Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
  • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
  • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
  • A61K38/1703—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
  • A61K38/1709—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/39533—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals
  • A61K39/3955—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum against materials from animals against proteinaceous materials, e.g. enzymes, hormones, lymphokines
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/22—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against growth factors ; against growth regulators
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
  • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto

Definitions

• Angiogenesis the development of new blood vessels from the endothelium of a preexisting vasculature, is a critical process in the growth, progression, and metastasis of solid tumors within the host.
• angiogenesis the autocrine, paracrine, and amphicrine interactions of the vascular endothelium with its surrounding stromal components are tightly regulated both spatially and temporally.
• the levels and activities of proangiogenic and angiostatic cytokines and growth factors are maintained in balance.
• the pathological angiogenesis 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. More recently, it has become apparent that certain types of leukemia are also influenced by signaling involved in angiogenesis.
• AvastinTM (bevacizumab), a monoclonal antibody that binds to Vascular Endothelial Growth Factor (VEGF), has proven to be effective in the treatment of a variety of cancers.
• Antagonists of the SDF/CXCR4 signaling pathway inhibit tumor neovascularization and are effective against cancer in mouse models (Guleng et al. Cancer Res. 2005 JuI 1 ;65(13):5864-71).
• the isocoumarin 2-(8-hydroxy-6-methoxy-l-oxo-l H-2-benzopyran-3-yl) propionic acid (NM-3) has completed phase I clinical evaluation as an orally bioavailable angiogenesis inhibitor.
• NM-3 directly kills both endothelial and tumor cells in vitro and is effective in the treatment of diverse human tumor xenografts in mice (Agata et al. Cancer Chemother Pharmacol. 2005 Jun lO).
• Angiogenesis is a feature of other, non-neoplastic disorders.
• Various ocular disorders particularly proliferative retinopathies and age-related macular degeneration, and
• DOC inflammatory disorders such as rheumatoid arthritis and psoriasis
• Anit-angiogenic agents are effective for the treatment of these disorders.
• MacugenTM an aptamer that binds to VEGF has proven to be effective in the treatment of neo vascular (wet) age-related macular degeneration.
• TNF- alpha antagonists in the treatment of rheumatoid arthritis is partially attributed to anti- angiogenic effects on the inflamed joint tissue (Feldmann et al. Annu Rev Immunol. 2001;19:163-96).
• Arteriogenesis a process related to but distinct from angiogenesis, occurs when the lumen of a pre-existing vessel increases to form a collateral.
• myocardial infarction or peripheral ischemia e.g., limb, kidney, etc.
• arterioles become more significant conductance vessels in order to maintain blood flow after occlusion of the major artery serving the affected tissue.
• agents that promote arteriogenesis may be used to treat myocardial infarction and other ischemic events, and may also be used to prevent an ischemic event where a partial arterial occlusion is detected or suspected.
• Notch pathway and particularly Notch 1 and Notch4, participates in angiogenic processes.
• Notch signalling is generally involved in the regulation of processes as diverse as cellular proliferation, differentiation, specification and survival (Artavanis-Tsakonas et al., 1999). Its complexity in vertebrates is illustrated by the existence of multiple Notch receptor and ligands, each with distinct patterns of expression. In mammals there are four Notch receptors (notchl-4) and five ligands (jaggedl, 2 and Dill, 3 and 4). Mutations of Notch receptors and ligands in mice lead to abnormalities in various organs, from all three germ lines, including the vascular system (Iso et al, 2003).
• the Notch pathway functions through local cell interactions, the extracellular domain of the ligand, present on the surface of one cell, interacts with the extracellular domain of the receptor on an adjacent cell. This interaction allows the action of two ADAM proteases on the extracellular domain of Notch followed by the action of a ⁇ -secretase on the transmembrane domain releasing the intracellular domain from the cell membrane and allowing it to be directed to the nucleus, where it functions with CSL to activate the expression of transcriptional repressors of the enhancer-of-split family (Mumra & Kopan, 2000).
• Notch homologues demonstrate the importance of this pathway in regulating the arterial versus venous endothelial differentiation, downstream of vascular endothelial growth factor and sonic-hedgehog and upstream of the ephrin pathway (Lawson et al, 2002), being the earliest genes expressed in an endothelial arterial specific fashion.
• Notch function is essential in the establishment of the arterial endothelial cell fate (Lawson et al, 2002; Fischer et al, 2004; Duarte et al, 2004).
• the disclosure provides uses for, and methods for identifying, agonists and antagonists of the Notch ligand Delta-like 4 (D114).
• D114 Notch ligand Delta-like 4
• both agonists and antagonists of D114 may be used to treat tumors undergoing angiogenesis or in other situations where it is desirable to inhibit or disrupt angiogenesis.
• the disclosure provides methods for stimulating arteriogenesis by administering a D114 agonist.
• Arteriogenesis is the process of collateral artery formation and growth, typically in ischemic tissues.
• D114 agonists may be used to treat patients suffering from, or at risk for, an ischemic event, such as a peripheral or coronary ischemia.
• the disclosure further relates to the discovery that upregulation of D114 causes endothelial cells to adopt an arterial identity, while inhibition of D114 causes endothelial cells to adopt a venous identity.
• the disclosure provides methods for altering venous or arterial identity by using, as appropriate an agonist or antagonist of D114.
• the disclosure provides biomarkers that may be used to assess whether an agent of interest is an agonist or antagonist of D114 signaling.
• the disclosure describes a method for treating cancer comprising administering to a subject in need thereof, an effective amount of an antagonist of D114.
• This antagonist may be a polypeptide, particularly a peptide comprising an extracellular region of D114.
• the polypeptide may be a monomer, but may also function as a dimer.
• examples of polypeptides that comprise the extracellular region of D114 may be selected from the DSL domain, a.a. 27-524, a.a. 1-486, a.a. 27-486, a.a. 1-442, and a.a. 27-442, or variants thereof, of SEQ ID NO: 1.
• a polypeptide may comprise at least one of, or a combination of, the following domains of D114: MNNL, DSL, EGF5, EGF5 (see Figure 20A).
• an antagonist of D114 may comprise an antibody, or a gragment thereof, that binds to an extracellular region of D114.
• Such an antibody may be monoclonal, human, or humanized.
• said antibodies may comprise at least one of SEQ ID NOs: 4-7. All of the above-mentioned antagonists of D114 may be covalently joined to a moiety that confers enhanced pharmacokinetic properties as disclosed throughout herein.
• the moiety may be selected from an Fc domain, His tag, or a polyoxyalkylene (e.g., PEG).
• antagonists of D114 stimulate, in a mammalian endothelial cell, at an effective concentration, expression of an arterial phenotype.
• a phenotype maybe be selected from, for example, expression of EphrinB2 and connexin37.
• antagonists of D114 inhibit, in a mammalian endothelial cell, at an effective conventration, expression of a venous phenotype.
• An example of such a phenotype may be the expression of EphB4.
• venous phenotypes may include the inhibition of Notch-regulated genes, such as Heyl, Hey2, Hesl and Hes2.
• the disclosure also provides methods for promoting the adoption of arterial characteristics in a blood vessel such as venous graft or saphenous vein graft.
• the method comprises administering to a subject in need thereof, an effective amount of a therapeutic polypeptide comprising an extracellular domain of D114.
• the polypeptides comprising an extracellular domain of D114 may be selected from the DSL domain, a.a. 27-524, a.a. 1-486, a.a. 27-486, a.a. 1-442, and a.a. 27-442 of SEQ ID NO: 1, all of which may be covalently linked to a moiety that confers enhanced pharmacokinetic properties as disclosed throughout herein.
• the moiety may be selected from an Fc domain, His tag, or a polyoxyalkylene (e.g., PEG).
• Such therapeutic polypeptides may be a monomer or a dimer as described above.
• the disclosure provides a method for inhibiting angiogenesis, the method comprising administering to a subject in need thereof, an effective amount of an antagonist of D114 signaling.
• this method is also useful for disrupting angiogenesis. That is, "inhibiting" angiogenesis may be defined not only as the prevention of vascular formation, but the prevention of functional vascular formation.
• the antagonist useful for angiogenesis inhibition may be a polypeptide, particularly a peptide comprising an extracellular region of D114.
• the polypeptide may be a monomer, but may also function as a dimer.
• Some examples of polypeptides that comprise the extracellular region of D114 may be selected from the DSL domain, a.a. 27-524, a.a.
• a polypeptide may comprise at least one of, or a combination of, the following domains of D114: MNNL, DSL, EGF5, EGF5 (see Figure 20A).
• an antagonist of D114 may comprise an antibody, or a fragment thereof, that binds to an extracellular region of D114. Such an antibody may be monoclonal, human, or humanized. In a particular embodiment, said antibodies may comprise at least one of SEQ ID NOs: 4-7.
