-20) +++ 50 Additional antisens e obesdescribed pr in the specification EphB4 GTG CAGGGATAGCAG GGCCAT (552-572) EphB4 AAG GAGGGGTGGTGC ACGGTG (952-972) EphB4 TTC CAGGTGCAGGGA GGAGCC (1007-1027) EphB4 GTG GTGACATTGACA GGCTCA (1263-1285) EphB4 TCT GGCTGTGATGTT CCTGGC (1555-1575) EphB4 GCC GCTCAGTTCCTC CCA (123-140) EphB4 TGA AGGTCTCCTTGC AGG (316-333) EphB4 CGC GGCCACCGTGTC CACCTT (408-428) as-8 EphB4 CTT CAGGGTCTTGAT TGCCAC (1929-1949) EphB4 ATG GAGGCCTCGCTC AGA (1980-1999) IEphb4 CAT GCCCACGAGCTG GATGAC (2138-2158) AS-ll I

Table 7. Inhibition of EphB4 Gene Expression by EphB4 I~NAi probes RNAi EphB4 RNAi sequence Inhibition Percent of EphB4 reduction Expression in viability 1 446 aaattggaaactgctgatctg466 2 447 aattggaaactgctgatctga467 +++ 70 3 453 aaactgctgatctgaagtggg473 ++++ 70 4 454 aactgctgatctgaagtgggt474 +++ 80 854 aatgtcaagacgctgcgtctg874 +++ 65 6 467 aagtgggtgacattccctcag487 + 35 7 848 aaggtgaatgtcaagacgctg868 ++ 50 8 698 aaggagaccttcaccgtcttc718 +++ 75 959 aaaaagtgcgcccagctgact979 + 40 1247 aatagccactctaacaccatt1267 ++ 50 11 1259 aacaccattggatcagccgtc1279 ++ 50 12 1652 aatgtcaccactgaccgagag1672 + 35 13 . 1784 aaataccatgagaagggcgcc1804 +++ 65 14 1832 aagacgtcagaaaaccgggca1852 + 30 l5 1938 aacatcacagccagacccaac19 ++ 50 16 2069 aagcagagcaatgggagagaa2089 ++++ 75 17 2078 aatgggagagaagcagaatat2098 +++ 65 18 2088 aagcagaatattcggacaaac2108 +++ 70 19 2094 aatattcggacaaacacggac2114 ++ 40 2105 aaacacggacagtatctcatc2125 ++ 50 21 2106 aacacggacagtatctcatcg2126 + 35 22 2197 aaaagagatcgatgtctccta2217 +++ 65 23 2174 aatgaggctgtgagggaattt2194 ++ 50 24 2166 aagaccctaatgaggctgtga2186 ++ 50 2198 aaagagatcgatgtctcctac2218 +++ 55 26 2199 aagagatcgatgtctcctaCg2219 +++ 70 27 2229 aagaggtgattggtgcaggtg2249 + 33 28 2222 aagattgaagaggtgattggt2242 + 30 29 2429 aacagcatgcccgtcatgatt2449 ++ 40 2291 aagaaggagagctgtgtggca2311 +++ 50 31 2294 aaggagagctgtgtggcaatc2314 +++ 60 32 2311 aatcaagaccctgaagggtgg2331 +++ 70 33 2497 aaacgacggacagttcacagt2517 + 35 