EP2291401A2 - Antagonistes de bmp9 et bmp10, alk1 et autres ligands alk1, et leurs utilisations - Google Patents

Antagonistes de bmp9 et bmp10, alk1 et autres ligands alk1, et leurs utilisations

Info

Publication number
EP2291401A2
EP2291401A2 EP09746978A EP09746978A EP2291401A2 EP 2291401 A2 EP2291401 A2 EP 2291401A2 EP 09746978 A EP09746978 A EP 09746978A EP 09746978 A EP09746978 A EP 09746978A EP 2291401 A2 EP2291401 A2 EP 2291401A2
Authority
EP
European Patent Office
Prior art keywords
alkl
bmp9
agent
antibody
bmplo
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP09746978A
Other languages
German (de)
English (en)
Inventor
Jasbir Seehra
John Knopf
Robert S. Pearsall
Asya Grinberg
Ravindra Kumar
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Acceleron Pharma Inc
Original Assignee
Acceleron Pharma Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Acceleron Pharma Inc filed Critical Acceleron Pharma Inc
Publication of EP2291401A2 publication Critical patent/EP2291401A2/fr
Withdrawn legal-status Critical Current

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Classifications

    • 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
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • 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
    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies

Definitions

  • Angiogenesis the process of forming new blood vessels, is critical in many normal and abnormal physiological states. Under normal physiological conditions, humans and animals undergo angiogenesis in specific and restricted situations. For example, angiogenesis is normally observed in wound healing, fetal and embryonic development and formation of the corpus luteum, endometrium and placenta. Undesirable or inappropriately regulated angiogenesis occurs in many disorders, in which abnormal endothelial growth may cause or participate in the pathological process. For example, angiogenesis participates in the growth of many tumors. Deregulated angiogenesis has been implicated in pathological processes such as rheumatoid arthritis, retinopathies, hemangiomas, and psoriasis. The diverse pathological disease states in which unregulated angiogenesis is present have been categorized as angiogenesis-associated diseases.
  • Capillary blood vessels are composed primarily of endothelial cells and pericytes, surrounded by a basement membrane.
  • Angiogenesis begins with the erosion of the basement membrane by enzymes released by endothelial cells and leukocytes. The endothelial cells, which line the lumen of blood vessels, then protrude through the basement membrane. Angiogenic factors induce the endothelial cells to migrate through the eroded basement membrane. The migrating cells form a "sprout" protruding from the parent blood vessel, where the endothelial cells undergo mitosis and proliferate. Endothelial sprouts merge with each other to form capillary loops, creating the new blood vessel.
  • 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.
  • MacugenTM an aptamer that binds to VEGF has proven to be effective in the treatment of neovascular (wet) age-related macular degeneration.
  • 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).
  • NM-3 The isocoumarin 2-(8-hydroxy-6- methoxy-l-oxo-1 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 Dec;56(6):610-4.).
  • Thalidomide and related compounds have shown beneficial effects in the treatment of cancer, and although the molecular mechanism of action is not clear, the inhibition of angiogenesis appears to be an important component of the anti-tumor effect (see, e.g., Dredge et al. Microvasc Res.
  • 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).
  • Anti-angiogenic therapies are widely expected to have beneficial effects on other inflammatory diseases, particularly psoriasis. Although many anti-angiogenic agents have an effect on angiogenesis regardless of the tissue that is affected, other angiogenic agents may tend to have a tissue-selective effect.
  • compositions and methods for inhibiting angiogenesis include methods and compositions which can inhibit the unwanted growth of blood vessels, either generally or in certain tissues and/or disease states.
  • the present disclosure presents a characterization of an activin-like kinase I (ALKl)-mediated regulatory system, including its ligands BMP9 and BMPlO, and the role of this system in angiogenesis.
  • ALKl activin-like kinase I
  • the disclosure provides antagonists of ALK-I ligands and the use of such antagonists as anti-angiogenic agents. Additionally, the disclosure provides antagonists of ALK-I itself, and the use of such antagonists as anti-angiogenic agents.
  • ALKl is a receptor for the GDF5 group of ligands, which includes GDF6 and GDF7, and also for the BMP9 group of ligands, which includes BMPlO.
  • the disclosure provides antagonists of the ALKl regulatory system, including antagonists of the receptor or one or more of the ligands, for use in inhibiting angiogenesis.
  • the disclosure provides antagonists of ALKl ligands for the treatment of cancers, particularly multiple myeloma, melanoma, lung cancer, rheumatoid arthritis, and disorders associated with pathological angiogenesis in the eye.
  • an ALKl ECD polypeptide comprises an amino acid sequence that is at least 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence of amino acids 22-118 of the human ALKl sequence of SEQ ID NO:1.
  • An ALKl ECD polypeptide may be used as a small monomeric protein or in a dimerized form (e.g., expressed as a fusion protein), particularly for local administration into tissues such as the eye.
  • An ALKl ECD may also be fused to a second polypeptide portion to provide improved properties, such as an increased half-life or greater ease of production or purification. Fusions to an Fc portion of an immunoglobulin or linkage to a polyoxyethylene moiety (e.g., polyethylene glycol) may be particularly useful to increase the serum half-life of the ALKl ECD polypeptide in systemic administration (e.g., intravenous, intraarterial and intraperitoneal administration).
  • systemic administration e.g., intravenous, intraarterial and intraperitoneal administration.
  • an ALKl-Fc fusion protein comprises a polypeptide having an amino acid sequence that is at least 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence of amino acids 22-118 of SEQ ID NO:1, which polypeptide is fused, either with or without an intervening linker, to an Fc portion of an immunoglobulin, and wherein the ALKl-Fc fusion protein binds to GDF5, GDF7, BMP9 and/or BMPlO with a K 0 of less than 1 x 10 "7 M and/or binds to TGF ⁇ -1 with a K D of greater than 1 x 10 "6 .
  • an Fc portion may be selected so as to be appropriate to the organism.
  • the Fc portion is an Fc portion of a human IgGl.
  • the ALKl-Fc fusion protein comprises amino acids 22-118 of SEQ ID NO:1.
  • the ALKl-Fc fusion protein comprises the amino acid sequence of SEQ ID NO: 3.
  • the ALKl-Fc fusion protein is the protein produced by expression of the nucleic acid of SEQ ID NO:4 in a mammalian cell line, particularly a Chinese Hamster Ovary (CHO) cell line.
  • ALKl-ECD polypeptides may be formulated as a pharmaceutical preparation that is substantially pyrogen free. The pharmaceutical preparation may be prepared for systemic delivery (e.g., intravenous, intraarterial or subcutaneous delivery) or local delivery (e.g., to the eye).
  • the disclosure identifies difficulties in developing relatively homogeneous preparations of ALKl-Fc fusion protein for use in a therapeutic setting.
  • the ALKl-Fc fusion protein tends to aggregate into higher order multimers.
  • the disclosure provides solutions to these difficulties and therefore provides pharmaceutical preparations comprising ALKl-Fc fusion proteins wherein such preparations are at least 85%, 90%, 95%, 96%, 97%, 98% or 99% composed of dimeric ALKl -Fc fusion protein.
  • the disclosure provides pharmaceutical preparations comprising an ALKl- Fc fusion protein comprising: a polypeptide having an amino acid sequence that is at least 97% identical to the sequence of amino acids 22-118 of SEQ ID NO: 1 , which polypeptide is fused to an Fc portion of an immunoglobulin, and wherein the ALKl- Fc fusion protein binds to GDF5, GDF7, BMP9 and/or BMPlO with a K 0 of less than I x IO 7 M and/or binds to TGF ⁇ -1 with a K 0 of greater than 1 x 10 "6 and wherein at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% of the ALKl-Fc fusion protein is present in a dimeric form.
  • the Fc portion of the ALKl-Fc fusion protein may be an Fc portion of a human IgGl .
  • the ALKl -Fc fusion protein may comprise the amino acid sequence of SEQ ID NO: 3.
  • the ALKl-Fc fusion protein may be produced by expression of the nucleic acid of SEQ ID NO:4 in a mammalian cell line, particularly a Chinese Hamster Ovary (CHO) cell line.
  • Such pharmaceutical preparations may formulated so as to be appropriate for administration to the eye, particularly by injection.
  • the disclosed pharmaceutical preparations may be used for a variety of therapeutic purposes described herein, including inhibiting angiogenesis, treating a tumors, treating rheumatoid arthritis, and treating ocular disorders associated with angiogenesis.
  • the ALKl-Fc pharmaceutical preparations and preparations comprising antibodies directed to ALKl or one or more ligands of ALKl may be used in conjunction with a second agent that inhibits angiogenesis, such as a VEGF antagonist (e.g., Avastin, sorafenib, and VEGF receptor traps).
  • a VEGF antagonist e.g., Avastin, sorafenib, and VEGF receptor traps.
  • the disclosure provides methods for inhibiting angiogenesis in a mammal by administering any of the ALKl ECD polypeptides described generally or specifically herein.
  • a method comprises administering to the mammal an effective amount of an ALKl -Fc fusion protein, wherein the ALKl Fc fusion protein comprises a polypeptide having an amino acid sequence that is at least 90% identical to the sequence of amino acids 22-1 18 of SEQ ID NO: 1, which polypeptide is fused to an Fc portion of an immunoglobulin, and wherein the ALKl-Fc fusion protein binds to TGF ⁇ -1 with a KQ of greater than 1 x 10 "6 .
  • the ALKl-Fc fusion protein binds to one or more ALKl ligands selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the ALKl -Fc fusion protein has a sequence of SEQ ID NO:3.
  • the ALKl ECD polypeptide may be delivered locally (e.g., to the eye) or systemically (e.g., intravenously, intraarterially or subcutaneously).
  • the disclosure provides a method for inhibiting angiogenesis in the eye of a mammal by administering an ALKl-Fc protein to the mammal at a location distal to the eye, e.g. by systemic administration.
  • the disclosure provides antibodies that bind to ALKl, particularly an epitope situated in the extracellular domain, amino acids 22-118 of SEQ ID NO: 1, and inhibit the binding of ALKl to at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • an antibody may bind with a K D of less than 5 x 10 '8 M, and optionally between 5 x 10 "8 and 1 x 10 '10 .
  • An antibody with affinity within this range would be expected to inhibit signaling by one or more of GDF5, GDF6, and GDF7 while having less effect on signaling by BMP9 and BMPlO.
  • Such an antibody preferably inhibits angiogenesis stimulated by at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, and GDF7. While not wishing to be bound to a particular mechanism, it is expected that such antibodies will act by inhibiting ALKl activity directly, which should be contrasted to the activity of an ALKl-Fc fusion protein, which is expected to inhibit the activity of ALKl ligands.
  • An anti-ALKl antibody is not expected to interfere with the ability of GDF5, GDF6, GDF7, BMP9 or BMPlO to signal through alternative receptor systems, such as the BMPRIa, BMPRIb and BMPRII complexes.
  • an anti-ALKl antibody is expected to interfere with the ability of low affinity ligands for ALKl (e.g., TGF- ⁇ , which is generally recognized as triggering significant signaling events through ALK-I even though binding is relatively weak) to signal through ALKl, even though an ALKl ECD may not bind to or inhibit such low affinity ligands.
  • An antibody may bind to the ALKl polypeptide with a K D of less than 1 x 10 "10 M.
  • An antibody with affinity within this range would be expected to inhibit signaling by BMP9 or BMPlO.
  • Such an antibody preferably inhibits binding of BMP9 and BMPlO to ALKl .
  • an antibody that binds relatively poorly to ALKl may inhibit TGF ⁇ binding to ALKl while failing to inhibit the tighter binding ligands such as GDF5 or BMP9.
  • the antibodies described herein are preferably recombinant antibodies, meaning an antibody expressed from a nucleic acid that has been constructed using the techniques of molecular biology, such as a humanized antibody or a fully human antibody developed from a single chain antibody. Fv, Fab and single chain antibodies are also included within the term "recombinant antibody”.
  • Antibodies may also be polyclonal or non- recombinant monoclonal antibodies (including human or murine forms, as well as human antibodies obtained from transgenic mice).
  • Antibodies and ALKl-ECD polypeptides may be formulated as a pharmaceutical preparation that is substantially pyrogen free.
  • the pharmaceutical preparation may be prepared for systemic delivery (e.g., intravenous, intraarterial or subcutaneous delivery) or local delivery (e.g., to the eye).
  • Antibodies described in WO 2007/040912 may be useful in the various methods described herein.