• All of the above-mentioned antagonists of D114 may be covalently joined to a moiety that confers enhanced pharmacokinetic properties as disclosed throughout herein.
• the moiety may be selected from an Fc domain, His tag, or a polyoxyalkylene (e.g., PEG).
• PEG polyoxyalkylene
• any of the aforementioned antagonists of D114 signaling inhibit, in a mammalian endothelial cell, at an effective concentration, VEGF-stimulated angiogenesis, and may be administered to treat angiogenesis-associated disease.
• angiogenesis-associated diseases include angiogenesis-dependent cancer, benign tumors, inflammatory disorders, chronic articular rheumatism and psoriasis, ocular angiogenic diseases, Osier- Webber Syndrome, myocardial angiogenesis, plaque neovascularization, telangiectasia, hemophiliac joints, angiofibroma, wound granulation, wound healing, telangiectasia psoriasis scleroderma, pyogenic granuloma, rubeosis, arthritis and diabetic neovascularization.
• angiogenesis may be inhibited by further administering, either simultaneously or sequentially, at least one additional anti-angiogenesis agent that inhibits angiogenesis in an additive or synergistic manner with said antagonist.
• said additional anti-angiogenesis agent may be an inhibitor of a Notch- receptor.
• a monomelic polypeptide comprising a portion of the extracellular domain of D114 promotes angiogenesis at low concentrations and inhibits VEGF-mediated angiogenesis at higher concentrations. Soluble D114 polypeptide promotes arterialization or arteriogenesis at all concentrations. Accordingly, by selecting the appropriate dose of monomelic soluble D114 polypeptide, differing effects on angiogenesis may be achieved.
• a soluble D114 polypeptide comprises the DSL domain of SEQ ID NO:1 (amino acids 173-233) but lacks the transmembrane and intracellular portions (amino acids 552-685).
• the D114 polypeptide comprises at least 200 amino acids in the region of amino acids 27-528 of SEQ ID NO: 1.
• the D114 polypeptide comprises amino acids 27-486 of SEQ ID NO:1 and preferably amino acids 27-524.
• the soluble D114 polypeptide includes a moiety that confers desirable pharmacokinetic properties, such as an Fc domain or a polyoxyalkylene moiety (e.g., PEG).
• the disclosure provides methods for stimulating arteriogenesis. Such methods may comprise administering to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the subject may have or be at risk for an ischemic condition.
• the subject may have coronary artery disease, including, for example, angina or may have had a myocardial infarction.
• the subject may have a peripheral artery disease, such as an ischemic event or partial occlusion in a limb, the brain or an organ, such as the kidney.
• the subject may be diagnosed as being at risk for an ischemic event.
• the disclosure provides methods for promoting the adoption of arterial characteristics in a blood vessel.
• a method may comprise administering to a blood vessel ex vivo or to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the blood vessel may be a venous graft, such as a saphenous vein graft.
• the disclosure provides methods for disrupting angiogenesis. Such methods may comprise administering to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the disclosure provides methods for disrupting tumor vasculature. Such methods may comprise administering to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the disclosure provides methods for evaluating the effects of a test agent on D114 signaling.
• a method may comprise (a) contacting a cell of endothelial lineage with the test agent; and (b) detecting a phenotype associated with arterial or venous phenotype.
• a test agent that promotes the adoption of an arterial phenotype or an agent that inhibits the adoption of a venous phenotype is an agonist of D114 signaling, while a test agent that inhibits the adoption of an arterial phenotype or promotes the adoption of a venous phenotype is an antagonist of D114 signaling.
• agonists of D114 signaling stimulate, in a mammalian endothelial cell, expression of an arterial phenotype and inhibit expression of a venous phenotype.
• antagonists of D114 signaling inhibit, in a mammalian endothelial cell, expression of an arterial phenotype and stimulate expression of a venous phenotype. Any known feature that distinguishes arterial and venous endothelial cells may be detected for the purpose of assessing arterial and venous phenotypes.
• expression of EphrinB2 and expression of connexin37 may be used as indicators of arterial phenotype.
• expression of EphB4 may be used as an indicator of venous phenotype.
• the disclosure provides methods for inhibiting alpha smooth muscle actin ( ⁇ -SMA) positive cell recruitment to a blood vessel, the method comprising, administering to a subject in need thereof, an effective amount of an inhibitor of D114 signaling.
• the inhibitor is selected from the group consisting of: an antibody to D114, a D114-His fusion or a D114-Fc fusion.
• the ⁇ — SMA positive cell is selected from the group consisting of: a pericyte, a smooth muscle cell, or a peri endothelial cell.
• the blood vessel is a venous graft.
• the venous graft is a saphenous vein graft.
• the subject has an angiogenesis-associated disease.
• the angiogenesis-associated disease is selected from the group described above.
• the methods further include administering at least one additional anti-angiogenesis agent that inhibits angiogenesis in an additive or synergistic manner with the inhibitor of D114 signaling.
• compositions of isolated monoclonal antibodies or antigen binding portion that binds to an epitope that is situated in the extracellular portion of D114.
• epitopes situated in the extracellular portion of D114 include the MNNL and DSL domains, as well as any one or more of the EGF repeats as illustrated in Figure 2OA.
• such antibodies may comprise any one of SEQ ID NOs: 4-7.
• Said antibodies may further be humanized antibodies.
• Figure 1 shows the amino acid sequence of the human Delta-like 4 protein (SEQ ID NO:1; GenBank NP_061947).
• the signal sequence amino acids 1-26, is underlined.
• the transmembrane domain amino acids 532-552, is bolded.
• the extracellular domain of the mature protein is amino acids 27-531, although imprecision in signal peptide processing may result in a protein that is slightly longer or shorter.
• the intracellular domain is amino acids 532-685.
• Figure 2 shows the nucleic acid sequence (cDNA) encoding the human Delta-like 4 protein (SEQ ID NO:2; GenBank NM_019074).
• the coding sequence is nucleic acids 321- 2378.
• Figure 3 shows pZ/EG-mD114 transgenesis vector and result of Cre activity.
• Figure 4 (a) LacZ staining of a ZEG-mD114 embryo at E8.0; (b) EGFP expression in the dt embryos at E8.5. (c) haemorrhaging and pericardial edema in dt embryos at E9.0.
• FIG. 5 Wholemount PECAMl immunostaining of E9.0 and E9.5 dt and control embryos, (a) control embryo at E9.0, (b) dt embryo at E9.0 showing a hypertrophied dorsal aorta (lower left arrow), ramified ACV (lower right arrow) and an immature vascular plexus in the head region (upper arrow) (c) control embryo at E9.5, (d) dt embryo at E9.5 showing hypertrophied dorsal aorta and almost no sign of an ACV, immature vascular plexus in the head region and hypertrophied sinus venosus and heart ventricle.
• FIG. 6 PECAMl immunostaining in cryosections and microangiography,
• a-g serial sections of a E9.5 dt embryo (anterior-posterior) showing fusion between the aorta (upper right arrow) and the ACV (upper left arrow) just prior to its connection to the sinus venosus (lower arrow).
• the ACV consists of a plexus of small capillaries (upper left arrow) which join to form a single vessel with a large lumen just prior to its fusion with the dorsal aorta.
• Section (e) shows the aortic atrophy in regions posterior to the sinus venosus.
• FIG. 7 Venous expression of arterial markers in dt embryos. In situ hybridization of cryosections from E9.0 dt embryos.with ephrin-B2(a,b,c) and connexin-37 (d,e,f) specific riboprobes. The mutant embryos show concomitant expression of these arterial specific markers in the both the dorsal aortae (AD) and anterior cardinal veins (VCA) In the control embryos (c,f), as expected, the expression is restricted to the aortae.
• AD dorsal aortae
• VCA anterior cardinal veins
• Figure 8 Upregulation of Notch signalling in the venous endothelium of the mutant embryos. In situ hybridization of cryosections from E9.0 dt embryos, with heyl (a,b,c) and Notchl (d,e,f) specific riboprobes. Both genes appear upregulated in the anterior cardinal veins (VCA). In the control embryos (c,f), as expected, the expression is restricted to the aortae.
• VCA anterior cardinal veins
• Figure 9 Downregulation of venous specific markers in dt embryos. In situ hybridization and immunostainings of cryosections from E9.0 dt embryos, (a) anti-Eph-B4 immunostain, (c) eph-b4 mRNA, and E9.0 control embryos, (b) anti-Eph-B4 immunostain, (d) eph-b4 mRNA.
• FIG. 10 Shows a schematic of the human D114 domain structure (top) and an annotated human D114 amino acid sequence (SEQ ID NO:1) (bottom). The signal sequence and DSL domain are underlined and indicated. The eighth EGF8 domain (EGF8) is shaded.
• the ⁇ XB ( ⁇ EGF8) construct contains 19 extra amino acids (RSPSCIYRRSWRSRGAQIL) (SEQ ID NO:3) at the C-terminus after the CAS residues of the EGF8 repeat.
