WO2006043954A1 - Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine - Google Patents

Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine Download PDF

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Publication number
WO2006043954A1
WO2006043954A1 PCT/US2004/034878 US2004034878W WO2006043954A1 WO 2006043954 A1 WO2006043954 A1 WO 2006043954A1 US 2004034878 W US2004034878 W US 2004034878W WO 2006043954 A1 WO2006043954 A1 WO 2006043954A1
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opn
antibody
polypeptide
osteopontin
cell
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PCT/US2004/034878
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English (en)
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Avi Ashkenazi
Robert Pitti
Thomas Wu
Zemin Zhang
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Genentech, Inc.
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Priority to CA002584028A priority Critical patent/CA2584028A1/fr
Priority to PCT/US2004/034878 priority patent/WO2006043954A1/fr
Priority to AU2004324192A priority patent/AU2004324192A1/en
Priority to EP04795965A priority patent/EP1805220A1/fr
Publication of WO2006043954A1 publication Critical patent/WO2006043954A1/fr
Priority to US11/536,489 priority patent/US20070041983A1/en

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    • 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
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • C07K16/24—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against cytokines, lymphokines or interferons
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/20—Fusion polypeptide containing a tag with affinity for a non-protein ligand
    • C07K2319/21—Fusion polypeptide containing a tag with affinity for a non-protein ligand containing a His-tag
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2799/00—Uses of viruses
    • C12N2799/02—Uses of viruses as vector
    • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid
    • C12N2799/026—Uses of viruses as vector for the expression of a heterologous nucleic acid where the vector is derived from a baculovirus

Definitions

  • the present invention is directed to compositions of matter useful for the treatment of tumor in mammals and to methods of using those compositions of matter for the same.
  • Osteopontin is a phosphorylated, acidic, glycoprotein with many physiological and pathological roles and is widely expressed at sites of injury and inflammation. In bone, osteopontin makes up about 2% of the non-collagenous matrix, where it plays a major role in mineralized tissue resorption, a normal tissue remodeling event (Roach, H.I., Cell Biology International, 18(6): 617-28 (1994)). The overexpression of OPN in many tumors suggests that it plays a significant role in cancer biology. While OPN appears to play a critical role in a number of physiological and pathological events, OPN is not essential for normal development and survival as evidenced from developmental studies with OPN null mice.
  • OPN is localized to cell-matrix and matrix-matrix interfaces, most prominantly in the lamina limitans and cement lines, where it is deposited by osteoclasts (Dodds, R.A et al., Journal of Bone & Mineral Research, 10(11): 1666-80 (1995)). After attachment of osteoclasts to bone, the cells then secrete acid and enzymes into a ventral pocket, where the bone tissue is dissolved. OPN is not essential for bone and teeth development which are normal in OPN null mice. (Rittling, et al, Journal of Bone & Mineral Research, 13(7): 1 101-1 1 ( 1998)).
  • OPN may also play both pro-inflammatory and anti-inflammatory roles in immunity but OPNs role in immunity is not as well understood as OPN's role in bone biology. OPN expression has been detected in several inflammatory cells in culture, including T cells, macrophages and NK cells
  • OPN has been suggested to be involved in regulating the ThI- mediated demyelinating disease, multiple sclerosis (Chabas et al., Science, 294(5547): 1731-5 (2001)) and in recruitment of T cells and macrophages in vitro (O'Regan et al., Journal of Immunolgoy, 162(2): 1024-31 (1999)).
  • OPN drives the Th I response by regulating IL-12 and IL-IO production in macrophages.
  • OPN induces IL-12 production through activation of the ⁇ v ⁇ 3 receptors and downregulates IL-IO production through the CD44 receptor (Ashkar, S.k G. F. Weber, et al. Science, 287(5454): 860-864 (2000)).
  • OPN null mice are also more vulnerable to infection to Herpes simplex and Listeria monocytogenes (Ashkar et al., Science, 287 (5454): 860-4 (2000)).
  • OPN drives an anti-inflammatory response by inhibiting nitric oxide (NO) production in macrophages and kidney tubule epithelial cells.
  • NO nitric oxide
  • OPN may play a variety of pro- and anti-inflammatory roles in immunity.
  • Osteopontin expression has been shown to be upregulated in a variety of tumor types, and it has been suggested that the increased OPN expression may correlate with malignancy grade, metastasis and clinical outcome.
  • OPN has been described as a useful marker of colon, breast, prostate, ovarian, lung and other cancers (Fedarko et al., Clinical Cancer Research, 7(12): 4060-6 (2001 ); Kim et al., JAMA, 287(13): 1671-9 (2002)).
  • OPN expression correlates inversely with survival and directly with metastasis to bone (Hotte et al., Cancer, 95(3): 506-512 (2002)).
  • the ⁇ v ⁇ 3 integrin which may be the preeminent receptor for OPN, has also been actively studied for its role in prostate cancer metastasis to the bone (Cooper et al., Neoplasia, 4(3): 191-4 (2002)) and has been found to be highly over-expressed in prostate as well as other cancers.
  • OPN may play an important role in tumor biology
  • OPN may play an important role in tumor biology
  • OPN may play in the tumor environment. Since tumor generated OPN is soluble and not incorporated into the surrounding matrix, OPN may play an important signaling role as an activator of receptor signals independent of matrix adhesion (Rittling et al., Journal of Biological Chemistry, 277(1 1 ): 9175082 (2002)). Further, the well established role of OPN in osteoclast-mediated bone resorption suggests a possible role for OPN in bone metastasis, especially in osteolytic metastases. Additionally, cancer cells themselves may secrete OPN and use it in an autocrine loop to attach to and migrate in the tumor environment, mimicking osteoclast attachment and migration in bone.
  • osteoclasts signal through Rho-A, which plays a critical role in actin stress fiber formation and focal adhesions, and thus, stimulates osteoclast podosome organization, motility and bone resorption (Chellaiah et al., Journal of Biological Chemistry, 275(16): 1 1993-2002 (2000)), a similar mechanism in cancer cells could support invasion, migration and metastasis.
  • matrix proteins such as OPN
  • the attachment is mediated by integrin receptors that mediate signals through focal adhesion kinase (FAK) or a closely related molecule PYK2, both adapter kinases which may be hubs in integrin signaling networks.
  • FAK focal adhesion kinase
  • PYK2 closely related molecule
  • ILK integrin-linked kinase
  • Osteopontin polypeptides are herein referred to as osteopontin ("OPN” polypeptides) or Tumor-associated Antigenic Target-234 (“TAT234" polypeptides) or PRO 1004 and are expected to serve as effective targets for cancer therapy and diagnosis in mammals.
  • OPN osteopontin
  • TAT234" Tumor-associated Antigenic Target-234
  • PRO 1004 are expected to serve as effective targets for cancer therapy and diagnosis in mammals.
  • the present invention relates to a method for modulating at least one biological activity of a cell expressing a receptor for an osteopontin polypeptide, or a neighboring cell that secretes an osteopontin polypeptide, said method comprising blocking an osteopontin polypeptide from contacting said receptor using an anti -osteopontin antibody, whereby said anti-osteopontin antibody binds to said osteopontin polypeptide and whereby said binding prevents said osteopontin polypeptide from interacting with said receptor, thereby modulating at least one biological activity of said cell.
  • the method concerns the inhibition of the binding of a cell expressing a receptor for an osteopontin polypeptide or a neighboring cell that secretes an osteopontin polypeptide to osteopontin.
  • the inhibition of binding to osteopontin results in inhibition of phosphorylation of signaling molecules. Even further, the inhibition of phosphorylation of signaling molecules results in inhibition of cell migration. Even further, the inhibition of phosphorylation of signaling molecules results in inhibition of cell proliferation. In an even further embodiment, the inhibition of phosphorylation of signaling molecules results in inhibition of cell survival.
  • the invention relates to a method for treatment or preventing a tumor, said method comprising administering to a subject in need of such treatment an effective amount of an agent that inhibits the activity of the osteopontin polypeptide, thereby effectively treating or preventing said tumor.
  • the inhibited activity of the osteopontin polypeptide is binding of the osteopontin polypeptide to an osteopontin receptor. Further, the inhibition of binding of the osteopontin polypeptide to an osteopontin receptor results in inhibition of phosphorylation of signaling molecules. Even further, the inhibition of phosphorylation of signaling molecules results in inhibition of cell migration.
  • the present invention relates to a method for preparing a pharmaceutical composition for the treatment of a tumor comprising incorporating a therapeutically effective amount of an agent that modulates the activity of the osteopontin polypeptide into a pharmaceutically acceptable carrier vehicle.
  • the agent is an anti-osteopontin antibody.
  • the anti-osteopontin antibody is 2H2 or 2G2 anti-osteopontin antibody.
  • the present invention relates to a method for inhibiting cell migration of a cell expressing a receptor for osteopontin, said method comprising blocking an osteopontin polypeptide from contacting said receptor using an anti-osteopontin antibody, whereby said anti- osteopontin antibody binds to said osteopontin polypeptide and whereby said binding prevents the osteopontin polypeptide from interacting with said receptor, thereby modulating at least one biological activity of said cell.
  • the present invention relates to a method for inhibiting growth of a tumor cell expressing a receptor for osteopontin, said method comprising blocking an osteopontin polypeptide from contacting said receptor using an anti-osteopontin antibody, whereby said anti- osteopontin antibody binds to said osteopontin polypeptide and whereby said binding prevents the osteopontin polypeptide from interacting with said receptor, thereby inhibiting tumor growth.
  • Figure 1 illustrates integrin receptor expression on a 293 cell line (a human embryonic kidney cell line), a MG63 cell line (an osteosarcoma cell line), and a MDA-MB-435 cell line (a highly metastatic human breast carcinoma line), from FACS using antibodies to ⁇ v ⁇ 3, ⁇ 4 ⁇ l and ⁇ 5 ⁇ l .
  • Figure 2 illustrates anti-OPN antibodies, 2G2 and 2H2, blocking attachment of MDA-MB-435 highly metastatic human breast carcinoma cells to the osteopontin antigen, OPN 20 .
  • Figure 3 illustrates anti-OPN antibodies, 2H2, blocking attachment of IGROV- I human ovarian cancer cells to the osteopontin antigen, OPN 20 -
  • Figure 4 illustrates anti-OPN antibodies, 2G2 and 2H2, blocking binding of purified ⁇ v ⁇ 3 to the osteopontin antigen, OPN 2O .
  • Figure 5 illustrates anti-OPN antibody, 2G2, inhibiting migration of MDA-MB-435 435 highly metastatic human breast carcinoma cells on solid-phase osteopontin (SP-OPN) in comparison with the assay medium control (A-Media).
  • Figure 6 illustrates inhibition of phosphorylation at tyrosine-397 of FAK in MDA-MB-435 cells by
  • Figure 7 illustrates reduction of tumor size of beige nude mice injected with IGROV-I human ovarian cancer cells using anti-OPN antibodies, 2G2, in comparison with anti-GP120 antibodies.
  • Figure 8 illustrates reduction of tumor size of beige nude mice injected with IGROV-I human ovarian cancer cells using anti-OPN antibodies, 2G2, administered at 13.5 mg/kg or 27 mg/kg.
  • Figure 9 shows a nucleic acid sequence (SEQ ID NO: 1) of a human osteopontin (referred herin as PRO10004) cDNA, wherein SEQ ID NO: 1 is a clone designated herein as "UNQl 002" and/or
  • Figure 10 shows the amino acid sequence of full-length human osteopontin (SEQ ID NO: 2) (referred herein as PRO 10004 and/or TAT234), derived from the coding sequence of SEQ ID NO: 1 shown in Figure 9 or SEQ ID NO: 3 shown in Figure 11.
  • SEQ ID NO: 2 referred herein as PRO 10004 and/or TAT234.
  • FIG. 11 shows a nucleic acid sequence (SEQ ID NO: 3) of a human osteopontin (referred herein as TAT234) cDNA wherein SEQ ID NO: 3 is a clone designated herein as "UNQ 1002" and/or “DNA92980” also herein referred as “DNA83139". '
  • OPN polypeptide refers to osteopontin, the phosphorylated, acidic, glycoprotein with many physiological and pathological roles and widely expressed at sites of injury and inflammation and in tumors.
  • Osteopontin or “OPN” is also referred to herein as "TAT234" (Tumor-associated Antigenic Target- 234) and/or as "PRO10004".
  • TAT234" Tumor-associated Antigenic Target- 234
  • PRO10004 Tumor-associated Antigenic Target- 234
  • the OPN polypeptides described herein encompass native sequence polypeptide, polypeptide variants and fragments of native sequence polypeptide and polypeptide variants (which are further defined herein).
  • OPN polypeptides described herein may be isolated from a variety of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods.
  • the term "OPN polypeptide” or “osteopontin polypeptide” also include variants of the osteopontin polypeptide disclosed herein.
  • OPN 36 refers to full-length osteopontin or OPN (SEQ ID NO: 2).
  • Full-length osteopontin may be encoded by the nucleic acid sequence of SEQ ID NO: 1 (DNA92980-1 ) or SEQ ID NO: 3 (DNA92980 also herein referred as DNA83139).
  • SEQ ID NO: 1 (DNA92980-1 ) includes more extensive nucleic acid regions flanking the region encoding for osteopontin than SEQ ID NO: 3 (DNA92980 also herein referred as DNA83139).
  • OPN 20 refers to an N-terminal fragment of osteopontin resulting from cleavage of osteopontin (SEQ ID NO: 2) lysine at amino acid residue 172 (K 172) of SEQ ID NO: 2.
  • a "native sequence OPN polypeptide” comprises a polypeptide having the same amino acid sequence as the corresponding OPN polypeptide derived from nature. Such native sequence OPN can be isolated from nature or can be produced by recombinant or synthetic means.
  • the term “native sequence OPN polypeptide” specifically encompasses naturally-occurring truncated or secreted forms of the specific OPN polypeptide (e.g.
  • the native sequence OPN polypeptide disclosed herein is mature or full-length native sequence polypeptide comprising the full-length amino acid sequence shown in the accompanying figures. Start and stop codon (if indicated) is shown in bold font and underlined in the figures ( Figure 9 and 1 1). Nucleic acid residues indicated as "N" in the accompanying figures are any nucleic acid residue.
  • the OPN polypeptide disclosed in the accompanying figures are any nucleic acid residue.
  • the C-terminal boundary of a signal peptide may vary, but most likely by no more than about 5 amino acids on either side of the signal peptide C-terminal boundary as initially identified herein, wherein the C-terminal boundary of the signal peptide may be identified pursuant to criteria routinely employed in the art for identifying that type of amino acid sequence element (e.g., Nielsen et al., Prot. Eng. 10:1-6
  • OPN polypeptide variant means an OPN polypeptide, preferably an active OPN polypeptide, as defined herein having at least about 80% amino acid sequence identity with a full- length native sequence OPN polypeptide sequence as disclosed herein, an OPN polypeptide sequence lacking the signal peptide as disclosed herein, or any other fragment of a full-length OPN polypeptide sequence as disclosed herein (such as those encoded by a nucleic acid that represents only a portion of the complete coding sequence for a full-length OPN polypeptide).
  • OPN polypeptide variants include, for instance, OPN polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C-terminus of the full-length native amino acid sequence.
  • a OPN polypeptide variant will have at least about 80% amino acid sequence identity, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity, to a full-length native sequence OPN polypeptide sequence as disclosed herein, an OPN polypeptide sequence lacking the signal peptide as disclosed herein, or any other specifically defined fragment of a full-length OPN polypeptide sequence as disclosed herein.
  • OPN variant polypeptides are at least about 10 amino acids in length, alternatively at least about 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600 amino acids in length, or more.
  • OPN variant polypeptides will have no more than one conservative amino acid substitution as compared to the native OPN polypeptide sequence, alternatively no more than 2, 3, 4, 5, 6, 7, 8, 9, or 10 conservative amino acid substitution as compared to the native OPN polypeptide sequence.
  • full-length coding region when used in reference to a nucleic acid encoding an OPN polypeptide refers to the sequence of nucleotides which encode the full-length OPN polypeptide of the invention (which is often shown between start and stop codons, inclusive thereof, in the accompanying figures).
  • full-length coding region when used in reference to an ATCC deposited nucleic acid refers to the OPN polypeptide-encoding portion of the cDNA that is inserted into the vector deposited with the ATCC (which is often shown between start and stop codons, inclusive thereof, in the accompanying figures).
  • Isolated when used to describe the OPN polypeptides disclosed herein, means polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
  • the polypeptide will be purified (1 ) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the OPN polypeptide natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • An "isolated" OPN polypeptide-encoding nucleic acid or other polypeptide-encoding nucleic acid is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the polypeptide-encoding nucleic acid.
  • An isolated polypeptide-encoding nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated polypeptide-encoding nucleic acid molecules therefore are distinguished from the specific polypeptide-encoding nucleic acid molecule as it exists in natural cells.
  • an isolated polypeptide-encoding nucleic acid molecule includes polypeptide- encoding nucleic acid molecules contained in cells that ordinarily express the polypeptide where! for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
  • control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
  • the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
  • Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
  • Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
  • a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
  • "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
  • epitope tagged when used herein refers to a chimeric polypeptide comprising an OPN polypeptide or anti-OPN antibody fused to a "tag polypeptide".
  • the tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the polypeptide to which it is fused.
  • the tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes.
  • Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 and 50 amino acid residues (preferably, between about 10 and 20 amino acid residues).
  • Active or “activity” for the purposes herein refers to form(s) of a OPN polypeptide which retain a biological and/or an immunological activity of native or naturally-occurring OPN, wherein "biological” activity refers to a biological function (either inhibitory or stimulatory) caused by a native or naturally-occurring OPN other than the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring OPN and an "immunological” activity refers to the ability to induce the production of an antibody against an antigenic epitope possessed by a native or naturally-occurring OPN.
  • the biological activity of OPN includes the ability to stimulate cell migration, to stimulate inflammatory response, to stimulate cell survival, to stimulate cell proliferation and to stimulate cell invasion.
  • the term "antagonist” is used in the broadest sense, and includes any molecule that partially or fully blocks, inhibits, or neutralizes a biological activity of a native OPN polypeptide disclosed herein.
  • the term "agonist” is used in the broadest sense and includes any molecule that mimics a biological activity of a native OPN polypeptide disclosed herein.
  • Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments or amino acid sequence variants of native OPN polypeptides, peptides, antisense oligonucleotides, small organic molecules, etc.
  • Methods for identifying agonists or antagonists of a OPN polypeptide may comprise contacting a OPN polypeptide with a candidate agonist or antagonist molecule and measuring a detectable change in one or more biological activities normally associated with the OPN polypeptide.
  • Treating” or “treatment” or “alleviation” refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition or disorder.
  • Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder is to be prevented.
  • a subject or mammal is successfully "treated" for a OPN polypeptide-expressing cancer if, after receiving a therapeutic amount of an anti-OPN antibody, OPN binding oligopeptide or OPN binding organic molecule according to the methods of the present invention, the patient shows observable and/or measurable reduction in or absence of one or more of the following: reduction in the number of cancer cells or absence of the cancer cells; reduction in the tumor size; inhibition (i.e., slow to some extent and preferably stop) of cancer cell infiltration into peripheral organs including the spread of cancer into soft tissue and bone; inhibition (i.e., slow to some extent and preferably stop) of tumor metastasis; inhibition, to some extent, of tumor growth; and/or relief to some extent, one or more of the symptoms associated with the specific cancer; reduced morbidity and mortality, and improvement in quality of life issues.
  • the anti-OPN antibody or OPN binding oligopeptide may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic. Reduction of
  • TTP time to disease progression
  • RR response rate
  • Metastasis can be determined by staging tests and by bone scan and tests for calcium level and other enzymes to determine spread to the bone.
  • CT scans can also be done to look for spread to the pelvis and lymph nodes in the area.
  • Chest X-rays and measurement of liver enzyme levels by known methods are used to look for metastasis to the lungs and liver, respectively.
  • Other routine methods for monitoring the disease include transrectal ultrasonography (TRUS) and transrectal needle biopsy (TRNB).
  • bladder cancer which is a more localized cancer
  • methods to determine progress of disease include urinary cytologic evaluation by cystoscopy, monitoring for presence of blood in the urine, visualization of the urothelial tract by sonography or an intravenous pyelogram, computed tomography (CT) and magnetic resonance imaging (MRI).
  • CT computed tomography
  • MRI magnetic resonance imaging
  • Chronic administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to maintain the initial therapeutic effect (activity) for an extended period of time.