  • the disclosure provides methods for inhibiting angiogenesis in a mammal by administering to the mammal an effective amount of an antibody that binds to an ALKl polypeptide, described herein either generally or specifically.
  • An antibody useful for this purpose may bind to the extracellular domain of ALKl (e.g., bind to a polypeptide consisting of amino acids 22-1 18 of SEQ ID NO: 1) or another portion of ALKl.
  • the antibody may bind to a polypeptide consisting of amino acids 22-118 of SEQ ID NO:1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the antibody may bind to the ALKl polypeptide with a K D of less than 5 x 10 "8 M, and optionally between 5 x 10 "8 and 1 x 10 "10 .
  • the antibody may inhibit angiogenesis stimulated by at least one ALKl ligand selected from the group consisting of: GDF5, GDF6 and GDF7.
  • An antibody that selectively inhibits signaling mediated by GDF5, GDF6, or GDF7 relative to signaling by BMP9 or BMPlO may be used as a selective inhibitor of angiogenesis that occurs in tissues where GDF5, GDF6, or GDF7 are localized: primarily bone or joints.
  • the antibody may bind to the ALKl polypeptide with a K D of less than 1 x 10 "10 M.
  • the antibody may inhibit the binding of ALKl to an ALKl ligand, wherein the ALKl ligand is selected from the group consisting of: BMP9 and BMPlO.
  • the anti-ALKl antibody may be delivered locally (e.g., to the eye) or systemically (e.g., intravenously, intraarterially or subcutaneously).
  • the disclosure provides a method for inhibiting angiogenesis in the eye of a mammal by administering an anti-ALKl antibody.
  • the disclosure provides a method for treating patients with multiple myeloma.
  • the disclosure provides a method for inhibiting angiogenesis in disorders that are associated with pathological angiogenesis as a consequence of multiple pro-angiogenic factors, such as VEGF, PDGF and/or FGF.
  • the disclosure provides antibodies that bind to an ALKl ligand disclosed herein and inhibit the binding of the ALKl ligand to ALKl . While not wishing to be bound to any particular mechanism, it is expected that antibodies that bind to ALKl ligands will have effects that are similar in nature to ALKl ECD polypeptides, because both types of agent bind to the ligands rather than the receptor itself.
  • the antibody binds to a ligand selected from the group consisting of GDF5, GDF6 and GDF7.
  • the antibody may bind to the ALKl ligand with a K D of less than 5 x 10 "8 M.
  • the antibody may be selected for inhibition of angiogenesis stimulated by the ALKl ligand.
  • a CAM assay is an appropriate assay system for selection of desirable antibodies.
  • Such antibodies are preferably recombinant antibodies, and may be formulated as a pharmaceutical preparation that is substantially pyrogen free.
  • the pharmaceutical preparation may be prepared for systemic delivery (e.g., intravenous, intraarterial or subcutaneous delivery) or local delivery (e.g., to the eye).
  • the disclosure provides antibodies that bind to an ALKl ligand and inhibit the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of BMP9 and BMPlO.
  • a neutralizing anti-BMP9 antibody inhibits angiogenesis in vivo.
  • BMP-I O stimulates angiogenesis while an antagonist of BMP-10 inhibits angiogenesis.
  • the antibody may bind to the ALKl ligand with a K D of less than 1 x 10 "10 M.
  • Such antibodies are preferably recombinant antibodies, and may be formulated as a pharmaceutical preparation that is substantially pyrogen free.
  • the pharmaceutical preparation may be prepared for systemic delivery (e.g., intravenous, intraarterial or subcutaneous delivery) or local delivery (e.g., to the eye).
  • the disclosure provides methods for inhibiting angiogenesis in a mammal, the method comprising, administering to the mammal an effective amount of an antibody that binds to an ALKl ligand and inhibits the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the antibody may inhibit angiogenesis stimulated by at least one ALKl ligand selected from the group consisting of: GDF5, GDF6 and GDF7.
  • an antibody that binds to an ALKl ligand and inhibits the ligand to ALKl is an antibody that binds at or near the type I receptor binding site of the ligand.
  • the disclosure provides methods for inhibiting angiogenesis in a mammal by administering other inhibitors of the ALKl signaling system disclosed herein.
  • inhibitors may include nucleic acids (e.g., antisense or RNAi constructs) that decrease the production of ALKl, GDF5, GDF6, GDF7, BMP9 or BMPlO).
  • affinity binding reagents can also be used, such as aptamers, random peptides, protein scaffolds that can be modified to allow binding to selected targets (examples of such scaffolds include anticalins and FNIII domains); in each case, an affinity binding reagent would be selected for the ability to disrupt the ALKl regulatory system disclosed herein, either by disrupting the ALKl-ligand interaction or by inhibiting the signaling that occurs after binding.
  • the disclosure describes the role of DAN as a regulator of the ALKl regulatory system.
  • DAN binds to the GDF5 group of ligands but fails to bind to the BMP9 group of ligands.
  • DAN is expected to inhibit angiogenesis mediated by GDF5, GDF6 or GDF7 but not angiogenesis mediated by BMP9 or BMPlO.
  • DAN may therefore be used as a selective agent for inhibiting angiogenesis in the bone or joints, where the GDF5 group of proteins is primarily expressed.
  • the disclosure provides DAN proteins for use as anti-angiogenic agents in the context of bone or joint angiogenesis, including rheumatoid arthritis and cancers that involve the bone or joints (e.g., multiple myeloma and bone metastases).
  • a DAN protein will generally bind to one or more ALKl ligands selected from the group consisting of: GDF5, GDF6 and GDF7, while having relatively poor binding to BMP9 or BMPlO.
  • a DAN protein may comprise an amino acid sequence that is at least 70%, 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the sequence of amino acids corresponding to amino acids 17-180 of SEQ ID NO: 10 (mature human DAN) or amino acids 21-125 of SEQ ID NO: 10 (conserved cysteine knot domain of DAN).
  • a DAN protein may also be encoded by a nucleic acid that comprises a sequence the complement of which hybridizes under stringent hybridization conditions to nucleotides 153-467 of SEQ ID NO: 11 or a variant of nucleotides 153-467 of SEQ ID NO: 1 1 that has the same coding sequence (a "silent" variant, such as a variant containing one or more alterations at a wobble position in the triplet code), or to nucleotides 93-635 of SEQ ID NO: 1 1 or a silent variant thereof.
  • the DAN protein is a fusion protein, such as an Fc fusion protein.
  • DAN is expected to be particularly useful for the inhibition of angiogenesis in bone and joints (including tumors located in the bone or joints, such as multiple myeloma and bone metastases), it may also be useful in other contexts, such as in a tumor located elsewhere, or in the eye.
  • a method of inhibiting angiogenesis in a mammal comprises administering to the mammal an effective amount of an antagonist of BMP9 and/or BMPlO.
  • the antagonist is an antibody that binds to BMP9 and/or BMPlO.
  • the antibody may be a polyclonal, monoclonal, and chimeric or a humanized antibody.
  • the antagonist may be a Fd, Fv, Fab, F(ab'), F(ab) 2 , or F(ab') 2 fragment, single chain Fv (scFv), diabody, triabody, tetrabody, minibody or a peptibody.
  • the antagonist is an aptamer (peptide or nucleic acid).
  • the disclosure provides for antagonists of both BMP9 and BMPlO, such as antibodies that cross-react and thus antagonize both proteins effectively (e.g., affinity less than 10 nM or less than 1 nM for both BMP9 and BMPlO).
  • antagonists of both BMP9 and BMPlO such as antibodies that cross-react and thus antagonize both proteins effectively (e.g., affinity less than 10 nM or less than 1 nM for both BMP9 and BMPlO).
  • ALK-I- Fc which binds to both BMP9 and BMPlO and inhibits the activities of both ligands.
  • the antagonist may be an inhibitor of BMP9 and/or BMPlO expression.
  • the antagonist is a nucleic acid that inhibits BMP9 and/or BMPlO expression.
  • the nucleic acid may be an antisense or RNAi nucleic acid.
  • the antagonist may be a non-antibody protein that binds to BMP9 and/or BMPlO.
  • the antagonist may be a member of a GDF Trap family. Examples of the GDF Trap family include but are not limited to follistatin, FLRG, noggin and gremlin.
  • the antagonist is a polypeptide that comprises an amino acid sequence was selected from a library of amino acid sequences by a method comprising a step of detecting binding to BMP9 and BMPlO.
  • the disclosure provides methods for treating rheumatoid arthritis in a mammal, the method comprising, administering to a mammal that has rheumatoid arthritis an effective amount of an agent selected from the group consisting of: an ALKl ECD protein; an antibody that binds to an ALKl ligand and inhibits the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of GDF5, GDF6, GDF7, BMP9 and BMPlO; an antibody that binds to an ALKl polypeptide consisting of amino acids 22-118 of
  • SEQ ID NO:1 inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO; and a DAN polypeptide.
  • the disclosure provides methods for treating a tumor in a mammal.
  • Such a method may comprise administering to a mammal that has a tumor an effective amount of an agent selected from the group consisting of: an ALKl ECD protein; an antibody that binds to an ALKl ligand and inhibits the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of GDF5, GDF6, GDF7, BMP9 and BMPlO; an antibody that binds to an ALKl polypeptide consisting of amino acids 22-1 18 of SEQ ID NO: 1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO; and a DAN polypeptide.
  • an agent selected from the group consisting of: an ALKl ECD protein
  • a method may further comprise administering a second agent that inhibits angiogenesis.
  • a tumor may be a tumor that is associated with bone, such as a leukemia, a bone marrow tumor, a multiple myeloma or bone metastases, such as those commonly associated with breast or prostate cancer.
  • a tumor may be a melanoma or lung cancer tumor.
  • a tumor may also be one that utilizes multiple pro-angiogenic factors, such as a tumor that is resistant to anti-VEGF therapy.
  • Such formulations may comprise an agent selected from the group consisting of: an ALKl ECD protein; an antibody that binds to an ALKl ligand and inhibits the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of GDF5, GDF6, GDF7, BMP9 and BMPlO; an antibody that binds to an ALKl polypeptide consisting of amino acids 22-118 of SEQ ID NO: 1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO; and a DAN polypeptide.
  • an agent selected from the group consisting of: an ALKl ECD protein
  • the disclosure provides methods for treating an angiogenesis related disease of the eye.
  • Such methods may comprise administering systemically or to said eye a pharmaceutical formulation comprising: an effective amount of an agent selected from the group consisting of: an ALKl ECD protein; an antibody that binds to an ALKl ligand and inhibits the binding of the ALKl ligand to ALKl, wherein the ALKl ligand is selected from the group consisting of GDF5, GDF6, GDF7, BMP9 and BMPlO; an antibody that binds to an ALKl polypeptide consisting of amino acids 22-118 of SEQ ID NO:1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPl O; and a DAN polypeptide.
  • an agent selected from the group consisting of: an ALKl ECD protein
  • an agent described herein may be administered in conjunction with a second agent that inhibits angiogenesis.
  • the agent may be administered in conjunction with a second agent that has an anti-cancer effect, such as a chemotherapeutic agent or a biologic anti-cancer agent.
  • the disclosure also provides an ophthalmic pharmaceutical formulation comprising an ALKl-Fc fusion protein having an amino acid sequence that is at least 97% identical to the sequence of amino acids 22-1 18 of SEQ ID NO: 1, which polypeptide is fused to an Fc portion of an immunoglobulin, and wherein the ALKl- Fc fusion protein binds to GDF5, GDF7, BMP9 and/or BMPlO with a K 0 of less than 1 x 10 "7 M and/or binds to TGF ⁇ -1 with a K 0 of greater than 1 x 10 "6 .
  • the fusion protein has the sequence of SEQ ID NO: 3.
  • the Fc portion is from human IgGl .
  • the fusion protein is produced by expression of the nucleic acid of SEQ ID NO:4 in a mammalian cell line.
  • the cell line is Chinese Hamster Ovary cell line.
  • the formulation may further comprise one or more of the following medicaments: pegaptanib, ranibizumab, or a glucocorticoid. In one embodiment, the formulation is substantially pyrogen free.
  • the application also provides for an ophthalmic pharmaceutical formulation comprising an antibody that binds to an ALKl polypeptide consisting of amino acids 22-1 18 of SEQ ID NO:1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the antibody inhibits angiogenesis stimulated by at least one ALKl ligand selected from the group consisting of: GDF5, GDF6 and GDF7.