• the P524-His construct ends at P524, 4 amino acids before the transmembrane domain, with a 6xHis tag at the C-terminus. Both constructs contain the receptor-binding domain, DSL domain. Full length constructs have either a Myc tag or no tag.
• Figure 11 shows the purified hD114-P524-6xHis protein (histidine tagged hD114-P524) after nickel column purification (SDS-PAGE: CBB-G250 Staining).
• hD114 inhibits tube formation in human arterial endothelial cells (HUAEC).
• VEGF was used at 50 ng/ml as a positive control.
• D114 at lower concentrations (30ng/ml or 100 ng/ml) promoted tube formation, while D114 at 500 ng/ml inhibited tube formation ⁇ (data not shown).
• Quantitative analysis for tube length and the number of junctions in sD114-treated HUVECs Bioquant Image Analysis; mean from triplicate wells in 2 repetition experiments). Similar results were seen with human arterial endothelial cell assay(data not shown).
• hD114 inhibits sprouting in human arterial endothelial cells (HUAEC).
• VEGF was used at 20 ng/ml as a positive control.
• D114 at 100ng/ml or 200 ng/ml promoted sprouting, while D114 at 500 ng/ml inhibited sproutingv (not shown).
• Quantitative analysis for vascular area is shown (Bioquant Image Analysis; mean from triplicate wells in 2 repetition experiments). Similar results were seen with sD114-Fc(data not shown).
• hD114 inhibits VEGF-stimulated sprouting in human arterial endothelial cells (HUAEC) at high concentrations.
• VEGF was used at 20 ng/ml.
• D114 at lOOng/ml had little effect, while D114 at 200 ng/ml inhibited VEGF-stimulated sprouting.
• FIG. 15 D114+/- mutant mice show defective increase in vascular proliferation:
• A The vasculature of wild type and D114+/- embryos were examined using PECAM wholemount immunostaining. Dorsal aorta and cardinal vein are labeled a and v. Absence of large vessels and an increase in vessel branching and density was seen in D114 +/" embryos at El 0.5 compared to wild type.
• B Vascular response in D114+/- adult mice was examined as in (A) after tumor implantation. Wild type mice showed organized vascular proliferation in the tumor (left half), while mutant mice showed markedly increased vascular response which lacks organization and vascular hierarchy.
• FIG. 16 Biochemical properties of sD114:
• Notch-Fc fusion protein was coated directly on ELISA plates.
• sD114-AP was allowed to bind Notch-Fc and the bound D114 was quantitated by the addition of AP substrate.
• sD114-AP bound efficiently to Notch 1 and not Notch 3 (left panel). Binding of sDll-4Fc and sD114-His to Notch 1 was examined.
• B HUVEC cells were transfected with expression vectors for sD114-Fc, sD114-His or vector alone. Notch responsive Hes-2 gene expression was not induced by sD114 proteins.
• FIG. 17 sD114 induces vessel response but lack perfusion in murine Matrigel assay:
• A Matrigel was injected subcutaneously into Balb/C nu/nu mice. After 6 days, plugs were removed and processed in paraffin. Individual sections were stained with H&E and representative photographs at x 20 magnification from triplicate plugs in 2 independent experiments are shown.
• B Matrigel plugs were stained for PECAM. Photomicrographs were taken with a Nikon Coolpix 5000 camera on a Nikon Eclipse E400 microscope with a 4 x/0.13 NA objective and a 10 x eyepiece. Quantitation of vascularized area averaged ( ⁇ SEM) from all plugs (Scion Image software) in bar graph. P value ⁇ 0.01.
• sD114 inhibits the tumor growth in a murine tumor xenograft model:
• B In assessing the effect of endogenous expression of sD114, HT29 were transfected with expression vector with D114-FL, sD114-Fc, sD114-His, or vector alone.
• Control group showed co-localization of ⁇ -SMA and PECAM, while sD114 group had paucity of ⁇ -SMA positive cells in the micro-vessels.
• Soluble D114 inhibits tumor growth in vivo in a murine zenograft model.
• D114-E6 (residues 1-422 of SEQ ID NO: 1) which lacks EGF-like domains 7 and 8 was administered intraperitoneally starting at day 5 post implantation at 5 mg/kg, three times a week.
• the combined effect of D114-E6 with a VEGF neutralizing antibody (Avastin) was also examined. Avastin was also administered intraperitoneally starting at day 5 post implantation at 10 mg/kg, three times a week.
• FIG. 20 Epitope mapping of anti-D114 antibodies:
• A Illustration of a complete set of D114 truncation mutants fused to alkaline phosphatase. Four individual clones were identified, each with a specific binding region to D114.
• B Coat 4ug/ml (10OuI) D114 antibodies on ELISA plate overnight in PBS at 4°C. Block the plate with 0.5% BSA for 2 hours, and then add 20ng of soluble D114 proteins fused with alkaline phosphatase. After 45 min incubation at room temperature, the plate is washed with PBST and incubated with PNPP at 37°C for 20 min. This experiment has been repeated at least three times.
• Figure 21 Protein sequence alignment of human D114 (hD114), mouse D114 (mD114), and human Dill (hDlll). From N terminus to C terminus, first shaded region indicates the epitope for antibody clone #2-6. Second shaded region represents the DSL region. Third shaded region, which comprises EGF-like 3 (E3) domain, indicates the epitope for antibody clone #6 IB.
• E3 EGF-like 3
• FIG. 22 Characterization of anti-D114 antibodies:
• A Human D114 antibodies were raised in mouse by immunization with soluble human D114-His protein (aa 1 -524 of SEQ ID NO: 1).
• B Two antibody clones designated #2-6 and #61B efficiently neutralize D114-Notchl interaction.
• FIG. 23 Sequence identifying the variable regions V H (SEQ ID NO: 4) and V L (SEQ ID NO: 5) of D114 antibody clone designated #61 B.
• Figure 24 Sequence identifying the variable regions V H (SEQ ID NO: 6) and V L (SEQ ID NO: 7) of D114 antibody clone designated #2-6.
• FIG. 25 D114-Fc fusion protein linker engineering.
• the linker region between fusion proteins may affect the function of protein of interest.
• Three different linkers between D114 (E6) and human IgGl Fc (starts at EPKS in Fc hinge region) were tested. There is a three-fold-difference between Ll and L2 fusion proteins.
• Dll4-L2-Fc was chosen for tumor xenograft study.
• ELISA plate was coated with 0.5ug/ml (10OuI) Notchl-Fc in PBS at 4°C for overnight, and then blocked with 0.5% BSA for 2 hours. Indicated amount of D114-Fc proteins or BSA were premixed with 50ng D114 (E8)-AP and then added. After 45min incubation at room temperature, the plate was washed with PBST and incubated with PNPP at 37 C for 1 hour.
• the current invention is based in part on the discovery that Delta-like 4 function is essential for angiogenesis in vivo, and, moreover, that an increase of Delta-like 4 activity is associated with increased proliferation of arterial endothelial cells and an increased adoption of an arterial identity by endothelial cells.
• Applicants generated mouse D114 knockout mutations that evinced dosage sensitive defects in angiogenesis.
• Applicants generated D114 overexpression models in mouse and demonstrated that increased expression of D114 causes, in some instances, hypertrophy of arterial tissue and, moreover, causes venous tissue to adopt an arterial identity.
• angiogenesis in which a system of arterial and venous microvessels is generated, is highly sensitive to D114 activity and may be perturbed (e.g., inhibited or caused to occur in a disorganized or ineffective manner) by inhibition or hyperactivation of D114.
• both agonists and antagonists of D114 may be used to treat tumors undergoing angiogenesis.
• the invention relates to the discovery that overexpression of D114 can stimulate arterial growth, and may therefore be used to stimulate arteriogenesis.
• Arteriogenesis is the process of collateral artery formation and growth, typically in ischemic tissues.
• D114 agonists may be used to treat patients suffering from, or at risk for, an ischemic event, such as a peripheral or coronary ischemia. Furthermore, the dislcosure demonstrates that a soluble monomelic or dimeric D114 polypeptide can act to inhibit or promote angiogenesis at low or high concentrations, respectively.
• the invention further relates to biomarkers that may be used to assess whether an agent of interest is an agonist or antagonist of D114 signaling.
• the scientific literature relating to Delta proteins generally, including D114, provides no clarity as to whether a particular agent activates or inhibits D114-mediated signaling.
• D114 and Delta extracelluar domains e.g., soluble monomelic or dimeric forms, forms with deleted intracellular domains, and soluble Fc fusions
• D114 and Delta extracelluar domains have been tested in a variety of assays and it remains unclear whether any of the observed effects are due to agonist or antagonist activity, or whether there is any meaningful activity at all.