  • Intermittent administration is treatment that is not consecutively done without interruption, but rather is cyclic in nature.
  • “Mammal” for purposes of the treatment of, alleviating the symptoms of a cancer refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, cats, cattle, horses, sheep, pigs, goats, rabbits, etc.
  • the mammal is human.
  • Administration "in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
  • Carriers as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution.
  • physiologically acceptable carriers include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as TWEEN®, polyethylene glycol (PEG), and PLURONICS®.
  • buffers such as phosphate, citrate, and other organic acids
  • antioxidants including ascorbic acid
  • proteins such as serum albumin,
  • solid phase or “solid support” is meant a non-aqueous matrix to which an antibody, OPN binding oligopeptide or OPN binding organic molecule of the present invention can adhere or attach.
  • solid phases encompassed herein include those formed partially or entirely of glass (e.g., controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones.
  • the solid phase can comprise the well of an assay plate; in others it is a purification column (e.g., an affinity chromatography column). This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S.
  • a “liposome” is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug (such as an OPN polypeptide, an antibody thereto or a OPN binding oligopeptide) to a mammal.
  • a drug such as an OPN polypeptide, an antibody thereto or a OPN binding oligopeptide
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.
  • a “small” molecule or “small” organic molecule is defined herein to have a molecular weight below about 500 Daltons.
  • an “effective amount” of a polypeptide, antibody, OPN binding oligopeptide, OPN binding organic molecule or an agonist or antagonist thereof as disclosed herein is an amount sufficient to carry out a specifically stated purpose.
  • An “effective amount” may be determined empirically and in a routine manner, in relation to the stated purpose.
  • the term "therapeutically effective amount” refers to an amount of an antibody, polypeptide, OPN binding oligopeptide, OPN binding organic molecule or other drug effective to "treat” a disease or disorder in a subject or mammal.
  • the therapeutically effective amount of the drug may reduce the number of cancer cells; reduce the tumor size; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer. See the definition herein of "treating”.
  • the drug may prevent growth and/or kill existing cancer cells, it may be cytostatic and/or cytotoxic.
  • a “growth inhibitory amount" of an anti-OPN antibody, OPN polypeptide, OPN binding oligopeptide or OPN binding organic molecule is an amount capable of inhibiting the growth of a cell, especially tumor, e.g., cancer cell, either in vitro or in vivo.
  • a “growth inhibitory amount" of an anti- OPN antibody, OPN polypeptide, OPN binding oligopeptide or OPN binding organic molecule for purposes of inhibiting neoplastic cell growth may be determined empirically and in a routine manner.
  • a "cytotoxic amount" of an anti-OPN antibody, OPN polypeptide, OPN binding oligopeptide or OPN binding organic molecule is an amount capable of causing the destruction of a cell, especially tumor, e.g., cancer cell, either in vitro or in vivo.
  • a "cytotoxic amount" of an anti-OPN antibody, OPN polypeptide, OPN binding oligopeptide or OPN binding organic molecule for purposes of inhibiting neoplastic cell growth may be determined empirically and in a routine manner.
  • antibody is used in the broadest sense and specifically covers, for example, single anti-OPN monoclonal antibodies (including agonist, antagonist, and neutralizing antibodies), anti-OPN antibody compositions with polyepitopic specificity, polyclonal antibodies, single chain anti-OPN antibodies, and fragments of anti-OPN antibodies (see below) as long as they exhibit the desired biological or immunological activity.
  • immunoglobulin Ig is used interchangeable with antibody herein.
  • an "isolated antibody” is one which has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials which would interfere with therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the antibody will be purified (1 ) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain.
  • Isolated antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
  • the basic 4-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light (L) chains and two identical heavy (H) chains (an IgM antibody consists of 5 of the basic heterotetramer unit along with an additional polypeptide called J chain, and therefore contain 10 antigen binding sites, while secreted IgA antibodies can polymerize to form polyvalent assemblages comprising 2-5 of the basic 4-chain units along with J chain).
  • the 4-chain unit is generally about 150,000 daltons.
  • Each L chain is linked to a H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype.
  • Each H and L chain also has regularly spaced intrachain disulfide bridges.
  • Each H chain has at the N-terminus, a variable domain (V H ) followed by three constant domains (C H ) for each of the ⁇ and ⁇ chains and four C H domains for ⁇ and ⁇ isotypes.
  • Each L chain has at the N-terminus, a variable domain (V L ) followed by a constant domain (C L ) at its other end.
  • the V L is aligned with the V H and the C L is aligned with the first constant domain of the heavy chain (C H I ).
  • Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable domains.
  • the pairing of a V (I and V L together forms a single antigen-binding site.
  • immunoglobulins can be assigned to different classes or isotypes. There are five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, having heavy chains designated ⁇ , ⁇ , ⁇ , ⁇ , and ⁇ , respectively.
  • the ⁇ and ⁇ classes are further divided into subclasses on the basis of relatively minor differences in C H sequence and function, e.g., humans express the following subclasses: IgGl , IgG2, IgG3, IgG4, IgAl , and IgA2.
  • variable refers to the fact that certain segments of the variable domains differ extensively in sequence among antibodies.
  • the V domain mediates antigen binding and define specificity of a particular antibody for its particular antigen.
  • variability is not evenly distributed across the 1 10-amino acid span of the variable domains.
  • the V regions consist of relatively invariant stretches called framework regions (FRs) of 15-30 amino acids separated by shorter regions of extreme variability called “hypervariable regions” that are each 9- 12 amino acids long.
  • FRs framework regions
  • hypervariable regions that are each 9- 12 amino acids long.
  • the variable domains of native heavy and light chains each comprise four FRs, largely adopting a ⁇ -sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases forming part of, the ⁇ -sheet structure.
  • the hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD. (1991)).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC).
  • hypervariable region when used herein refers to the amino acid residues of an antibody which are responsible for antigen-binding.
  • the hypervariable region generally comprises amino acid residues from a "complementarity determining region" or "CDR" (e.g. around about residues 24-34 (Ll ), 50-56 (L2) and 89-97 (L3) in the V L) and around about 1-35 (Hl ), 50-65 (H2) and 95-102 (H3) in the V H ; Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD. (1991)) and/or those residues from a "hypervariable loop" (e.g.
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations which include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies. The modifier "monoclonal" is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies useful in the present invention may be prepared by the hybridoma methodology first described by Kohler et al., Nature, 256:495 (1975), or may be made using recombinant DNA methods in bacterial, eukaryotic animal or plant cells (see, e.g., U.S. Patent No. 4,816,567).
  • the "monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:624-628 (1991 ) and Marks et al., J. MoI. Biol., 222:581-597 (1991), for example.
  • the monoclonal antibodies herein include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see U.S. Patent No. 4,816,567; and Morrison et al., Proc. Natl. Acad. Sci. USA, 81:6851 -6855 (1984)).
  • Chimeric antibodies of interest herein include "primatized" antibodies comprising variable domain antigen- binding sequences derived from a non-human primate (e.g. Old World Monkey, Ape etc), and human constant region sequences.
  • an “intact” antibody is one which comprises an antigen-binding site as well as a C L and at least heavy chain constant domains, C H I, C H 2 and C H 3.
  • the constant domains may be native sequence constant domains (e.g. human native sequence constant domains) or amino acid sequence variant thereof.
  • the intact antibody has one or more effector functions.
  • “Antibody fragments” comprise a portion of an intact antibody, preferably the antigen binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab', F(ab') 2 , and Fv fragments; diabodies; linear antibodies (see U.S. Patent No. 5,641,870, Example 2; Zapata et al., Protein Eng.
  • F(ab') 2 antibody fragments differ from Fab fragments by having additional few residues at the carboxy terminus of the C H 1 domain including one or more cysteines from the antibody hinge region.
  • Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab') 2 antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • the Fc fragment comprises the carboxy-terminal portions of both H chains held together by disulfides.
  • the effector functions of antibodies are determined by sequences in the Fc region, which region is also the part recognized by Fc receptors (FcR) found on certain types of cells.
  • Fv is the minimum antibody fragment which contains a complete antigen-recognition and - binding site. This fragment consists of a dimer of one heavy- and one light-chain variable region domain in tight, non-covalent association. From the folding of these two domains emanate six hypervariable loops (3 loops each from the H and L chain) that contribute the amino acid residues for antigen binding and confer antigen binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
  • Single-chain Fv also abbreviated as “sFv” or “scFv” are antibody fragments that comprise the V H and V L antibody domains connected into a single polypeptide chain.
  • the sFv polypeptide further comprises a polypeptide linker between the V H and V L domains which enables the sFv to form the desired structure for antigen binding.
  • diabodies refers to small antibody fragments prepared by constructing sFv fragments (see preceding paragraph) with short linkers (about 5-10 residues) between the V H and V L domains such that inter-chain but not intra-chain pairing of the V domains is achieved, resulting in a bivalent fragment, i.e., fragment having two antigen-binding sites.
  • Bispecific diabodies are heterodimers of two "crossover" sFv fragments in which the V H and V L domains of the two antibodies are present on different polypeptide chains.
  • Diabodies are described more fully in, for example, EP 404,097; WO 93/11 161 ; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993).
  • Humanized forms of non-human (e.g., rodent) antibodies are chimeric antibodies that contain minimal sequence derived from the non-human antibody.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or non-human primate having the desired antibody specificity, affinity, and capability.
  • donor antibody such as mouse, rat, rabbit or non-human primate having the desired antibody specificity, affinity, and capability.
  • framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
  • the humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • a "species-dependent antibody,” e.g., a mammalian anti-human IgE antibody, is an antibody which has a stronger binding affinity for an antigen from a first mammalian species than it has for a homologue of that antigen from a second mammalian species.
  • the species-dependent antibody "bind specifically" to a human antigen (i.e., has a binding affinity (Kd) value of no more than about 1 x 10 ⁇ 7 M, preferably no more than about 1 x 10 "8 and most preferably no more than about 1 x 10 '9 M) but has a binding affinity for a homologue of the antigen from a second non-human mammalian species which is at least about 50 fold, or at least about 500 fold, or at least about 1000 fold, weaker than its binding affinity for the human antigen.
  • the species-dependent antibody can be of any of the various types of antibodies as defined above, but preferably is a humanized or human antibody.
  • OPN binding oligopeptide is an oligopeptide that binds, preferably specifically, to a OPN polypeptide as described herein.
  • OPN binding oligopeptides may be chemically synthesized using known oligopeptide synthesis methodology or may be prepared and purified using recombinant technology.
  • OPN binding oligopeptides are usually at least about 5 amino acids in length, alternatively at least about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 , 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51 , 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81 , 82, 83, 84, 85, 86, 87, 88, 89, 90, 91 , 92, 93, 94, 95, 96, 97, 98, 99, or 100 amino acids in length or more, wherein such oligopeptides that are capable of binding, preferably specifically
  • OPN binding oligopeptides may be identified without undue experimentation using well known techniques.
  • techniques for screening oligopeptide libraries for oligopeptides that are capable of specifically binding to a polypeptide target are well known in the art (see, e.g., U.S. Patent Nos. 5,556,762, 5,750,373, 4,708,871 , 4,833,092, 5,223,409, 5,403,484, 5,571,689, 5,663,143; PCT Publication Nos. WO 84/03506 and WO84/03564; Geysen et al., Proc.
  • OPN binding organic molecule is an organic molecule other than an oligopeptide or antibody as defined herein that binds, preferably specifically, to a OPN polypeptide as described herein.
  • OPN binding organic molecules may be identified and chemically synthesized using known methodology (see, e.g., PCT Publication Nos. WOOO/00823 and WO00/39585).
  • OPN binding organic molecules are usually less than about 2000 daltons in size, alternatively less than about 1500, 750, 500, 250 or 200 daltons in size, wherein such organic molecules that are capable of binding, preferably specifically, to a OPN polypeptide as described herein may be identified without undue experimentation using well known techniques.
  • an antibody, oligopeptide or other organic molecule "which binds" an antigen of interest e.g. a tumor-associated polypeptide antigen target
  • an antigen of interest e.g. a tumor-associated polypeptide antigen target
  • an antigen of interest e.g. a tumor-associated polypeptide antigen target
  • the extent of binding of the antibody, oligopeptide or other organic molecule to a "non- target" protein will be less than about 10% of the binding of the antibody, oligopeptide or other organic molecule to its particular target protein as determined by fluorescence activated cell sorting (FACS) analysis or radioimmunoprecipitation (RIA).
  • FACS fluorescence activated cell sorting
  • RIA radioimmunoprecipitation
  • the term "specific binding” or “specifically binds to” or is “specific for” a particular polypeptide or an epitope on a particular polypeptide target means binding that is measurably different from a non-specific interaction.
  • Specific binding can be measured, for example, by determining binding of a molecule compared to binding of a control molecule, which generally is a molecule of similar structure that does not have binding activity.
  • specific binding can be determined by competition with a control molecule that is similar to the target, for example, an excess of non-labeled target.
  • binding is indicated if the binding of the labeled target to a probe is competitively inhibited by excess unlabeled target.
  • the term “specific binding” or “specifically binds to” or is “specific for” a particular polypeptide or an epitope on a particular polypeptide target as used herein can be exhibited, for example, by a molecule having a Kd for the target of at least about 10 "4 M, alternatively at least about 10 "5 M, alternatively at least about 10 " 6 M, alternatively at least about 10 "7 M, alternatively at least about 10 “8 M, alternatively at least about 10 “9 M, alternatively at least about 10 " '° M, alternatively at least about 10 " " M, alternatively at least about 10 "12 M, or greater.
  • the term “specific binding” refers to binding where a molecule binds to a particular polypeptide or epitope on a particular polypeptide without substantially binding to any other polypeptide or polypeptide epitope.
  • An antibody, oligopeptide or other organic molecule that "inhibits the growth of tumor cells expressing a OPN polypeptide" or a “growth inhibitory” antibody, oligopeptide or other organic molecule is one which results in measurable growth inhibition of cancer cells expressing or overexpressing the appropriate OPN polypeptide.
  • the OPN polypeptide may be a polypeptide that is produced and secreted by a cancer cell.
  • Preferred growth inhibitory anti-OPN antibodies, oligopeptides or organic molecules inhibit growth of OPN-expressing tumor cells by greater than 20%, preferably from about 20% to about 50%, and even more preferably, by greater than 50% (e.g., from about 50% to about 100%) as compared to the appropriate control, the control typically being tumor cells not treated with the antibody, oligopeptide or other organic molecule being tested.
  • growth inhibition can be measured at an antibody concentration of about 0.1 to 30 ⁇ g/ml or about 0.5 nM to 200 nM in cell culture, where the growth inhibition is determined 1-10 days after exposure of the tumor cells to the antibody. Growth inhibition of tumor cells in vivo can be determined in various ways such as is described in the Experimental Examples section below.
  • the antibody is growth inhibitory in vivo if administration of the anti-OPN antibody at about 1 ⁇ g/kg to about 100 mg/kg body weight results in reduction in tumor size or tumor cell proliferation within about 5 days to 3 months from the first administration of the antibody, preferably within about 5 to 30 days.
  • An antibody, oligopeptide or other organic molecule which "induces apoptosis" is one which induces programmed cell death as determined by binding of annexin V, fragmentation of DNA, cell shrinkage, dilation of endoplasmic reticulum, cell fragmentation, and/or formation of membrane vesicles (called apoptotic bodies).
  • the cell is usually one which expresses or overexpresses an OPN polypeptide.
  • the cell is a tumor cell, e.g., breast cancer, lung cancer colon cancer, prostate cancer, pancrease cancer, bone cancer, ovarian cancer, brain cancer cells.
  • phosphatidyl serine (PS) translocation can be measured by annexin binding; DNA fragmentation can be evaluated through
  • DNA laddering; and nuclear/chromatin condensation along with DNA fragmentation can be evaluated by any increase in hypodiploid cells.
  • the antibody, oligopeptide or other organic molecule which induces apoptosis is one which results in about 2 to 50 fold, preferably about 5 to 50 fold, and most preferably about 10 to 50 fold, induction of annexin binding relative to untreated cell in an annexin binding assay.
  • Antibody effector functions refer to those biological activities attributable to the Fc region (a native sequence Fc region or amino acid sequence variant Fc region) of an antibody, and vary with the antibody isotype. Examples of antibody effector functions include: CIq binding and complement dependent cytotoxicity; Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor); and B cell activation.
  • ADCC antibody-dependent cell-mediated cytotoxicity
  • FcRs Fc receptors
  • cytotoxic cells e.g., Natural Killer (NK) cells, neutrophils, and macrophages
  • NK cells Natural Killer cells
  • neutrophils neutrophils
  • macrophages cytotoxic cells
  • the antibodies “arm” the cytotoxic cells and are absolutely required for such killing.
  • the primary cells for mediating ADCC, NK cells express Fc ⁇ RIII only, whereas monocytes express Fc ⁇ RI, Fc ⁇ RII and Fc ⁇ RIII.
  • ADCC activity of a molecule of interest is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol. 9:457-92 (1991 ).
  • an in vitro ADCC assay such as that described in US Patent No. 5,500,362 or 5,821 ,337 may be performed.
  • Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells.
  • PBMC peripheral blood mononuclear cells
  • NK Natural Killer
  • ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al. (USA) 95:652- 656 (1998).
  • Fc receptor or “FcR” describes a receptor that binds to the Fc region of an antibody.
  • the preferred FcR is a native sequence human FcR.
  • a preferred FcR is one which binds an IgG antibody (a gamma receptor) and includes receptors of the Fc ⁇ RI, Fc ⁇ RII and Fc ⁇ RIII subclasses, including allelic variants and alternatively spliced forms of these receptors.
  • Fc ⁇ RII receptors include Fc ⁇ RIIA (an “activating receptor”) and Fc ⁇ RIIB (an “inhibiting receptor”), which have similar amino acid sequences that differ primarily in the cytoplasmic domains thereof.
  • Activating receptor Fc ⁇ RIIA contains an immunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmic domain.
  • ITAM immunoreceptor tyrosine-based activation motif
  • Inhibiting receptor Fc ⁇ RIIB contains an immunoreceptor tyrosine-based inhibition motif (ITIM) in its cytoplasmic domain, (see review M. in Daeron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed in Ravetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991); Capel et al., Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med. 126:330-41 (1995). Other FcRs, including those to be identified in the future, are encompassed by the term "FcR" herein.
  • ITIM immunoreceptor tyrosine-based inhibition motif
  • the term also includes the neonatal receptor, FcRn, which is responsible for the transfer of maternal IgGs to the fetus (Guyer et al., J. Immunol. 1 17:587 (1976) and Kim et al., J. Immunol. 24:249 (1994)).
  • FcRn neonatal receptor
  • Human effector cells are leukocytes which express one or more FcRs and perform effector functions. Preferably, the cells express at least Fc ⁇ RIII and perform ADCC effector function. Examples of human leukocytes which mediate ADCC include peripheral blood mononuclear cells
  • PBMC natural killer cells
  • monocytes monocytes
  • cytotoxic T cells neutrophils
  • neutrophils neutrophils
  • the effector cells may be isolated from a native source, e.g., from blood.
  • “Complement dependent cytotoxicity” or “CDC” refers to the lysis of a target cell in the presence of complement. Activation of the classical complement pathway is initiated by the binding of the first component of the complement system (CIq) to antibodies (of the appropriate subclass) which are bound to their cognate antigen.
  • CIq first component of the complement system
  • a CDC assay e.g., as described in Gazzano-Santoro et al., J. Immunol. Methods 202:163 (1996), may be performed.
  • cancer and “cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth.
  • examples of cancer include, but are not limited to tumors, such as bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • MDA-MB-4305 refers to a highly metastatic human breast carcinoma line, known to express high levels of OPN.
  • MG63 refers to an osteosarcoma cell line, known to express high levels of ⁇ vb3.
  • IGF-I refers to a human ovarian cancer cell line, known to express high levels of OPN and its ⁇ v receptors.
  • cell proliferative disorder refers to disorders that are associated with some degree of abnormal cell proliferation.
  • the cell proliferative disorder is cancer.
  • Tumor refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
  • An antibody, oligopeptide or other organic molecule which "induces cell death" is one which causes a viable cell to become nonviable.
  • the cell is one which specifically expresses or overexpresses a nucleic acid encoding an OPN polypeptide and specifically expresses or overexpresses an OPN polypeptide.
  • the cell may be a cancerous or a normal cell.
  • the OPN polypeptide may be a polypeptide that is produced and secreted by a cancer cell.
  • Cell death in vitro may be determined in the absence of complement and immune effector cells to distinguish cell death induced by antibody- dependent cell-mediated cytotoxicity (ADCC) or complement dependent cytotoxicity (CDC).