34 2498 aacgacggacagttcacagtc2518 + 40 2609 aacatcctagtcaacagcaac2629 ++ 50 36 2621 aacagcaacctcgtctgcaaa2641 + 35 37 2678 aactcttccgatcccacctac2698 ++ 50 38 2640 aagtgtctgactttggccttt2660 +++ 70 39 2627 aacctcgtctgcaaagtgtct2647 ++ 50 2639 aaagtgtctgactttggcctt2659 + 25 41 2852 aatcaggacgtgatcaatgcc2872 +++ 75 42 2716 aaagattcccatccgatggac2736 ++ 50 43 2717 aagattcccatccgatggact2737 ++ 60 44 2762 aagttcacttccgccagtgat2782 +++ 70 3142 aagatacgaagaaagtttcgc3162 ++ 50 46 3136 aatgggaagatacgaagaaag3156 +++ 66 47 2867 aatgccattgaacaggactac2887 48 3029 aaaatcgtggcccgggagaat3049 + 33 49 3254 aaaatcttggccagtgtccag3274 ++ 50 50 3255 aaatcttggccagtgtccagc3275 +++ 75 51 3150 aagaaagtttcgcagccgctg3170 +++ 80 52 3251 aagaaaatcttggccagtgtc3271 ++ 50 53 3256 aatcttggccagtgtccagca3276 ++ 50 AdditionalRNAi probes describedin specification the Eph B4 50 gagacccugcugaacacaauu Eph B4 472 ggugaaugucaagacgcuguu Eph B4 1562 caucacagccagacccaacuu siRNA cucuuccgaucccaccuacuu Eph B4 2302 cucuuccgaucccaccuacuu Example 9. Inhibition of Epllrin B2 Gene Expression b~phrin B2 antisense probes and RNAi probes KS SLK, a cell line expressing endogenous high level of ephrin B2. Cell viability was tested using fixed dose of each oligonuceotide (SUM). Gene expression downregulation was done using cell line 293 engineered to stably express full-length ephrin B2.
KS SLK
expressing EphrinB2 were also used to test the viability in response to RNAi probes tested at the fixed dose of 50 nM. Protein expression levels were measured using 293 cells stably expressing full-length EphrinB2, in cell lysates after 24 hr treatment with fixed 50 nM of I~NAi probes.
The results on Ephrin B2 antisense probes were summarized below in Table 8.
The results on Ephrin B2 P.I~TAi probes were summarized below in Table 9.
Table 8. Ephrin B2 antisense ~I~Ns.
sequence Coding Percent Inhibition region reduction of Ephrin in B2 viability Expression EphrinAS- TCAGACCTTGTAGTA GT (983-1002)35 ++
AAT