• reagents may affect D114 signaling in a variety of ways.
• a reagent may affect Notch 1 and/or Notch 4 activation, or activation of retrograde D114 signaling, possibly mediated by the D114 intracellular domain.
• a reagent may also affect the activity of preseniline protease activity, which may affect both Notch 1 and Notch4.
• D114 hyperactivation causes endothelial cells to adopt an arterial phenotype, typified by expression of EphrinB2 and connexin37, while D114 loss of function causes endothelial cells to adopt a venous identity, typified by expression of EphB4. This information about the genetically-determined, in vivo effects of D114 activity will permit the identification of both known and newly discovered agents as agonists or antagonists of DU4 signaling.
• 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.
• D114 is a Notch ligand and contains a signal sequence, a DSL domain, eight epidermal growth factor-like repeats, a transmembrane domain, and an intracellular region, all of which are characteristics of members of the Delta protein family.
• the tissue distribution of Delta-4 mRNA resembles that previously described for Notch-4 (Int-3) transcripts. Soluble forms of the extracellular portion of Delta-4 inhibit the apparent proliferation of human aortic endothelial cells, but not human pulmonary arterial endothelial cells. Yoneya et al. J. Biochem. Vol. 129, pp. 27-34 (2001).
• Notch family of proteins are transmembrane receptors that contain characteristic multiple epidermal growth factor (EGF)-like repeats as well as conserved domains such as RAM, ankyrin-like repeat, and PEST sequences.
• Ligands for Notch proteins include Delta and Serrate in Drosophila melanogaster, LAG-2 and APX-I in Caenorhabditis elegans, and Delta and Serrate (or Jagged) in vertebrates. These ligands are also transmembrane proteins and contain a highly conserved DSL (Delta-Serrate-LAG-2) motif upstream of a variable number of EGF-like repeats.
• the DSL domain is a characteristic feature of Notch ligands and is important for protein function; thus, point mutation of the DSL domain in LAG-2 results in a loss of activity.
• Delta and Jagged (Serrate) proteins of vertebrates exhibit similar structures, each group of proteins also possesses several distinct features. Thus, whereas vertebrate Delta proteins contain eight EGF-like repeats, Jagged proteins contain 16 such repeats. Furthermore, the EGF domains are followed by a cysteine-rich domain in Jagged proteins but not in Delta proteins. However, the consequences of these structural differences remain unclear.
• NOTCH4 Li et al. (Genomics. 1998 JuI l ;51(l):45-58) reported that the human NOTCH4 gene contains 30 exons and spans approximately 30 kb. They isolated cDNAs corresponding to 6.7-kb NOTCH4(S) and 9.3 -kb NOTCH4(L) mRNA isoforms.
• the predicted protein encoded by NOTCH4(S) is 2,003 amino acids long and contains the characteristic Notch motifs: a signal peptide, 29 epidermal growth factor (EGF)-like repeats, 3 Notch/lin-12 repeats, a transmembrane region, 6 cdclO (603151 )/ankyrin repeats, and the PEST conserved region at the C terminus.
• GEF epidermal growth factor
• NOTCH4(S) is the major transcript and is expressed in a wide variety of tissues.
• Candidate agonists and antagonists will generally be any antibody that binds to, or soluble portions of, proteins involved in the D114 signaling pathway, including, for example, D114, Notchl, Notch4 and presenilin.
• Candidate agonists and antagonists may also be small molecules or other agents that bind to or effect members of the pathway.
• Antisense or RNAi nucleic acids may be used as antagonists of D114, Notchl, Notch4 or presenilin or other members of the signaling pathway.
• agents examples include:
• the agent is a soluble polypeptide comprising an extracellular domain of a D114 protein, e.g., as shown in amino acids 27-531 of SEQ ID NO:1.
• the D114 soluble polypeptide comprises a DSL domain of a D114 protein.
• the D114 soluble polypeptide is a truncate comprising at least domains 5 or 6 of the EGF-like domains.
• the subject soluble polypeptides include fragments, functional variants, and modified forms of D114 soluble polypeptide. These fragments, functional variants, and modified forms of the subject soluble polypeptides may be tested for activity as agonists or antagonists of D114 by assessing effects on arterial or venous phenotype in endothelial cells.
• 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 D114.
• 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 modulate D114 signaling.
• a functional variant of an D114 soluble polypeptide comprises an amino acid sequence that is at least 90%, 95%, 97%, 99% or 100% identical to residues 27-531 of the amino acid sequence of SEQ ID NO:1.
• the present invention contemplates making 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).
• Modified soluble polypeptides can be produced, for instance, by amino acid substitution, deletion, or addition.
• the purpose of screening such combinatorial libraries may be to generate, for example, soluble polypeptide variants which can act as agonists or antagonists of D114.
• 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.
• mutagenesis can give rise to variants which have intracellular half-lives dramatically different than the corresponding wild-type soluble polypeptide.
• 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 can be utilized to alter the subject soluble polypeptide levels by modulating their half- life.
• 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.
• proteins, and particularly their recombinant nucleic acid constructs can be used in gene therapy protocols.
• 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.
• soluble polypeptide variants e.g., the antagonist forms
• soluble polypeptide variants 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.
• 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.
• the soluble polypeptides of the invention may further comprise post-translational modifications.
• modifications include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
• 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 agonist or antagonist effects on D114.
• functional variants or modified forms of the subject soluble polypeptides include fusion proteins having at least a portion of the soluble polypeptide and one or more fusion domains.
• 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.
• relevant matrices for affinity chromatography such as glutathione-, amylase-, and nickel- or cobalt- conjugated resins are used.
• Fusion domains also include "epitope tags," which are usually short peptide sequences for which a specific antibody is available.
• epitope tags for which specific monoclonal antibodies are readily available include FLAG, influenza virus haemagglutinin (HA), and c-myc tags.
• 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.
• the soluble polypeptides of the present invention contain one or more modifications that are capable of stabilizing the soluble polypeptides.
• 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.
• soluble polypeptides (unmodified or modified) of the invention can be produced by a variety of art-known techniques.
• 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).
• automated peptide synthesizers are commercially available (e.g., Advanced ChemTech Model 396; Milligen/Biosearch 9600).
• 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).
• the invention relates to isolated and/or recombinant nucleic acids encoding a D114 polypeptide.
• the subject nucleic acids may be single-stranded or double- stranded, DNA or RNA 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.
• 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 SEQ ID NO:2.
• nucleic acid sequences complementary to the subject nucleic acids, and variants of the subject nucleic acids are also within the scope of this invention.
• nucleic acid sequences of the invention can be isolated, recombinant, and/or fused with a heterologous nucleotide sequence, or in a DNA library.
• nucleic acids of the invention also include nucleotide sequences that hybridize under highly stringent conditions to the nucleotide sequence depicted in SEQ ID NO:2, or complement sequences thereof.
• appropriate stringency conditions which promote DNA hybridization can be varied.
• 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 0 C.
• SSC sodium chloride/sodium citrate
• 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 0 C.
• 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.
• 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 subject 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, CAU and CAC are synonyms for histidine) may result in "silent" 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.
• nucleotides up to about 3-5% of the nucleotides
• 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.
• 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.
• 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 occurring 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.
• 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.
• the subject nucleic acid is provided in an expression vector comprising a nucleotide sequence encoding a D114 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.
• the term regulatory sequence includes promoters, enhancers, and other expression control elements. Exemplary regulatory sequences are described in Goeddel; Gene Expression Technology: Methods in Enzymology, 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 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 polymerase, the major operator and promoter regions of phage lambda , the control regions for fd coat protein, the promoter for 3-phosphoglycerate kinase or other glycolytic enzymes, the promoters of acid phosphatase, e.g., Pho5, the promoters of the yeast ⁇ -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.
• T7 promoter whose expression is directed by T7 RNA polymerase
• the major operator and promoter regions of phage lambda the control regions for f
• 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.
• 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.
• the present invention further pertains to methods of producing the subject soluble polypeptides.
• a host cell transfected with an expression vector encoding a D114 soluble polypeptide can be cultured under appropriate conditions to allow expression of the D114 soluble polypeptide to occur.
• the D114 soluble polypeptide may be secreted and isolated from a mixture of cells and medium containing the soluble polypeptides.
• 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 known in the art for purifying proteins, including ion- exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for particular epitopes of the soluble polypeptides.
• 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 portion 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.
• 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 prokaryotic 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, pko-neo and pHyg derived vectors are examples of mammalian expression vectors suitable for transfection of eukaryotic cells.
• vectors are modified with sequences from bacterial plasmids, such as pBR322, to facilitate replication and drug resistance selection in both prokaryotic and eukaryotic cells.
• bacterial plasmids such as pBR322
• derivatives of viruses such as the bovine papilloma virus (BPV-I), or Epstein-Barr virus (pHEBo, pREP-derived and p205) can be used for transient expression of proteins in eukaryotic cells.