  • ADCC antibody- dependent cell-mediated cytotoxicity
  • CDC complement dependent cytotoxicity
  • the assay for cell death may be performed using heat inactivated serum (i.e., in the absence of complement) and in the absence of immune effector cells.
  • heat inactivated serum i.e., in the absence of complement
  • immune effector cells i.e., in the absence of immune effector cells.
  • loss of membrane integrity as evaluated by uptake of propidium iodide (PI), trypan blue (see Moore et al. Cytotechnology 17: 1-1 1 (1995)) or 7AAD can be assessed relative to untreated cells.
  • Preferred cell death-inducing antibodies, oligopeptides or other organic molecules are those which induce PI uptake in the PI uptake assay in BT474 cells.
  • a “OPN-expressing cell” is a cell which expresses an endogenous or transfected nucleic acid which encodes for an OPN polypeptide or which expresses an endogenous or transfected OPN polypeptide in a secreted form.
  • a “OPN-expressing cancer” is a cancer comprising cell that expresses a nucleic acid which encodes an OPN polypeptide and which may produce and secrete a OPN polypeptide.
  • a “OPN-expressing cancer” optionally produces sufficient levels of OPN polypeptide thereof, such that an anti-OPN antibody, oligopeptide to other organic molecule can bind to OPN polypeptide and have a therapeutic effect with respect to the cancer.
  • the antagonist may be an antisense oligonucleotide which reduces, inhibits or prevents production and secretion of the secreted OPN polypeptide by tumor cells.
  • a cancer which "overexpresses" a OPN polypeptide is one which has significantly higher levels of OPN polypeptide that is produced and secreted, compared to a noncancerous cell of the same tissue type. Such overexpression may be caused by gene amplification or by increased transcription or translation.
  • OPN polypeptide overexpression may be determined in a detection or prognostic assay by evaluating increased levels of the OPN protein secreted by the cell (e.g., via an immunohistochemistry assay using anti-OPN antibodies prepared against an isolated OPN polypeptide which may be prepared using recombinant DNA technology from an isolated nucleic acid encoding the OPN polypeptide; FACS analysis, etc.).
  • OPN polypeptide-encoding nucleic acid or mRNA may be measured levels of OPN polypeptide-encoding nucleic acid or mRNA in the cell, e.g., via fluorescent in situ hybridization using a nucleic acid based probe corresponding to a OPN- encoding nucleic acid or the complement thereof; (FISH; see WO98/45479 published October, 1998), Southern blotting, Northern blotting, or polymerase chain reaction (PCR) techniques, such as real time quantitative PCR (RT-PCR).
  • FISH fluorescent in situ hybridization using a nucleic acid based probe corresponding to a OPN- encoding nucleic acid or the complement thereof;
  • PCR polymerase chain reaction
  • RT-PCR real time quantitative PCR
  • immunoadhesin designates antibody-like molecules which combine the binding specificity of a heterologous protein (an “adhesin”) with the effector functions of immunoglobulin constant domains.
  • the immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity which is other than the antigen recognition and binding site of an antibody (i.e., is “heterologous"), and an immunoglobulin constant domain sequence.
  • the adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand.
  • the immunoglobulin constant domain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG-I , IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-I and IgA-2), IgE, IgD or IgM.
  • immunoglobulin such as IgG-I , IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-I and IgA-2), IgE, IgD or IgM.
  • label when used herein refers to a detectable compound or composition which is conjugated directly or indirectly to the antibody, oligopeptide or other organic molecule so as to generate a "labeled" antibody, oligopeptide or other organic molecule.
  • the label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable.
  • cytotoxic agent refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells.
  • the term is intended to include radioactive isotopes
  • chemotherapeutic agents e.g., At 2 ", I 131 , 1 125 , Y 90 , Re 186 , Re 188 , Sm 153 , Bi 212 , P 32 and radioactive isotopes of Lu
  • chemotherapeutic agents e.g., At 2 ", I 131 , 1 125 , Y 90 , Re 186 , Re 188 , Sm 153 , Bi 212 , P 32 and radioactive isotopes of Lu
  • chemotherapeutic agents e.g., At 2 ", I 131 , 1 125 , Y 90 , Re 186 , Re 188 , Sm 153 , Bi 212 , P 32 and radioactive isotopes of Lu
  • methotrexate adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents, enzymes and fragments thereof such as nucleolytic enzymes, antibiotics, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof, and the various antitumor or anticancer agents disclosed below. Other cytotoxic agents are described below.
  • a tumoricidal agent causes destruction of tumor cells.
  • a “growth inhibitory agent” when used herein refers to a compound or composition which inhibits growth of a cell, especially a OPN-producing cancer cell, either in vitro or in vivo.
  • the growth inhibitory agent may be one which significantly reduces the percentage of OPN-producing cells in S phase.
  • growth inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce Gl arrest and M-phase arrest.
  • Classical M-phase blockers include the vincas (vincristine and vinblastine), taxanes, and topoisomerase II inhibitors such as doxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin.
  • DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further information can be found in The Molecular Basis of Cancer. Mendelsohn and Israel, eds., Chapter 1 , entitled “Cell cycle regulation, oncogenes, and antineoplastic drugs” by Murakami et al. (WB Saunders: Philadelphia, 1995), especially p. 13.
  • the taxanes paclitaxel and docetaxel are anticancer drugs both
  • Docetaxel (TAXOTERE®, Rhone-Poulenc Rorer), derived from the European yew, is a semisynthetic analogue of paclitaxel (TAXOL®, Bristol-Myers Squibb). Paclitaxel and docetaxel promote the assembly of microtubules from tubulin dimers and stabilize microtubules by preventing depolymerization, which results in the inhibition of mitosis in cells. "Doxorubicin” is an anthracycline antibiotic.
  • doxorubicin The full chemical name of doxorubicin is (8S- cis)-10-[(3-amino-2,3,6-trideoxy- ⁇ -L-lyxo-hexapyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,l 1-trihydroxy- 8-(hydroxyacetyl)- 1 -methoxy-5, 12-naphthacenedione.
  • cytokine is a generic term for proteins released by one cell population which act on another cell as intercellular mediators.
  • cytokines are lymphokines, monokines, and traditional polypeptide hormones. Included among the cytokines are growth hormone such as human growth hormone, N-methionyl human growth hormone, and bovine growth hormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin; prorelaxin; glycoprotein hormones such as follicle stimulating hormone (FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH); hepatic growth factor; fibroblast growth factor; prolactin; placental lactogen; tumor necrosis factor- ⁇ and - ⁇ ; mullerian-inhibiting substance; mouse gonadotropin-associated peptide; inhibin; activin; vascular endothelial growth factor; integrin; thrombopoietin (TPO); nerve growth factors such as NGF- ⁇ ; platelet-growth factor;
  • cytokine includes proteins from natural sources or from recombinant cell culture and biologically active equivalents of the native sequence cytokines.
  • package insert is used to refer to instructions customarily included in commercial packages of therapeutic products, that contain information about the indications, usage, dosage, administration, contraindications and/or warnings concerning the use of such therapeutic products.
  • the present invention provides anti-OPN antibodies which may find use herein as therapeutic agents.
  • Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies.
  • Polyclonal antibodies are preferably raised in animals by multiple subcutaneous (sc) or intraperitoneal (ip) injections of the relevant antigen and an adjuvant. It may be useful to conjugate the relevant antigen (especially when synthetic peptides are used) to a protein that is immunogenic in the species to be immunized.
  • KLH keyhole limpet hemocyanin
  • serum albumin serum albumin
  • bovine thyroglobulin or soybean trypsin inhibitor
  • a bifunctional or derivatizing agent e.g., maleimidobenzoyl sulfosuccinimide ester (conjugation through cysteine residues), N-hydroxysuccinimide (through lys
  • Animals are immunized against the antigen, immunogenic conjugates, or derivatives by combining, e.g., 100 ⁇ g or 5 ⁇ g of the protein or conjugate (for rabbits or mice, respectively) with 3 volumes of Freund's complete adjuvant and injecting the solution intradermally at multiple sites.
  • the animals are boosted with 1/5 to 1/10 the original amount of peptide or conjugate in Freund's complete adjuvant by subcutaneous injection at multiple sites.
  • the animals are bled and the serum is assayed for antibody titer. Animals are boosted until the titer plateaus.
  • Conjugates also can be made in recombinant cell culture as protein fusions. Also, aggregating agents such as alum are suitably used to enhance the immune response.
  • Monoclonal antibodies may be made using the hybridoma method first described by Kohler et al., Nature, 256:495 (1975), or may be made by recombinant DNA methods (U.S. Patent No. 4,816,567).
  • lymphocytes In the hybridoma method, a mouse or other appropriate host animal, such as a hamster, is immunized as described above to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the protein used for immunization.
  • lymphocytes may be immunized in vitro. After immunization, lymphocytes are isolated and then fused with a myeloma cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell
  • the hybridoma cells thus prepared are seeded and grown in a suitable culture medium which medium preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells (also referred to as fusion partner).
  • a suitable culture medium which medium preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells (also referred to as fusion partner).
  • the parental myeloma cells lack the enzyme hypoxanthine guanine phosphoribosyl transferase (HGPRT or HPRT)
  • HGPRT or HPRT the selective culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
  • Preferred fusion partner myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a selective medium that selects against the unfused parental cells.
  • Preferred myeloma cell lines are murine myeloma lines, such as those derived from MOPC-21 and MPC-1 1 mouse tumors available from the SaIk Institute Cell Distribution Center, San Diego, California USA, and SP-2 and derivatives e.g., X63- Ag8-653 cells available from the American Type Culture Collection, Manassas, Virginia, USA.
  • Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); and Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp. 51 -63 (Marcel Dekker, Inc., New York, 1987)).
  • Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the antigen.
  • the binding specificity of monoclonal antibodies produced by hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunosorbent assay (ELISA).
  • RIA radioimmunoassay
  • ELISA enzyme-linked immunosorbent assay
  • the binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis described in Munson et al., Anal. Biochem., 107:220 (1980).
  • the clones may be subcloned by limiting dilution procedures and grown by standard methods (Goding, Monoclonal Antibodies: Principles and Practice, pp.59-103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D-MEM or RPMI- 1640 medium.
  • the hybridoma cells may be grown in vivo as ascites tumors in an animal e.g,, by i.p. injection of the cells into mice.
  • the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional antibody purification procedures such as, for example, affinity chromatography (e.g., using protein A or protein G-Sepharose) or ion-exchange chromatography, hydroxylapatite chromatography, gel electrophoresis, dialysis, etc.
  • affinity chromatography e.g., using protein A or protein G-Sepharose
  • ion-exchange chromatography e.g., ion-exchange chromatography
  • hydroxylapatite chromatography hydroxylapatite chromatography
  • gel electrophoresis e.g., dialysis, etc.
  • DNA encoding the monoclonal antibodies is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains'of murine antibodies).
  • the hybridoma cells serve as a preferred source of such DNA.
  • the DNA may be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese Hamster Ovary (CHO) cells, or myeloma cells that do not otherwise produce antibody protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells.
  • host cells such as E. coli cells, simian COS cells, Chinese Hamster Ovary (CHO) cells, or myeloma cells that do not otherwise produce antibody protein.
  • Review articles on recombinant expression in bacteria of DNA encoding the antibody include Skerra et al., Curr. Opinion in Immunol., 5:256-262
  • monoclonal antibodies or antibody fragments can be isolated from antibody phage libraries generated using the techniques described in McCafferty et al., Nature, 348:552-554 (1990). Clackson et al., Nature, 352:624-628 (1991) and Marks et al., J. MoI. Biol.,
  • the DNA that encodes the antibody may be modified to produce chimeric or fusion antibody polypeptides, for example, by substituting human heavy chain and light chain constant domain (C H and C L ) sequences for the homologous murine sequences (U.S. Patent No. 4,816,567; and Morrison, et al., Proc. Natl Acad. Sci. USA, 81 :6851 (1984)), or by fusing the immunoglobulin coding sequence with all or part of the coding sequence for a non-immunoglobulin polypeptide (heterologous polypeptide).
  • C H and C L constant domain
  • the non-immunoglobulin polypeptide sequences can substitute for the constant domains of an antibody, or they are substituted for the variable domains of one antigen-combining site of an antibody to create a chimeric bivalent antibody comprising one antigen-combining site having specificity for an antigen and another antigen-combining site having specificity for a different antigen.
  • the anti-OPN antibodies of the invention may further comprise humanized antibodies or human antibodies.
  • Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab', F(ab') 2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • Humanized antibodies include human immunoglobulins (recipient antibody) in which residues from a complementary determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity and capacity.
  • CDR complementary determining region
  • Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • Humanized antibodies may also comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence.
  • the humanized antibody optimally also will comprise at least a portioff of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-329 (1988); and Presta, Curr. Qp. Struct. Biol.. 2:593-596 (1992)].
  • Fc immunoglobulin constant region
  • Humanization can be essentially performed following the method of Winter and co-workers [Jones et al., Nature, 321 :522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.
  • such "humanized" antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species.
  • humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
  • variable domains both light and heavy
  • HAMA response human anti- mouse antibody
  • the sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable domain sequences.
  • the human V domain sequence which is closest to that of the rodent is identified and the human framework region (FR) within it accepted for the humanized antibody (Sims et al., J. Immunol. 151 :2296 (1993); Chothia et al., J. MoI. Biol.. 196:901 (1987)).
  • Another method uses a particular framework region derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains.
  • the same framework may be used for several different humanized antibodies (Carter et al., Proc. Natl. Acad. Sci. USA. 89:4285 (1992); Presta et al., J. Immunol. 151 :2623 (1993)).
  • humanized antibodies are prepared by a process of analysis of the parental sequences and ⁇ various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
  • Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art.
  • Computer programs are available which illustrate and display probable three- dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, i.e., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen.
  • FR residues can be selected and combined from the recipient and import sequences so that the desired antibody characteristic, such as increased affinity for the target antigen(s), is achieved.
  • the hypervariable region residues are directly and most substantially involved in influencing antigen binding.
  • humanized anti-OPN antibody may be an antibody fragment, such as a Fab, which is optionally conjugated with one or more cytotoxic agent(s) in order to generate an immunoconjugate.
  • the humanized antibody may be an intact antibody, such as an intact IgGl antibody.
  • human antibodies can be generated. For example, it is now possible to produce transgenic animals (e.g., mice) that are capable, upon immunization, of producing a full repertoire of human antibodies in the absence of endogenous immunoglobulin production.
  • J H antibody heavy-chain joining region
  • phage display technology can be used to produce human antibodies and antibody fragments in vitro, from immunoglobulin variable (V) domain gene repertoires from unimmunized donors.
  • V domain genes are cloned in-frame into either a major or minor coat protein gene of a filamentous bacteriophage, such as Ml 3 or fd, and displayed as functional antibody fragments on the surface of the phage particle.
  • the filamentous particle contains a single-stranded DNA copy of the phage genome, selections based on the functional properties of the antibody also result in selection of the gene encoding the antibody exhibiting those properties.
  • the phage mimics some of the properties of the B-cell.
  • Phage display can be performed in a variety of formats, reviewed in, e.g., Johnson, Kevin S. and Chiswell. David J., Current Opinion in Structural Biology 3:564-571 (1993).
  • V-gene segments can be used for phage display. Clackson et al., Nature, 352:624-628
  • human antibodies may also be generated by in vitro activated B cells (see U.S. Patents 5,567,610 and 5,229,275).
  • Antibody fragments In certain circumstances there are advantages of using antibody fragments, rather than whole antibodies. The smaller size of the fragments allows for rapid clearance, and may lead to improved access to solid tumors.
  • F(ab') 2 fragments can be isolated directly from recombinant host cell culture.
  • Fab and F(ab') 2 fragment with increased in vivo half-life comprising a salvage receptor binding epitope residues are described in U.S. Patent No. 5,869,046.
  • Other techniques for the production of antibody fragments will be apparent to the skilled practitioner.
  • the antibody of choice is a single chain Fv fragment (scFv). See WO 93/16185;
  • Fv and sFv are the only species with intact combining sites that are devoid of constant regions; thus, they are suitable for reduced nonspecific binding during in vivo use.
  • sFv fusion proteins may be constructed to yield fusion of an effector protein at either the amino or the carboxy terminus of an sFv. See Antibody Engineering, ed. Borrebaeck, supra.
  • the antibody fragment may also be a "linear antibody", e.g., as described in U.S.
  • Patent 5,641 ,870 for example.
  • Such linear antibody fragments may be monospecific or bispecific.
  • Bispecific antibodies are antibodies that have binding specificities for at least two different epitopes. Exemplary bispecific antibodies may bind to two different epitopes of a OPN protein as described herein. Other such antibodies may combine a OPN binding site with a binding site for another protein. Alternatively, an anti-OPN arm may be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD3), or Fc receptors for IgG (Fc ⁇ R), such as Fc ⁇ RI (CD64), Fc ⁇ RII (CD32) and Fc ⁇ RIII (CDl 6), so as to focus and localize cellular defense mechanisms to the OPN-expressing cell.
  • a triggering molecule such as a T-cell receptor molecule (e.g. CD3), or Fc receptors for IgG (Fc ⁇ R), such as Fc ⁇ RI (CD64), Fc ⁇ RII (CD32) and Fc ⁇ RIII (CDl 6), so as to
  • Bispecific antibodies may also be used to localize cytotoxic agents to cells which express OPN. These antibodies possess a OPN-binding arm and an arm which binds the cytotoxic agent (e.g., saporin, anti-interferon- ⁇ , vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten). Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g., F(ab') 2 bispecific antibodies).
  • cytotoxic agent e.g., saporin, anti-interferon- ⁇ , vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten.
  • Bispecific antibodies can be prepared as full length antibodies or antibody fragments (e.g., F(ab') 2 bispecific antibodies).
  • WO 96/16673 describes a bispecific anti-ErbB2/anti-Fc ⁇ RIII antibody and U.S. Patent No. 5,837,234 discloses a bispecific anti-ErbB2/anti-Fc ⁇ RI antibody. A bispecific anti-ErbB2/Fc ⁇ antibody is shown in WO98/02463.
  • U.S. Patent No. 5,821 ,337 teaches a bispecific anti-ErbB2/anti- CD3 antibody.
  • bispecific antibodies are known in the art. Traditional production of full length bispecific antibodies is based on the co-expression of two immunoglobulin heavy chain-light chain pairs, where the two chains have different specificities (Millstein et al., Nature 305:537-539
  • antibody variable domains with the desired binding specificities are fused to immunoglobulin constant domain sequences.
  • the fusion is with an Ig heavy chain constant domain, comprising at least part of the hinge, C H 2, and C H 3 regions. It is preferred to have the first heavy-chain constant region (C H 1) containing the site necessary for light chain bonding, present in at least one of the fusions.
  • DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co-transfected into a suitable host cell.
  • the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh et al.. Methods in Enzymology 121 :210 (1986).
  • the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture.
  • the preferred interface comprises at least a part of the C H 3 domain.
  • one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g., tyrosine or tryptophan).
  • Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers.
  • Bispecific antibodies include cross-linked or "heteroconjugate" antibodies.
  • one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin.
  • Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/200373, and EP 03089).
  • Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross- linking agents are well known in the art, and are disclosed in U.S. Patent No. 4,676,980, along with a number of cross-linking techniques.
  • bispecific antibodies can be prepared using chemical linkage.
  • bispecific antibody F(ab') 2 molecule Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody.
  • the bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.
  • Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al., J. Immunol. 148(5): 1547-1553 (1992).
  • the leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion.
  • the antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
  • the "diabody” technology described by Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments.
  • the fragments comprise a V H connected to a V L by a linker which is too short to allow pairing between the two domains on the same chain.
  • V H and V L domains of one fragment are forced to pair with the complementary V L and V H domains of another fragment, thereby forming two antigen-binding sites.
  • Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dinners has also been reported. See Gruber et al., J. Immunol., 152:5368 (1994).
  • Antibodies with more than two valencies are contemplated.
  • trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60 (1991).
  • Heteroconjugate antibodies are also within the scope of the present invention.
  • Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells [U.S. Patent No. 4,676,980], and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP 03089].
  • the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents.
  • immunotoxins may be constructed using a disulfide exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980.
  • a multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind.
  • the antibodies of the present invention can be multivalent antibodies (which are other than of the IgM class) with three or more antigen binding sites (e.g. tetravalent antibodies), which can be readily produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody.