EphrinAS- TCGCCGGGCTCTGCGGGGGC (963-982) 50 +++

EphrinAS- ATCTCCTGGACGATGTACAC (943-962) 45 ++

EphrinAS- CGGGTGCCCGTAGTCCCCGC (923-942) 35 ++

EphrinAS- TGACCTTCTCGTAGTGAGGG (903-922) 40 +++

EphrinAS- CAG ACGCTGTCCGCAGT (883-902) 40 ++
AAG

EphrinAS- CCTTAGCGGGATGATAATGT (863-882) 35 ++

EphrinAS- CACTGGGCTCTGAGCCGTTG (843-862) 60 +++

EphrinAS- TTGTTGCCGCTGCGCTTGGG (823-842) 40 ++

EphrinAS- TGTGGCCAGTGTGCTGAGCG (803-822) 40 ++

EphrinAS- ACAGCGTGGTCGTGTGCTGC (783-802)70 +++

EphrinAS- GGCGAGTGCTTCCTGTGTCT (763-782)80 ++++

EphrinAS- CCTCCGGTACTTCAGCAAGA (743-762)50 +++

EphrinAS- GGACCACCAGCGTGATGATG (723-742)60 +++

EphrinAS- ATGACGATGAAGATGATGCA (703-722)70 +++

EphrinAS- TCCTGAAGCAATCCCTGCAA (683-702)60 +++

EphrinAS- ATAAGGCCACTTCGGAACCG (663-682)45 ++

EphrinAS- AGGATGTTGTTCCCCGAATG (643-662)50 +++

EphrinAS- TCCGGCGCTGTTGCCGTCTG (623-642)75 +++

EphrinAS- TGCTAGAACCTGGATTTGGT (603-622)60 +++

EphrinAS- TTTACAAAGGGACTTGTTGT (583-602)66 +++

EphrinAS- CGAACTTCTTCCATTTGTAC (563-582)50 ++

EphrinAS- CAGCTTCTAGTTCTGGACGT (543-562)50 +++

EphrinAS- CTTGTTGGATCTTTATTCCT (523-542)70 +++

EphrinAS- GGTTGATCCAGCAGAACTTG (503-522)65 +++

EphrinAS- CATCTTGTCCAACTTTCATG (483-502)75 +++

EphrinAS- AGGATCTTCATGGCTCTTGT (463-482)60 +++

EphrinAS- CTGGCACACCCCTCCCTCCT (443-462)45 ++

EphrinAS- GGTTATCCAGGCCCTCCAAA (423-442)50 +++

EphrinAS- GACCCATTTGATGTAGATAT (403-422)50 +++

EphrinAS- AATGTAATAATCTTTGTTCT (383-402)60 +++

EphrinAS- TCTGAAATTCTAGACCCCAG (363-382)60 +++

EphrinAS- AGGTTAGGGCTGAATTCTTG (343-362)75 +++

EphrinAS- AAACTTGATGGTGAATTTGA (323-342)60 +++

EphrinAS- TATCTTGGTCTGGTTTGGCA (303-322)50 ++

EphrinAS- CAGTTGAGGAGAGGGGTATT (283-302)40 ++

EphrinAS- TTCCTTCTTAATAGTGCATC (263-282)66 +++

EphrinAS- TGTCTGCTTGGTCTTTATCA (243-262)70 ++++

EphrinAS- ACCATATAAACTTTATAATA (223-242)50 +++

EphrinAS- TTCATACTGGCCAACAGTTT (203-222)50 +++

EphrinAS- TAGAGTCCACTTTGGGGCAA (183-202)70 ++++

EphrinAS- ATAATATCCAATTTGTCTCC (163-182)70 ++++

EphrinAS- I CTGTGGGTATAGTACCA (143-l62)80 ++++
TAT

EphrinAS- GTCCTTGTCCAGGTA (123-142)60 +++
GAA
AT

EphrinAS- TTGGAGTTCGAGGAA CA (103-122)80 ++++
TTC

EphrinAS- ATAGATAGGCTCTAA TA (83-102) 70 +++
AAC

EphrinAS- TCGATTTGG TCG TT (63-82) 50 +++
AAA CAG

EphrinAS- CTGCAT ATC AC (43-62) 80 ++++
AAA AAA
ACC

EphrinAS- ACCCCAGCAGTACTT CA (23-42) 85 ++++
CCA

EphrinAS- CGGAGTCCCTTCTCA CC (3-22) 70 +++
CAG

EphrinAS- GAGTCCCTTCTCACA AT (1-20) 80 ++++
GCC

Table 9. Ephrin B2 I~NAi probes.
RNAi other Percent Inhibition RNAi Sequence reduction of Ephrin no.
and in B2 homology viability Expression with human genes.