• BBV-I bovine papilloma virus
• pHEBo Epstein-Barr virus
• pREP-derived and p205 Epstein-Barr virus
• 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.
• 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 ⁇ -gal containing pBlueBac III).
• pVL-derived vectors such as pVL1392, pVL1393 and pVL941
• pAcUW-derived vectors such as pAcUWl
• pBlueBac-derived vectors such as the ⁇ -gal containing pBlueBac III.
• fusion genes are well known. Essentially, the joining of various DNA fragments coding for different polypeptide sequences is performed in accordance with conventional techniques, employing blunt-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.
• the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
• 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, Current Protocols in Molecular Biology, eds. Ausubel et al., John Wiley & Sons: 1992).
• the present invention provides antibodies that have agonist or antagonist effects on D114 signaling.
• Such antibodies may bind to antigens such as D114, Notchl or Notch4.
• the antibody binds to an extracellular domain of such antigens.
• antibodies may be polyclonal or monoclonal; intact or truncated, e.g., F(ab')2, Fab, Fv; xenogeneic, allogeneic, syngeneic, fully human or modified forms thereof, e.g., humanized, chimeric.
• Fully human antibodies may be selected from transgenic animals that express human immunoglobulin genes or assembled from recombinant libraries expressing antibody fragments.
• 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).
• 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.
• An immunogenic portion of an antigen 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.
• antibody-producing cells 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.
• Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with D114, Notchl, Notch4 or other target polypeptide and monoclonal antibodies isolated from a culture comprising such hybridoma cells.
• antibody as used herein is intended to include fragments thereof which are also specifically reactive with antigen. 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 antigen 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.
• transgenic mice or other organisms including other mammals may be used to express humanized antibodies.
• 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).
• an antibody of the invention is a monoclonal antibody, and in certain embodiments the invention makes available methods for generating novel antibodies.
• a method for generating a monoclonal antibody that binds specifically to D114, Notchl or Notch4 may comprise administering to a mouse an amount of an immunogenic composition comprising the antigen 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 hybridoma that produces a monocolonal antibody that binds specifically to the antigen.
• a hybridoma can be propagated in a cell culture, optionally in culture conditions where the hybridoma-derived cells produce the monoclonal antibody.
• the monoclonal antibody may be purified from the cell culture.
• the disclosure provides humanized versions of any of the antibodies disclosed herein, as well as antibodies and antigen binding portions thereof that comprise at least one CDR portion derived from an antibody disclosed herein, particularly the CDR3.
• the antibody is a monoclonal antibody that is immunocompatible with the subject to which it is to be administered, and preferably is clinically acceptable for administration to a human.
• single chain antibodies, and chimeric, humanized or primatized (CDR-grafted) antibodies, as well as chimeric or CDR-grafted single chain antibodies, comprising portions derived from different species, are also encompassed by the present invention as antigen binding portions of an antibody.
• the various portions of these antibodies can be joined together chemically by conventional techniques, or can be prepared as a contiguous protein using genetic engineering techniques.
• nucleic acids encoding a chimeric or humanized chain can be expressed to produce a contiguous protein. See, e.g., Cabilly et al, U.S. Pat. No. 4,816,567; Cabilly et al., European Patent No.
• functional fragments of antibodies including fragments of chimeric, humanized, primatized or single chain antibodies, can also be produced.
• Functional fragments of the subject antibodies retain at least one binding function and/or modulation function of the full-length antibody from which they are derived.
• Preferred functional fragments retain an antigen binding function of a corresponding full-length antibody (e.g., specificity for D114).
• Certain preferred functional fragments retain the ability to inhibit one or more functions characteristic of D114, such as a binding activity, a signaling activity, and/or stimulation of a cellular response.
• Applicants have generated monoclonal antibodies against D114 as well as hybridoma cell lines producing D114 monoclonal antibodies. These antibodies were further characterized in many ways, such as, their ability to inhibit interaction between D114 and Notch and their cross-reactivity. Further, epitope mapping studies reveals that these D114 antibodies may specifically bind to one or more regions of D114. For example, as illustrated in Figure 21 , the antibody clone designated #2-6 binds to a region that spans an area that includes the MNNL domain, while a clone designated #61 B binds to a region that includes the EGF-like 3 domain. Other antibody clones that have been identified bind to other EGF-like domains, as shown in Figure 2OA.
• 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.
• 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.
• the disclosure provides isolated nucleic acid compounds comprising at least a portion that hybridizes to a D114 transcript under physiological conditions and decreases the expression of D114 in a cell.
• Such nucleic acids may be used as D114 antagonists, as described herein.
• the D114 transcript may be any pre-splicing transcript (i.e., including introns), post-splicing transcript, as well as any splice variant.
• the D114 transcript has a sequence corresponding to the cDNA set forth in SEQ ID NO:2, and particularly the coding portion thereof.
• the disclosure provides isolated nucleic acid compounds comprising at least a portion that hybridizes to a Notch 1 or Notch4 transcript under physiological conditions and decreases the expression of Notchl or Notch4 in a cell. These may be used as D114 antagonists also.
• the Notchl or Notch4 transcript may be any pre-splicing transcript (i.e., including introns), post-splicing transcript, as well as any splice variant.
• nucleic acid compounds examples include antisense nucleic acids, RNAi constructs and catalytic nucleic acid constructs.
• a nucleic acid compound may be single or double stranded.
• a double stranded compound may also include regions of overhang or non-complementarity, where one or the other of the strands is single stranded.
• a single stranded compound may include regions of self-complementarity, meaning that the compound forms a so-called "hairpin” or "stem-loop” structure, with a region of double helical structure.
• a nucleic acid compound may comprise a nucleotide sequence that is complementary to a region consisting of no more than 1000, no more than 500, no more than 250, no more than 100 or no more than 50 nucleotides of the D114, Notchl or Notch4 nucleic acid sequence.
• the region of complementarity will preferably be at least 8 nucleotides, and optionally at least 10 or at least 15 nucleotides.
• a region of complementarity may fall within an intron, a coding sequence or a noncoding sequence of the target transcript, such as the coding sequence portion.
• a nucleic acid compound will have a length of about 8 to about 500 nucleotides or base pairs in length, and optionally the length will be about 14 to about 50 nucleotides.
• a nucleic acid may be a DNA (particularly for use as an antisense), RNA or RNA:DNA hybrid. Any one strand may include a mixture of DNA and RNA, as well as modified forms that cannot readily be classified as either DNA or RNA.
• a double stranded compound may be DNA:DNA, DNA:RNA or RNA:RNA, and any one strand may also include a mixture of DNA and RNA, as well as modified forms that cannot readily be classified as either DNA or RNA.
• a nucleic acid compound may include any of a variety of modifications, including one or modifications to the backbone (the sugar-phosphate portion in a natural nucleic acid, including internucleotide linkages) or the base portion (the purine or pyrimidine portion of a natural nucleic acid).
• An antisense nucleic acid compound will preferably have a length of about 15 to about 30 nucleotides and will often contain one or more modifications to improve characteristics such as stability in the serum, in a cell or in a place where the compound is likely to be delivered, such as the stomach in the case of orally delivered compounds and the lung for inhaled compounds.
• the strand complementary to the target transcript will generally be RNA or modifications thereof.
• the other strand may be RNA, DNA or any other variation.
• the duplex portion of double stranded or single stranded "hairpin" RNAi construct will preferably have a length of 18 to 40 nucleotides in length and optionally about 21 to 23 nucleotides in length, so long as it serves as a Dicer substrate.
• Catalytic or enzymatic nucleic acids may be ribozymes or DNA enzymes and may also contain modified forms.
• Nucleic acid compounds may inhibit expression of the target by about 50%, 75%, 90% or more when contacted with cells under physiological conditions and at a concentration where a nonsense or sense control has little or no effect. Preferred concentrations for testing the effect of nucleic acid compounds are 1, 5 and 10 micromolar. Nucleic acid compounds may also be tested for effects on cellular phenotypes, such as arterial or venous identity. Methods of screening/assays
• agonists of D114 signaling stimulate, in a mammalian endothelial cell, expression of an arterial phenotype and inhibit expression of a venous phenotype.
• antagonists of D114 signaling inhibit, in a mammalian endothelial cell, expression of an arterial phenotype and stimulate expression of a venous phenotype. Any known feature that distinguishes arterial and venous endothelial cells may be detected for the purpose of assessing arterial and venous phenotypes.
• expression of EphrinB2 and expression of connexin37 may be used as indicators of arterial phenotype.
• expression of EphB4 may be used as an indicator of venous phenotype.
• Agents may also be screened for binding activity to D114, Notch 1 or Notch4, or for the ability to stimulate or inhibit the production of the active intracellular domain of Notch 1 (NICD), Notch4 or D114.