  • the multivalent antibody can comprise a dimerization domain and three or more antigen binding sites.
  • the preferred dimerization domain comprises (or consists of) an Fc region or a hinge region. In this scenario, the antibody will comprise an Fc region and three or more antigen binding sites amino-terminal to the Fc region.
  • the preferred multivalent antibody herein comprises (or consists of) three to about eight, but preferably four, antigen binding sites.
  • the multivalent antibody comprises at least one polypeptide chain (and preferably two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable domains.
  • the polypeptide chain(s) may comprise VDl -(Xl ) n -VD2-(X2) n -Fc, wherein VDl is a first variable domain, VD2 is a second variable domain, Fc is one polypeptide chain of an Fc region, Xl and X2 represent an amino acid or polypeptide, and n is 0 or 1.
  • the polypeptide chain(s) may comprise: VH-CHl -flexible linker- VH-CHl -Fc region chain; or VH-CHl- VH-CHl-Fc region chain.
  • the multivalent antibody herein preferably further comprises at least two (and preferably four) light chain variable domain polypeptides.
  • the multivalent antibody herein may, for instance, comprise from about two to about eight light chain variable domain polypeptides.
  • the light chain variable domain polypeptides contemplated here comprise a light chain variable domain and, optionally, further comprise a CL domain.
  • effector Function Engineering It may be desirable to modify the antibody of the invention with respect to effector function, e.g., so as to enhance antigen-dependent cell-mediated cyotoxicity (ADCC) and/or complement dependent cytotoxicity (CDC) of the antibody. This may be achieved by introducing one or more amino acid substitutions in an Fc region of the antibody. Alternatively or additionally, 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 internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med.
  • Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross-linkers as described in Wolff et al., Cancer Research 53:2560-2565 (1993).
  • an antibody can be engineered which has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al., Anti-Cancer Drug Design 3:219-230 (1989).
  • a salvage receptor binding epitope into the antibody (especially an antibody fragment) as described in U.S. Patent 5,739,277, for example.
  • the term "salvage receptor binding epitope” refers to an epitope of the Fc region of an IgG molecule (e.g., IgG 1 , IgG 2 , IgG 3 , or IgG 4 ) that is responsible for increasing the in vivo serum half-life of the IgG molecule.
  • the invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • a cytotoxic agent such as a chemotherapeutic agent, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).
  • Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes.
  • radionuclides are available for the production of radioconjugated antibodies. Examples include 212 Bi, 131 I, 131 In, 90 Y, and 186 Re. Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein- coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p- azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)- ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis
  • a ricin immunotoxin can be prepared as described in Vitetta et ai, Science, 238: 1098 (1987).
  • Carbon- 14-labeled l-isothiocyanatobenzyl-3- methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/1 1026.
  • Conjugates of an antibody and one or more small molecule toxins, such as a calicheamicin, maytansinoids, a trichothene, and CCl 065, and the derivatives of these toxins that have toxin activity, are also contemplated herein.
  • an anti-OPN antibody (full length or fragments) of the invention is conjugated to one or more maytansinoid molecules.
  • Maytansinoids are mitototic inhibitors which act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Patent No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Patent No. 4,151,042). Synthetic maytansinol and derivatives and analogues thereof are disclosed, for example, in U.S. Patent Nos. 4, 137,230; 4,248,870;
  • Mavtansinoid-antibodv conjugates In an attempt to improve their therapeutic index, maytansine and maytansinoids have been conjugated to antibodies specifically binding to tumor cell antigens.
  • Immunoconjugates containing maytansinoids and their therapeutic use are disclosed, for example, in U.S. Patent Nos. 5,208,020, 5,416,064 and European Patent EP 0425 235 B 1 , the disclosures of which are hereby expressly incorporated by reference. Liu et al., Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) described immunoconjugates comprising a maytansinoid designated DMl linked to the monoclonal antibody
  • C242 directed against human colorectal cancer.
  • the conjugate was found to be highly cytotoxic towards cultured colon cancer cells, and showed antitumor activity in an in vivo tumor growth assay.
  • Chari et al., Cancer Research 52:127-131 (1992) describe immunoconjugates in which a maytansinoid was conjugated via a disulfide linker to the murine antibody A7 binding to an antigen on human colon cancer cell lines, or to another murine monoclonal antibody TA.1 that binds the HER-2/neu oncogene.
  • the cytotoxicity of the TA.1 -maytansonoid conjugate was tested in vitro on the human breast cancer cell line SK-BR-3, which expresses 3 x 10 5 HER-2 surface antigens per cell.
  • the drug conjugate achieved a degree of cytotoxicity similar to the free maytansonid drug, which could be increased by increasing the number of maytansinoid molecules per antibody molecule.
  • the A7-maytansinoid conjugate showed low systemic cytotoxicity in mice.
  • Anti-OPN polypeptide antibodv-mavtansinoid conjugates immunoconjugates
  • Anti-OPN antibody-maytansinoid conjugates are prepared by chemically linking an anti-OPN antibody to a maytansinoid molecule without significantly diminishing the biological activity of either the antibody or the maytansinoid molecule.
  • An average of 3-4 maytansinoid molecules conjugated per antibody molecule has shown efficacy in enhancing cytotoxicity of target cells without negatively affecting the function or solubility of the antibody, although even one molecule of toxin/antibody would be expected to enhance cytotoxicity over the use of naked antibody.
  • Maytansinoids are well known in the art and can be synthesized by known techniques or isolated from natural sources. Suitable maytansinoids are disclosed, for example, in U.S. Patent No.
  • Preferred maytansinoids are maytansinol and maytansinol analogues modified in the aromatic ring or at other positions of the maytansinol molecule, such as various maytansinol esters.
  • linking groups known in the art for making antibody-maytansinoid conjugates, including, for example, those disclosed in U.S. Patent No. 5,208,020 or EP Patent 0 425 235 Bl, and Chari et al., Cancer Research 52:127-131 (1992).
  • the linking groups include disufide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups, or esterase labile groups, as disclosed in the above-identified patents, disulfide and thioether groups being preferred.
  • Conjugates of the antibody and maytansinoid may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-
  • SPDP N-succinimidyl-3-(2-pyridyldithio) propionate
  • succinimidyl- succinimidyl-
  • imidoesters such as dimethyl adipimidate HCL
  • active esters such as disuccinimidyl suberate
  • aldehydes such as glutareldeh
  • Particularly preferred coupling agents include N-succinimidyl-3-(2- pyridyldithio) propionate (SPDP) (Carlsson et al., Biochem. J. 173:723-737 [1978]) and N- succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for a disulfide linkage.
  • SPDP N-succinimidyl-3-(2- pyridyldithio) propionate
  • SPP N- succinimidyl-4-(2-pyridylthio)pentanoate
  • the linker may be attached to the maytansinoid molecule at various positions, depending on the type of the link.
  • an ester linkage may be formed by reaction with a hydroxyl group using conventional coupling techniques. The reaction may occur at the C-3 position having a hydroxyl group, the C-14 position modified with hyrdoxymethyl, the C-15 position modified with a hydroxyl group, and the C-20 position having a hydroxyl group.
  • the linkage is formed at the C-3 position of maytansinol or a maytansinol analogue.
  • Another immunoconjugate of interest comprises an anti-OPN antibody conjugated to one or more calicheamicin molecules.
  • the calicheamicin family of antibiotics are capable of producing double-stranded DNA breaks at sub-picomolar concentrations.
  • For the preparation of conjugates of the calicheamicin family see U.S. patents 5,712,374, 5,714,586, 5,739,1 16, 5,767,285, 5,770,701,
  • Structural analogues of calicheamicin which may be used include, but are not limited to, ⁇ /, ⁇ 2 ', ⁇ 3 ', N-acetyl- ⁇ , 1 , PSAG and ⁇ (Hinman et al., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research 58:2925-2928 ( 1998) and the aforementioned U.S. patents to American Cyanamid).
  • Another anti-tumor drug that the antibody can be conjugated is QFA which is an antifolate.
  • QFA is an antifolate.
  • Both calicheamicin and QFA have intracellular sites of action and do not readily cross the plasma membrane. Therefore, cellular uptake of these agents through antibody mediated internalization greatly enhances their cytotoxic effects.
  • cytotoxic agents include BCNU, streptozoicin, vincristine and 5-fluorouracil, the family of agents known collectively LL-E33288 complex described in U.S. patents 5,053,394, 5,770,710, as well as esperamicins (U.S. patent 5,877,296).
  • Enzymatically active toxins and fragments thereof which can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes.
  • diphtheria A chain nonbinding active fragments of diphtheria toxin
  • exotoxin A chain from Pseudomonas aeruginosa
  • ricin A chain abrin A chain
  • modeccin A chain alpha-s
  • the present invention further contemplates an immunoconjugate formed between an antibody and a compound with nucleolytic activity (e.g., a ribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).
  • a compound with nucleolytic activity e.g., a ribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase.
  • the antibody may comprise a highly radioactive atom.
  • radioactive isotopes are available for the production of radioconjugated anti-OPN antibodies. Examples include At 2 ", I 131 , 1 125 , Y 90 , Re 186 , Re 188 , Sm 153 , Bi 212 , P 32 , Pb 212 and radioactive isotopes of Lu.
  • the conjugate When used for detection, it may comprise a radioactive atom for scintigraphic studies, for example tc 99m or I 123 , or a spin label for nuclear magnetic resonance (NMR) imaging (also known as magnetic resonance imaging, mri), such as iodine-123 again, iodine-131 , indium- 111, fluorine- 19, carbon-] 3, nitrogen- 15, oxygen- 17, gadolinium, manganese or iron.
  • NMR nuclear magnetic resonance
  • mri nuclear magnetic resonance
  • the radio- or other labels may be incorporated in the conjugate in known ways.
  • the peptide may be biosynthesized or may be synthesized by chemical amino acid synthesis using suitable amino acid precursors involving, for example, fluorine-19 in place of hydrogen.
  • Labels such as tc 99m or I 123 , .Re 186 , Re 188 and In" 1 can be attached via a cysteine residue in the peptide.
  • Yttrium-90 can be attached via a lysine residue.
  • the IODOGEN method (Fraker et al (1978) Biochem. Biophys. Res. Commun. 80: 49-57 can be used to incorporate iodine-123. "Monoclonal Antibodies in
  • Conjugates of the antibody and cytotoxic agent may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl- 4-(N-maleimidomethyI) cyclohexane-1-carboxylate, iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCL), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as 1 ,
  • a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238: 1098 (1987).
  • Carbon- 14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/1 1026.
  • the linker may be a "cleavable linker" facilitating release of the cytotoxic drug in the cell.
  • an acid-labile linker for example, an acid-labile linker, peptidase-sensitive linker, photolabile linker, dimethyl linker or disulfide-containing linker (Chari et al., Cancer Research 52: 127- 131 (1992); U.S. Patent No. 5,208,020) may be used.
  • a fusion protein comprising the anti-OPN antibody and cytotoxic agent may be made, e.g., by recombinant techniques or peptide synthesis.
  • the length of DNA may comprise respective regions encoding the two portions of the conjugate either adjacent one another or separated by a region encoding a linker peptide which does not destroy the desired properties of the conjugate.
  • the antibody may be conjugated to a "receptor” (such streptavidin) for utilization in tumor pre-targeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand” (e.g., avidin) which is conjugated to a cytotoxic agent (e.g., a radionucleotide).
  • a "receptor” such streptavidin
  • a ligand e.g., avidin
  • cytotoxic agent e.g., a radionucleotide
  • the anti-OPN antibodies disclosed herein may also be formulated as immunoliposomes.
  • a "liposome” is a small vesicle composed of various types of lipids, phospholipids and/or surfactant which is useful for delivery of a drug to a mammal.
  • the components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes.
  • Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al.,
  • Particularly useful liposomes can be generated by the reverse phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol and PEG-derivatized phosphatidylethanolamine (PEG-PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter.
  • Fab' fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al., J. Biol. Chem. 257:286-288 (1982) via a disulfide interchange reaction.
  • a chemotherapeutic agent is optionally contained within the liposome. See Gabizon et al., J. National Cancer Inst. 81 (19): 1484 (1989).
  • OPN binding oligopeptides of the present invention are oligopeptides that bind, preferably specifically, to a OPN polypeptide as described herein.
  • OPN binding oligopeptides may be chemically synthesized using known oligopeptide synthesis methodology or may be prepared and purified using recombinant technology.
  • OPN binding oligopeptides are usually at least about 5 amino acids in length, alternatively at least about 6, 7, 8, 9, 10, U , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61 , 62, 63, 64, 65, 66, 67, 68, 69, 70, 71 , 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 amino acids in length or more, wherein such oligopeptides that are capable of binding, preferably specifically, to
  • OPN binding oligopeptides may be identified without undue experimentation using well known techniques.
  • techniques for screening oligopeptide libraries for oligopeptides that are capable of specifically binding to a polypeptide target are well known in the art (see, e.g., U.S. Patent Nos. 5,556,762, 5,750,373, 4,708,871 , 4,833,092, 5,223,409, 5,403,484, 5,571,689, 5,663,143; PCT Publication Nos. WO 84/03506 and WO84/03564;
  • Geysen et al. Proc. Natl. Acad. Sci. U.S.A.. 81 :3998-4002 (1984); Geysen et al., Proc. Natl. Acad. Sci. U.S.A., 82: 178-182 (1985); Geysen et al., in Synthetic Peptides as Antigens, 130-149 ( 1986); Geysen et al.. J. Immunol. Meth., 102:259-274 (1987); Schoofs et al.. J. Immunol., 140:61 1-616 (1988), Cwirla, S. E. et al. (1990) Proc. Natl. Acad. Sci. USA.
  • bacteriophage (phage) display is one well known technique which allows one to screen large oligopeptide libraries to identify member(s) of those libraries which are capable of specifically binding to a polypeptide target.
  • Phage display is a technique by which variant polypeptides are displayed as fusion proteins to the coat protein on the surface of bacteriophage particles (Scott, J.K. and Smith, G. P. (1990) Science. 249: 386).
  • the utility of phage display lies in the fact that large libraries of selectively randomized protein variants (or randomly cloned cDNAs) can be rapidly and efficiently sorted for those sequences that bind to a target molecule with high affinity. Display of peptide (Cwirla, S. E. et al. (1990) Proc. Natl. Acad. Sci. USA. 87:6378) or protein
  • Sorting phage libraries of random mutants requires a strategy for constructing and propagating a large number of variants, a procedure for affinity purification using the target receptor, and a means of evaluating the results of binding enrichments.
  • phage display libraries have been used to analyze and control bimolecular interactions (WO 98/20169; WO 98/20159) and properties of constrained helical peptides (WO 98/20036).
  • WO 97/35196 describes a method of isolating an affinity ligand in which a phage display library is contacted with one solution in which the ligand will bind to a target molecule and a second solution in which the affinity ligand will not bind to the target molecule, to selectively isolate binding ligands.
  • WO 97/46251 describes a method of biopanning a random phage display library with an affinity purified antibody and then isolating binding phage, followed by a micropanning process using microplate wells to isolate high affinity binding phage.
  • Staphlylococcus aureus protein A as an affinity tag has also been reported (Li et al. (1998) MoI Biotech., 9: 187).
  • WO 97/47314 describes the use of substrate subtraction libraries to distinguish enzyme specificities using a combinatorial library which may be a phage display library.
  • a method for selecting enzymes suitable for use in detergents using phage display is described in WO 97/09446. Additional methods of selecting specific binding proteins are described in U.S. Patent Nos. 5,498,538, 5,432,018, and WO
  • OPN binding organic molecules are organic molecules other than oligopeptides or antibodies as defined herein that bind, preferably specifically, to a OPN polypeptide as described herein.
  • OPN binding organic molecules may be identified and chemically synthesized using known methodology (see, e.g., PCT Publication Nos. WO00/00823 and WOOO/39585).
  • OPN binding organic molecules are usually less than about 2000 daltons in size, alternatively less than about 1500, 750, 500, 250 or 200 daltons in size, wherein such organic molecules that are capable of binding, preferably specifically, to a OPN polypeptide as described herein may be identified without undue experimentation using well known techniques.
  • OPN binding organic molecules may be, for example, aldehydes, ketones, oximes, hydrazones, semicarbazones, carbazides, primary amines, secondary amines, tertiary amines, N-substituted hydrazines, hydrazides, alcohols, ethers, thiols, thioethers, disulfides, carboxylic acids, esters, amides, ureas, carbamates, carbonates, ketals, thioketals, acetals, thioacetals, aryl halides, aryl sulfonates, alkyl halides, alkyl sulfonates, aromatic compounds, heterocyclic compounds, anilines, alkenes, alkynes, diols, amino alcohols, oxazolidines, oxazolines, thiazolidines, thiazolines, enamines, sulfonamides, ep
  • Organic Molecules with the Desired Properties Techniques for generating antibodies, oligopeptides and organic molecules that bind to OPN polypeptides have been described above.
  • an anti-OPN antibody, oligopeptide or other organic molecule of the invention may be assessed by methods known in the art, e.g., using cells which express a OPN polypeptide either endogenously or exogenously following transfection with the OPN gene or exogenously adding OPN polypeptide.
  • appropriate tumor cell lines and OPN-transfected cells may be treated with an anti-OPN monoclonal antibody, oligopeptide or other organic molecule of the invention at various concentrations for a few days (e.g., 2-7) days and stained with crystal violet or MTT or analyzed by some other colorimetric assay.
  • Another method of measuring proliferation would be by comparing 3 H-thymidine uptake by the cells treated in the presence or absence an anti-OPN antibody, OPN binding oligopeptide or OPN binding organic molecule of the invention. After treatment, the cells are harvested and the amount of radioactivity incorporated into the DNA quantitated in a scintillation counter. Appropriate positive controls include treatment of a selected cell line with a growth inhibitory antibody known to inhibit growth of that cell line. Growth inhibition of tumor cells in vivo can be determined in various ways known in the art.
  • the source of the OPN polyepepide may be from endogenous or exongeous expression of the OPN polypeptide or from transfection with the OPN gene or exogenous adding of OPN polypeptide.
  • the anti-OPN antibody, OPN binding oligopeptide or OPN binding organic molecule will inhibit cell proliferation of a OPN- producing tumor cell or a OPN-receptor-expressing tumor cell in vitro or in vivo by about 25-100% compared to the untreated tumor cell, more preferably, by about 30-100%, and even more preferably by about 50-100% or 70-100%, in one embodiment, at an antibody concentration of about 0.5 to 30 ⁇ g/ml. Growth inhibition can be measured at an antibody concentration of about 0.5 to 30 ⁇ g/ml or about 0.5 nM to 200 nM in cell culture, where the growth inhibition is determined 1-10 days after exposure of the tumor cells to the antibody.
  • the antibody is growth inhibitory in vivo if administration of the anti-OPN antibody at about 1 ⁇ g/kg to about 100 mg/kg body weight results in reduction in tumor size or reduction of tumor cell proliferation within about 5 days to 3 months from the first administration of the antibody, preferably within about 5 to 30 days.
  • OPN binding oligopeptide or OPN binding organic molecule which induces cell death, loss of membrane integrity as indicated by, e.g., propidium iodide (PI), trypan blue or 7AAD uptake may be assessed relative to control.
  • a PI uptake assay can be performed in the absence of complement and immune effector cells.
  • OPN polypeptide-expressing tumor cells are incubated with medium alone or medium containing the appropriate anti-OPN antibody (e.g, at about lO ⁇ g/ml), OPN binding oligopeptide or OPN binding organic molecule. The cells are incubated for a 3 day time period.
  • Those anti-OPN antibodies, OPN binding oligopeptides or OPN binding organic molecules that induce statistically significant levels of cell death as determined by PI uptake may be selected as cell death-inducing anti- OPN antibodies, OPN binding oligopeptides or OPN binding organic molecules.
  • a routine cross-blocking assay such as that described in Antibodies. A Laboratory Manual, Cold Spring Harbor Laboratory, Ed Harlow and David Lane (1988), can be performed. This assay can be used to determine if a test antibody, oligopeptide or other organic molecule binds the same site or epitope as a known anti-OPN antibody.
  • epitope mapping can be performed by methods known in the art .
  • the antibody sequence can be mutagenized such as by alanine scanning, to identify contact residues. The mutant antibody is initially tested for binding with polyclonal antibody to ensure proper folding.
  • peptides corresponding to different regions of an OPN polypeptide can be used in competition assays with the test antibodies or with a test antibody and an antibody with a characterized or known epitope.