  • the antibody binds to the ALKl polypeptide with a K D of less than 5 x 10 '8 M.
  • the antibody binds to the ALKl polypeptide with a K D of less than 1 x 10 '10 M.
  • the antibody inhibits angiogenesis stimulated by GDF5, GDF6, GDF7, BMP9, or BMPlO.
  • the formulation may further comprise one or more of the following medicaments: pegaptanib, ranibizumab, or a glucocorticoid.
  • the formulation is substantially pyrogen free.
  • the disclosure provides for an ophthalmic pharmaceutical formulation comprising an antibody that binds to an ALKl ligand disclosed herein and inhibits the binding of the ALKl ligand to ALKl .
  • the antibody binds to a ligand selected from the group consisting of GDF5, GDF6 and GDF7.
  • the antibody may bind to the ALKl ligand with a K D of less than 5 x 10 "8 M.
  • the antibody may be selected for inhibition of angiogenesis stimulated by the ALKl ligand.
  • a CAM assay is an appropriate assay system for selection of desirable antibodies.
  • an antibody to BMP9 inhibits VEGF- mediated angiogenesis in a CAM assay.
  • Such antibodies are preferably recombinant antibodies.
  • the formulation may further comprise one or more of the following medicaments: pegaptanib, ranibizumab, or a glucocorticoid. In one embodiment, the formulation is substantially pyrogen free.
  • the application also provides methods of treating an angiogenesis related disease of the eye comprising administering to said eye an ophthalmic pharmaceutical formulation comprising an ALKl-Fc fusion protein comprising: a polypeptide having an amino acid sequence that is at least 97% identical to the sequence of amino acids 22-118 of SEQ ID NO:1, which polypeptide is fused to an Fc portion of an immunoglobulin, and wherein the ALKl-Fc fusion protein binds to GDF5, GDF7, BMP9 and/or BMPlO with a K D of less than 1 x 10 '7 M and/or binds to TGF ⁇ -1 with a K D of greater than 1 x 10 "6 .
  • the fusion protein has the sequence of SEQ ID NO: 3.
  • the Fc portion is from human IgGl .
  • the fusion protein is produced by expression of the nucleic acid of SEQ ID NO:4 in a mammalian cell line.
  • the cell line is Chinese Hamster Ovary cell line.
  • the formulation may further comprise one or more of the following medicaments: pegaptanib, ranibizumab, or a glucocorticoid. In one embodiment, the formulation is substantially pyrogen free.
  • the application also provides methods of treating an angiogenesis related disease of the eye comprising administering to said eye an ophthalmic pharmaceutical formulation comprising an antibody that binds to an ALKl polypeptide consisting of amino acids 22-1 18 of SEQ ID NO:1 and inhibits the binding of at least one ALKl ligand selected from the group consisting of: GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the antibody inhibits angiogenesis stimulated by at least one ALKl ligand selected from the group consisting of: GDF5, GDF6 and GDF7.
  • the antibody binds to the ALKl polypeptide with a K D of less than 5 x 10 "8 M.
  • the antibody binds to the ALKl polypeptide with a K D of less than 1 x 10 '10 M.
  • the antibody inhibits angiogenesis stimulated by GDF5, GDF6, GDF7, BMP9, or BMPlO.
  • the formulation may further comprise one or more of the following medicaments: pegaptanib, ranibizumab, or a glucocorticoid. In one embodiment, the formulation is substantially pyrogen free.
  • the angiogenesis related disease is selected from the group consisting of a tumor, a tumor that is resistant to anti-VEGF therapy, a multiple myeloma tumor, a tumor that has metastasized to the bone, joint or bone inflammation, rheumatoid arthritis, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, and retrolental fibroplasias.
  • Figure 1 shows the amino acid sequence for the human Activin Like Kinase 1, ALKl (SEQ ID NO:1). Single underlining shows the predicted extracellular domain. Double underlining shows the intracellular domain. The signal peptide and the transmembrane domain are not underlined.
  • Figure 2 shows the nucleic acid sequence of a human ALKl cDNA (SEQ ID NO:2).
  • the coding sequence is underlined.
  • the portion encoding the extracellular domain is double underlined.
  • Figure 3 shows an example of a fusion of the extracellular domain of human ALKl to an Fc domain (SEQ ID NO:3).
  • the hALKl-Fc protein includes amino acids 22-120 of the human ALKl protein, fused at the C-terminus to a linker (underlined) and an IgGl Fc region.
  • Figure 4 shows the nucleic acid sequence for expression of the hALKl-Fc polypeptide of SEQ ID NO:3. The encoded amino acid sequence is also shown. The leader sequence is cleaved such that Asp 22 is the N-terminal amino acid of the secreted protein.
  • Figure 5 shows the anti-angiogenic effect of murine ALKl-Fc (“RAP”) and human ALKl-Fc (“ACE”) in an endothelial cell tube forming assay. All concentrations of RAP and ACE reduced the level of tube formation in response to Endothelial Cell Growth Supplement (ECGF) to a greater degree than the positive control, Endostatin.
  • RAP murine ALKl-Fc
  • ACE human ALKl-Fc
  • Figure 6 shows the angiogenic effect of GDF7 in a chick chorioallantoic membrane (CAM) assay.
  • the GDF7 effect is comparable to that of VEGF.
  • Figure 7 shows the anti-angiogenic effect of the human ALKl-Fc fusion in the CAM assay.
  • hALKl-Fc inhibits angiogenesis stimulated by VEGF, FGF and GDF7.
  • Figure 8 shows comparative anti-angiogenic effects of murine ALKl-Fc (mALKl-Fc), hALKl-Fc, a commercially available anti-ALKl monoclonal antibody (Anti-ALKl mAb) and a commercially available, neutralizing anti-VEGF monoclonal antibody.
  • the anti-angiogenic effect of the ALKl-Fc constructs is comparable to the effects of the anti-VEGF antibody.
  • Figure 9 shows the anti-angiogenic effects of hALKl-Fc and the anti-VEGF antibody in vivo.
  • hALKl-Fc and anti-VEGF had comparable effects on angiogenesis in the eye as measured by the mouse corneal micropocket assay.
  • Figure 10 shows the effects of mALKl-Fc in the murine collagen-induced arthritis (ClA) model of rheumatoid arthritis.
  • the graph shows mean group arthritic scores determined during the 42 day observation period in the collagen-induced male DBA/1 arthritic mice.
  • RAP-041 is mALKl-Fc.
  • AvastinTM is the anti-VEGF antibody bevacizumab.
  • Figure 1 1 shows resolution of hALKl-Fc (SEQ ID NO: 3) and an hALKl-Fc fusion protein from R&D Systems (Minneapolis, MN) by Superose 12 10/300 GL Size Exclusion column (Amersham Biosciences, Piscataway, NJ).
  • the R&D Systems material contains approximately 13% aggregated protein, as shown by the peaks on the left hand side of the graph, as well as some lower molecular weight species.
  • the material of SEQ ID NO:3 is greater than 99% composed of dimers of the appropriate molecular size.
  • Figure 13 shows the effect of recombinant human BMP9 (“rhB9”) and a commercially available anti-BMP9 monoclonal antibody (“mabB9”) on VEGF- mediated angiogenesis in the CAM assay.
  • rhB9 recombinant human BMP9
  • mabB9 commercially available anti-BMP9 monoclonal antibody
  • FIG. 14 shows the effects of mALKl-Fc on an orthotopic xenograft model using the MDA-MB-231 cell line, a cell line derived from ER- breast cancer cells. At a dose of 30 mg/kg, the mALKl-Fc has a significant growth-delaying effect on the xenograft tumor.
  • Figure 15 shows the effects of hALKl-Fc on an orthotopic xenograft model using the MCF7 cell line, a cell line derived from ER+ breast cancer cells.
  • the hALKl-Fc has a significant growth-delaying effect on the xenograft tumor.
  • Figure 16 shows the ability of hALKl-Fc to inhibit by more than 80% the transcriptional reporter activity induced by BMPlO in a cell-based assay.
  • Figure 17 shows the effects of a BMP9/10 antagonist or hALKl-Fc on
  • VEGF- or BMPlO-stimulated angiogenesis in a chick chorioallantoic membrane (CAM) assay Data are means ⁇ SEM; ***, p ⁇ 0.0001.
  • BMP9/10 antagonist reduced both VEGF-stimulated angiogenesis and BMPlO-stimulated angiogenesis by more than 50%, and effects of similar magnitude were obtained with hALKl-Fc.
  • Figure 18 shows a dose-dependent inhibition of BMPlO-stimulated angiogenesis by a BMP9/10 antagonist in a chick chorioallantoic membrane (CAM) assay. Data are means ⁇ SEM; **, p ⁇ 0.01.
  • Figure 19 shows an alignment of the mature portions of the human BMP9 (SEQ ID NO: 12) and BMPlO (SEQ ID NO: 13) proteins. Regions of identity are shown with asterisks.
  • ALKl is a type I cell-surface receptor for the TGF- ⁇ superfamily of ligands and is also known as ACVRLl and ACVRLKl .
  • ALKl has been implicated as a receptor for TGF- ⁇ l, TGF- ⁇ 3 and BMP-9 (Marchuk et al., Hum MoI Genet. 2003; Brown et al., J Biol Chem. 2005 JuI 1 ;280(26):251 1 1-8).
  • loss-of-function mutations in ALKl lead to a variety of abnormalities in the developing vasculature (Oh et al., Proc. Natl Acad. Sci. USA 2000, 97, 2626-2631 ; Urness et al., Nat. Genet. 2000, 26, 328-331).
  • HHT hereditary hemorrhagic telangiectasia
  • Typical symptoms of patients with HHT include recurrent epistaxis, gastrointestinal hemorrhage, cutaneous and mucocutaneous telangiectases, and arteriovenous malformations (AVM) in the pulmonary, cerebral, or hepatic vasculature.
  • ALM arteriovenous malformations
  • ALKl ECD polypeptides may be used to inhibit angiogenesis in vivo, including VEGF-independent angiogenesis and angiogenesis that is mediated by multiple angiogenic factors, including VEGF, FGF and PDGF.
  • ALKl ECD polypeptides may be used to inhibit angiogenesis in vivo, including VEGF-independent angiogenesis and angiogenesis that is mediated by multiple angiogenic factors, including VEGF, FGF and PDGF.
  • ALKl ECD polypeptides may be used to inhibit angiogenesis in vivo, including VEGF-independent angiogenesis and angiogenesis that is mediated by multiple angiogenic factors, including VEGF, FGF and PDGF.
  • ALKl ECD polypeptide can exert an anti-angiogenic effect even in the case where the ALKl ECD polypeptide does not exhibit meaningful binding to TGF- ⁇ l.
  • ALKl ECD polypeptides inhibit angiogenesis that is stimulated by many different pro-angiogenic factors, including VEGF, FGF, and GDF7.
  • the disclosure provides a description of an ALKl regulatory system, in which ALKl is a receptor for the GDF5 group of ligands, which includes GDF6 and GDF7, and also for the BMP9 group of ligands, which includes BMPlO, with different affinities for the two groups of ligands.
  • ALKl signaling pathway is effective against tumors or cancers including, for example, breast, lung, estrogen receptor positive (ER+), estrogen receptor negative (ER-), bone, tumor or cancer metastasized to bone, melanoma, multiple myeloma (see, for example WO2008/057461). Further, the disclosure demonstrates that signaling mediated by ALKl and the ligands described above is pro-angiogenic in vivo, and that inhibition of this regulatory system has a potent anti-angiogenic effect in vivo.
  • ER+ estrogen receptor positive
  • ER- estrogen receptor negative
  • the disclosure provides antagonists of the ALKl regulatory system, including antagonists of the receptor or one or more of the ligands, for use in inhibiting angiogenesis, including both VEGF-dependent angiogenesis and VEGF-independent angiogenesis.
  • antagonists of the ALKl regulatory system including antagonists of the receptor or one or more of the ligands, for use in inhibiting angiogenesis, including both VEGF-dependent angiogenesis and VEGF-independent angiogenesis.
  • antibodies directed to ALKl itself are expected to have different effects from an ALKl ECD polypeptide.
  • a pan- neutralizing antibody against ALKl (one that inhibits the binding of all strong and weak ligands) would be expected to inhibit the signaling of such ligands through ALKl but would not be expected to inhibit the ability of such ligands to signal through other receptors (e.g., BMPRIa, BMPRIb, BMPRlI in the case of GDF5-7 and BMP9-10 and TBRI and TBRII in the case of TGF ⁇ ).