• Notch 1 Notch 1
• Notch4 Notch4
• Expression from hairy/enhancer of split (HES) sensitive promoters may also be useful in determining whether Notch signaling is activated.
• NICD stimulates expression of HES and HES-driven promoters.
• Compounds identified through any screening system can then be tested in animals to assess their effects on angiogenesis, arteriogenesis, or anti-tumor activity in vivo, as well as effects on arterial or venous identity in vivo
• Test agents can be any chemical (element, molecule, compound, drug), made synthetically, made by recombinant techniques or isolated from a natural source.
• test agents can be peptides, polypeptides, peptoids, sugars, hormones, or nucleic acid molecules.
• 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.
• an assay can be carried out to screen for compounds that specifically inhibit binding of D114 (ligand) to Notch 1/Notch4(receptor), or vice- versa, e.g., by inhibition of binding of labeled ligand- or receptor-Fc fusion proteins to immortalized cells.
• samples of cells expressing one type of cell surface molecule are contacted with either labeled ligand 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 compound(s) is an indication that the test compound(s) interferes with binding.
• the reciprocal assay using cells expressing a ligand 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 D114 and Notchl/Notch4 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.
• an isolated or purified protein 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 can 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.
• a change in the ionic strength or pH of the elution buffer can lead to a release of compounds.
• 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 linked to a second moiety not occurring 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 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.
• a fusion protein in one aspect of this embodiment, 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.
• 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).
• compound elution buffer can be formulated to permit retention of the fusion protein by the affinity matrix, but can be formulated to interfere with binding of the compound(s) tested to the receptor or ligand protein portion of the fusion protein.
• 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 ligands 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.
• fusion protein with compound bound thereto can be eluted from the affinity matrix with a suitable elution buffer (a matrix elution buffer).
• a suitable elution buffer a matrix elution buffer
• 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.
• 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 modulators of D114 signaling as described above. These methods are particularly aimed at therapeutic and prophylactic treatments of animals, and more particularly, humans.
• 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 inflammation; 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; Osier-Webber Syndrome, corneal diseases, rubeosis, arthritis, diabetic neovascularization.
• angiogenesis-dependent cancer including, for example, solid tumors, blood born tumors such as leukemias, and tumor metastases; benign tumors, for
• 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.
• a cancer tumor
• the subject methods of the invention can be used alone.
• 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).
• proliferative disorders e.g., tumor
• 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.
• one or more therapeutic agents of the disclosure can be administered, together (simultaneously) or at different times (sequentially).
• therapeutic agents can be administered with another type of compounds for treating cancer or for inhibiting angiogenesis.
• 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.
• 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.
• a therapeutic agent of the present invention When a 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, beg, bicalutamide, bleomycin, buserelin, busulfan, campothecin, capecitabine, carboplatin, carmustine, 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, geni
• 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 alkaloids (vinblastine, vincristine, and vinorelbine), microtubule disrupters such as taxane (paclitaxel, docetaxel), vincristin, vinblastin, nocodazole, epothilones and navelbine, epidipodophyllotoxins (etoposide, teniposide), DNA damaging agents (actinomycin, amsacrine, anthracycl
• 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- ⁇ bFGF antibodies; and (3) inhibitors of endothelial cell response to angiogenic stimuli, including collagenase inhibitor, basement membrane turnover inhibitors, angiostatic steroids, fungal-derived angiogenesis inhibitors, platelet factor 4, thrombospondin, arthritis drugs such as D-penicillamine and gold thiomalate, vitamin D 3 analogs, alpha-interferon, and the like.
• angiogenic molecules such as bFGF (basic fibroblast growth factor)
• neutralizers of angiogenic molecules such as an anti- ⁇ bFGF antibodies
• inhibitors of endothelial cell response to angiogenic stimuli including collagenase inhibitor, basement membrane turnover inhibitors, angiostatic steroids, fungal-derived angiogenesis inhibitors, platelet factor 4,
• angiogenesis 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 ⁇ v ⁇ 3 , 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.
• plasminogen fragments e.g., Kringles 1-3 of plasminogen
• tropoin subunits e.g., antagonist
• administration of the 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 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.
• the disclosure provides methods for stimulating arteriogenesis. Such methods may comprise administering to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the subject may have or be at risk for an ischemic condition.
• the subject may have coronary artery disease, including, for example, angina or may have had a myocardial infarction.
• the subject may have a peripheral artery disease, such as an ischemic event or partial occlusion in a limb, the brain or an organ, such as the kidney.
• the subject may be diagnosed as being at risk for an ischemic event.
• the disclosure provides methods for promoting the adoption of arterial characteristics in a blood vessel.
• a method may comprise administering to a blood vessel ex vivo or to a subject in need thereof, an effective amount of an agonist of D114 signaling.
• the blood vessel may be a venous graft, such as a saphenous vein graft, such as may be used in a coronary bypass surgery.
• the subject therapeutic agents 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, emulsif ⁇ ers 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.
• compositions comprising any of the various nucleic acid compounds targeted to D114, Notchl , Notch4 or other members of the pathway.
• a pharmaceutical composition will generally include a pharmaceutically acceptable carrier.
• 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.
• aqueous and nonaqueous carriers examples include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate.
• polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
• vegetable oils such as olive oil
• 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.
• 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, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption, such as aluminum monostearate and gelatin.
• 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, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium
• Injectable 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) and poly( anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.
• 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 carrier material to produce a single dosage form will generally be that amount of the compound which produces a therapeutic effect.
• 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.
• 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 therapeutic agent as an active ingredient.
• lozenges using a flavored basis, usually sucrose and acacia or tragacanth
• 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, mannitol, 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 sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds; (7) wetting agents, such as par
• 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 and the like.
• Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs.
• 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, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.
• 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.
• suspending agents such as ethoxylated isostearyl alcohols, polyoxyethylene sorbitol, and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
• 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 azone. 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. Keratolytic 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.
• Formulations for intravaginal or rectal 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 nonirritating 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.
• suitable nonirritating 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.
• polypeptide therapeutic agents of the instant invention can be expressed within cells from eukaryotic promoters.
• a soluble polypeptide of D114 or Notch 1/Notch4 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.
• the vectors stably introduced in and persist in target cells.
• viral vectors can be used that provide for transient expression. Such vectors can be repeatedly administered as necessary.
• Delivery of vectors encoding the subject 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).
• Example 1 Dosage-sensitive requirement for mouse D114 in artery development.
• Duarte et al. (Genes Dev. 2004 Oct 15;18(20):2474-8) demonstrated that loss-of- function mutations in mouse D114 cause defects in vasculogenesis and angiogenesis, and that these defects are dosage dependent, with D114 +/" mice showing a less severe phenotype that homozygous D114 "7" mice. Additionally, the loss of D114 function causes a loss of arterial vessel identity. These results demonstrate a level of sensitivity to D114 signaling that is unprecedented in the Notch pathway. The sensitivity of vascular development to D114 dosage indicates that antagonists of the D114-Notchl/4 signaling pathway will be highly effective in inhibiting angiogenesis.
• Example 2 mDLL4 overexpression causes arterial hypertrophy and loss of venous identity in developing mouse embryos.
• the rnDlU cDNA was cloned in pCALL2-MigR (Lobe et al, 1999) to produce the pZ/EG-mDll4 transgenesis vector (Fig.7), which was electroporated into Rl mouse embryonic stem (ES) cells.
• the transgenic mouse lines derived from electroporated ES cells by standard methods (Nagy & Rossant, 2000), were crossed to the constitutive ere line, CAG-Cre. Resulting embryos were analysed for EGFP fluorescence, the secondary reporter, which is co-expressed with mDll4 in those cells where the Cre recombination has taken place.
• EGFP expression was found to be strong and generalized in double transgenic embryos (dt) (Fig.8), which occurred in normal Mendelian ratios at E8.5 through E9.5. These embryos displayed severe haemorrhaging in the head, heart, branchial arches and posterior ventral region, pericardial edema and incomplete turning at E9.0 (Fig.8 c). After El 0.5 no double- transgenic embryos were recovered.
• hematopoietic clusters which are normally specific of major arteries in the ⁇ ort ⁇ -gon ⁇ d-mesonephros region, were detected in the sinus venosus region of the mutant embryos at E9.0 (not shown), providing evidence for functional arteriolization of venous structures.
• mDll4 overexpression causes aortic hypertrophy and arteriovenous shunting, localized angiogenic arrest, ectopic expression of endothelial arterial identity markers in venous vessels and downregulation of endothelial venous identity markers.
• Example 3 Human Delta-like (hdll4) Regulates Endothelial Cell Tube Formation and Endothelial Cell Sprouting.