89 aactgcgatttccaaatcgat109 80 ++++ 1 141 aactccaaatttctacctgga161 70 ++++ 2 148 aatttctacctggacaaggac168 75 +++ 3 147 aaatttctacctggacaagga167 60 +++ 4 163 aaggactggtactatacccac183 40 ++ 5 217 aagtggactctaaaactgttg237 80 ++++ 6 229 aaactgttggccagtatgaat249 50 +++ 7 228 aaaactgttggccagtatgaa248 80 ++++ 8 274 aagaccaagcagacagatgca294 80 ++++ 11 273 aaagaccaagcagacagatgc293 60 +++ 12 363 aagtttcaagaattcagccct383 66 +++ 13 370 aagaattcagccctaacctct390 50 +++ 14 373 aattcagccctaacctctggg393 50 +++ 15 324 aactgtgccaaaccagaccaa344 90 ++++ 16 440 aaatgggtctttggagggcct460 80 ++++ l7 501 aagatcctcatgaaagttgga521 50 +++ 18 513 aaagttggacaagatgcaagt533 50 +++ 19 491 aagagccatgaagatcctcat511 50 +++ 20 514 aagttggacaagatgcaagtt534 66 +++ 21 523 aagatgcaagttctgctggat543 66 +++ 22 530 aagttctgctggatcaaccag550 50 +++ 23 545 aaccaggaataaagatccaac565 35 ++ 24 555 aaagatccaacaagacgtcca575 40 ++ 25 556 aagatccaacaagacgtccag576 60 +++ 26 563 aacaagacgtccagaactaga583 60 +++ 27 566 aagacgtccagaactagaagc586 70 +++ 2g 593 aaatggaagaagttcgacaac613 75 ++++ 29 577 aactagaagctggtacaaatg597 66 +++ 30 594 aatggaagaagttcgacaaca614 35 ++ 31 583 aagctggtacaaatggaagaa603 50 +++ 32 611 aacaagtccctttgtaaaacc631 70 ++++ 33 599 aagaagttcgacaacaagtcc619 70 ++++ 34 602 aagttcgacaacaagtccctt622 80 ++++ 35 626 aaaaccaaatccaggttctag646 50 +++ 36 627 aaaccaaatccaggttctagc647 25 + 37 628 aaccaaatccaggttctagca648 30 ++ 38 632 aaatccaggttctagcacaga652 60 +++ 39 633 aatccaggttctagcacagac653 40 ++ 40 678 aacaacatcctcggttccgaa698 30 ++ 41 681 aacatcctcggttccgaagtg701 20 + 42 697 aagtggccttatttgcaggga717 30 ++ 43 Additional Ephrin probesdescribedin B2 RNAi the specification GCAGACAGAUGCACUAUUAUU ephrin CUGCGAUUUCCAAAUCGAUUU ephrin GGACUGGUACUAUACCCACUU ephrin Example 10. EphB4 antibodies inhibit tumor growth Figure 57 shows results on comparison of EphB4. monoclonal antibodies by 6250 and in Pull-down assay.
Figure 58 shows that EphB4 antibodies, in the presence of matrigel and growth factors, inhibit the ih vivo tumor growth of SCC15 cells.
BaIbC nude mice were injected subcutaneously with 2.5 x 10~ viable tumor cells SCC15 is a head and neck squamous cell carcinoma line. Tumors were initiated in nu/nu mice by injecting 2.5-Sx106 cells premixed with matrigel and Growth factors, and Ab's subcutaneously to initiate tumor xenografts. Mice were opened 14 days after injections.
SCC15 is a head and neck squamous cell carcinoma line, B16 is a melanoma cell line, and MCF-7 is a breast carcinoma line. The responses of tumors to these treatments were compared to control treated mice, which receive PBS injections. Animals were observed daily for tumor growth and subcutaneous tumors were measured using a caliper every 2 days.