  • an ALKl ECD polypeptide would be expected to inhibit all of the ligands that it binds to tightly, including, for a construct such as that shown in the Examples, GDF5-7 and BMP9-10, but would not affect ligands that it binds to weakly, such as TGF- ⁇ . So, while a pan-neutralizing antibody against ALKl would block BMP9 and TGF- ⁇ signaling through ALKl it would not block BMP9 and TGF- ⁇ signaling through another receptor, and while an ALKl ECD polypeptide may inhibit BMP9 signaling through all receptors (even receptors other than ALKl) it would not be expected to inhibit TGF- ⁇ signaling through any receptor, even ALKl .
  • Proteins described herein are the human forms, unless otherwise specified. Genbank references for the proteins are as follows: human GDF5, CAA56874; human GDF6, AAH43222; human GDF7, NP_878248; human BMP9, Q9UK05; human BMPlO, O95393; human DAN, BAA92265. ALKl sequences are set forth in Figures 1-5.
  • the conserved cysteine knot domain of Dan corresponds to amino acids 21-125 (underlined).
  • the coding sequence for DAN precursor corresponds to nucleic acids 93- 635.
  • the coding sequence for the mature DAN protein corresponds to nucleic acids 141-632.
  • the coding sequence for the conserved cysteine knot portion of DAN corresponds to nucleic acids 153-467.
  • Naturally occurring ALKl proteins are transmembrane proteins, with a portion of the protein positioned outside the cell (the extracelluar portion) and a portion of the protein positioned inside the cell (the intracellular portion). Aspects of the present disclosure encompass polypeptides comprising a portion of the extracellular domain of ALKl .
  • the disclosure provides "ALKl ECD polypeptides".
  • ALKl ECD polypeptide is intended to refer to a polypeptide consisting of or comprising an amino acid sequence of an extracellular domain of a naturally occurring ALKl polypeptide, either including or excluding any signal sequence and sequence N-terminal to the signal sequence, or an amino acid sequence that is at least 33 percent identical to an extracellular domain of a naturally occurring ALKl polypeptide, and optionally at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identical to the sequence of an extracellular domain of a naturally occurring ALKl polypeptide, as exemplified by the cysteine knot region of amino acids 34-95 of SEQ ID NO: 1 or the cysteine knot plus additional amino acids at the N- and C- termini of the extracellular domain, such as amino acids 22-118 of SEQ ID NO.
  • an ALKl ECD polypeptide may comprise a polypeptide that is encoded by nucleotides 100-285 of SEQ ID NO:2, or silent variants thereof or nucleic acids that hybridize to the complement thereof under stringent hybridization conditions (generally, such conditions are known in the art but may, for example, involve hybridization in 50% v/v formamide, 5x SSC, 2% w/v blocking agent, 0.1% N- lauroylsarcosine, 0.3% SDS at 65 C° overnight and washing in, for example, 5xSSC at about 65 C 0 ).
  • an ALKl ECD polypeptide may comprise a polypeptide that is encoded by nucleotides 64-384 of SEQ ID NO:2, or silent variants thereof or nucleic acids that hybridize to the complement thereof under stringent hybridization conditions (generally, such conditions are known in the art but may, for example, involve hybridization in 50% v/v formamide, 5x SSC, 2% w/v blocking agent, 0.1% N-lauroylsarcosine, 0.3% SDS at 65 C 0 overnight and washing in, for example, 5xSSC at about 65 C 0 ).
  • ALKl ECD polypeptide accordingly encompasses isolated extracellular portions of ALKl polypeptides, variants thereof (including variants that comprise, for example, no more than 2, 3, 4, 5 or 10 amino acid substitutions, additions or deletions in the sequence corresponding to amino acids 22-118 of SEQ ID NO:1 and including variants that comprise no more than 2, 3, 4, 5, or 10 amino acid substitutions, additions or deletions in the sequence corresponding to amino acids 34-95 of SEQ ID NO: 1), fragments thereof and fusion proteins comprising any of the preceding, but in each case preferably any of the foregoing ALKl ECD polypeptides will retain substantial affinity for one or more of GDF5, GDF6, GDF7, BMP9 or BMPlO.
  • ALKl ECD polypeptide is explicitly intended to exclude any full-length, naturally occurring ALKl polypeptide. Generally, an ALKl ECD polypeptide will be designed to be soluble in aqueous solutions at biologically relevant temperatures, pH levels and osmolarity.
  • the disclosure provides ALKl ECD polypeptides sharing a specified degree of sequence identity or similarity to a naturally occurring ALKl polypeptide.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • the amino acid residues at corresponding amino acid positions are then compared. When a position in the first sequence is occupied by the same amino acid residue as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid "identity" is equivalent to amino acid "homology").
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • the comparison of sequences and determination of percent identity and similarity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using the Needleman and Wunsch (J MoI. Biol. (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com).
  • the following parameters are used in the GAP program: either a Blosum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (Devereux, J., et al, Nucleic Acids Res.
  • Exemplary parameters include using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. Unless otherwise specified, percent identity between two amino acid sequences is to be determined using the GAP program using a Blosum 62 matrix, a GAP weight of 10 and a length weight of 3, and if such algorithm cannot compute the desired percent identity, a suitable alternative disclosed herein should be selected.
  • the percent identity between two amino acid sequences is determined using the algorithm of E. Myers and W. Miller (CABIOS, 4:11-17 (1989)) which has been incorporated into the ALIGN program (version 2.0), using a PAM 120 weight residue table, a gap length penalty of 12 and a gap penalty of4.
  • Another embodiment for determining the best overall alignment between two amino acid sequences can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. BioscL, 6:237-245 (1990)).
  • a sequence alignment the query and subject sequences are both amino acid sequences. The result of said global sequence alignment is presented in terms of percent identity.
  • amino acid sequence identity is performed using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci., 6:237-245 (1990)).
  • ALKl ECD polypeptides comprise an extracellular portion of a naturally occurring ALKl protein such as a sequence of SEQ ID NO:1, and preferably a ligand binding portion of the ALKl extracellular domain.
  • a soluble ALKl polypeptide comprises an amino acid sequence that is at least 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence of amino acids 22-118 of the SEQ ID NO:1.
  • a truncated extracellular ALKl polypeptide comprises at least 30, 40 or 50 consecutive amino acids of an amino acid sequence of an extracellular portion of SEQ ID NO: 1.
  • an ALKl ECD polypeptide binds to one or more of GDF5, GDF6, GDF7, BMP9 and BMPlO.
  • the ALKl polypeptide does not show substantial binding to TGF- ⁇ l or TGF- ⁇ 3. Binding may be assessed using purified proteins in solution or in a surface plasmon resonance system, such as a BiacoreTM system. Preferred soluble ALKl polypeptides will exhibit an anti- angiogenic activity.
  • Bioassays for angiogenesis inhibitory activity include the chick chorioallantoic membrane (CAM) assay, the mouse corneal micropocket assay, an assay for measuring the effect of administering isolated or synthesized proteins on implanted tumors.
  • the CAM assay is described by O'Reilly, et al. in "Angiogenic Regulation of Metastatic Growth” Cell, vol. 79 (2), Oct. 1, 1994, pp. 315-328. Briefly, 3 day old chicken embryos with intact yolks are separated from the egg and placed in a petri dish. After 3 days of incubation, a methylcellulose disc containing the protein to be tested is applied to the CAM of individual embryos. After 48 hours of incubation, the embryos and CAMs are observed to determine whether endothelial growth has been inhibited.
  • the mouse corneal micropocket assay involves implanting a growth factor-containing pellet, along with another pellet containing the suspected endothelial growth inhibitor, in the cornea of a mouse and observing the pattern of capillaries that are elaborated in the cornea. Other assays are described in the Examples.
  • ALKl ECD polypeptides may be produced by removing the cytoplasmic tail and the transmembrane region of an ALKl polypeptide.
  • the transmembrane domain may be inactivated by deletion, or by substitution of the normally hydrophobic amino acid residues which comprise a transmembrane domain with hydrophilic ones. In either case, a substantially hydrophilic hydropathy profile is created which will reduce lipid affinity and improve aqueous solubility. Deletion of the transmembrane domain is preferred over substitution with hydrophilic amino acid residues because it avoids introducing potentially immunogenic epitopes.
  • ALKl ECD polypeptides may additionally include any of various leader sequences at the N-terminus.
  • Such a sequence would allow the peptides to be expressed and targeted to the secretion pathway in a eukaryotic system. See, e.g., Ernst et al., U.S. Pat. No. 5,082,783 (1992).
  • a native ALKl signal sequence may be used to effect extrusion from the cell.
  • Possible leader sequences include native, tPa and honeybee mellitin leaders (SEQ ID Nos. 7-9, respectively).
  • Processing of signal peptides may vary depending on the leader sequence chosen, the cell type used and culture conditions, among other variables, and therefore actual N-terminal start sites for mature ALKl ECD polypeptides, including that of SEQ ID NO:5, may shift by 1-5 amino acids in either the N-terminal or C-terminal direction.
  • the present disclosure contemplates specific mutations of the ALKl polypeptides so as to alter the glycosylation of the polypeptide.
  • Such mutations may be selected so as to introduce or eliminate one or more glycosylation sites, such as O-linked or N-linked glycosylation sites.
  • Asparagine-linked glycosylation recognition sites generally comprise a tripeptide sequence, asparagine-X-threonine (or asparagines-X-serine) (where "X" is any amino acid) which is specifically recognized by appropriate cellular glycosylation enzymes.
  • the alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the wild-type ALKl polypeptide (for O-linked glycosylation sites).
  • a variety of amino acid substitutions or deletions at one or both of the first or third amino acid positions of a glycosylation recognition site (and/or amino acid deletion at the second position) results in non-glycosylation at the modified tripeptide sequence.
  • Another means of increasing the number of carbohydrate moieties on an ALKl polypeptide is by chemical or enzymatic coupling of glycosides to the ALKl polypeptide.
  • the sugar(s) may be attached to (a) arginine and histidine; (b) free carboxyl groups; (c) free sulfhydryl groups such as those of cysteine; (d) free hydroxyl groups such as those of serine, threonine, or hydroxyproline; (e) aromatic residues such as those of phenylalanine, tyrosine, or tryptophan; or (f) the amide group of glutamine.
  • Removal of one or more carbohydrate moieties present on an ALKl polypeptide may be accomplished chemically and/or enzymatically.
  • Chemical deglycosylation may involve, for example, exposure of the ALKl polypeptide to the compound trifluoromethanesulfonic acid, or an equivalent compound. This treatment results in the cleavage of most or all sugars except the linking sugar (N-acetylglucosamine or N-acetylgalactosamine), while leaving the amino acid sequence intact.
  • Chemical deglycosylation is further described by Hakimuddin et al. (1987) Arch. Biochem. Biophys. 259:52 and by Edge et al. (1981) Anal. Biochem. 118: 131.
  • Enzymatic cleavage of carbohydrate moieties on ALKl polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al. (1987) Meth. Enzymol. 138:350.
  • the sequence of an ALKl polypeptide may be adjusted, as appropriate, depending on the type of expression system used, as mammalian, yeast, insect and plant cells may all introduce differing glycosylation patterns that can be affected by the amino acid sequence of the peptide.
  • ALKl proteins for use in humans will be expressed in a mammalian cell line that provides proper glycosylation, such as HEK293 or CHO cell lines, although other mammalian expression cell lines, yeast cell lines with engineered glycosylation enzymes and insect cells are expected to be useful as well.
  • This disclosure further contemplates a method of generating mutants, particularly sets of combinatorial mutants of an ALKl polypeptide, as well as truncation mutants; pools of combinatorial mutants are especially useful for identifying functional variant sequences.
  • the purpose of screening such combinatorial libraries may be to generate, for example, ALKl polypeptide variants which can act as either agonists or antagonist, or alternatively, which possess novel activities all together.
  • a variety of screening assays are provided below, and such assays may be used to evaluate variants.
  • an ALKl polypeptide variant may be screened for ability to bind to an ALKl ligand, to prevent binding of an ALKl ligand to an ALKl polypeptide or to interfere with signaling caused by an ALKl ligand.
  • the activity of an ALKl polypeptide or its variants may also be tested in a cell-based or in vivo assay, particularly any of the assays disclosed in the Examples.