  • ADPT Antibody Dependent Enzyme Mediated Prodrug Therapy
  • the antibodies of the present invention may also be used in ADEPT by conjugating the antibody to a prodrug-activating enzyme which converts a prodrug (e.g., a peptidyl chemotherapeutic agent, see WO81/01 145) to an active anti-cancer drug.
  • a prodrug e.g., a peptidyl chemotherapeutic agent, see WO81/01 145.
  • the enzyme component of the immunoconjugate useful for ADEPT includes any enzyme capable of acting on a prodrug in such a way so as to covert it into its more active, cytotoxic form.
  • Enzymes that are useful in the method of this invention include, but are not limited to, alkaline phosphatase useful for converting phosphate-containing prodrugs into free drugs; arylsulfatase useful for converting sulfate-containing prodrugs into free drugs; cytosine deaminase useful for converting non-toxic 5-fluorocytosine into the anti-cancer drug, 5-fluorouracil; proteases, such as serratia protease, thermolysin, subtilisin, carboxypeptidases and cathepsins (such as cathepsins B and L), that are useful for converting peptide-containing prodrugs into free drugs; D- alanylcarboxypeptidases, useful for converting prodrugs that contain D-amino acid substituent
  • antibodies with enzymatic activity can be used to convert the prodrugs of the invention into free active drugs (see, e.g., Massey, Nature 328:457-458 (1987)).
  • Antibody-abzyme conjugates can be prepared as described herein for delivery of the abzyme to a tumor cell population.
  • the enzymes of this invention can be covalently bound to the anti-OPN antibodies by techniques well known in the art such as the use of the heterobifunctional crosslinking reagents discussed above.
  • fusion proteins comprising at least the antigen binding region of an antibody of the invention linked to at least a functionally active portion of an enzyme of the invention can be constructed using recombinant DNA techniques well known in the art (see, e.g., Neuberger et al., Nature 312:604-608 (1984).
  • the present invention relates to isolated nucleotide sequences encoding polypeptides referred to in the present application as OPN polypeptides.
  • OPN polypeptides referred to in the present application as OPN polypeptides.
  • cDNAs partial and full-length encoding various OPN polypeptides are disclosed in further detail in the Examples below.
  • anti-OPN antibody and OPN polypeptide variants can be prepared.
  • Anti-OPN antibody and OPN polypeptide variants can be prepared by introducing appropriate nucleotide changes into the encoding DNA, and/or by synthesis of the desired antibody or polypeptide.
  • amino acid changes may alter post- translational processes of the anti-OPN antibody or OPN polypeptide, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.
  • Variations in the anti-OPN antibodies and OPN polypeptides described herein can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S. Patent No. 5,364,934.
  • Variations may be a substitution, deletion or insertion of one or more codons encoding the antibody or polypeptide that results in a change in the amino acid sequence as compared with the native sequence antibody or polypeptide.
  • the variation is by substitution of at least one amino acid with any other amino acid in one or more of the domains of the anti-OPN antibody or OPN polypeptide.
  • Guidance in determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the anti-OPN antibody or OPN polypeptide with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology.
  • Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.e., conservative amino acid replacements.
  • Insertions or deletions may optionally be in the range of about 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the full-length or mature native sequence.
  • Anti-OPN antibody and OPN polypeptide fragments are provided herein. Such fragments may be truncated at the N-terminus or C-terminus, or may lack internal residues, for example, when compared with a full length native antibody or protein. Certain fragments lack amino acid residues that are not essential for a desired biological activity of the anti-OPN antibody or OPN polypeptide. Anti-OPN antibody and OPN polypeptide fragments may be prepared by any of a number of conventional techniques. Desired peptide fragments may be chemically synthesized.
  • An alternative approach involves generating antibody or polypeptide fragments by enzymatic digestion, e.g., by treating the protein with an enzyme known to cleave proteins at sites defined by particular amino acid residues, or by digesting the DNA with suitable restriction enzymes and isolating the desired fragment.
  • Yet another suitable technique involves isolating and amplifying a DNA fragment encoding a desired antibody or polypeptide fragment, by polymerase chain reaction (PCR). Oligonucleotides that define the desired termini of the DNA fragment are employed at the 5' and 3' primers in the PCR.
  • anti-OPN antibody and OPN polypeptide fragments share at least one biological and/or immunological activity with the native anti-OPN antibody or OPN polypeptide disclosed herein.
  • conservative substitutions of interest are shown in Table 6 under the heading of preferred substitutions. If such substitutions result in a change in biological activity, then more substantial changes, denominated exemplary substitutions in Table 6, or as further described below in reference to amino acid classes, are introduced and the products screened.
  • Substantial modifications in function or immunological identity of the anti-OPN antibody or OPN polypeptide are accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • Amino acids may be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)):
  • Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Such substituted residues also may be introduced into the conservative substitution sites or, more preferably, into the remaining (non-conserved) sites.
  • oligonucleotide-mediated (site-directed) mutagenesis alanine scanning, and PCR mutagenesis.
  • Site-directed mutagenesis Carter et al., Nucl. Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)]
  • cassette mutagenesis [Wells et al., Gene, 34:315 (1985)]
  • restriction selection mutagenesis [Wells et al., Philos.
  • Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous sequence.
  • preferred scanning amino acids are relatively small, neutral amino acids.
  • amino acids include alanine, glycine, serine, and cysteine.
  • Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant [Cunningham and Wells, Science, 244:1081-1085 (1989)].
  • Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions [Creighton, The Proteins, (W. H. Freeman & Co., N.Y.); Chothia, J. MoI. Biol., 150:1 (1976)]. If alanine substitution does not yield adequate amounts of variant, an isoteric amino acid can be used.
  • cysteine residues not involved in maintaining the proper conformation of the anti-OPN antibody or OPN polypeptide also may be substituted, generally with serine, to improve the oxidative stability of the molecule and prevent aberrant crosslinking.
  • cysteine bond(s) may be added to the anti-OPN antibody or OPN polypeptide to improve its stability (particularly where the antibody is an antibody fragment such as an Fv fragment).
  • a particularly preferred type of substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g., a humanized or human antibody).
  • a parent antibody e.g., a humanized or human antibody
  • the resulting variant(s) selected for further development will have improved biological properties relative to the parent antibody from which they are generated.
  • a convenient way for generating such substitutional variants involves affinity maturation using phage display. Briefly, several hypervariable region sites (e.g., 6-7 sites) are mutated to generate all possible amino substitutions at each site.
  • the antibody variants thus generated are displayed in a monovalent fashion from filamentous phage particles as fusions to the gene III product of Ml 3 packaged within each particle.
  • the phage-displayed variants are then screened for their biological activity (e.g., binding affinity) as herein disclosed.
  • alanine scanning mutagenesis can be performed to identify hypervariable region residues contributing significantly to antigen binding.
  • the panel of variants is subjected to screening as described herein and antibodies with superior properties in one or more relevant assays may be selected for further development.
  • Nucleic acid molecules encoding amino acid sequence variants of the anti-OPN antibody are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non-variant version of the anti-OPN antibody.
  • H. Modifications of Anti-OPN Antibodies and OPN Polypeptides Covalent modifications of anti-OPN antibodies and OPN polypeptides are included within the scope of this invention.
  • One type of covalent modification includes reacting targeted amino acid residues of an anti-OPN antibody or OPN polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the anti-OPN antibody or OPN polypeptide.
  • Derivatization with bifunctional agents is useful, for instance, for crosslinking anti-OPN antibody or OPN polypeptide to a water-insoluble support matrix or surface for use in the method for purifying anti-OPN antibodies, and vice-versa.
  • crosslinking agents include, e.g., l ,l-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3'-dithiobis(succinimidylpropionate), bifunctional maleimides such as bis-N- maleimido-l ,8-octane and agents such as methyl-3-[(p-azidophenyl)dithio]propioimidate.
  • Another type of covalent modification of the anti-OPN antibody or OPN polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the antibody or polypeptide.
  • "Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence anti-OPN antibody or OPN polypeptide (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), and/or adding one or more glycosylation sites that are not present in the native sequence anti-OPN antibody or OPN polypeptide.
  • the phrase includes qualitative changes in the glycosylation of the native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.
  • Glycosylation of antibodies and other polypeptides is typically either N-linked or O-linked.
  • N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
  • the tripeptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain.
  • the presence of either of these tripeptide sequences in a polypeptide creates a potential glycosylation site.
  • O-linked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine may also be used.
  • Addition of glycosylation sites to the anti-OPN antibody or OPN polypeptide is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above- described tripeptide sequences (for N-linked glycosylation sites).
  • 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 original anti-OPN antibody or OPN polypeptide (for O-linked glycosylation sites).
  • the anti-OPN antibody or OPN polypeptide amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the anti-OPN antibody or OPN polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.
  • Another means of increasing the number of carbohydrate moieties on the anti-OPN antibody or OPN polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330 published 11 September 1987, and in Aplin and Wriston, CRC Crit. Rev. Biochem., pp. 259-306 ( 1981 ).
  • Removal of carbohydrate moieties present on the anti-OPN antibody or OPN polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid residues that serve as targets for glycosylation.
  • Chemical deglycosylation techniques are known in the art and described, for instance, by Hakimuddin, et al., Arch. Biochem. Biophvs., 259:52 (1987) and by Edge et al., Anal. Biochem.. JJ_8:131 (1981).
  • Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al., Meth. Enzvmol,. 138:350 (1987).
  • Another type of covalent modification of anti-OPN antibody or OPN polypeptide comprises linking the antibody or polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S.
  • nonproteinaceous polymers e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes
  • the antibody or polypeptide also may be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization (for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively), in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules), or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • the anti-OPN antibody or OPN polypeptide of the present invention may also be modified in a way to form chimeric molecules comprising an anti-OPN antibody or OPN polypeptide fused to another, heterologous polypeptide or amino acid sequence.
  • a chimeric molecule comprises a fusion of the anti-OPN antibody or OPN polypeptide with a tag polypeptide which provides an epitope to which an anti-tag antibody can selectively bind.
  • the epitope tag is generally placed at the amino- or carboxyl- terminus of the anti- OPN antibody or OPN polypeptide. The presence of such epitope-tagged forms of the anti-OPN antibody or OPN polypeptide can be detected using an antibody against the tag polypeptide.
  • the epitope tag enables the anti-OPN antibody or OPN polypeptide to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag.
  • Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-his) or poly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptide and its antibody 12CA5 [Field et al., MoI. Cell.
  • tag polypeptides include the Flag- peptide [Hopp et al., BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin et al., Science, 255: 192- 194 ( 1992)] ; an ⁇ -tubul i n epitope peptide [Ski nner et al . , J. Biol. Chem., 266: 15163-
  • the chimeric molecule may comprise a fusion of the anti-OPN antibody or OPN polypeptide with an immunoglobulin or a particular region of an immunoglobulin.
  • an immunoglobulin also referred to as an "immunoadhesin”
  • a fusion could be to the Fc region of an IgG molecule.
  • the Ig fusions preferably include the substitution of a soluble (transmembrane domain deleted or inactivated) form of an anti-OPN antibody or OPN polypeptide in place of at least one variable region within an Ig molecule.
  • the immunoglobulin fusion includes the hinge, CH 2 and CH 3 , or the hinge, CHi, CH 2 and CH 3 regions of an IgGl molecule.
  • anti-OPN antibodies and OPN polypeptides by culturing cells transformed or transfected with a vector containing anti-OPN antibody- and OPN polypeptide-encoding nucleic acid. It is, of course, contemplated that alternative methods, which are well known in the art, may be employed to prepare anti-OPN antibodies and OPN polypeptides.
  • the appropriate amino acid sequence, or portions thereof may be produced by direct peptide synthesis using solid-phase techniques [see, e.g., Stewart et al., Solid-Phase Peptide Synthesis. W.H. Freeman Co., San Francisco, CA (1969); Merrifield, J. Am. Chem. Soc, 85:2149- 2154 (1963)]. In vitro protein synthesis may be performed using manual techniques or by automation.
  • DNA encoding anti-OPN antibody or OPN polypeptide may be obtained from a cDNA library prepared from tissue believed to possess the anti-OPN antibody or OPN polypeptide mRNA and to express it at a detectable level.
  • human anti-OPN antibody or OPN polypeptide DNA can be conveniently obtained from a cDNA library prepared from human tissue.
  • the anti-OPN antibody- or OPN polypeptide-encoding gene may also be obtained from a genomic library or by known synthetic procedures (e.g., automated nucleic acid synthesis).
  • Probes such as oligonucleotides of at least about 20-80 bases
  • Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (New York: Cold Spring Harbor
  • the oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized.
  • the oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 32 P-labeled ATP, biotinylation or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency, are provided in Sambrook et al., supra. Sequences identified in such library screening methods can be compared and aligned to other known sequences deposited and available in public databases such as GenBank or other private sequence databases.
  • Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined using methods known in the art and as described herein.
  • Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook et al., supra, to detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. 2. Selection and Transformation of Host Cells
  • Host cells are transfected or transformed with expression or cloning vectors described herein for anti-OPN antibody or OPN polypeptide production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the culture conditions such as media, temperature, pH and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook et al., supra.
  • Methods of eukaryotic cell transfection and prokaryotic cell transformation are known to the ordinarily skilled artisan, for example, CaCl 2 , CaPO 4 , liposome-mediated and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells.
  • the calcium treatment employing calcium chloride, as described in Sambrook et al., supra, or electroporation is generally used for prokaryotes.
  • Infection with Agrobacte ⁇ um tumefaciens is used for transformation of certain plant cells, as described by Shaw et al., Gene, 23:315 (1983) and WO 89/05859 published 29 June 1989.
  • Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells.
  • Suitable. prokaryotes include but are not limited to eubacteria, such as
  • E. coli Kl 2 strain MM294 ATCC 31 ,446
  • E. coli Xl 776 ATCC 31,537
  • E. coli strain W3110 ATCC 27,325)
  • K5 772 ATCC 53,635
  • Other suitable prokaryotic host cells include Enterobacteriaceae such as Escherichia, e.g., E.
  • Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations.
  • strain W31 10 may be modified to effect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. coli W3110 strain 1A2, which has the complete genotype tonA ; E. coli W31 10 strain 9E4, which has the complete genotype tonA ptr3; E. coli W31 10 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3 phoA El 5 (argF-lac)169 degP ompTkan r ; E.
  • coli W31 10 strain 37D6 which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT rbs7 UvG kan r ;.E. coli W3110 strain 40B4, which is strain 37D6 with a non-kanamycin resistant degP deletion mutation; and an E. coli strain having mutant periplasmic protease disclosed in U.S. Patent No. 4,946,783 issued 7 August 1990.
  • in vitro methods of cloning e.g., PCR or other nucleic acid polymerase reactions, are suitable.
  • Full length antibody, antibody fragments, and antibody fusion proteins can be produced in bacteria, in particular when glycosylation and Fc effector function are not needed, such as when the therapeutic antibody is conjugated to a cytotoxic agent (e.g., a toxin) and the immunoconjugate by itself shows effectiveness in tumor cell destruction.
  • Full length antibodies have greater half life in circulation. Production in E. coli is faster and more cost efficient.
  • a cytotoxic agent e.g., a toxin
  • the antibody is isolated from the E. coli cell paste in a soluble fraction and can be purified through, e.g., a protein A or G column depending on the isotype. Final purification can be carried out similar to the process for purifying antibody expressed e.g,, in CHO cells.
  • eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for anti-OPN antibody- or OPN polypeptide-encoding vectors.
  • Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism.
  • Others include Schizosaccharomyces pombe (Beach and Nurse, Nature. 290: 140 [1981]; EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Patent No. 4,943,529; Fleer et al., Bio/Technology, 9:968-975
  • K. laciis such as, e.g., K. laciis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J. Bacteriol., 154(2):737-742 [1983]), K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al., Bio/Technology. 8:135 (1990)), K. thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al., J. Basic Microbiol.. 28:265-278 [ 1988]); Candida;
  • Trichoderma reesia (EP 244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76:5259-5263 [1979]); Schwanniomyces such as Schwanniomyces occidentalis (EP 394,538 published 31 October 1990); and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 January 1991), and Aspergillus hosts such as A. nidulans (Ballance et al., Biochem. Biophvs. Res. Commun., 1 12:284-289 [1983]; Tilburn et al., Gene. 26:205-221 [1983];
  • Methylotropic yeasts are suitable herein and include, but are not limited " to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia, Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs.
  • Suitable host cells for the expression of glycosylated anti-OPN antibody or OPN polypeptide are derived from multicellular organisms.
  • invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells, such as cell cultures of cotton, corn, potato, soybean, petunia, tomato, and tobacco.
  • Numerous baculoviral strains and variants and corresponding permissive insect host cells from hosts such as Spodoptera frugiperda (caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori have been identified.
  • a variety of viral strains for transfection are publicly available, e.g., the L-I variant of Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV, and such viruses may be used as the virus herein according to the present invention, particularly for transfection of Spodoptera frugiperda cells.
  • vertebrate cells have been greatest in vertebrate cells, and propagation of vertebrate cells in culture (tissue culture) has become a routine procedure.
  • useful mammalian host cell lines are monkey kidney CVl line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham et al., J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse Sertoli cells (TM4, Mather, Biol. Reprod.
  • monkey kidney cells (CVl ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL- 1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (Wl 38, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N. Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
  • Host cells are transformed with the above-described expression or cloning vectors for anti- OPN antibody or OPN polypeptide production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the nucleic acid encoding anti-OPN antibody or OPN polypeptide may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression.
  • a replicable vector for cloning (amplification of the DNA) or for expression.
  • the vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage.
  • the appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art.
  • Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan.
  • the OPN may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • a heterologous polypeptide which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • the signal sequence may be a component of the vector, or it may be a part of the anti-OPN antibody- or OPN polypeptide-encoding DNA that is inserted into the vector.
  • the signal sequence may be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders.
  • the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader (including Saccharomyces and Kluyveromyces ⁇ -factor leaders, the latter described in U.S. Patent No. 5,010,182), or acid phosphatase leader, the C albicans glucoamylase leader (EP 362,179 published 4 April 1990), or the signal described in WO 90/13646 published 15 November 1990.
  • mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram- negative bacteria, the 2 ⁇ plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • Selection genes will typically contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • selectable markers for mammalian cells are those that enable the identification of cells competent to take up the anti-OPN antibody- or OPN polypeptide-encoding nucleic acid, such as DHFR or thymidine kinase.
  • An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub et al., Proc. Natl. Acad. Sci. USA, 77:4216 (1980).
  • a suitable selection gene for use in yeast is the trp ⁇ gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature, 282:39 (1979); Kingsman et al., Gene, 7: 141 (1979); Tschemper et al., Gene, 10:157 (1980)].
  • the trp ⁇ gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No.
  • Expression and cloning vectors usually contain a promoter operably linked to the anti-OPN antibody- or OPN polypeptide-encoding nucleic acid sequence to direct mRNA synthesis. Promoters recognized by a variety of potential host cells are well known. Promoters suitable for use with prokaryotic hosts include the ⁇ -lactamase and lactose promoter systems [Chang et al., Nature, 275:615
  • Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S. D.) sequence operably linked to the DNA encoding anti- OPN antibody or OPN polypeptide.
  • Suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase [Hitzeman et al., J. Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al., J. Adv.
  • yeast promoters which are inducible promoters having the additional advantage of transcription controlled by growth conditions, are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for use in yeast expression are further described in EP 73,657.
  • Anti-OPN antibody or OPN polypeptide transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus (UK 2,21 1 ,504 published 5 July 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, and from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • viruses such as polyoma virus, fowlpox virus (UK 2,21 1 ,504 published 5 July 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus,
  • Enhancers are cis- acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription.
  • Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus.
  • Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the anti-OPN antibody or OPN polypeptide coding sequence, but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells yeast, fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms
  • sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding anti-OPN antibody or OPN polypeptide.
  • U.S. Patent Re. 30,985 may be used as culture media for the host cells. Any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCINTM drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art.
  • the culture conditions such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan. 5. Detecting Gene Amplification/Expression
  • Gene amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA [Thomas, Proc. Natl. Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, based on the sequences provided herein.
  • antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes.
  • the antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • Gene expression may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product.
  • Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native sequence OPN polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to OPN DNA and encoding a specific antibody epitope.
  • anti-OPN antibody and OPN polypeptide may be recovered from culture medium or from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g. Triton-X 100) or by enzymatic cleavage. Cells employed in expression of anti- OPN antibody and OPN polypeptide can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell lysing agents.