Antibodies #1 and #23 showed significant regression of SCC15 tumor size compared to control, especially with no additional growth factor added.
Figure 59 shows that EphB4 antibodies cause apoptosis, necrosis and decreased angiogenesis in SCC15, head and neck carcinoma tumor type.
Angiogenesis was assessed by CD-31 immunohistochemistry. Tumor tissue sections from treated and untreated mice were stained for CD31. Apoptosis was assessed by immunohistochemical TUNNEL, and proliferation by BrdU assay. Following surgical removal, tumors were immediately sliced into 2 mm serial sections and embedded in paraffin using standard procedures. Paraffin embedded tissue were sectioned at 5 Vim, the wax removed and the tissue rehydrated. The rehydrated tissues were microwave irradiated in antigen retreival solution. . Slides were rinsed in PBS, and TUNNEL reaction mixture (Terminal deoxynucleotidyl transferase and flourescein labeled nucleotide soluti~n), and BrdU were added in a humidity chamber completely shielded from light. The TUNNEL and BrdU reaction mixture were then removed, slides were rinsed and anti-flourescein antibody conjugated with horseradish peroxidase was added. After incubation and rinsing, 3, 3'diaminobenzidine was added. IVIasson's Trichrome and PIematoxylin and Eosin were also used to stain the slides to visualize morphology. Ii~Iasson's Trichrome allows to visualize necrosis and fibrosis. The tumor gets blood support from tumor/skin, muscle boundaxy. As tumor grows, inner regions get depleted ~f nutrients. This leads to necrosis (cell death), preferably at the tumor center. After cells die, (tumor) tissue gets replaced with fibroblastic tissue. Slides were visualized under 20-fold magnification with digital images acquired. A
different morphology was obtained on SCC tumors with each antibody administered. Ab #1 showed an increase in necrosis and fibrosis but not apoptosis. Ab #23 showed an increase in apoptosis, necrosis and fibrosis and a decrease in vessel infiltration. Ab #35 showed an increase in necrosis and fibrosis, and a small increase in apoptosis and a decrease in vessel infiltration. Ab #79 showed a large increase in apoptosis, and necrossis and fibrosis. Ab #91 showed no change in apoptosis but an increase in proliferation. And Ab #138 showed an increase in apoptosis, necrosis, fibrosis and a decrease in proliferation and vessel infiltration.
Tumors treated with control PBS displayed abundant tumor density and a robust angiogenic response. Tumors treated with EphB4 antibodies displayed a decrease in tumor cell density and a marked inhibition of tumor angiogenesis in regions with viable tumor cells, as well as tumor necrosis and apoptosis.
- loo -Figure 60 shows that systemic administration of antibodies on xenografts leads to tumor regression in SCC15 tumor xenografts.
Alternate day treatment with EphB4 monoclonal antibody or an equal volume of PBS
as control were initiated on day 4, after the tumors have established, and continued for 14 days. Systemic administration was administered either IP or SC with no significant difference. All the experiments were carried out in a double-blind manner to eliminate investigator bias. Mice were sacrificed at the conclusion of the two week treatment period.
Tumors were harvested immediately postmortem and fixed and processed for immunohistochemistry. EphB4 antibodies 40 mg per kg body weight were administered.
Treatment with EphB4 antibody significantly inhibited human SCC tumor growth compared with control-treated mice (p<0.05). Treatment with EphB4 antibody significantly inhibited tumor weight compared with control-treated mice (p<0.05).
lIVC~l~P~I~ATI~I~T BY I~EFEI~EIVCE
All publications and patents mentioned herein are hereby incorporated by reference in their entirety as if each individual publication or patent was specifically and individually indicated to be incorporated by reference.
while specific embodiments of the subj ect invention have been discussed, the above specification is illustrative and not restrictive. Many variations of the invention will become apparent to those skilled in the aut upon review of this specification and the claims below.
The full scope of the invention should be determined by reference to the claims, along with their full scope of equivalents, and the specification, along with such variations.

Claims (61)

1. An isolated soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide.

2. The soluble polypeptide of claim 1, comprising a globular domain of an EphB4 protein.

3. The soluble polypeptide of claim 1, comprising a sequence at least 90%
identical to residues 1-522 of the amino acid sequence defined by Figure 65.

4. The soluble polypeptide of claim 1, comprising a sequence at least 90%
identical to residues 1-412 of the amino acid sequence defined by Figure 65.

5. The soluble polypeptide of claim 1, comprising a sequence at least 90%
identical to residues 1-312 of the amino acid sequence defined by Figure 65.

6. The soluble polypeptide of claim 1, comprising a sequence defined by Figure 1 or 2.

7. The soluble polypeptide of claim 1, wherein the soluble polypeptide inhibits the interaction between Ephrin B2 and EphB4.

8. The soluble polypeptide of claim 1, wherein the soluble polypeptide inhibits clustering of Ephrin B2 or EphB4.

9. The soluble polypeptide of claim 1, wherein the soluble polypeptide inhibits phosphorylation of Ephrin B2 or EphB4.

10. The soluble polypeptide of claim 1, wherein the soluble polypeptide is a fusion protein.

11. The soluble polypeptide of claim 1, wherein the soluble polypeptide comprises one or more modified amino acid residues.

12. An isolated soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephuin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.

13. The soluble polypeptide of claim 12, comprising residues 1-225 of the amino acid sequence defined by Figure 66.

14. The soluble polypeptide of claim 12, comprising a sequence defined by Figure 3

15. The soluble polypeptide of claim 12, wherein the soluble polypeptide inhibits the interaction between Ephrin B2 and EphB4.