  • Combinatorially-derived variants can be generated which have a selective or generally increased potency relative to an ALKl ECD polypeptide comprising an extracellular domain of a naturally occurring ALKl polypeptide.
  • mutagenesis can give rise to variants which have serum half-lives dramatically different than the corresponding a wild-type ALKl ECD polypeptide.
  • the altered protein can be rendered either more stable or less stable to proteolytic degradation or other processes which result in destruction of, or otherwise elimination or inactivation of a native ALKl ECD polypeptide.
  • Such variants, and the genes which encode them can be utilized to alter ALKl ECD polypeptide levels by modulating the half-life of the ALKl polypeptides.
  • a short half-life can give rise to more transient biological effects and can allow tighter control of recombinant ALKl ECD polypeptide levels within the patient.
  • mutations may be made in the linker (if any) and/or the Fc portion to alter the half-life of the protein.
  • a combinatorial library may be produced by way of a degenerate library of genes encoding a library of polypeptides which each include at least a portion of potential ALKl polypeptide sequences.
  • a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential ALKl polypeptide nucleotide sequences are expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display).
  • the library of potential ALKl ECD variants 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 vector for expression.
  • the synthesis of degenerate oligonucleotides is well known in the art (see for example, Narang, SA (1983) Tetrahedron 39:3; Itakura et al., (1981) Recombinant DNA, Proc. 3rd Cleveland Sympos. Macromolecules, ed. AG Walton, Amsterdam: Elsevier pp273-289; Itakura et al., (1984) Annu.
  • ALKl 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 ALKl 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.
  • Preferred assays include ALKl ligand binding assays and ligand-mediated cell signaling assays.
  • the ALKl ECD polypeptides of the disclosure may further comprise post-translational modifications in addition to any that are naturally present in the ALKl polypeptides.
  • modifications include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
  • the modified ALKl ECD 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 an ALKl ECD polypeptide may be tested as described herein for other ALKl ECD polypeptide variants.
  • an ALKl ECD polypeptide When an ALKl ECD polypeptide is produced in cells by cleaving a nascent form of the ALKl polypeptide, post-translational processing may also be important for correct folding and/or function of the protein.
  • Different cells such as CHO, HeLa, MDCK, 293, WI38, NIH-3T3 or HEK293 have specific cellular machinery and characteristic mechanisms for such post-translational activities and may be chosen to ensure the correct modification and processing of the ALKl polypeptides.
  • functional variants or modified forms of the ALKl ECD polypeptides include fusion proteins having at least a portion of the ALKl ECD polypeptides 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, an immunoglobulin heavy chain constant region (Fc), maltose binding protein (MBP), or human serum albumin.
  • GST glutathione S transferase
  • Fc immunoglobulin heavy chain constant region
  • MBP maltose binding protein
  • human serum albumin human serum albumin.
  • a fusion domain may be selected so as to confer a desired property. For example, some fusion domains are particularly useful for isolation of the fusion proteins by affinity chromatography.
  • matrices for affinity chromatography such as glutathione-, amylase-, and nickel- or cobalt- conjugated resins are used.
  • Many of such matrices are available in "kit” form, such as the Pharmacia GST purification system and the QIAexpressTM system (Qiagen) useful with (HIS 6 ) fusion partners.
  • a fusion domain may be selected so as to facilitate detection of the ALKl ECD polypeptides. Examples of such detection domains include the various fluorescent proteins (e.g., GFP) as well as "epitope tags," which are usually short peptide sequences for which a specific antibody is available.
  • 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.
  • an ALKl ECD polypeptide is fused with a domain that stabilizes the ALKl polypeptide in vivo (a "stabilizer" domain).
  • stabilizing is meant anything that increases serum half life, regardless of whether this is because of decreased destruction, decreased clearance by the kidney, or other pharmacokinetic effect. Fusions with the Fc portion of an immunoglobulin are known to confer desirable pharmacokinetic properties on a wide range of proteins. Likewise, fusions to human serum albumin can confer desirable properties. Other types of fusion domains that may be selected include multimerizing (e.g., dimerizing, tetramerizing) domains and functional domains.
  • the present disclosure provides a fusion protein comprising a soluble extracellular domain of ALKl fused to an Fc domain (e.g., SEQ ID NO: 6).
  • THTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCWVp A) VSHEDPEVKF NWYVDGVEVHNAKTKPREEQYNSTYRWSVLTVLHQDWLNGKEYKCK (A) VSNKAL PVPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESN GQPENNYKTTPPVLDSDGPFFLYSKLTVDKSRWQQGNVFSCSVMHEALHN (A) HYT QKSLSLSPGK*
  • the Fc domain has one or more mutations at residues such as Asp-265, lysine 322, and Asn-434.
  • the mutant Fc domain having one or more of these mutations e.g., Asp-265 mutation
  • the mutant Fc domain having one or more of these mutations has increased ability of binding to the MHC class I-related Fc-receptor (FcRN) relative to a wildtype Fc domain.
  • an ALKl ECD polypeptide may be placed C-terminal to a heterologous domain, or, alternatively, a heterologous domain may be placed C-terminal to an ALKl ECD polypeptide.
  • the ALKl ECD polypeptide domain and the heterologous domain need not be adjacent in a fusion protein, and additional domains or amino acid sequences may be included C- or N-terminal to either domain or between the domains.
  • an immunoglobulin Fc region or simply “Fc” is understood to mean the carboxyl-terminal portion of an immunoglobulin chain constant region, preferably an immunoglobulin heavy chain constant region, or a portion thereof.
  • an immunoglobulin Fc region may comprise 1) a CHl domain, a CH2 domain, and a CH3 domain, 2) a CHl domain and a CH2 domain, 3) a CHl domain and a CH3 domain, 4) a CH2 domain and a CH3 domain, or 5) a combination of two or more domains and an immunoglobulin hinge region.
  • the immunoglobulin Fc region comprises at least an immunoglobulin hinge region a CH2 domain and a CH3 domain, and preferably lacks the CHl domain.
  • the class of immunoglobulin from which the heavy chain constant region is derived is IgG (Ig ⁇ ) ( ⁇ subclasses 1, 2, 3, or 4).
  • Other classes of immunoglobulin, IgA (Ig ⁇ ), IgD (Ig ⁇ ), IgE (Ig ⁇ ) and IgM (Ig ⁇ ) may be used.
  • IgG immunoglobulin
  • IgA Ig ⁇
  • IgD IgD
  • IgE Ig ⁇
  • IgM IgM
  • the portion of the DNA construct encoding the immunoglobulin Fc region preferably comprises at least a portion of a hinge domain, and preferably at least a portion of a CH 3 domain of Fc gamma or the homologous domains in any of IgA, IgD, IgE, or IgM.
  • substitution or deletion of amino acids within the immunoglobulin heavy chain constant regions may be useful in the practice of the methods and compositions disclosed herein.
  • One example would be to introduce amino acid substitutions in the upper CH2 region to create an Fc variant with reduced affinity for Fc receptors (Cole et al. (1997) J. Immunol. 159:3613).
  • the present disclosure makes available isolated and/or purified forms of the ALKl ECD polypeptides, which are isolated from, or otherwise substantially free of (e.g., at least 80%, 90%, 95%, 96%, 97%, 98%, or 99% free of), other proteins and/or other ALKl ECD polypeptide species.
  • ALKl polypeptides will generally be produced by expression from recombinant nucleic acids.
  • the disclosure includes nucleic acids encoding soluble ALKl polypeptides comprising the coding sequence for an extracellular portion of an ALKl proteins. In further embodiments, this disclosure also pertains to a host cell comprising such nucleic acids.
  • the host cell may be any prokaryotic or eukaryotic cell.
  • a polypeptide of the present disclosure may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells.
  • Other suitable host cells are known to those skilled in the art. Accordingly, some embodiments of the present disclosure further pertain to methods of producing the ALKl ECD polypeptides. It has been established that an ALKl -Fc fusion protein set forth in SEQ ID NO:3 and expressed in CHO cells has potent anti-angiogenic activity.
  • DAN polypeptides including variants of wild type DAN, and fusion proteins containing DAN proteins may be generated and characterized as described above with respect to ALKl ECD proteins.
  • the disclosure provides isolated and/or recombinant nucleic acids encoding any of the ALKl polypeptides (e.g., ALKl ECD polypeptides), including fragments, functional variants and fusion proteins disclosed herein.
  • ALKl polypeptides e.g., ALKl ECD polypeptides
  • SEQ ID NO: 2 encodes the naturally occurring human ALKl precursor polypeptide
  • SEQ ID NO: 4 encodes the precursor of an ALKl extracellular domain fused to an IgGl Fc domain.
  • the subject nucleic acids may be single-stranded or double stranded.
  • Such nucleic acids may be DNA or RNA molecules. These nucleic acids may be used, for example, in methods for making ALKl polypeptides or as direct therapeutic agents (e.g., in an antisense, RNAi or gene therapy approach).
  • the subject nucleic acids encoding ALKl polypeptides are further understood to include nucleic acids that are variants of SEQ ID NO: 2 or 4.
  • Variant nucleotide sequences include sequences that differ by one or more nucleotide substitutions, additions or deletions, such as allelic variants.
  • the disclosure provides isolated or recombinant nucleic acid sequences that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO: 2 or 4.
  • nucleic acid sequences complementary to SEQ ID NO: 2 or 4, and variants of SEQ ID NO: 2 or 4 are also within the scope of this disclosure.
  • the nucleic acid sequences of the disclosure can be isolated, recombinant, and/or fused with a heterologous nucleotide sequence, or in a DNA library.
  • nucleic acids of the disclosure also include nucleotide sequences that hybridize under highly stringent conditions to the nucleotide sequence designated in SEQ ID NO: 2 or 4, complement sequence of SEQ ID NO: 2 or 4, or fragments 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 0 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 0 C, to high stringency conditions at about 65 0 C. Both temperature and salt may be varied, or temperature or salt concentration may be held constant while the other variable is changed.
  • the disclosure 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 nucleic acids as set forth in SEQ ID NOs: 2 or 4 due to degeneracy in the genetic code are also within the scope of the disclosure.
  • 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.
  • CAU and CAC are synonyms for histidine
  • 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 disclosure.
  • the recombinant nucleic acids of the disclosure may be operably linked to one or more regulatory nucleotide sequences in an expression construct.
  • Regulatory nucleotide sequences will generally be appropriate to the host cell used for expression.
  • 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 disclosure.
  • 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 an ALKl polypeptide and operably linked to at least one regulatory sequence.
  • Regulatory sequences are art-recognized and are selected to direct expression of the ALKl 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 an ALKl polypeptide.
  • Such useful expression control sequences include, for example, the early and late promoters of SV40, tet promoter, adenovirus or cytomegalovirus immediate early promoter, RSV promoters, 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. It should be understood that the design of the expression vector may depend on such factors as the choice of the host cell to be transformed and/or the type of protein desired to
  • 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.
  • a recombinant nucleic acid included in the disclosure 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 ALKl 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.
  • Some 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 in 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.
  • a vector will be designed for production of the subject ALKl polypeptides in CHO cells, such as a Pcmv-Script vector (Stratagene, La Jolla, Calif.), pcDNA4 vectors (Invitrogen, Carlsbad, Calif.) and pCI-neo vectors (Promega, Madison, Wise).
  • a vector will be designed for production of the subject ALKl polypeptides in CHO cells, such as a Pcmv-Script vector (Stratagene, La Jolla, Calif.), pcDNA4 vectors (Invitrogen, Carlsbad, Calif.) and pCI-neo vectors (Promega, Madison, Wise).
  • the subject gene constructs can be used to cause expression of the subject ALKl polypeptides in cells propagated in culture, e.g., to produce proteins, including fusion proteins or variant proteins, for purification.
  • This disclosure also pertains to a host cell transfected with a recombinant gene including a coding sequence (e.g., SEQ ID NO: 2 or 4) for one or more of the subject ALKl polypeptides.
  • the host cell may be any prokaryotic or eukaryotic cell.
  • an ALKl polypeptide disclosed herein may be expressed in bacterial cells such as E. coli, insect cells (e.g., using a baculovirus expression system), yeast, or mammalian cells. Other suitable host cells are known to those skilled in the art. Accordingly, the present disclosure further pertains to methods of producing the subject ALKl polypeptides, including ALKl ECD polypeptides.
  • a host cell transfected with an expression vector encoding an ALKl polypeptide can be cultured under appropriate conditions to allow expression of the ALKl polypeptide to occur.