• dll4 The extacellular domain of human dll4 (amino acids 26-524 of SEQ ID NO:1) was cloned in mammalian expression vector with His tag or Fc tag, and expressed as secreted protein in 293 cell and CHO-K cells. Purified dll4 was first shown to bind Notch 1 and then tested for its in vitro activity on endothelial cell when cultivated on matrigel. See Figures 10 and 11. Endothelial cells organized to make tube like structures within 8-24 hr, and the tube formation was minimal in growth factor deprived condition. Addition of VEGF at 20ng/ml induces tube formation.
• D114 when tested in growth factor deficient conditions, induced tube formation at lower dose levels (100 and 200 ng/ml) while the higher dose level of 500ng/ml failed to induce tube formation (Figure 12). D114 however did not induce tube formation when added to VEGF containing cultures..
• Endothelial cell and smooth muscle cell spheroids of defined cell number were generated.
• SM or HUVE cells were suspended in corresponding culture medium containing 0.25% (w/v) carboxymethylcellulose and seeded in nonadherent round-bottom 96- well plates. Under these conditions, all suspended cells contribute to the formation of a single spheroid per well of defined size and cell number (standard size: 2250 cells/spheroid; in vitro angiogenesis: 750-1000 cells/spheroid).
• SM and HUVE cells were mixed and seeded in nonadherent round-bottom 96-well plates as described above. Spheroids were cultured for at least 24 h and used for the corresponding experiments.
• This stock solution (0.5 ml) was mixed with 0.5 ml room temperature medium (ECGM basal medium [PromoCell] with 40% FCS containing 0.5% (w/v) carboxymethylcellulose to prevent sedimentation of spheroids prior to polymerization of the collagen gel, 50 spheroids, and the corresponding test substance.
• ECGM basal medium [PromoCell] with 40% FCS containing 0.5% (w/v) carboxymethylcellulose to prevent sedimentation of spheroids prior to polymerization of the collagen gel, 50 spheroids, and the corresponding test substance.
• the spheroid containing gel was rapidly transferred into prewarmed 24-well plates and allowed to polymerize (1 min), after which 0.1 ml ECGM basal medium was pipetted on top of the gel. The gels were incubated at 37°C, 5% CO2, and 100% humidity.
• in vitro angiogenesis was digitally quantitated by measuring the length of the sprouts that had grown out of each spheroid (ocular grid at 10Ox magnification) using the digital imaging software DP-Soft (Olympus) analyzing at least 10 spheroids per experimental group and experiment.
• SMC and HUVEC were labeled using the fluorescent dyes PKH26 (red fluorescence) and PKH67 (green fluorescence) following manufacturer's instructions. After trypsinization, suspended cells were washed once with HBSS, membrane labeled with PKH26 or PKH67 for 5 min, and washed three times using corresponding culture medium. Quality of cell labeling was examined using fluorescence microscopy.
• Spheroids were fixed in Karnovsky's fixative, postfixed in 1.0% osmium tetroxide, dehydrated in a graded series of ethanol, and embedded in Epon. Sections of 0.5 ⁇ m were cut and stained with azure 1 1 methylene blue for light microscopic evaluation. Ultrathin sections (50-80 nm) were cut, collected on copper grids, and automatically stained with uranyl acetate and lead citrate for observation with a Zeiss EM 10 electron microscope.
• Spheroids were harvested and centrifuged for 3 min at 200 g. Cultured monolayer cells were harvested by trypsinization and collected by centrifugation. Spheroids and pelleted monolayer cells were fixed in HBSS containing 4% paraformaldehyde and processed for paraffin embedding; after dehydration (graded series of ethanol and isopropanol, 1 h each), the specimens were first immersed with paraffin I (melting temperature 42°C) for 12 h at 60°C. Spheroids and monolayer cells were again collected by centrifugation and immersed with paraffin II (melting temperature 56°C) for 12 h at 70 0 C. Finally, the resulting paraffin block was cooled to room temperature and trimmed for sectioning.
• paraffin sections (4 ⁇ m) were cut, deparaffinized, and rehydrated. Sections were then incubated with 3% H2O2 in H2O to inhibit endogenous peroxidase. After washings in phosphate-buffered saline, the sections were incubated for 30 min with blocking solution (10% normal goat serum), followed by incubation with the corresponding primary antibody in a humid chamber at 4°C overnight.
• Apoptotic cells were visualized by histochemical detection of nucleosomal fragmentation products (TUNEL) applying the In Situ Cell Death Detection Kit, following the manufacturer's instructions.
• TUNEL nucleosomal fragmentation products in sections of paraffin-embedded spheroids were detected after deparaffination and proteinase K digestion by 3' end labeling with fluorescein-dUTP using terminal deoxynucleotidyl transferase. Labeling was visualized either directly by fluorescence microscopy or indirectly after incubating the sections with peroxidase-labeled anti-fluorescein antibody and developing with diaminobenzidine as substrate.
• Fragmented DNA of 10 spheroids was extracted by lysis for 60 min at room temperature with vigorous shaking. The extracts were centrifuged for 10 min at 13,000 g and 300 ⁇ l of the supernatant was incubated with peroxidase-labeled anti-DNA antibody and biotinylated anti-histone antibody in streptavidin-coated microtiter plates following the manufacturer's instructions.
• Example 4 Vascular proliferation in embryonic and adult D114 +/- mutant mice.
• D114 + * mice showed an even greater increase in the vascular response (1.5 fold increase, P ⁇ 0,05). Furthermore the vessels showed lack of architecture and loss of hierarchy. Thus vascular response was increased but maturation was lacking. Maturation of newly forming vessels accompanies the recruitment of pericytes. We hypothesized that newly forming vessels in D114 +/" mice may be defective in pericyte recruitment. Thus localization of pericytes with ⁇ -SMA antibodies showed abundant signal in tumor vessels in wild type mice, whereas tumor vessels in D114 +/" mice showed a profound deficiency in pericyte coverage (Fig 15D). Reduced recruitment of pericytes may contribute to the lack of vascular hierarchy in D114 +/" mice tumor vessels.
• Example 5 Soluble D114 inhibits D114-Notch signaling.
• Example 6 sD114 induces vascularization of Matrigel plugs in vivo.
• sD114 can directly inhibit angiogenesis in vivo.
• Matrigel was supplemented with VEGF, sD114-Fc, sD114-His or various combinations, and injected into the ventral abdominal subcutaneous tissue of Balb/C nu/nu mice.
• Matrigel plugs without growth factors had virtually no vascularization after 6 days (Figure 17A), while VEGF recruited endothelial cells and formed various stages of vascular structures including those with open lumen containing red blood cells throughout the plug.
• sD114 in the context of VEGF showed a marked increase in vascular structures (Fig 17) which appeared like thin strings, and mostly lacked lumen.
• sD114 alone in the absence of VEGF was also capable of inducing angiogenesis.
• Immuno-chemical examination with PECAM further demonstrates the contrast between VEGF induced large vessel filled with red blood cells and sD114 induced vessels which express PECAM but lack lumen and lack perfusion defined by the presence of red blood cells (Fig 17B).
• Hemoglobin was also quantitated specifically by the Drabkin method using a Drabkin reagent kit. and fold change was compared with control measurement represented as 1.
• Median hemoglobin levels were thus were 1, 9.7, and 2.5, and 3 in control, VEGF, D114- Fc, and D114-His groups.
• Example 7 sD114 inhibits the growth of human tumors in athymic mice.
• D114 is one of the genes induced in tumor vessels in certain human and murine tumors (Fig 15C). D114 induction may be a generalized feature of tumor vessels, one which could be beneficial for tumor growth. D114 expression is seen predominantly in the tumor vasculature.
• sD114 tumor cell viability in vitro with various concentrations of sD114 was tested (HT29, MCF-7, SCC-15, B 16, PC3 and KS-SLK cell lines), and no effect was observed (data not shown).
• sD114 may modulate tumor growth in vivo.
• HT29 human colon carcinoma cell line
• KS- SLK human Kaposi's sarcoma cell line
• Tumor volume was similar in vector alone and D114-FL, while sD114-Fc and sD114-His had markedly reduced tumor volume (over 70% reduction with sD114-His) (Fig 18B).
• Harvested tumors harvested at the time were examined for vascular density using PECAM immuno-staining.
• Tumors expressing D114-FL or vector alone showed highly structured vessels (Fig 18C).
• sD114 expressing tumors showed marked changes in the vessel architecture.
• KS-SLK tumor xenografts Remarkably the vessels appeared thin and often lacking apparent lumen.
• DH4 knock out mice were generated in CDl background and described previously 16 .
• DlU ' ' ' and most Dll4 +/' mouse embryos have a lethal phenotype.
• the vasculature of Dll4 +/ ⁇ embryos was visualized with platelet endothelial cell adhesion molecule (PECAM) and alpha smooth muscle actin ( a - SMA) staining.