16. The soluble polypeptide of claim 12, wherein the soluble polypeptide inhibits clustering of Ephrin B2 or EphB4.

17. The soluble polypeptide of claim 12, wherein the soluble polypeptide inhibits phosphorylation of Ephrin B2 or EphB4.

18. The soluble polypeptide of claim 12, wherein the soluble polypeptide is a fusion protein.

19. The soluble polypeptide of claim 12, wherein the soluble polypeptide comprises one or more modified amino acid residues.

20. A pharmaceutical composition comprising the soluble polypeptide of claim 1, and a pharmaceutically acceptable carrier.

21. A pharmaceutical composition comprising the soluble polypeptide of claim 12, and a pharmaceutically acceptable carrier.

22. A cosmetic composition comprising the soluble polypeptide of claim 1, and a pharmaceutically acceptable carrier.

23. A cosmetic composition comprising the soluble polypeptide of claim 12, and a pharmaceutically acceptable carrier.
23. A diagnostic kit comprising the soluble polypeptide of claim 1 and a pharmaceutically acceptable carrier.

24. A diagnostic kit comprising the soluble polypeptide of claim 12 and a carrier.

25. An antagonist antibody selected from the group consisting of:
(a) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (b) aa1 antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

26. The antagonist antibody of claim 25, wherein the antagonist antibody inhibits the interaction between Ephrin B2 and EphB4.

27. The antagonist antibody of claim 25, wherein the antagonist antibody inhibits clustering of Ephrin B2 or EphB4.

28. The antagonist antibody of claim 25, wherein the antagonist antibody inhibits phosphorylation of Ephrin B2 or EphB4.

29. The antagonist antibody of claim 25, wherein the antagonist antibody is a monoclonal antibody.

30. The antagonist antibody of claim25, wherein the antagonist antibody is a polyclonal antibody.

31. A pharmaceutical composition comprising the antagonist antibody of claim 25, and a pharmaceutically acceptable carrier.

32. A cosmetic compostion comprising the antagonist antibody of claim 25, and a pharmaceutically acceptable carrier.

33. A diagnostic lit comprising the antagonist antibody of claim 25, and a carrier.

34. A method of inhibiting signaling through Ephrin B2/EphB4 pathway in a cell, comprising contacting the cell with an effective amount of a soluble polypeptide of claim 1.

35. A method of inhibiting signaling through Ephrin B2/EphB4 pathway in a cell, comprising contacting the cell with an effective amount of a soluble polypeptide of claim 12.

36. A method of inhibiting signaling through Ephrin B2/EphB4 pathway in a cell, comprising contacting the cell with an effective amount of a soluble polypeptide of claim 25.

37. A method of reducing the growth rate of a tumor, comprising administering an amount of a polypeptide agent sufficient to reduce the growth rate of the tumor, wherein the polypeptide agent is selected from the group consisting of:
(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

38. The method of claim 37, wherein the tumor comprises cells expressing a higher level of EphB4 and/or EphrinB2 than noncancerous cells of a comparable tissue.

39. A method for treating a patient suffering from a cancer, comprising administering to the patient a polypeptide agent selected from the group consisting of (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;

(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.

(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

40. The method of claim 39, wherein the cancer comprises cancer cells expressing EphrinB2 and/or EphB4 at a higher level than noncancerous cells of a comparable tissue.

41. The method of claim 39, wherein the cancer is metastatic cancer.

42. The method of claim 39, wherein the tumor is selected from the group consisting of colon carcinoma, breast tumor, mesothelioma, prostate tumor, squamous cell carcinoma, Kaposi sarcoma, and leukemia.

43. The method of claim 39, wherein the cancer is an angiogenesis-dependent cancer.

44. The method of claim 39, wherein the cancer is an angiogenesis-independent cancer.

45. The method of claim 39, wherein the polypeptide agent inhibits the interaction between Ephrin B2 and EphB4.

46. The method of claim 39, wherein the polypeptide agent inhibits clustering of Ephrin B2 or EphB4.

47. The method of claim 39, wherein the polypeptide agent inhibits phosphorylation of Ephrin B2 or EphB4.

48. The method of claim 39, wherein the polypeptide agent is formulated with a pharmaceutically acceptable carrier.

49. The method of claim 39, further including administering at least one additional anti-cancer chemotherapeutic agent that inhibits cancer cells in an additive or synergistic mariner with the polypeptide agent.