  • the ALKl polypeptide may be secreted and isolated from a mixture of cells and medium containing the ALKl polypeptide.
  • the ALKl polypeptide 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 subject ALKl 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, immunoaffinity purification with antibodies specific for particular epitopes of the ALKl polypeptides and affinity purification with an agent that binds to a domain fused to the ALKl polypeptide (e.g., a protein A column may be used to purify an ALKl-Fc fusion).
  • the ALKl polypeptide is a fusion protein containing a domain which facilitates its purification.
  • purification is achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography.
  • the purification could be completed with viral filtration and buffer exchange.
  • a fusion gene coding for a purification leader sequence such as a poly-(His)/enterokinase cleavage site sequence at the N- terminus of the desired portion of the recombinant ALKl polypeptide, can allow purification of the expressed fusion protein by affinity chromatography using a Ni 2+ metal resin.
  • the purification leader sequence can then be subsequently removed by treatment with enterokinase to provide the purified ALKl polypeptide (e.g., see Hochuli et al., (1987) J. Chromatography 411 :177; and Janknecht et al., PNAS USA 88:8972).
  • 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).
  • 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, 35, 30, 25, 22, 20 or 18 nucleotides of the full-length ALKl nucleic acid sequence or ligand nucleic acid sequence.
  • the region of complementarity will preferably be at least 8 nucleotides, and optionally at least 10 or at least 15 nucleotides, and optionally between 15 and 25 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, for example, angiogenesis.
  • Nucleic acids encoding DAN polypeptides including variants of wild type DAN, and those encoding fusion proteins containing DAN proteins may be generated and characterized as described above with respect to nucleic acids encoding ALKl ECD proteins.
  • Another aspect of the disclosure pertains to an antibody reactive with an extracellular portion of an ALKl polypeptide, preferably antibodies that are specifically reactive with ALKl polypeptide.
  • such antibody may interfere with ALKl binding to a ligand such as GDF5, GDF6, GDF7 BMP-9 or BMP-IO - it will be understood that an antibody against a ligand of ALKl should bind to the mature, processed form of the relevant protein.
  • the disclosure also provides antibodies that bind to GDF5, GDF6, GDF7, BMP9 and/or BMPlO and inhibit ALKl binding to such ligands.
  • Preferred antibodies will exhibit an anti-angiogenic activity in a bioassay, such as a CAM assay or corneal micropocket assay (see above).
  • a preferred anti-BMP9 antibody is described in Example 10, below.
  • an antibody that inhibits both BMP9 and BMPlO may be desirable; such an antibody may inhibit both ligands in an ALK- 1 binding assay, in an angiogenesis assay (e.g. HUVEC tube forming assay, CAM assay, Matrigel assay, or other such assays described herein).
  • antibody as used herein is intended to include whole antibodies, e.g., of any isotype (IgG, IgA, IgM, IgE, etc), and includes fragments or domains of immunoglobulins which are reactive with a selected antigen.
  • Antibodies can be fragmented using conventional techniques and the fragments screened for utility and/or interaction with a specific epitope of interest.
  • the term includes segments of proteolytically-cleaved or recombinantly-prepared portions of an antibody molecule that are capable of selectively reacting with a certain protein.
  • Non-limiting examples of such proteolytic and/or recombinant fragments include Fab, F(ab')2, Fab' , Fv, and single chain antibodies (scFv) containing a V[L] and/or V[H] domain joined by a peptide linker.
  • the scFv's may be covalently or non- covalently linked to form antibodies having two or more binding sites.
  • the term antibody also includes polyclonal, monoclonal, or other purified preparations of antibodies and recombinant antibodies.
  • the term "recombinant antibody” means an antibody, or antigen binding domain of an immunoglobulin, expressed from a nucleic acid that has been constructed using the techniques of molecular biology, such as a humanized antibody or a fully human antibody developed from a single chain antibody. Single domain and single chain antibodies are also included within the term "recombinant antibody”.
  • Antibodies may be generated by any of the various methods known in the art, including administration of antigen to an animal, administration of antigen to an animal that carries human immunoglobulin genes, or screening with an antigen against a library of antibodies (often single chain antibodies or antibody domains). Once antigen binding activity is detected, the relevant portions of the protein may be grafted into other antibody frameworks, including full-length IgG frameworks. For example, by using immunogens derived from an ALKl polypeptide or an ALKl ligand (e.g., BMP9 or BMPlO, or an immunogen common to both BMP9 and
  • BMPlO anti-protein/anti-peptide antisera or monoclonal antibodies
  • BMP9 and BMPlO have considerable amino acid identity, and therefore, each protein may be used as an immunogen to generate antibodies that can cross-react with both BMP9 and BMPlO. Fragments of highly similar sequence may also be used as immunogens.
  • a mammal such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide (e.g., a ALKl 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 ALKl polypeptide or an antigenic fragment which is capable of eliciting an antibody response, or a fusion protein.
  • Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art.
  • An immunogenic portion preferably an extracellular portion
  • an ALKl polypeptide or an ALKl ligand such as BMP9 or BMPlO
  • 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.
  • anti-ALKl or anti-ligand antisera can be obtained and, if desired, polyclonal antibodies can be isolated from the serum.
  • antibody-producing cells lymphocytes
  • immortalizing cells such as myeloma cells to yield hybridoma cells.
  • Such techniques are well known in the art, and include, for example, the hybridoma technique (originally developed by Kohler and Milstein, (1975) Nature, 256: 495-497), the human B cell hybridoma technique (Kozbar et al., (1983) Immunology Today, 4: 72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., (1985) Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. pp. 77-96).
  • Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with a mammalian ALKl polypeptide of the present disclosure or ligands such as BMP9 or BMPlO and monoclonal antibodies isolated from a culture comprising such hybridoma cells.
  • Antibodies with specificity for both BMP9 and BMPlO may be selected from hybridomas that are obtained from animals inoculated with either BMP9 or BMPlO alone.
  • antibody as used herein is intended to include fragments thereof which are also specifically reactive with one of the subject ALKl polypeptides or ALKl ligand polypeptides or a combination of target antigens (e.g., BMP9 and BMPlO).
  • 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 disclosure is further intended to include bispecific, single-chain, and chimeric and humanized molecules having affinity for an ALKl polypeptide conferred by at least one CDR region of the antibody.
  • the antibody further comprises a label attached thereto and is able to be detected, (e.g., the label can be a radioisotope, fluorescent compound, enzyme or enzyme co-factor).
  • an antibody of the disclosure is a recombinant antibody, particularly a humanized monoclonal antibody or a fully human recombinant antibody.
  • the adjective "specifically reactive with” as used in reference to an antibody is intended to mean, as is generally understood in the art, that the antibody is sufficiently selective between the antigen of interest (e.g. an ALKl polypeptide or an ALKl ligand) and other antigens that are not of interest that the antibody is useful for, at minimum, detecting the presence of the antigen of interest in a particular type of biological sample.
  • the antibody is sufficiently selective between the antigen of interest (e.g. an ALKl polypeptide or an ALKl ligand) and other antigens that are not of interest that the antibody is useful for, at minimum, detecting the presence of the antigen of interest in a particular type of biological sample.
  • a higher degree of specificity in binding may be desirable.
  • an antibody for use in detecting a low abundance protein of interest in the presence of one or more very high abundance protein that are not of interest may perform better if it has a higher degree of selectivity between the antigen of interest and other cross-reactants.
  • Monoclonal antibodies generally have a greater tendency (as compared to polyclonal antibodies) to discriminate effectively between the desired antigens and cross- reacting polypeptides.
  • an antibody that is effective at selectively identifying an antigen of interest in one type of biological sample may not be as effective for selectively identifying the same antigen in a different type of biological sample (e.g. a blood sample).
  • an antibody that is effective at identifying an antigen of interest in a purified protein preparation that is devoid of other biological contaminants may not be as effective at identifying an antigen of interest in a crude biological sample, such as a blood or urine sample.
  • the application provides antibodies that have demonstrated specificity for an antigen of interest in a sample type that is likely to be the sample type of choice for use of the antibody.
  • One characteristic that influences the specificity of an antibody:antigen interaction is the affinity of the antibody for the antigen.
  • affinity a dissociation constant
  • the GDF5,6,7 group of ligands bind with a KD of approximately 5xlO '8 M and the BMP9,10 ligands bind with a K D of approximately IxIO "10 M.
  • antibodies of appropriate affinity may be selected to interfere with the signaling activities of these ligands.
  • 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.
  • ELISAs ELISAs
  • surface plasmon resonance binding assays e.g.
  • an antibody disclosed herein is an antibody that binds to the mature portion of human BMP9, the amino acid sequence of which is shown below:
  • HLKFPTKVGK ACCVPTKLSP ISVLYKDDMG VPTLKYHYEG MSVAECGCR (SEQ ID NO: 12)
  • an antibody disclosed herein is an antibody that binds to the mature portion of human BMPlO, the amino acid sequence of which is shown below:
  • non-antibody proteins that bind to BMP9 or BMPlO may be generated by selection from libraries.
  • a wide variety of technologies are available for selecting random peptides, as well as framework based proteins, that bind to a particular ligand.
  • an approach to identifying a useful non-antibody protein will involve screening or selecting from a library those proteins that bind to BMP9 and/or BMPlO or inhibit a BMP9 or BMPlO activity, such as receptor (e.g., ALKl) binding or cellular signaling (e.g, SMAD 1/5 signaling).
  • receptor e.g., ALKl
  • cellular signaling e.g, SMAD 1/5 signaling
  • DAN-Fc fusion proteins with engineered or variant Fc regions Such antibodies and Fc fusion proteins may be useful, for example, in modulating effector functions, such as, antigen-dependent cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Additionally, the modifications may improve the stability of the antibodies and Fc fusion proteins.
  • Amino acid sequence variants of the antibodies and Fc fusion proteins are prepared by introducing appropriate nucleotide changes into the DNA, or by peptide synthesis. Such variants include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the antibodies and Fc fusion proteins disclosed herein.
  • amino acid changes also may alter post-translational processes of the antibodies and Fc fusion proteins, such as changing the number or position of glycosylation sites.
  • Antibodies and Fc fusion proteins with reduced effector function may be produced by introducing changes in the amino acid sequence, including, but are not limited to, the Ala-Ala mutation described by Bluestone et al. (see WO 94/28027 and WO 98/47531; also see Xu et al. 2000 Cell Immunol 200; 16-26).
  • antibodies and Fc fusion proteins of the disclosure with mutations within the constant region including the Ala-Ala mutation may be used to reduce or abolish effector function.
  • antibodies and Fc fusion proteins may comprise a mutation to an alanine at position 234 or a mutation to an alanine at position 235, or a combination thereof.
  • the antibody or Fc fusion protein comprises an IgG4 framework, wherein the Ala-Ala mutation would describe a mutation(s) from phenylalanine to alanine at position 234 and/or a mutation from leucine to alanine at position 235.
  • the antibody or Fc fusion protein comprises an IgGl framework, wherein the Ala-Ala mutation would describe a mutation(s) from leucine to alanine at position 234 and/or a mutation from leucine to alanine at position 235.
  • the antibody or Fc fusion protein may alternatively or additionally carry other mutations, including the point mutation K322A in the CH2 domain (Hezareh et al. 2001 J Virol. 75: 12161-8).
  • the antibody or Fc fusion protein may be modified to either enhance or inhibit complement dependent cytotoxicity (CDC).
  • Modulated CDC activity may be achieved by introducing one or more amino acid substitutions, insertions, or deletions in an Fc region (see, e.g., U.S. Pat. No. 6, 194,551).
  • cysteine residue(s) may be introduced in the Fc region, thereby allowing interchain disulfide bond formation in this region.
  • the homodimeric antibody thus generated may have improved or reduced internalization capability and/or increased or decreased complement-mediated cell killing. See Caron et al., J. Exp Med. 176: 1 191-1 195 (1992) and Shopes, B. J.
  • the disclosure provides methods of inhibiting angiogenesis in a mammal by administering to a subject an effective amount of a an ALKl ECD polypeptide, such as an ALKl -Fc fusion protein, a DAN protein, such as a DAN-Fc fusion protein, or an antibody disclosed herein, such as an antibody against GDF5, GDF6, GDF7, BMP9, BMPlO, or the ECD of ALKl, or nucleic acid antagonists (e.g., antisense or siRNA) of any of the foregoing hereafter collectively referred to as "therapeutic agents".