  • the following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation; reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS- PAGE; ammonium sulfate precipitation; gel filtration using, for example, Sephadex G-75; protein A Sepharose columns to remove contaminants such as IgG; and metal chelating columns to bind epitope- tagged forms of the anti-OPN antibody and OPN polypeptide.
  • the purification step(s) selected will depend, for example, on the nature of the production process used and the particular anti-OPN antibody or OPN polypeptide produced.
  • the antibody can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, are removed, for example, by centrifugation or ultrafiltration.
  • the antibody composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being the preferred purification technique.
  • affinity chromatography is the preferred purification technique.
  • the suitability of protein A as an affinity ligand depends on the species and isotype of any immunoglobulin Fc domain that is present in the antibody.
  • Protein A can be used to purify antibodies that are based on human ⁇ l , ⁇ 2 or ⁇ 4 heavy chains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G is recommended for all mouse isotypes and for human ⁇ 3 (Guss et al., EMBO J. 5:15671575 (1986)).
  • the matrix to which the affinity ligand is attached is most often agarose, but other matrices are available.
  • Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose.
  • the antibody comprises a C H 3 domain
  • Bakerbond ABXTMresin J. T. Baker, Phillipsburg, NJ
  • Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSETM chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS- PAGE, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.
  • the mixture comprising the antibody of interest and contaminants may be subjected to low pH hydrophobic interaction chromatography using an elution buffer at a pH between about 2.5-4.5, preferably performed at low salt concentrations (e.g., from about 0-0.25M salt).
  • Therapeutic formulations of the anti-OPN antibodies, OPN binding oligopeptides, OPN binding organic molecules and/or OPN polypeptides used in accordance with the present invention are prepared for storage by mixing the antibody, polypeptide, oligopeptide or organic molecule having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers
  • Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as acetate, Tris, phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin,
  • the formulations herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • an anti-OPN antibody, OPN binding oligopeptide, or OPN binding organic molecule it may be desirable to include in the one formulation, an additional antibody, e.g., a second anti-OPN antibody which binds a different epitope on the OPN polypeptide, or an antibody to some other target such as a growth factor that affects the growth of the particular cancer.
  • the composition may further comprise a chemotherapeutic agent, cytotoxic agent, cytokine, growth inhibitory agent, anti-hormonal agent, and/or cardioprotectant. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • the active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsules and poly-(methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semi-permeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained- release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No.
  • copolymers of L-glutamic acid and ⁇ ethyl- L-glutamate copolymers of L-glutamic acid and ⁇ ethyl- L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT® (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3-hydroxybutyric acid.
  • LUPRON DEPOT® injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate
  • poly-D-(-)-3-hydroxybutyric acid poly-D-(-)-3-hydroxybutyric acid.
  • the formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.
  • OPN polypeptide overexpression may be analyzed by immunohistochemistry (IHC).
  • IHC immunohistochemistry
  • Parrafin embedded tissue sections from a tumor biopsy may be subjected to the IHC assay and accorded a OPN protein staining intensity criteria as follows:
  • Score 2+ - a weak to moderate complete membrane staining is observed in more than 10% of the tumor cells.
  • Score 3+ - a moderate to strong complete membrane staining is observed in more than 10% of the tumor cells.
  • Those tumors with 0 or 1 + scores for OPN polypeptide expression may be characterized as not overexpressing OPN, whereas those tumors with 2+ or 3+ scores may be characterized as overexpressing OPN.
  • FISH assays such as the INFORM® (sold by Ventana, Arizona) or PATHVISION® (Vysis, Illinois) may be carried out on formalin-fixed, paraffin-embedded tumor tissue to determine the extent (if any) of OPN overexpression in the tumor.
  • OPN overexpression or amplification may be evaluated using an in vivo detection assay, e.g., by administering a molecule (such as an antibody, oligopeptide or organic molecule) which binds the molecule to be detected and is tagged with a detectable label (e.g., a radioactive isotope or a fluorescent label) and externally scanning the patient for localization of the label.
  • a detectable label e.g., a radioactive isotope or a fluorescent label
  • the anti-OPN antibodies, oligopeptides and organic molecules of the invention have various non-therapeutic applications.
  • the anti-OPN antibodies, oligopeptides and organic molecules of the present invention can be useful for staging of OPN polypeptide-expressing cancers (e.g., in radioimaging).
  • the antibodies, oligopeptides and organic molecules are also useful for purification or immunoprecipitation of OPN polypeptide from cells, for detection and quantitation of OPN polypeptide in vitro, e.g., in an ELISA or a Western blot, to kill and eliminate OPN-expressing cells from a population of mixed cells as a step in the purification of other cells.
  • cancer treatment involves one or a combination of the following therapies: surgery to remove the cancerous tissue, radiation therapy, and chemotherapy.
  • Anti-OPN antibody, oligopeptide or organic molecule therapy may be especially desirable in elderly patients who do not tolerate the toxicity and side effects of chemotherapy well and in metastatic disease where radiation therapy has limited usefulness.
  • the tumor targeting anti-OPN antibodies, oligopeptides and organic molecules of the invention are useful to alleviate OPN- expressing cancers upon initial diagnosis of the disease or during relapse.
  • the anti-OPN antibody, oligopeptide or organic molecule can be used alone, or in combination therapy with, e.g., hormones, antiangiogens, or radiolabeled compounds, or with surgery, cryotherapy, and/or radiotherapy.
  • Anti-OPN antibody, oligopeptide or organic molecule treatment can be administered in conjunction with other forms of conventional therapy, either consecutively with, pre- or post- conventional therapy.
  • Chemotherapeutic drugs such as TAXOTERE® (docetaxel), TAXOL®
  • the cancer patient can be administered anti-OPN antibody, oligopeptide or organic molecule in conjunction with treatment with the one or more of the preceding chemotherapeutic agents.
  • combination therapy with palictaxel and modified derivatives is contemplated.
  • the anti-OPN antibody, oligopeptide or organic molecule will be administered with a therapeutically effective dose of the chemotherapeutic agent.
  • the anti-OPN antibody, oligopeptide or organic molecule is administered in conjunction with chemotherapy to enhance the activity and efficacy of the chemotherapeutic agent, e.g., paclitaxel.
  • the Physicians' Desk Reference (PDR) discloses dosages of these agents that have been used in treatment of various cancers.
  • the dosing regimen and dosages of these aforementioned chemotherapeutic drugs that are therapeutically effective will depend on the particular cancer being treated, the extent of the disease and other factors familiar to the physician of skill in the art and can be determined by the physician.
  • a conjugate comprising an anti-OPN antibody, oligopeptide or organic molecule conjugated with a cytotoxic agent is administered to the patient.
  • the immunoconjugate bound to the OPN protein is internalized by the cell, resulting in increased therapeutic efficacy of the immunoconjugate in killing the cancer cell to which it binds.
  • the cytotoxic agent targets or interferes with the nucleic acid in the cancer cell. Examples of such cytotoxic agents are described above and include maytansinoids, calicheamicins, ribonucleases and DNA endonucleases.
  • the anti-OPN antibodies, oligopeptides, organic molecules or toxin conjugates thereof are administered to a human patient, in accord with known methods, such as intravenous administration, e.g.,, as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes.
  • Intravenous or subcutaneous administration of the antibody, oligopeptide or organic molecule is preferred.
  • Other therapeutic regimens may be combined with the administration of the anti-OPN antibody, oligopeptide or organic molecule.
  • the combined administration includes co-administration, using separate formulations or a single pharmaceutical formulation, and consecutive administration in either order, wherein preferably there is a time period while both (or all) active agents simultaneously exert their biological activities.
  • Preferably such combined therapy results in a synergistic therapeutic effect.
  • the therapeutic treatment methods of the present invention involves the combined administration of an anti-OPN antibody (or antibodies), oligopeptides or organic molecules and one or more chemotherapeutic agents or growth inhibitory agents, including co ⁇ administration of cocktails of different chemotherapeutic agents.
  • Chemotherapeutic agents include estramustine phosphate, prednimustine, cisplatin, 5-fluorouracil, melphalan, cyclophosphamide, hydroxyurea and hydroxyureataxanes (such as paclitaxel and doxetaxel) and/or anthracycline antibiotics. Preparation and dosing schedules for such chemotherapeutic agents may be used according to manufacturers' instructions or as determined empirically by the skilled practitioner.
  • the antibody, oligopeptide or organic molecule may be combined with an anti-hormonal compound; e.g., an anti-estrogen compound such as tamoxifen; an anti-progesterone such as onapristone (see, EP 616 812); or an anti-androgen such as flutamide, in dosages known for such molecules.
  • an anti-hormonal compound e.g., an anti-estrogen compound such as tamoxifen; an anti-progesterone such as onapristone (see, EP 616 812); or an anti-androgen such as flutamide
  • the patient may previously have been subjected to anti-androgen therapy and, after the cancer becomes androgen independent, the anti-OPN antibody, oligopeptide or organic molecule (and optionally other agents as described herein) may be administered to the patient.
  • a cardioprotectant to prevent or reduce myocardial dysfunction associated with the therapy
  • one or more cytokines to the patient.
  • the patient may be subjected to surgical removal of cancer cells and/or radiation therapy, before, simultaneously with, or post antibody, oligopeptide or organic molecule therapy.
  • Suitable dosages for any of the above co-administered agents are those presently used and may be lowered due to the combined action (synergy) of the agent and anti-OPN antibody, oligopeptide or organic molecule.
  • the dosage and mode of administration will be chosen by the physician according to known criteria.
  • the appropriate dosage of antibody, oligopeptide or organic molecule will depend on the type of disease to be treated, as defined above, the severity and course of the disease, whether the antibody, oligopeptide or organic molecule is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the antibody, oligopeptide or organic molecule, and the discretion of the attending physician.
  • the antibody, oligopeptide or organic molecule is suitably administered to the patient at one time or over a series of treatments.
  • the antibody, oligopeptide or organic molecule is administered by intravenous infusion or by subcutaneous injections.
  • about 1 ⁇ g/kg to about 50 mg/kg body weight (e.g., about 0.1-15mg/kg/dose) of antibody can be an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion.
  • a dosing regimen can comprise administering an initial loading dose of about 4 mg/kg, followed by a weekly maintenance dose of about 2 mg/kg of the anti-OPN antibody.
  • other dosage regimens may be useful.
  • a typical daily dosage might range from about 1 ⁇ g/kg to 100 mg/kg or more, depending on the factors mentioned above.
  • the treatment is sustained until a desired suppression of disease symptoms occurs. The progress of this therapy can be readily monitored by conventional methods and assays and based on criteria known to the physician or other persons of skill in the art.
  • the present application contemplates administration of the antibody by gene therapy.
  • administration of nucleic acid encoding the antibody is encompassed by the expression "administering a therapeutically effective amount of an antibody”. See, for example, WO96/07321 published March 14, 1996 concerning the use of gene therapy to generate intracellular antibodies.
  • nucleic acid (optionally contained in a vector) into the patient's cells
  • in vivo and ex vivo the nucleic acid is injected directly into the patient, usually at the site where the antibody is required.
  • ex vivo treatment the patient's cells are removed, the nucleic acid is introduced into these isolated cells and the modified cells are administered to the patient either directly or, for example, encapsulated within porous membranes which are implanted into the patient (see, e.g., U.S. Patent Nos. 4,892,538 and 5,283,187).
  • U.S. Patent Nos. 4,892,538 and 5,283,187 There are a variety of techniques available for introducing nucleic acids into viable cells.
  • the techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or in vivo in the cells of the intended host.
  • Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc.
  • a commonly used vector for ex vivo delivery of the gene is a retroviral vector.
  • the currently preferred in vivo nucleic acid transfer techniques include transfection with viral vectors (such as adenovirus, Herpes simplex I virus, or adeno-associated virus) and lipid-based systems (useful lipids for lipid-mediated transfer of the gene are DOTMA, DOPE and DC-Choi, for example).
  • viral vectors such as adenovirus, Herpes simplex I virus, or adeno-associated virus
  • lipid-based systems useful lipids for lipid-mediated transfer of the gene are DOTMA, DOPE and DC-Choi, for example.
  • the anti-OPN antibodies of the invention can be in the different forms encompassed by the definition of "antibody” herein.
  • the antibodies include full length or intact antibody, antibody fragments, native sequence antibody or amino acid variants, humanized, chimeric or fusion antibodies, immunoconjugates, and functional fragments thereof.
  • fusion antibodies an antibody sequence is fused to a heterologous polypeptide sequence.
  • the antibodies can be modified in the Fc region to provide desired effector functions.
  • the naked antibody bound on the cell surface can induce cytotoxicity, e.g., via antibody-dependent cellular cytotoxicity (ADCC) or by recruiting complement in complement dependent cytotoxicity, or some other mechanism.
  • ADCC antibody-dependent cellular cytotoxicity
  • certain other Fc regions may be used.
  • the antibody competes for binding or bind substantially to, the same epitope as the antibodies of the invention.
  • Antibodies having the biological characteristics of the present anti-OPN antibodies of the invention are also contemplated, specifically including the in vivo tumor targeting and any cell proliferation inhibition or cytotoxic characteristics.
  • the present anti-OPN antibodies, oligopeptides and organic molecules are useful for treating a OPN-expressing cancer or alleviating one or more symptoms of the cancer in a mammal.
  • a cancer includes, but is not limited to, breast, such as metastatic mammary carcinoma, lung, colon, prostate, pancrease, bone, ovary, brain tumor, such as glioma.
  • the cancers encompass metastatic cancers of any of the preceding.
  • the antibody, oligopeptide or organic molecule is able to bind to at least a portion of the cancer cells that express OPN polypeptide in the mammal.
  • the antibody, oligopeptide or organic molecule is effective to destroy or kill OPN- expressing tumor cells or inhibit the growth of such tumor cells, in vitro or in vivo, upon binding to OPN polypeptide.
  • Such an antibody includes a naked anti-OPN antibody (not conjugated to any agent). Naked antibodies that have cytotoxic or cell growth inhibition properties can be further harnessed with a cytotoxic agent to render them even more potent in tumor cell destruction. Cytotoxic properties can be conferred to an anti-OPN antibody by, e.g., conjugating the antibody with a cytotoxic agent, to form an immunoconjugate as described herein.
  • the cytotoxic agent or a growth inhibitory agent is preferably a small molecule. Toxins such as calicheamicin or a maytansinoid and analogs or derivatives thereof, are preferable.
  • compositions comprising an anti-OPN antibody, oligopeptide or organic molecule of the invention, and a carrier.
  • compositions can be administered to the patient in need of such treatment, wherein the composition can comprise one or more anti-OPN antibodies present as an immunoconjugate or as the naked antibody.
  • the compositions can comprise these antibodies, oligopeptides or organic molecules in combination with other therapeutic agents such as cytotoxic or growth inhibitory agents, including chemotherapeutic agents.
  • the invention also provides formulations comprising an anti-OPN antibody, oligopeptide or organic molecule of the invention, and a carrier.
  • the formulation is a therapeutic formulation comprising a pharmaceutically acceptable carrier.
  • nucleic acids encoding the anti-OPN antibodies are encompassed.
  • the invention also provides methods useful for treating a OPN polypeptide-expressing cancer or alleviating one or more symptoms of the cancer in a mammal, comprising administering a therapeutically effective amount of an anti-OPN antibody, oligopeptide or organic molecule to the mammal.
  • the antibody, oligopeptide or organic molecule therapeutic compositions can be administered short term (acute) or chronic, or intermittent as directed by physician. Also provided are methods of inhibiting the growth of, and killing a OPN polypeptide-expressing cell.
  • kits and articles of manufacture comprising at least one anti-OPN antibody, oligopeptide or organic molecule.
  • Kits containing anti-OPN antibodies, oligopeptides or organic molecules find use, e.g., for OPN cell killing assays, for purification or immunoprecipitation of OPN polypeptide from cells.
  • the kit can contain an anti-OPN antibody, oligopeptide or organic molecule coupled to beads (e.g., sepharose beads).
  • Kits can be provided which contain the antibodies, oligopeptides or organic molecules for detection and quantitation of OPN in vitro, e.g., in an ELISA or a Western blot.
  • Such antibody, oligopeptide or organic molecule useful for detection may be provided with a label such as a fluorescent or radiolabel.
  • a label such as a fluorescent or radiolabel.
  • Another embodiment of the invention is an article of manufacture containing materials useful for the treatment of anti-OPN expressing cancer.
  • the article of manufacture comprises a container and a label or package insert on or associated with the container.
  • Suitable containers include, for example, bottles, vials, syringes, etc.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition which is effective for treating the cancer condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • At least one active agent in the composition is an anti-OPN antibody, oligopeptide or organic molecule of the invention.
  • the label or package insert indicates that the composition is used for treating cancer.
  • the label or package insert will further comprise instructions for administering the antibody, oligopeptide or organic molecule composition to the cancer patient.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.
  • Kits are also provided that are useful for various purposes , e.g., for OPN-expressing cell killing assays, for purification or immunoprecipitation of OPN polypeptide from cells.
  • the kit can contain an anti-OPN antibody, oligopeptide or organic molecule coupled to beads (e.g., sepharose beads).
  • Kits can be provided which contain the antibodies, oligopeptides or organic molecules for detection and quantitation of OPN polypeptide in vitro, e.g., in an ELISA or a Western blot.
  • the kit comprises a container and a label or package insert on or associated with the container.
  • the container holds a composition comprising at least one anti-OPN antibody, oligopeptide or organic molecule of the invention. Additional containers may be included that contain, e.g., diluents and buffers, control antibodies.
  • the label or package insert may provide a description of the composition as well as instructions for the intended in vitro or detection use.
  • Nucleotide sequences (or their complement) encoding OPN polypeptides have various applications in the art of molecular biology, including uses as hybridization probes, in chromosome and gene mapping and in the generation of anti-sense RNA and DNA probes.
  • OPN-encoding nucleic acid will also be useful for the preparation of OPN polypeptides by the recombinant techniques described herein, wherein those OPN polypeptides may find use, for example, in the preparation of anti-OPN antibodies as described herein.
  • the full-length native sequence OPN gene, or portions thereof, may be used as hybridization probes for a cDNA library to isolate the full-length OPN cDNA or to isolate still other cDNAs (for instance, those encoding naturally-occurring variants of OPN or OPN from other species) which have a desired sequence identity to the native OPN sequence disclosed herein.
  • the length of the probes will be about 20 to about 50 bases.
  • the hybridization probes may be derived from at least partially novel regions of the full length native nucleotide sequence wherein those regions may be determined without undue experimentation or from genomic sequences including promoters, enhancer elements and introns of native sequence OPN.
  • a screening method will comprise isolating the coding region of the OPN gene using the known DNA sequence to synthesize a selected probe of about 40 bases.
  • Hybridization probes may be labeled by a variety of labels, including radionucleotides such as 32 P or 35 S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems. Labeled probes having a sequence complementary to that of the OPN gene of the present invention can be used to screen libraries of human cDNA, genomic DNA or mRNA to determine which members of such libraries the probe hybridizes to. Hybridization techniques are described in further detail in the Examples below.
  • any EST sequences disclosed in the present application may similarly be employed as probes, using the methods disclosed herein.
  • Other useful fragments of the OPN-encoding nucleic acids include antisense or sense oligonucleotides comprising a singe-stranded nucleic acid sequence (either RNA or DNA) capable of binding to target OPN mRNA (sense) or OPN DNA (antisense) sequences.
  • Antisense or sense oligonucleotides, according to the present invention comprise a fragment of the coding region of OPN DNA. Such a fragment generally comprises at least about 14 nucleotides, preferably from about 14 to 30 nucleotides.
  • Stein and Cohen Cancer Res. 48:2659
  • binding of antisense or sense oligonucleotides to target nucleic acid sequences results in the formation of duplexes that block transcription or translation of the target sequence by one of several means, including enhanced degradation of the duplexes, premature termination of transcription or translation, or by other means.
  • the antisense oligonucleotides thus may be used to block expression of OPN proteins, wherein those OPN proteins may play a role in the induction of cancer in mammals.
  • Antisense or sense oligonucleotides further comprise oligonucleotides having modified sugar-phosphodiester backbones (or other sugar linkages, such as those described in WO 91/06629) and wherein such sugar linkages are resistant to endogenous nucleases.
  • Such oligonucleotides with resistant sugar linkages are stable in vivo (i.e., capable of resisting enzymatic degradation) but retain sequence specificity to be able to bind to target nucleotide sequences.
  • Preferred intragenic sites for antisense binding include the region incorporating the translation initiation/start codon (5'-AUG / 5'-ATG) or termination/stop codon (5'-UAA, 5'-UAG and 5-UGA / 5'- TAA, 5'-TAG and 5'-TGA) of the open reading frame (ORF) of the gene. These regions refer to a portion of the mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5' or 3') from a translation initiation or termination codon.