• PECAM platelet endothelial cell adhesion molecule
• a - SMA alpha smooth muscle actin
• RT-PCR analysis First-strand cDNA was synthesized from total RNA using a Superscript Preamplification System kit (GIBCOBRL) and used (0.1 ⁇ g) for PCR with specific primers for DU4, GAPDH, $-actin, Heyl, Hey2, Hesl, Hes2 (primer pairs used in this study are available on request), PCR products were visualized by ethidium bromide staining.
• GIBCOBRL Superscript Preamplification System kit
• Antibodies and other reagents Anti-PECAM (M20) from Santa Cruz Biotechnology (Santa Cruz, CA), anti- ⁇ -SMA (Dako, Carpinteria, CA), IgG-Fc fragment and antihuman Fc from Jackson Laboratories (Bar Harbor, ME), Notchl-Fc and Notch3-Fc from R&D (R&D systems), Hypoxyprobe-1 from Chemicon (Chemicon International, Temecula, CA), Rhodamine labeled Ricinus Communis Agglutinin I (RCA) from Vector labs (Vector labs, Burlingame, CAsi), and alkaline phosphatase substrate PNPP was purchased from Sigma (Sigma Chemicals, St. Louis, MO).
• HUVECs Normal human umbilical vein endothelial cells
• HUAECs human umbilical arterial endothelial cells
• Cambrex Walkersville, MD
• EGM2-supplemented medium Invitrogen
• HUVECs and HUAECs were used at passages 4 or below and collected from a confluent dish.
• ChoK cell line was obtained from American Type Culture Collection (Manassas, VA) and cultured under recommended conditions.
• D114 constructs Full length human D114 gene was cloned by PCR amplification from human cDNA (Clonetech) made from fetal lung tissues. Both full length (amino acid residues 1-685) and C-terminally His-tagged extracellular domain (amino acid residues 1 -486) proteins were expressed from pcDNA3.1 expression vector (Invitrogen). Fc fusion protein was expressed from pCXFc vector (Invitrogen). AP fusion protein was expressed from pAPtag-2 vector (GeneHunter Corp.). All proteins were transiently expressed in ChoK cells (ATCC) using Lipofectamine 2000 (Invitrogen). His-tagged and Fc-fusion D114 proteins were purified through Nickel-NTA column and Protein A-Sepharose column 19 .
• Notch receptor binding and activation pathway Five ⁇ g/ml Notchl-Fc and Notch3-Fc were coated overnight at 4°C in PBS on 96-well plates. D114-AP was diluted in PBS and 0.1% Tween-20 (PBST), 50 ⁇ l of each dilution was incubated with Notch-Fc and blocked with 5% milk in PBS for one hour. Wells were washed three times with PBST, developed with PNPP and read at OD405.
• PBST Tween-20
• human umbilical vein endothelial cells were grown in 100-mm dishes until 80% confluence and were co-cultured with choK cells transiently expressing full length D114 (1 :1 ration) or choK cells transfected with vector alone. Co- cultures were treated with either rD114-His or rD114-Fc for a period of 24 hr, cells were harvested and total RNA was isolated for further analysis .
• MACSelect 4.1 transfected cell selection kit was used as per manufacturer's instructions. In brief, cells were cotransfected with expression vector containing the plasmid of interest and pMACS 4.1 plasmid. After 36 hr, cells were harvested with 5 mM EDTA and incubated with MACSelect 4 Microbeads for 15 min at 4°C. The cell suspension was then passed via an MS+ column in a magnetic field. After 3 washes, the column was removed from the field and selected cells eluted in culture medium. Selection efficiency was confirmed by FACS analysis of sorted cells with fluorescent D114 monoclonal antibody (data not shown).
• EC tube formation assay Matrigel (250 ⁇ L; BD Biosciences, Palo Alto, CA) was placed in each well of an ice-cold 24-well plate. The plate was allowed to sit at room temperature for 15 minutes, and 37°C for 30 minutes for Matrigel to polymerize. HUVECs in EGM2 medium were plated at a concentration of 1x10 4 cells/well with test material at various concentrations in triplicates. After 6-hour and 24-hour incubations, pictures were taken for each concentration using a Bioquant Image Analysis system (Bioquant, Arlington, TN). Length of cords formed and number of junctions were compared among various groups using ImageJ software (NIH, Bethesda, MD). Experiments were repeated twice 19 .
• Endothelial cell spheroids were generated by suspending equal number of endothelial cells (1000 cells/well) in culture medium containing 0.25% (w/v) carboxymethylcellulose and seeded in nonadherent round-bottom 96-well plates. Endothelial cells were suspended to form a single spheroid per well. Spheroids were embedded into collagen gels and cultured for at least 24 h. Sprouting was recorded digitally (ocular grid at 10Ox magnification) using the digital imaging DP-Soft (Olympus) analyzing at least 10 spheroids per experimental group and experiment. Sprouting was also quantitated by measuring the length of the sprouts by ImageJ 19 .
• Murine Matrigel plug angiogenesis assay In vivo angiogenesis was assayed using the Matrigel plug assay. 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 vehicle alone (PBS containing 0.25% BSA) or VEGF, or sD114, or VEGF and sD114 together. Matrigel (0.5 mL) was injected into the abdominal subcutaneous tissue of female Balb/C nu/nu mice (6 weeks old, 5 mice per group) along the peritoneal midline.
• mice were humanely killed and plugs were recovered * weighed, and divided for hemoglobin measurement and immuno-histochemical analysis.
• Vascular identity of the infiltrating cells was established with PECAM immuno- staining. The experiment was repeated three times. The vascularized area in each section was calculated using ImageJ.
• Hemoglobin in one-half of the Matrigel plug was measured using the Drabkin method (Drabkin reagent kit 525; Sigma, St. Louis, MO) using the manufacturer's recommended protocol.
• Immunohistochemistry and immunofluorescence Sections (5 ⁇ m) of formalin-fixed paraffin- embedded tissues were processed using standard methods 16 19 . Sections were incubated with primary antibody overnight at 4° C and appropriate secondary antibody for 1 hour at room temperature. Antibody binding was localized with ABC staining kit form Vector Laboratories (Burlingame, CA) according to the manufacturer's instructions and peroxidase activity detected using DAB substrate solution (Vector Laboratories).. Routine negative controls were exclusion of primary and secondary antibody and substitution of normal IgG isotope for primary antibody. The positive staining area was estimated using ImageJ and analyzed by Student t test.
• Fluorescent immunostaining was performed in a similar fashion to detect the expression level of EC-specific markers including PECAM.
• Appropriate fluorescein-conjugated secondary antibodies (Sigma- Aldrich, St Louis, MO) were used and nuclei were counterstained with 4', 6-diamidino-2-phenylindoledihydrochloride hydrate (DAPI).
• Slides were mounted with Vectashield antifade mounting solution (Vector Laboratories) and images obtained using an Olympus AX70 fluorescence microscope and Spot v2.2.2 (Diagnostic Instruments, Sterling Heights, MI) digital imaging system.
• Murine tumor xenografts Tumor cells (1.5 x 10 6 ) HT29 (human colon cancer cell line) or KS-IMM (human Kaposi's sarcoma cancer cell line) were implanted subcutaneously in flanks of male athymic BaIbC nu/nu mice (6-8 weeks old, 6 mice/group and repeated twice).
• Tumor cells were mixed with Matrigel (1 :1 vol/vol; BD Biosciences) with or without 5 ⁇ g/ml of sD114. Tumor volume was measured on day 14 estimated as 0.52 x a x b 2 , where a and b are the largest and smallest lengths of the palpable tumor.
• the Student t test was used to compare tumor volumes, with P ⁇ .05 being considered significant.
• Animals were humanely killed and tumor and adjacent normal tissues were harvested. Harvested tissues were divided to either fixed in formalin or frozen in OCT for analysis. Distribution and intensity of hypoxia was studied using hypoxyprobe-1 (HPl-100, Chemicon) infused intraperitoneally at a dose of 60mg/kg one hour prior to the tumor harvest and localized using recommended protocol. Vessel perfusion was studied using rhodamine labeled Ricinus Communis Agglutinin 1 (Vector Labs) infused 10-15 minutes prior to the tumor harvest and analyzed using the manufacturer recommended protocol. All procedures were approved by our Institutional Animal Care and Use Committees and performed in accordance with the Animal Welfare Act regulations.
• Ferrara N Carver-Moore K, Chen H, et al. Heterozygous embryonic lethality induced by targeted inactivation of the VEGF gene. Nature. 1996;380:439-442.
• Gerety SS Wang HU, Chen ZF, Anderson DJ. Symmetrical mutant phenotypes of the receptor EphB4 and its specific transmembrane ligand ephrin-B2 in cardiovascular development. MoI Cell. 1999;4:403-414.
• EphB4 The soluble extracellular domain of EphB4 (sEphB4) antagonizes EphB4-EphrinB2 interaction, modulates angiogenesis, and inhibits tumor growth. Blood. 2006;107:2330-2338.

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