  • the data presented indicate specifically that the anti-angiogenic therapeutic agents disclosed herein may be used to inhibit angiogenesis in the eye of a mammal. It is expected that these therapeutic agents will also be useful in inhibiting angiogenesis in bones and joints, and in tumors, particularly tumors associated with bones and joints.
  • 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; rheumatoid arthritis; psoriasis; rubeosis; Osier- Webber Syndrome; myocardial angiogenesis; plaque neovascularization; telangiectasia; hemophiliac joints; and angiofibroma.
  • 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; rheumatoid arthritis; psoriasis; rubeosis;
  • polypeptide therapeutic agents of the present disclosure are useful for treating or preventing a cancer (tumor), and particularly such cancers as are known to rely on angiogenic processes to support growth.
  • a cancer tumor
  • ALKl ECD polypeptides affect angiogenesis that is stimulated by multiple factors. This is highly relevant in cancers, where a cancer will frequently acquire multiple factors that support tumor angiogenesis.
  • the therapeutic agents disclosed herein will be particularly effective in treating tumors that are resistant to treatment with a drug that targets a single angiogenic factor (e.g., bevacizumab, which targets VEGF).
  • an ALKl-Fc fusion protein is effective in reducing the pathological effects of melanoma, lung cancer and multiple myeloma. Multiple myeloma is widely recognized as a cancer that includes a significant angiogenic component. Accordingly, it is expected that ALKl-Fc fusion proteins and other therapeutic agents disclosed herein will be useful in treating multiple myeloma and other tumors associated with the bone. As demonstrated herein, therapeutic agents disclosed herein may be used to ameliorate the bone damage associated with multiple myeloma, and therefore may be used to ameliorate bone damage associated with bone metastases of other tumors, such as breast or prostate tumors. As noted herein, the GDF5-7 ligands are highly expressed in bone, and, while not wishing to be limited to any particular mechanism, interference with these ligands may disrupt processes that are required for tumor development in bone.
  • polypeptide therapeutic agents can be administered, together (simultaneously) or at different times (sequentially).
  • polypeptide therapeutic agents can be administered with another type of compounds for treating cancer or for inhibiting angiogenesis.
  • the subject methods of the disclosure 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.
  • conventional cancer therapies e.g., chemotherapy, radiation therapy, phototherapy, immunotherapy, and surgery
  • a wide array of conventional compounds have been shown to have antineoplastic activities.
  • a polypeptide therapeutic agent disclosed herein When a polypeptide therapeutic agent disclosed herein is administered in combination with another conventional anti-neoplastic agent, either concomitantly or sequentially, such therapeutic agent may 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.
  • the antiangiogenic agents described herein may be used in combination with other compositions and procedures for the treatment of diseases.
  • a tumor may be treated conventionally with surgery, radiation or chemotherapy combined with the ALKl or ALKl ligand antagonist and then the antagonist may be subsequently administered to the patient to extend the dormancy of micrometastases and to stabilize any residual primary tumor.
  • Angiogenesis-inhibiting agents can also be given prophylactically to individuals known to be at high risk for developing new or re-current cancers. Accordingly, an aspect of the disclosure encompasses methods for prophylactic prevention of cancer in a subject, comprising administrating to the subject an effective amount of an ALKl or ALKl ligand antagonist and/or a derivative thereof, or another angiogenesis-inhibiting agent of the present disclosure. As demonstrated herein, ALKl-Fc is effective for diminishing the phenotype of a murine model of rheumatoid arthritis. Accordingly, therapeutic agents disclosed herein may be used for the treatment of rheumatoid arthritis and other type of bone or joint inflammation.
  • angiogenesis inhibiting proteins of the present disclosure are useful in the treatment of disease of excessive or abnormal stimulation of endothelial cells. These diseases include, but are not limited to, intestinal adhesions, atherosclerosis, scleroderma, and hypertrophic scars, i.e., keloids. They are also useful in the treatment of diseases that have angiogenesis as a pathologic consequence such as cat scratch disease (Rochele minalia quintosa) and ulcers (Helicobacter pylori).
  • General angiogenesis inhibiting proteins can be used as a birth control agent by reducing or preventing uterine vascularization required for embryo implantation.
  • the present disclosure provides an effective birth control method when an amount of the inhibitory protein sufficient to prevent embryo implantation is administered to a female.
  • an amount of the inhibiting protein sufficient to block embryo implantation is administered before or after intercourse and fertilization have occurred, thus providing an effective method of birth control, possibly a "morning after" method. While not wanting to be bound by this statement, it is believed that inhibition of vascularization of the uterine endometrium interferes with implantation of the blastocyst.
  • Administration methods may include, but are not limited to, pills, injections (intravenous, subcutaneous, intramuscular), suppositories, vaginal sponges, vaginal tampons, and intrauterine devices. It is also believed that administration of angiogenesis inhibiting agents of the present disclosure will interfere with normal enhanced vascularization of the placenta, and also with the development of vessels within a successfully implanted blastocyst and developing embryo and fetus.
  • angiogenesis is associated with, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, and retrolental fibroplasias.
  • the therapeutic agents disclosed herein may be administered intra-ocularly or by other local administration to the eye.
  • ALKl-Fc may be administered systemically and yet have the desired effect on ocular angiogenesis.
  • diseases associated with angiogenesis in the eye include, but are not limited to, epidemic keratoconjunctivitis, Vitamin A deficiency, contact lens overwear, atopic keratitis, superior limbic keratitis, pterygium keratitis sicca, sjogrens, acne rosacea, phylectenulosis, syphilis, Mycobacteria infections, lipid degeneration, chemical burns, bacterial ulcers, fungal ulcers, Herpes simplex infections, Herpes zoster infections, protozoan infections, Kaposi sarcoma, Mooren ulcer, Terrien's marginal degeneration, mariginal keratolysis, rheumatoid arthritis, systemic lupus, polyarteritis, trauma, Wegeners sarcoidosis, Scleritis, Steven's Johnson disease, periphigoid radial keratotomy, and corneal graft rejection, sickle cell anemia,
  • Conditions of the eye can be treated or prevented by, e.g., systemic, topical, intraocular injection of a therapeutic agent, or by insertion of a sustained release device that releases a therapeutic agent.
  • a therapeutic agent may be delivered in a pharmaceutically acceptable ophthalmic vehicle, such that the compound is maintained in contact with the ocular surface for a sufficient time period to allow the compound to penetrate the corneal and internal regions of the eye, as for example the anterior chamber, posterior chamber, vitreous body, aqueous humor, vitreous humor, cornea, iris/ciliary, lens, choroid/retina and sclera.
  • the pharmaceutically- acceptable ophthalmic vehicle may, for example, be an ointment, vegetable oil or an encapsulating material.
  • the therapeutic agents of the disclosure may be injected directly into the vitreous and aqueous humour.
  • the compounds may be administered systemically, such as by intravenous infusion or injection, for treatment of the eye.
  • One or more therapeutic agents can be administered.
  • the methods of the disclosure also include co-administration with other medicaments that are used to treat conditions of the eye.
  • administration can occur simultaneously or sequentially in time.
  • the therapeutic agents and/or medicaments may be administered by different routes of administration or by the same route of administration.
  • a therapeutic agent and a medicament are administered together in an ophthalmic pharmaceutical formulation.
  • a therapeutic agent is used to treat a disease associated with angiogenesis in the eye by concurrent administration with other medicaments that act to block angiogenesis by pharmacological mechanisms.
  • Medicaments that can be concurrently administered with a therapeutic agent of the disclosure include, but are not limited to, pegaptanib (MacugenTM), ranibizumab (LucentisTM), squalamine lactate (EvizonTM), heparinase, and glucocorticoids (e.g.
  • a method is provided to treat a disease associated with angiogenesis is treated by administering an ophthalmic pharmaceutical formulation containing at least one therapeutic agent disclosed herein and at least one of the following medicaments: pegaptanib (MacugenTM), ranibizumab (LucentisTM), squalamine lactate (EvizonTM), heparinase, and glucocorticoids (e.g. Triamcinolone).
  • an ophthalmic pharmaceutical formulation containing at least one therapeutic agent disclosed herein and at least one of the following medicaments: pegaptanib (MacugenTM), ranibizumab (LucentisTM), squalamine lactate (EvizonTM), heparinase, and glucocorticoids (e.g. Triamcinolone).
  • compositions for use in accordance with the present disclosure may be formulated in conventional manner using one or more physiologically acceptable carriers or excipients. Such formulations will generally be substantially pyrogen free, in compliance with most regulatory requirements.
  • the therapeutic method of the disclosure includes administering the composition systemically, or locally as an implant or device.
  • the therapeutic composition for use in this disclosure is in a pyrogen-free, physiologically acceptable form.
  • Therapeutically useful agents other than the ALKl signaling antagonists which may also optionally be included in the composition as described above, may be administered simultaneously or sequentially with the subject compounds (e.g., ALKl ECD polypeptides or any of the antibodies disclosed herein) in the methods disclosed herein.
  • compositions suitable for parenteral administration may comprise one or more ALKl ECD polypeptides or other antibodies 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.
  • the antibodies and ALKl ECD proteins disclosed herein are administered in an ophthalmic pharmaceutical formulation.
  • the ophthalmic pharmaceutical formulation is a sterile aqueous solution, preferable of suitable concentration for injection, or a salve or ointment.
  • Such salves or ointments typically comprise one or more antibodies or ALKl ECD proteins disclosed herein dissolved or suspended in a sterile pharmaceutically acceptable salve or ointment base, such as a mineral oil-white petrolatum base.
  • a sterile pharmaceutically acceptable salve or ointment base such as a mineral oil-white petrolatum base.
  • anhydrous lanolin may also be included in the formulation.
  • Thimerosal or chlorobutanol are also preferably added to such ointment compositions as antimicrobial agents.
  • the sterile aqueous solution is as described in U.S. Pat. No. 6,071,958.
  • the disclosure provides formulations that may be varied to include acids and bases to adjust the pH; and buffering agents to keep the pH within a narrow range. Additional medicaments may be added to the formulation. These include, but are not limited to, pegaptanib, heparinase, ranibizumab, or glucocorticoids.
  • the ophthalmic pharmaceutical formulation according to the disclosure is prepared by aseptic manipulation, or sterilization is performed at a suitable stage of preparation.
  • compositions and formulations may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient.
  • the pack may for example comprise metal or plastic foil, such as a blister pack.
  • the pack or dispenser device may be accompanied by instructions for administration.
  • hALKl -Fc a soluble ALKl fusion protein that has the extracellular domain of human ALKl fused to a human Fc or mouse ALKl fused to a murine Fc domain with a minimal linker in between.
  • the constructs are referred to as hALKl -Fc and mALKl-Fc, respectively.
  • hALKl-Fc is shown as purified from CHO cell lines in Figure 3 (SEQ ID
  • ALKl ECD polypeptides including Fc fusion proteins having a c-terminus of the ALKl derived sequence that is anywhere from 1 to 5 amino acids upstream (113-1 17 relative to SEQ ID NO:1) or downstream (119- 123) of Ql 18.
  • the hALKl-Fc and mALKl-Fc proteins were expressed in CHO cell lines. Three different leader sequences were considered:
  • Tissue Plasminogen Activator Tissue Plasminogen Activator (TPA): MDAMKRGLCCVLLLCGA VFVSP (SEQ ID NO: 8)
  • TAA Tissue Plasminogen Activator
  • Native MTLGSPRKGLLMLLMALVTQG (SEQ ID NO: 9).
  • the selected form employs the TPA leader and has the unprocessed amino acid sequence shown in Figure 4 (SEQ ID NO:5).
  • This polypeptide is encoded by the nucleic acid sequence shown in Figure 4 (SEQ ID NO:4).
  • Purification can be achieved by a series of column chromatography steps, including, for example, three or more of the following, in any order: protein A chromatography, Q sepharose chromatography, phenylsepharose chromatography, size exclusion chromatography, and cation exchange chromatography.
  • the purification can be completed with viral filtration and buffer exchange.
  • the hALKl-Fc protein was purified to a purity of >98% as determined by size exclusion chromatography and >95% as determined by SDS PAGE.
  • hALKl-Fc tends to be expressed in a mixture of dimers and higher order aggregates which, while appearing pure under denaturing, reducing conditions (e.g., reducing SDS-PAGE), are problematic for administration to a patient.
  • the aggregates may be immunogenic or poorly bioavailable, and because of their heterogeneity, these aggregates make it difficult to characterize the pharmaceutical preparation at a level that is desirable for drug development.