  • Other preferred regions for antisense binding include: introns; exons; intron-exon junctions; the open reading frame (ORF) or "coding region,” which is the region between the translation initiation codon and the translation termination codon; the 5' cap of an mRNA which comprises an N7-methylated guanosine residue joined to the 5'-most residue of the mRNA via a 5'-5' triphosphate linkage and includes 5' cap structure itself as well as the first 50 nucleotides adjacent to the cap; the 5' untranslated region (5'UTR), the portion of an mRNA in the 5' direction from the translation initiation codon, and thus including nucleotides between the 5' cap site and the translation initiation codon of an mRNA or corresponding nucleotides on the gene; and the 3' untranslated region (3'UTR), the portion of an mRNA in the 3' direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3' end of an mRNA or
  • oligonucleotides containing modified backbones or non-natural internucleoside linkages include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone.
  • modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.
  • Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotri-esters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates, 5'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, selenophosphates and borano-phosphates having normal 3'-5' linkages, 2'- 5' linked analogs of these, and those having inverted polarity wherein one or more internucleotide linkages is a 3' to 3', 5' to 5' or 2' to 2' linkage.
  • Preferred oligonucleotides having inverted polarity comprise a single 3' to 3' linkage at the 3'-most internucleotide linkage i.e. a single inverted nucleoside residue which may be abasic (the nucleobase is missing or has a hydroxyl group in place thereof).
  • Various salts, mixed salts and free acid forms are also included.
  • Representative United States patents that teach the preparation of phosphorus-containing linkages include, but are not limited to, U.S. Pat.
  • Preferred modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages.
  • morpholino linkages formed in part from the sugar portion of a nucleoside
  • siloxane backbones sulfide, sulfoxide and sulfone backbones
  • formacetyl and thioformacetyl backbones methylene formacetyl and thioformacetyl backbones
  • riboacetyl backbones alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH.sub.2 component parts.
  • both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups.
  • the base units are maintained for hybridization with an appropriate nucleic acid target compound.
  • One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties is referred to as a peptide nucleic acid (PNA).
  • PNA peptide nucleic acid
  • the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone.
  • nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone.
  • Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos.: 5,539,082; 5,714,331 ; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.
  • Preferred antisense oligonucleotides incorporate phosphorothioate backbones and/or heteroatom backbones, and in particular -CH 2 -NH-O-CH 2 -, -CH 2 -N(CH 3 )-O-CH 2 - [known as a methylene (methylimino) or MMI backbone], -CH 2 -O-N(CH 3 )-CH 2 -, -CH 2 -N(CH 3 )-N(CH 3 )-CH 2 - and -O-N(CH 3 )-CH 2 -CH 2 - [wherein the native phosphodiester backbone is represented as -0-P-O-CH 2 -] described in the above referenced U.S. Pat.
  • Modified oligonucleotides may also contain one or more substituted sugar moieties.
  • Preferred oligonucleotides comprise one of the following at the 2' position: OH; F; O-alkyl, S-alkyl, or N-alkyl; O-alkenyl, S-alkeynyl, or N-alkenyl; O-alkynyl, S-alkynyl or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted Ci to C
  • oligonucleotides comprise one of the following at the 2' position: Ci to C, o lower alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH 3 , OCN, Cl, Br, CN, CF 3 , OCF 3 , SOCH 3 , SO 2 CH 3 , ONO 2 , NO 2 , N 3 , NH 2 , heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties.
  • a preferred modification includes 2'-methoxyethoxy (2'-0-CH 2 CH 2 OCH 3 , also known as 2'-O-(2-methoxyethyl) or 2'-MOE) (Martin et al., HeIv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxyalkoxy group.
  • a further preferred modification includes 2'-dimethylaminooxyethoxy, i.e., a O(CH 2 ) 2 ON(CH 3 ) 2 group, also known as 2'-DMAOE, as described in examples hereinbelow, and T- dimethylaminoethoxyethoxy (also known in the art as 2'-O-dimethylaminoethoxyethyl or T- DMAEOE), i.e., 2'-0-CH 2 -O-CH 2 -N(CH 2 ).
  • 2'-dimethylaminooxyethoxy i.e., a O(CH 2 ) 2 ON(CH 3 ) 2 group
  • T- dimethylaminoethoxyethoxy also known in the art as 2'-O-dimethylaminoethoxyethyl or T- DMAEOE
  • a further prefered modification includes Locked Nucleic Acids (LNAs) in which the T- hydroxyl group is linked to the 3' or 4' carbon atom of the sugar ring thereby forming a bicyclic sugar moiety.
  • the linkage is preferably a methelyne (-CH 2 -) n group bridging the T oxygen atom and the 4' carbon atom wherein n is 1 or 2.
  • LNAs and preparation thereof are described in WO 98/39352 and WO 99/14226.
  • Other preferred modifications include 2'-methoxy (2'-0-CH 3 ), 2'-aminopropoxy (2 1 -
  • Oligonucleotides may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.
  • Representative United States patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat.
  • Oligonucleotides may also include nucleobase (often referred to in the art simply as “base”) modifications or substitutions.
  • nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U).
  • nucleobases include tricyclic pyrimidines such as phenoxazine cytidine(lH-pyrimido[5,4-b][l ,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1 H-pyrimido[5,4-b][l ,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g.
  • nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7- deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S.
  • nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6 substituted purines, including 2-aminopropyladenine, 5-propynyIuracil and 5-propynylcytosine.
  • 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2.degree. C. (Sanghvi et al, Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are preferred base substitutions, even more particularly when combined with 2'-O-methoxyethyl sugar modifications.
  • Representative United States patents that teach the preparation of modified nucleobases include, but are not limited to: U.S. Pat. No. 3,687,808, as well as U.S. Pat.
  • the compounds of the invention can include conjugate groups covalently bound to functional groups such as primary or secondary hydroxyl groups.
  • Conjugate groups of the invention include intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers.
  • Typical conjugates groups include cholesterols, lipids, cation lipids, phospholipids, cationic phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes.
  • Groups that enhance the pharmacodynamic properties include groups that improve oligomer uptake, enhance oligomer resistance to degradation, and/or strengthen sequence-specific hybridization with RNA.
  • Groups that enhance the pharmacokinetic properties include groups that improve oligomer uptake, distribution, metabolism or excretion.
  • Conjugate moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-
  • a thioether e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306- 309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl.
  • Acids Res., 1990, 18, 3777-3783 a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino- carbonyl-oxycholesterol moiety.
  • Oligonucleotides of the invention may also be conjugated to active drug substances, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.
  • active drug substances for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen
  • the present invention also includes antisense compounds which are chimeric compounds.
  • "Chimeric” antisense compounds or “chimeras,” in the context of this invention, are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound.
  • oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid.
  • An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids.
  • RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex.
  • Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above.
  • Preferred chimeric antisense oligonucleotides incorporate at least one 2' modified sugar (preferably 2'-0-(CH 2 ⁇ -O-CH 3 ) at the 3' terminal to confer nuclease resistance and a region with at least 4 contiguous 2'-H sugars to confer RNase H activity.
  • 2' modified sugar preferably 2'-0-(CH 2 ⁇ -O-CH 3 ) at the 3' terminal to confer nuclease resistance and a region with at least 4 contiguous 2'-H sugars to confer RNase H activity.
  • Such compounds have also been referred to in the art as hybrids or gapmers.
  • Preferred gapmers have a region of 2' modified sugars (preferably 2'-O-(CH 2 ) 2 -O-CH 3 ) at the 3'-terminal and at the 5' terminal separated by at least one region having at least 4 contiguous 2'-H sugars and preferably incorporate phosphorothioate backbone linkages.
  • Representative United States patents that teach the preparation of such hybrid structures include, but are not limited to, U.S. Pat. Nos. 5,013,830; 5,149,797; 5,220,007;
  • antisense compounds used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis.
  • Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.).
  • any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.
  • the compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption.
  • Representative United States patents that teach the preparation of such uptake, distribution and/or absorption assisting formulations include, but are not limited to, U.S. Pat. Nos.
  • sense or antisense oligonucleotides include those oligonucleotides which are covalently linked to organic moieties, such as those described in WO 90/10048, and other moieties that increases affinity of the oligonucleotide for a target nucleic acid sequence, such as poly-(L-lysine).
  • intercalating agents such as ellipticine, and alkylating agents or metal complexes may be attached to sense or antisense oligonucleotides to modify binding specificities of the antisense or sense oligonucleotide for the target nucleotide sequence.
  • Antisense or sense oligonucleotides may be introduced into a cell containing the target nucleic acid sequence by any gene transfer method, including, for example, CaPO/i-mediated DNA transfection, electroporation, or by using gene transfer vectors such as Epstein-Barr virus.
  • an antisense or sense oligonucleotide is inserted into a suitable retroviral vector.
  • retroviral vectors include, but are not limited to, those derived from the murine retrovirus M-MuLV, N2 (a retrovirus derived from M-MuLV), or the double copy vectors designated DCT5A, DCT5B and DCT5C (see WO 90/13641 ).
  • Sense or antisense oligonucleotides also may be introduced into a cell containing the target nucleotide sequence by formation of a conjugate with a ligand binding molecule, as described in WO
  • Suitable ligand binding molecules include, but are not limited to, cell surface receptors, growth factors, other cytokines, or other ligands that bind to cell surface receptors.
  • conjugation of the ligand binding molecule does not substantially interfere with the ability of the ligand binding molecule to bind to its corresponding molecule or receptor, or block entry of the sense or antisense oligonucleotide or its conjugated version into the cell.
  • a sense or an antisense oligonucleotide may be introduced into a cell containing the target nucleic acid sequence by formation of an oligonucleotide-lipid complex, as described in WO
  • the sense or antisense oligonucleotide-lipid complex is preferably dissociated within the cell by an endogenous lipase.
  • Antisense or sense RNA or DNA molecules are generally at least about 5 nucleotides in length, alternatively at least about 6, 7, 8, 9, 10, 1 1 , 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 1 10, 1 15, 120, 125,
  • the probes may also be employed in PCR techniques to generate a pool of sequences for identification of closely related OPN coding sequences.
  • Nucleotide sequences encoding a OPN can also be used to construct hybridization probes for mapping the gene which encodes that OPN and for the genetic analysis of individuals with genetic disorders.
  • the nucleotide sequences provided herein may be mapped to a chromosome and specific regions of a chromosome using known techniques, such as in situ hybridization, linkage analysis against known chromosomal markers, and hybridization screening with libraries.
  • the OPN can be used in assays to identify the other proteins or molecules involved in the binding interaction. By such methods, inhibitors of the receptor/ligand binding interaction can be identified. Proteins involved in such binding interactions can also be used to screen for peptide or small molecule inhibitors or agonists of the binding interaction. Also, the receptor OPN can be used to isolate correlative ligand(s). Screening assays- can be designed to find lead compounds that mimic the biological activity of a native OPN or a receptor for OPN.
  • screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.
  • Small molecules contemplated include synthetic organic or inorganic compounds.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays and cell based assays, which are well characterized in the art.
  • Nucleic acids which encode OPN or its modified forms can also be used to generate either transgenic animals or "knock out" animals which, in turn, are useful in the development and screening of therapeutically useful reagents.
  • a transgenic animal e.g., a mouse or rat
  • a transgenic animal is an animal having cells that contain a transgene, which transgene was introduced into the animal or an ancestor of the animal at a prenatal, e.g., an embryonic stage.
  • a transgene is a DNA which is integrated into the genome of a cell from which a transgenic animal develops.
  • cDNA encoding OPN can be used to clone genomic DNA encoding OPN in accordance with established techniques and the genomic sequences used to generate transgenic animals that contain cells which express DNA encoding OPN.
  • transgenic animals particularly animals such as mice or rats
  • transgenic animals have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009.
  • particular cells would be targeted for OPN transgene incorporation with tissue-specific enhancers.
  • Transgenic animals that include a copy of a transgene encoding OPN introduced into the germ line of the animal at an embryonic stage can be used to examine the effect of increased expression of DNA encoding OPN.
  • Such animals can be used as tester animals for reagents thought to confer protection from, for example, pathological conditions associated with its overexpression.
  • an animal is treated with the reagent and a reduced incidence of the pathological condition, compared to untreated animals bearing the transgene, would indicate a potential therapeutic intervention for the pathological condition.
  • non-human homologues of OPN can be used to construct a OPN "knock out" animal which has a defective or altered gene encoding OPN as a result of homologous recombination between the endogenous gene encoding OPN and altered genomic DNA encoding OPN introduced into an embryonic stem cell of the animal.
  • cDNA encoding OPN can be used to clone genomic DNA encoding OPN in accordance with established techniques.
  • a portion of the genomic DNA encoding OPN can be deleted or replaced with another gene, such as a gene encoding a selectable marker which can be used to monitor integration.
  • flanking DNA typically, several kilobases of unaltered flanking DNA (both at the 5' and 3' ends) are included in the vector [see e.g., Thomas and Capecchi, Cell, 51 :503 (1987) for a description of homologous recombination vectors].
  • the vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA are selected [see e.g., Li et al., Cell, 69:915 (1992)].
  • the selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras [see e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 1 13-152].
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a "knock out" animal.
  • Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA.
  • Knockout animals can be characterized for instance, for their ability to defend against certain pathological conditions and for their development of pathological conditions due to absence of the OPN polypeptide.
  • Nucleic acid encoding the OPN polypeptides may also be used in gene therapy.
  • genes are introduced into cells in order to achieve in vivo synthesis of a therapeutically effective genetic product, for example for replacement of a defective gene.
  • Gene therapy includes both conventional gene therapy where a lasting effect is achieved by a single treatment, and the administration of gene therapeutic agents, which involves the one time or repeated administration of a therapeutically effective DNA or mRNA.
  • Antisense RNAs and DNAs can be used as therapeutic agents for blocking the expression of certain genes in vivo. It has already been shown that short antisense oligonucleotides can be imported into cells where they act as inhibitors, despite their low intracellular concentrations caused by their restricted uptake by the cell membrane.
  • oligonucleotides can be modified to enhance their uptake, e.g. by substituting their negatively charged phosphodiester groups by uncharged groups.
  • nucleic acids there are a variety of techniques available for introducing nucleic acids into viable cells.
  • the techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or in vivo in the cells of the intended host.
  • Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, cell fusion, DEAE-dextran, the calcium phosphate precipitation method, etc.
  • the currently preferred in vivo gene transfer techniques include transfection with viral (typically retroviral) vectors and viral coat protein- liposome mediated transfection (Dzau et al., Trends in Biotechnology 1 1, 205-210 [1993]).
  • the nucleic acid source with an agent that targets the target cells, such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cell, etc.
  • an agent that targets the target cells such as an antibody specific for a cell surface membrane protein or the target cell, a ligand for a receptor on the target cell, etc.
  • proteins which bind to a cell surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g. capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half-life.
  • the technique of receptor-mediated endocytosis is described, for example, by Wu et al., J. Biol. Chem.
  • OPN nucleic acid molecules encoding the OPN polypeptides or fragments thereof described herein are useful for chromosome identification.
  • OPN nucleic acid molecule of the present invention can be used as a chromosome marker.
  • OPN polypeptides and nucleic acid molecules of the present invention may also be used diagnostically for tissue typing, wherein the OPN polypeptides of the present invention may be differentially expressed in one tissue as compared to another, preferably in a diseased tissue as compared to a normal tissue of the same tissue type.
  • OPN nucleic acid molecules will find use for generating probes for PCR, Northern analysis, Southern analysis and Western analysis. This invention encompasses methods of screening compounds to identify those that mimic the
  • Screening assays for antagonist drug candidates are designed to identify compounds that bind or complex with the OPN polypeptides encoded by the genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins, including e.g., inhibiting the expression of OPN polypeptide from cells.
  • Screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.
  • the assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, and cell-based assays, which are well characterized in the art.
  • All assays for antagonists are common in that they call for contacting the drug candidate with a OPN polypeptide encoded by a nucleic acid identified herein under conditions and for a time sufficient to allow these two components to interact.
  • the interaction is binding and the complex formed can be isolated or detected in the reaction mixture.
  • the OPN polypeptide encoded by the gene identified herein or the drug candidate is immobilized on a solid phase, e.g., on a microtiter plate, by covalent or non-covalent attachments.
  • Non-covalent attachment generally is accomplished by coating the solid surface with a solution of the OPN polypeptide and drying.
  • an immobilized antibody e.g., a monoclonal antibody, specific for the OPN polypeptide to be immobilized can be used to anchor it to a solid surface.
  • the assay is performed by adding the non- immobilized component, which may be labeled by a detectable label, to the immobilized component, e.g., the coated surface containing the anchored component.
  • the non- reacted components are removed, e.g., by washing, and complexes anchored on the solid surface are detected.
  • the detection of label immobilized on the surface indicates that complexing occurred.
  • complexing can be detected, for example, by using a labeled antibody specifically binding the immobilized complex.
  • the candidate compound interacts with but does not bind to a particular OPN polypeptide encoded by a gene identified herein, its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions.
  • assays include traditional approaches, such as, e.g., cross-linking, co-immunoprecipitation, and co-purification through gradients or chromatographic columns.
  • protein-protein interactions can be monitored by using a yeast- based genetic system described by Fields and co-workers (Fields and Song, Nature (London “ ), 340:245- 246 (1989); Chien et al., Proc. Natl. Acad. Sci. USA.
  • yeast GAL4 consist of two physically discrete modular domains, one acting as the DNA-binding domain, the other one functioning as the transcription-activation domain.
  • the yeast expression system described in the foregoing publications (generally referred to as the "two-hybrid system") takes advantage of this property, and employs two hybrid proteins, one in which the target protein is fused to the DNA-binding domain of GAL4, and another, in which candidate activating proteins are fused to the activation domain.
  • GALl -lacL reporter gene under control of a GAL4-activated promoter depends on reconstitution of GAL4 activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with a chromogenic substrate for ⁇ -galactosidase.
  • a complete kit (MATCHMAKERTM) for identifying protein-protein interactions between two specific proteins using the two-hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions.
  • a reaction mixture is prepared containing the product of the gene and the intra- or extracellular component under conditions and for a time allowing for the interaction and binding of the two products.
  • a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound.
  • a placebo may be added to a third reaction mixture, to serve as positive control.
  • the binding (complex formation) between the test compound and the intra- or extracellular component present in the mixture is monitored as described hereinabove. The formation of a complex in the control reaction(s) but not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.
  • the OPN polypeptide may be added to a cell along with the compound to be screened for a particular activity and the ability of the compound to inhibit the activity of interest in the presence of the OPN polypeptide indicates that the compound is an antagonist to the OPN polypeptide.
  • antagonists may be detected by combining the OPN polypeptide and a potential antagonist with membrane-bound OPN polypeptide receptors or recombinant receptors under appropriate conditions for a competitive inhibition assay.
  • the OPN polypeptide can be labeled, such as by radioactivity, such that the number of OPN polypeptide molecules bound to the receptor can be used to determine the effectiveness of the potential antagonist.
  • the gene encoding the receptor can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. Coligan et al.. Current Protocols in Immun., 1 (2): Chapter 5 (1991 ).
  • expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the OPN polypeptide and a cDNA library created from this RNA is divided into pools and used to transfect
  • COS cells or other cells that are not responsive to the OPN polypeptide Transfected cells that are grown on glass slides are exposed to labeled OPN polypeptide.
  • the OPN polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transfected using an interactive sub- pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.
  • labeled OPN polypeptide can be photoaffinity-linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and exposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro- sequencing. The amino acid sequence obtained from micro- sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.
  • mammalian cells or a membrane preparation expressing the receptor would be incubated with labeled OPN polypeptide in the presence of the candidate compound.
  • potential antagonists include an oligonucleotide that binds to the fusions of immunoglobulin with OPN polypeptide, and, in particular, antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodies, anti- idiotypic antibodies, and chimeric or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments.
  • a potential antagonist may be a closely related protein, for example, a mutated form of the OPN polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the OPN polypeptide.
  • OPN polypeptide antagonist is an antisense RNA or DNA construct prepared using antisense technology, where, e.g., an antisense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation.
  • Antisense technology can be used to control gene expression through triple-helix formation or antisense DNA or RNA, both of which methods are based on binding of a polynucleotide to DNA or RNA.
  • the 5' coding portion of the polynucleotide sequence, which encodes the mature OPN polypeptides herein, is used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length.