50. A method of inhibiting angiogenesis, comprising contacting a cell an amount of a polypeptide agent sufficient to inhibit angiogenesis, wherein the polypeptide agent is selected from the group consisting of:
(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;

(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin-in B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.

(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

51. The method of claim 50, wherein the cell expresses EphB4 or Ephrin B2.

52. A method for treating a patient suffering from an angiogenesis-associated disease, comprising administering to the patient a polypeptide agent selected from the group consisting of:
(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

53. The method of claim 52, wherein the soluble polypeptide is formulated with a pharmaceutically acceptable carrier.

54. The method of claim 52, wherein the angiogenesis-associated disease is selected from the group consisting of angiogenesis-dependent cancer, benign tumors, inflammatory disorders, chronic articular rheumatism and psoriasis, ocular angiogenic diseases, Osler-Webber Syndrome, myocardial angiogenesis, plaque neovascularization, telangiectasia, hemophiliac joints, angiofibroma, wound granulation, wound healing, telangiectasia psoriasis scleroderma, pyogenic granuloma, cororany collaterals, ischemic limb angiogenesis, rubeosis, arthritis, diabetic neovascularization, fractures, vasculogenesis, and hematopoiesis.

55. The method of claim 52, further including administering at least one additional anti-angiogenesis agent that inhibits angiogenesis in an additive or synergistic manner with the soluble polypeptide.

56. Use of a polypeptide agent in the manufacture of medicament for the treatment of cancer, wherein the polypeptide agent is selected from the group consisting of (a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

57. Use of a polypeptide agent in the manufacture of medicament for the treatment of an angiogenesis-associated disease, wherein the polypeptide agent is selected from the group consisting of:
(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(c) an antibody which binds to an extracellular domain of an EphB4. protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

58. A method for treating a patient suffering from a cancer, comprising:
(a) identifying in the patient a tumor having a plurality of cancer cells that express EphB4 and/or EphrinB2; and (b) administering to the patient a polypeptide agent selected from the group consisting of:
(i) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;

(ii) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(iii) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (iv) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.

59. A method for treating a patient suffering from a cancer, comprising:
(a) identifying in the patient a,tumor having a plurality of cancer cells having a gene amplification of the EphB4 and/or EphrinB2 gene; and (b) administering to the patient a polypeptide agent selected from the group consisting of:
(i) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(ii) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(iii) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (iv) an antibody which binds to an extracellular domain of an Ephrin 132 protein and inhibits an activity of the Ephrin B2.

60. A method for identifying a tumor that is suitable for treatment with an EphrinB2 or EphB4 antagonist, the method comprising detecting in the tumor cell one or more of the following characteristics:
(a) expression of EphB4 protein and/or mRNA;
(b) expression of EphrinB2 protein and/or mRNA;
(c) gene amplification of the EphB4 gene; and (d) gene amplification of the EphrinB2 gene, wherein a tumor cell having one or more of characteristics (a)-(d) is suitable for treatment with an EphrinB2 or EphB4 antagonist.

61. The method of claim 60, wherein the EphrinB2 or EphB4 antagonist is selected from the group consisting of:

(a) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an EphB4 protein, wherein the EphB4 polypeptide is a monomer and binds specifically to an Ephrin B2 polypeptide;
(b) a soluble polypeptide comprising an amino acid sequence of an extracellular domain of an Ephrin B2 protein, wherein the soluble Ephrin B2 polypeptide is a monomer and binds with high affinity to an EphB4 polypeptide.
(c) an antibody which binds to an extracellular domain of an EphB4 protein and inhibits an activity of the EphB4; and (d) an antibody which binds to an extracellular domain of an Ephrin B2 protein and inhibits an activity of the Ephrin B2.