  • various approaches were tested to reduce the amount of aggregate in final preparations. In one approach, a number of different cell culture media were tested. IS CHO-CD (Cat. No.
  • ALKl is a type 1 receptor for ligands of the TGF ⁇ family. Multiple members of the TGF ⁇ family were tested for binding to a human ALKl-Fc fusion protein, using a BiacoreTM system. TGF ⁇ itself, GDF8, GDFl 1, BMP2 and BMP4 all failed to show substantial binding to the hALKl-Fc protein, while BMP2 and BMP4 showed only limited binding. In contrast, GDF5 and GDF7 displayed significant binding, with K D values of approximately 5 x 10 '8 M in both cases.
  • GDF6 will bind the fusion protein with similar affinity.
  • the highest binding affinity to hALKl-Fc was observed for BMP9, with K D values ranging from 1 x 10 "10 to 2 x 10 '9 , and BMPlO, with a K 0 of approximately 3 x 10 '9 .
  • Example 3 Characterization of ALKl-Fc and anti-ALKl Antibody Effects on Endothelial Cells
  • luciferase reporter construct under the control of four sequential consensus SBE sites (SBE4-luc), which are responsive to Smadl/5/8-mediated signaling
  • BMP-9 mediated activity in the presence and absence of hALKl-Fc drug or neutralizing ALKl specific monoclonal antibody in HMVEC cells.
  • HMVEC cells were stimulated with rhBMP-9 (50ng/ml), which induced Smadl/5/8-mediated transcriptional activation, evidenced here by the increase in SBE4-luc modulated transcriptional upregulation.
  • the hALKl-Fc compound (lO ⁇ g/ml) or antibody (lO ⁇ g/ml) diminished this transcriptional response, each by nearly 60%, indicating that the presence of ALKl-Fc significantly reduces BMP9 signaling, and moreover, that the BMP9 signaling is related to ALKl activity.
  • SMAD phosphorylation is commonly used to assay activation of upstream activin receptors.
  • ALKl is known to modulate phosphorylation of SMAD proteins 1,5 and 8 upon activation by its ligand.
  • rhBMP-9 50ng/ml
  • HUVEC cells a human endothelial cell line which innately expresses ALKl receptor
  • Phosphorylation of SMAD 1/5/8 was seen 5 minutes after treatment of cells with ligand and phosphorylation was maintained for the entirety of the 30 minute period.
  • hALKl-Fc 250ng/ml
  • SMAD 1/5/8 phosphorylation was reduced, confirming that this agent inhibits Smadl/5/8 activation in endothelial cells.
  • hALKl-Fc and mALKl-Fc in the presence of the strongly pro-angiogenic factor ECGS maintained strong inhibition of neovascularization demonstrating even more potent anti-angiogenic activity than the negative control endostatin (100ng/ml).
  • VEGF and FGF are well-known to stimulate angiogenesis.
  • a CAM (chick chorioallantoic membrane) assay system was used to assess the angiogenic effects of GDF7. As shown in Figure 6, GDF7 stimulates angiogenesis with a potency that is similar to that of VEGF. Similar results were observed with GDF5 and GDF6.
  • ALKl-Fc fusions were tested for anti-angiogenic activity in the CAM assay. These fusion proteins showed a potent anti-angiogenic effect on angiogenesis stimulated by VEGF, FGF and GDF7. See Figure 7. BMP9 and PDGF showed a relatively poor capability to induce angiogenesis in this assay, but such angiogenesic effect of these factors was nonetheless inhibited by ALKl .
  • ALKl-Fc proteins and a commercially available, anti-angiogenic anti-VEGF monoclonal antibody were compared in the CAM assay.
  • the ALKl-Fc proteins had similar potency as compared to anti-VEGF.
  • the anti-VEGF antibody bevacizumab is currently used in the treatment of cancer and macular degeneration in humans. See Figure 8.
  • an anti-ALKl antibody failed to significantly inhibit angiogenesis in this assay system. We expect that this may reflect the difference in the ALKl sequence in different species.
  • Example 5 Mouse Corneal Micropocket Assay The mouse corneal micropocket assay was used to assess the effects of ALKl-Fc on angiogenesis in the mouse eye.
  • hALKl-Fc administered intraperitoneally, significantly inhibited ocular angiogenesis.
  • hALKl-Fc inhibited ocular angiogenesis to the same degree as anti-VEGF.
  • hALKl- Fc and anti-VEGF were used at identical weight/weight dosages. Similar data were obtained when a Matrigel plug impregnated with VEGF was implanted in a non- ocular location.
  • the ligands for ALKl fall into two categories, with the GDF5,6,7 grouping having an intermediate affinity for ALKl and the BMP9,10 grouping having a high affinity for ALKl .
  • GDF5, GDF6, and GDF7 are primarily localized to bone and joints, while BMP9 is circulated in the blood.
  • BMP9 is circulated in the blood.
  • a pro-angiogenic system of the bones and joints that includes ALKl, GDF5, GDF6, and GDF7 and a systemic angiogenic system that includes ALKl and BMP9 (and possibly BMPlO).
  • the murine collagen-induced arthritis model is a well-accepted model of rheumatoid arthritis.
  • groups of 10 mice were treated with vehicle, anti- VEGF (bevacizumab - as a negative control, because bevacizumab does not inhibit murine VEGF), or doses of mALKl-Fc ("RAP-041") at 1 mg/kg, 10 mg/kg or 25 mg/kg.
  • mALKl-Fc mALKl-Fc
  • Example 7 Ligand Binding Characteristics of DAN DAN is a member of a family of secreted cystine knot proteins that inhibit
  • DAN is known to bind to and antagonize GDF5. We determined that DAN also binds tightly to GDF7, but not to BMP9. Thus, we conclude that DAN inhibits the suite of bone and joint localized ligands for ALKl, and DAN is expected to be a potent antagonist of bone and joint related angiogenesis. Thus DAN may be useful in treating cancers of the bone, e.g., multiple myeloma and bone metastases, as well as rheumatoid arthritis and osteoarthritis.
  • the findings disclosed in these Examples provide numerous reagents, described herein, for inhibiting angiogenesis in vivo, and particularly ocular angiogenesis. These findings also indicate that agents targeted to GDF5, GDF6, and GDF7 can be used to selectively inhibit bone and joint angiogenesis. These findings further indicate that such agents can be used to treat cancers and rheumatoid arthritis.
  • Example 8 ALKl-Fc Reduces Tumor Angiogenesis in a CAM Assay Tumors, as with any tissue, have a basic nutrient and oxygen requirement.
  • small tumors are capable of acquiring adequate amounts via diffusion from neighboring blood vessels, as the tumor increases in size, it must secure nutrients by recruiting and maintaining existing capillaries.
  • ALKl-Fc proteins In order to test the capacity of ALKl-Fc proteins to limit tumor growth through vessel inhibition, we tested varying concentrations of m ALKl -Fc in a melanoma explant CAM assay. As with CAM assays described above, small windows were made in the surface of each egg through which 5xlO 5 B16 melanoma cells were implanted. Eggs were then treated daily with 0.02 mg/ml mALKl-Fc, 0.2 mg/ml mALKl-Fc, or left untreated for a period of a week.
  • tumors were carefully removed, weighed and digital images were captured.
  • Tumors originating from CAMs treated with mALKl-Fc showed a significant decrease in size as compared to untreated CAM tumors.
  • Quantification of tumor weight demonstrated that weight of tumors treated daily with either 0.02 mg/ml or 0.2 mg/ml mALKl-Fc showed a reduction of 65% and 85% compared to the untreated CAMs.
  • neovascularization and tumor growth was significantly suppressed upon addition of ALKl-Fc in a dose-responsive manner, indicating that ALKl-Fc is a powerful anti- angiogenic agent.
  • 10mg/kg mALKl-Fc 10mg/kg mALKl
  • CAM chorioallantoic membrane
  • rhB9 recombinant human BMP9
  • mabB9 anti-BMP9 monoclonal antibody
  • This antibody is known to neutralize BMP9/ALK1 signaling. See, e.g., Scharpfenecker et al., JCe// ScL 2007 Mar 15; 120(Pt 6):964-72; David et al. Blood Mar l;109(5): 1953-61 ; 2007; David et al., Circ Res. 2008 Apr 25;102(8):914-22.
  • this murine monoclonal antibody could be humanized to provide a therapeutic agent for use in humans.
  • the antibody may be humanized by a variety of art-recognized techniques, including chimerization, CDR-grafting, resurfacing, back mutations, superhumanization, human string content optimization, and empirical methods, such as FR library generation and selection, FR shuffling and humaneering. See, e.g, Almagro and Fransson, Frontiers in Biosciences, 13: 1619-1633, 2008.
  • Example 11 Effects of ALKl-Fc Fusion Protein on Breast Cancer Tumor Models mALKl-Fc was effective in delaying the growth of breast cancer tumor cell lines derived from both estrogen receptor positive (ER+) and estrogen receptor negative tumor cells (ER-).
  • ER+ estrogen receptor positive
  • ER- estrogen receptor negative tumor cells
  • the MDA-MB-231 breast cancer cell line (derived from ER- cells) was stably transfected with the luciferase gene to allow for the in vivo detection of tumor growth and potential metastasis.
  • 1 x 10 6 MDA-MB-231 -Luc cells were implanted orthotopically in the mammary fat pad of athymic nude mice (Harlan). Tumor progression was followed by bioluminescent detection using an IVIS Spectrum imaging system (Caliper Life Sciences). An increase in the luminescence (number of photons detected) corresponds to an increase in tumor burden.
  • mice Thirty female nude mice were injected with 1 x 10 6 tumor cells into the mammary fat pad. Three days after tumor implantation the mice were treated with either vehicle control or mALKl-Fc (30 mg/kg) twice per week by subcutaneous (SC) injection. Treatment was continued and tumor progression was monitored by bioluminescent imaging for 10 weeks. mALKl-Fc treatment at 30 mg/kg slowed tumor progression as determined by bioluminescent detection when compared to vehicle treated controls ( Figure 14). Treatment with mALKl-Fc delayed, but did not reverse tumor growth in this model. This may be expected of an antiangiogenic compound in that tumors may be able to survive to a certain size before requiring new blood vessel formation to support continued growth. In a similar experiment, hALKl-Fc produced similar, if slightly lesser, effects at dose levels as low as 3 mg/kg.
  • ER+ estrogen-receptor-positive
  • MCF-7 luciferase expressing cell line
  • Example 13 BMP9/10 Antagonists Inhibit VEGF- and BMPlO-induced Angiogenesis in a CAM Assay
  • VEGF and BMPlO were used separately to promote angiogenesis.
  • VEGF 50 ng daily
  • BMP9/10 antagonist 82 pmol daily
  • Figure 17 A chick chorioallantoic membrane (CAM) assay system was used to investigate the effect of BMP9/10 antagonists on angiogenesis.
  • VEGF and BMPlO were used separately to promote angiogenesis.
  • VEGF 50 ng daily
  • BMP9/10 antagonist 82 pmol daily
  • FIG. 17 A chick chorioallantoic membrane

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Abstract

Sous certains aspects, la présente invention est fondée sur l'idée qu'un polypeptide renfermant une partie de liaison à un ligand du domaine extracellulaire du polypeptide d'activine-like kinase I (ALK1) peut être utilisé pour inhiber l'angiogenèse in vivo, en particulier chez des mammifères souffrant de troubles se rapportant à l'angiogenèse. Sous certains aspects, l'invention démontre que des antagonistes de BMP9 et/ou BMP10 et des ligands pour ALK1 peuvent également être utilisés pour inhiber l'angiogenèse in vivo.
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RU2559532C2 (ru) 2006-11-02 2015-08-10 Акселерон Фарма, Инк. Антагонисты рецептора и лигандов alk1 и их применение
US10059756B2 (en) 2006-11-02 2018-08-28 Acceleron Pharma Inc. Compositions comprising ALK1-ECD protein
CA2723449C (fr) * 2008-05-02 2020-01-21 Acceleron Pharma Inc. Methodes et compositions fondees sur des antagonistes alk1 servant a la modulation d'angiogenese et de couverture pericyte
US20160228509A9 (en) * 2009-05-08 2016-08-11 Novartis Ag Diagnostic BioMarkers for Fibrotic Disorders
US9809636B2 (en) 2012-04-06 2017-11-07 Acceleron Pharma Inc. Methods for increasing red blood cell levels comprising administering BMP9
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