  • a DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription (triple helix - see Lee et al., Nucl. Acids Res., 6:3073 ( 1979); Cooney et al., Science, 241 : 456 (1988); Dervan et al., Science. 251 : 1360 (1991 )), thereby preventing transcription and the production of the OPN polypeptide.
  • the antisense RNA oligonucleotide hybridizes to the mRNA in vivo and blocks translation of the mRNA molecule into the OPN polypeptide (antisense - Okano, Neurochem., 56:560 (1991 ); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton, FL, 1988).
  • the oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the OPN polypeptide.
  • antisense DNA is used, oligodeoxyribonucleotides derived from the translation-initiation site, e.g., between about -10 and +10 positions of the target gene nucleotide sequence, are preferred.
  • Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the OPN polypeptide, thereby blocking the normal biological activity of the OPN polypeptide.
  • small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non- peptidyl organic or inorganic compounds.
  • Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage. Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see, e.g., Rossi, Current Biology, 4:469-471
  • Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single- stranded and composed of deoxynucleotides.
  • the base composition of these oligonucleotides is designed such that it promotes triple-helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex.
  • Hoogsteen base-pairing rules which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex.
  • Isolated OPN polypeptide-encoding nucleic acid can be used herein for recombinantly producing OPN polypeptide using techniques well known in the art and as described herein.
  • the produced OPN polypeptides can be employed for generating anti-OPN antibodies using techniques well known in the art and as described herein.
  • Antibodies specifically binding a OPN polypeptide identified herein, as well as other molecules identified by the screening assays disclosed hereinbefore, can be administered for the treatment of various disorders, including cancer, in the form of pharmaceutical compositions.
  • OPN polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies are preferred.
  • lipofections or liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred.
  • peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al, Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993).
  • the formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • the composition may comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth- inhibitory agent.
  • cytotoxic agent such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth- inhibitory agent.
  • Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • EXAMPLE 1 Expression of OPN in E. coli This example illustrates preparation of an unglycosylated form of OPN by recombinant expression in E. coli.
  • the DNA sequence encoding OPN is initially amplified using selected PCR primers.
  • the primers should contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector.
  • restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector.
  • a variety of expression vectors may be employed.
  • An example of a suitable vector is pBR322 (derived from E. coli; see Bolivar et al., Gene, 2:95 (1977)) which contains genes for ampicillin and tetracycline resistance.
  • the vector is digested with restriction enzyme and dephosphorylated.
  • the PCR amplified sequences are then ligated into the vector.
  • the vector will preferably include sequences which encode for an antibiotic resistance gene, a trp promoter, a polyhis leader (including the first six STII codons, polyhis sequence, and enterokinase cleavage site), the OPN coding region, lambda transcriptional terminator, and an argU gene.
  • the ligation mixture is then used to transform a selected E. coli strain using the methods described in Sambrook et al., supra. Transformants are identified by their ability to grow on LB plates and antibiotic resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing. Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics. The overnight culture may subsequently be used to inoculate a larger scale culture. The cells are then grown to a desired optical density, during which the expression promoter is turned on. After culturing the cells for several more hours, the cells can be harvested by centrifugation.
  • the cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized OPN protein can then be purified using a metal chelating column under conditions that allow tight binding of the protein.
  • OPN may be expressed in E. coli in a poly-His tagged form, using the following procedure.
  • the DNA encoding OPN is initially amplified using selected PCR primers.
  • the primers will contain restriction enzyme sites which correspond to the restriction enzyme sites on the selected expression vector, and other useful sequences providing for efficient and reliable translation initiation, rapid purification on a metal chelation column, and proteolytic removal with enterokinase.
  • the PCR- amplified, poly-His tagged sequences are then ligated into an expression vector, which is used to transform an E. coli host based on strain 52 (W3110 fuhA(tonA) Ion galE rpoHts(htpRts) clpP(lacIq).
  • Transformants are first grown in LB containing 50 mg/ml carbenicillin at 30 0 C with shaking until an O.D.600 of 3-5 is reached. Cultures are then diluted 50-100 fold into CRAP media (prepared by mixing 3.57 g (NH 4 ) 2 SO 4 , 0.71 g sodium citrate «2H2O, 1.07 g KCl, 5.36 g Difco yeast extract, 5.36 g Sheffield hycase SF in 500 mL water, as well as 1 10 mM MPOS, pH 7.3, 0.55% (w/v) glucose and 7 mM MgSO 4 ) and grown for approximately 20-30 hours at 30°C with shaking. Samples are removed to verify expression by SDS-PAGE analysis, and the bulk culture is centrifuged to pellet the cells. Cell pellets are frozen until purification and refolding.
  • CRAP media prepared by mixing 3.57 g (NH 4 ) 2 SO 4 , 0.71 g sodium citrate «2H2O, 1.07 g
  • E. coli paste from 0.5 to 1 L fermentations (6-10 g pellets) is resuspended in 10 volumes (w/v) in 7 M guanidine, 20 mM Tris, pH 8 buffer. Solid sodium sulfite and sodium tetrathionate is added to make final concentrations of 0.1M and 0.02 M, respectively, and the solution is stirred overnight at
  • the protein is eluted with buffer containing 250 mM imidazole. Fractions containing the desired protein are pooled and stored at 4°C. Protein concentration is estimated by its absorbance at 280 nm using the calculated extinction coefficient based on its amino acid sequence.
  • the proteins are refolded by diluting the sample slowly into freshly prepared refolding buffer consisting of: 20 mM Tris, pH 8.6, 0.3 M NaCl, 2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA. Refolding volumes are chosen so that the final protein concentration is between 50 to 100 micrograms/ml. The refolding solution is stirred gently at 4 0 C for 12-36 hours.
  • the refolding reaction is quenched by the addition of TFA to a final concentration of 0.4% (pH of approximately 3). Before further purification of the protein, the solution is filtered through a 0.22 micron filter and acetonitrile is added to 2-10% final concentration.
  • the refolded protein is chromatographed on a Poros Rl /H reversed phase column using a mobile buffer of 0.1 % TFA with elution with a gradient of acetonitrile from 10 to 80%. Aliquots of fractions with A280 absorbance are analyzed on SDS polyacrylamide gels and fractions containing homogeneous refolded protein are pooled.
  • the properly refolded species of most proteins are eluted at the lowest concentrations of acetonitrile since those species are the most compact with their hydrophobic interiors shielded from interaction with the reversed phase resin. Aggregated species are usually eluted at higher acetonitrile concentrations.
  • the reversed phase step also removes endotoxin from the samples. Fractions containing the desired folded OPN polypeptide are pooled and the acetonitrile removed using a gentle stream of nitrogen directed at the solution.
  • Proteins are formulated into 20 mM Hepes, pH 6.8 with 0.14 M sodium chloride and 4% mannitol by dialysis or by gel filtration using G25 Superfine (Pharmacia) resins equilibrated in the formulation buffer and sterile filtered.
  • Human OPN disclosed herein has been successfully expressed and purified using this technique(s).
  • Human OPN was generated by ligating a full-length cDNA of human osteopontin into the poly His pET19b plasmid (Novagen) and expressing the OPN protein in E. coli strain 45G2.
  • the protein recovered from the Ni2+ affinity purification was predominantly a peptide fragment with a molecular mass measured by mass spectrometry of 20442.5 Daltons.
  • N-terminal sequencing of the recovered protein revealed that the protein had an intact N-terminus of OPN and may herein be ' referred to as OPN 36 (SEQ ID NO: 2).
  • a second fragment, believed to be a cleavage product was a N- terminal fragment of OPN, cleaved at amino acid residue Kl 73 and may herein be referred to as OPN 20 .
  • EXAMPLE 2 Expression of OPN in mammalian cells This example illustrates preparation of a potentially glycosylated form of OPN by recombinant expression in mammalian cells.
  • the vector, pRK5 (see EP 307,247, published March 15, 1989), is employed as the expression vector.
  • the OPN DNA is ligated into pRK5 with selected restriction enzymes to allow insertion of the OPN DNA using ligation methods such as described in Sambrook et al., supra.
  • the resulting vector is called pRK5-OPN.
  • the selected host cells may be 293 cells.
  • Human 293 cells (ATCC CCL 1573) are grown to confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics.
  • About 10 ⁇ g pRK5-OPN DNA is mixed with about 1 ⁇ g DNA encoding the VA RNA gene [Thimmappaya et al., Cell, 31:543 (1982)] and dissolved in 500 ⁇ l of 1 mM Tris-HCl, 0.1 mM EDTA, 0.227 M CaCl 2 .
  • the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 ⁇ Ci/ml 35 S-cysteine and 200 ⁇ Ci/ml 35 S-methionine.
  • culture medium alone
  • culture medium containing 200 ⁇ Ci/ml 35 S-cysteine and 200 ⁇ Ci/ml 35 S-methionine After a 12 hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of OPN polypeptide.
  • the cultures containing transfected cells may undergo further incubation (in serum free medium) and the medium is tested in selected bioassays.
  • OPN may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyrac et al., Proc. Natl. Acad. Sci., 12:7575 (1981 ). 293 cells are grown to maximal density in a spinner flask and 700 ⁇ g pRK5-OPN DNA is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA- dextran precipitate is incubated on the cell pellet for four hours.
  • the cells are treated with 20% glycerol for 90 seconds, washed with tissue culture medium, and re-introduced into the spinner flask containing tissue culture medium, 5 ⁇ g/ml bovine insulin and 0.1 ⁇ g/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris. The sample containing expressed OPN can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.
  • OPN can be expressed in CHO cells.
  • the pRK5-OPN can be transfected into CHO cells using known reagents such as CaPO 4 or DEAE-dextran.
  • the cell cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as 35 S-methionine.
  • the culture medium may be replaced with serum free medium.
  • the cultures are incubated for about 6 days, and then the conditioned medium is harvested.
  • the medium containing the expressed OPN can then be concentrated and purified by any selected method.
  • Epitope-tagged OPN may also be expressed in host CHO cells.
  • the OPN may be subcloned out of the pRK5 vector.
  • the subclone insert can undergo PCR to fuse in frame with a selected epitope tag such as a poly-his tag into a Baculovirus expression vector.
  • the poly-his tagged OPN insert can then be subcloned into a SV40 driven vector containing a selection marker such as DHFR for selection of stable clones.
  • the CHO cells can be transfected (as described above) with the SV40 driven vector. Labeling may be performed, as described above, to verify expression.
  • the culture medium containing the expressed poly-His tagged OPN can then be concentrated and purified by any selected method, such as by Ni 2+ -chelate affinity chromatography.
  • OPN may also be expressed in CHO and/or COS cells by a transient expression procedure or in CHO cells by another stable expression procedure. Stable expression in CHO cells is performed using the following procedure.
  • the proteins are expressed as an IgG construct (immunoadhesin), in which the coding sequences for the soluble forms (e.g. extracellular domains) of the respective proteins are fused to an IgGl constant region sequence containing the hinge, CH2 and CH2 domains and/or is a poly-His tagged form.
  • CHO expression vectors are constructed to have compatible restriction sites 5' and 3' of the DNA of interest to allow the convenient shuttling of cDNA's.
  • the vector used expression in CHO cells is as described in Lucas et al., Nucl. Acids Res. 24:9 (1774-1779 (1996), and uses the SV40 early promoter/enhancer to drive expression of the cDNA of interest and dihydrofolate reductase (DHFR).
  • DHFR expression permits selection for stable maintenance of the plasmid following transfection.
  • Twelve micrograms of the desired plasmid DNA is introduced into approximately 10 million CHO cells using commercially available transfection reagents Superfect ® (Quiagen), Dosper ® or Fugene ® (Boehringer Mannheim). The cells are grown as described in Lucas et al., supra. Approximately 3 x 10 7 cells are frozen in an ampule for further growth and production as described below.
  • the ampules containing the plasmid DNA are thawed by placement into water bath and mixed by vortexing.
  • the contents are pipetted into a centrifuge tube containing 10 mLs of media and centrifuged at 1000 rpm for 5 minutes.
  • the supernatant is aspirated and the cells are resuspended in 10 mL of selective media (0.2 ⁇ m filtered PS20 with 5% 0.2 ⁇ m diaf ⁇ ltered fetal bovine serum).
  • the cells are then aliquoted into a 100 mL spinner containing 90 mL of selective media. After 1-2 days, the cells are transferred into a 250 mL spinner filled with 150 mL selective growth medium and incubated at 37 0 C.
  • spinners After another 2-3 days, 250 mL, 500 mL and 2000 mL spinners are seeded with 3 x 10 5 cells/mL.
  • the cell media is exchanged with fresh media by centrifugation and resuspension in production medium.
  • any suitable CHO media may be employed, a production medium described in U.S. Patent No. 5, 122,469, issued June 16, 1992 may actually be used.
  • a 3L production spinner is seeded at 1.2 x 10 6 cells/mL. On day 0, the cell number pH ie determined. On day 1 , the spinner is sampled and sparging with filtered air is commenced.
  • the spinner On day 2, the spinner is sampled, the temperature shifted to 33°C, and 30 mL of 500 g/L glucose and 0.6 mL of 10% antifoam (e.g., 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion) taken. Throughout the production, the pH is adjusted as necessary to keep it at around 7.2. After 10 days, or until the viability dropped below 70%, the cell culture is harvested by centrifugation and filtering through a 0.22 ⁇ m filter. The filtrate was either stored at 4 0 C or immediately loaded onto columns for purification. For the poly-His tagged constructs, the proteins are purified using a Ni-NTA column (Qiagen).
  • 10% antifoam e.g., 35% polydimethylsiloxane emulsion, Dow Corning 365 Medical Grade Emulsion
  • imidazole is added to the conditioned media to a concentration of 5 mM.
  • the conditioned media is pumped onto a 6 ml Ni-NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4 0 C.
  • the column is washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole.
  • the highly purified protein is subsequently desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, with a 25 ml
  • Immunoadhesin (Fc-containing) constructs are purified from the conditioned media as follows.
  • the conditioned medium is pumped onto a 5 ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading, the column is washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5.
  • the eluted protein is immediately neutralized by collecting 1 ml fractions into tubes containing 275 ⁇ L of 1 M Tris buffer, pH 9.
  • the highly purified protein is subsequently desalted into storage buffer as described above for the poly-His tagged proteins.
  • the homogeneity is assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation. Certain of the OPN polypeptides disclosed herein have been successfully expressed and purified using this technique(s).
  • EXAMPLE 3 Expression of OPN in Yeast
  • yeast expression vectors are constructed for intracellular production or secretion of OPN from the ADH2/GAPDH promoter.
  • DNA encoding OPN and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of OPN.
  • DNA encoding OPN can be cloned into the selected plasmid, together with DNA encoding the ADH2/GAPDH promoter, a native OPN signal peptide or other mammalian signal peptide, or, for example, a yeast alpha-factor or invertase secretory signal/leader sequence, and linker sequences (if needed) for expression of OPN.
  • yeast cells such as yeast strain ABl 10
  • yeast cells can then be transformed with the expression plasmids described above and cultured in selected fermentation media.
  • the transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.
  • Recombinant OPN can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters.
  • the concentrate containing OPN may further be purified using selected column chromatography resins. Certain of the OPN polypeptides disclosed herein may be expressed and purified using this technique(s).
  • the following method describes recombinant expression of OPN in Baculovirus infected insect cells.
  • the sequence coding for OPN is fused upstream of an epitope tag contained within a baculovirus expression vector.
  • epitope tags include poly-his tags and immunoglobulin tags (like Fc regions of IgG).
  • a variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, the sequence encoding OPN or the desired portion of the coding sequence of OPN such as the sequence encoding an extracellular domain of a transmembrane protein or the sequence encoding the mature protein if the protein is extracellular is amplified by PCR with primers complementary to the 5' and 3' regions. The 5' primer may incorporate flanking (selected) restriction enzyme sites. The product is then digested with those selected restriction enzymes and subcloned into the expression vector. Recombinant baculovirus is generated by co-transfecting the above plasmid and
  • BaculoGoldTM virus DNA (Pharmingen) into Spodoptera frugiperda (“Sf9”) cells (ATCC CRL 171 1 ) using lipofectin (commercially available from GIBCO-BRL). After 4 - 5 days of incubation at 28 0 C, the released viruses are harvested and used for further amplifications. Viral infection and protein expression are performed as described by O'Reilley et al., Baculovirus expression vectors: A Laboratory Manual, Oxford: Oxford University Press (1994). Expressed poly-his tagged OPN can then be purified, for example, by Ni 2+ -chelate affinity chromatography as follows.
  • Extracts are prepared from recombinant virus-infected Sf9 cells as described by Rupert et al., Nature, 362: 175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl 2 ; 0.1 mM EDTA; 10% glycerol; 0.1 % NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice.
  • sonication buffer 25 mL Hepes, pH 7.9; 12.5 mM MgCl 2 ; 0.1 mM EDTA; 10% glycerol; 0.1 % NP-40; 0.4 M KCl
  • the sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% glycerol, pH 7.8) and filtered through a 0.45 ⁇ m filter.
  • loading buffer 50 mM phosphate, 300 mM NaCl, 10% glycerol, pH 7.8
  • a Ni 2+ -NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 mL, washed with 25 mL of water and equilibrated with 25 mL of loading buffer.
  • the filtered cell extract is loaded onto the column at 0.5 mL per minute.
  • the column is washed to baseline A 28 o with loading buffer, at which point fraction collection is started.
  • the column is washed with a secondary wash buffer (50 mM phosphate; 300 mM NaCl, 10% glycerol, pH 6.0), which elutes nonspecifically bound protein.
  • a secondary wash buffer 50 mM phosphate; 300 mM NaCl, 10% glycerol, pH 6.0
  • the column is developed with a 0 to 500 mM Imidazole gradient in the secondary wash buffer.
  • One mL fractions are collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni 2+ -NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted Hisio- tagged OPN are pooled and dialyzed against loading buffer.
  • purification of the IgG tagged (or Fc tagged) OPN can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography.
  • OPN polypeptides disclosed herein may be expressed and purified using this technique(s).
  • This example illustrates preparation of monoclonal antibodies which can specifically bind OPN.
  • Techniques for producing the monoclonal antibodies are known in the art and are described, for instance, in Goding, supra.
  • Immunogens that may be employed include purified OPN, fusion proteins containing OPN, and cells expressing recombinant OPN on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation.
  • mice such as Balb/c are immunized with the OPN immunogen emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1 -100 micrograms.
  • the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical Research, Hamilton, MT) and injected into the animal's hind foot pads.
  • MPL-TDM adjuvant Ribi Immunochemical Research, Hamilton, MT
  • the immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections.
  • Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELlSA assays to detect anti-OPN antibodies. After a suitable antibody titer has been detected, the animals "positive" for antibodies can be injected with a final intravenous injection of OPN. Three to four days later, the mice are sacrificed and the spleen cells are harvested. The spleen cells are then fused (using 35% polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU.l , available from ATCC, No. CRL 1597. The fusions generate hybridoma cells which can then be plated in 96 well tissue culture plates containing
  • HAT hypoxanthine, aminopterin, and thymidine
  • hybridoma cells will be screened in an ELISA for reactivity against OPN. Determination of "positive" hybridoma cells secreting the desired monoclonal antibodies against OPN is within the skill in the art.
  • the positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-OPN monoclonal antibodies.
  • the hybridoma cells can be grown in tissue culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium sulfate precipitation, followed by gel exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.
  • Antibodies directed against certain of the OPN polypeptides disclosed herein have been successfully produced using this technique(s). More specifically, two functional monoclonal antibodies that are capable of recognizing and binding to OPN protein (as measured by standard ELISA, FACS sorting analysis and/or immunohistochemistry analysis) have been successfully generated against the human OPN protein and are herein referred to as 2G2 and 2H2. Hybridomas expressing 2G2 and 2H2 antibodies have been deposited with ATCC on October 8, 2004.
  • the antigen used for generation of the 2G2 and 2H2 antibodies was human OPN purified by DEAE ion exchange chromatography from human breast milk.
  • various cDNA clones have been deposited with the ATCC.
  • the actual nucleotide sequences of those clones can readily be determined by the skilled artisan by sequencing of the deposited clone using routine methods in the art.
  • the predicted amino acid sequence can be determined from the nucleotide sequence using routine skill.
  • Applicants have identified what is believed to be the reading frame best identifiable with the sequence information available at the time.
  • toxin e.g., DM l
  • monoclonal antibodies directed against the OPN polypeptides as described herein
  • many of those monoclonal antibodies have been successfully conjugated to a cell toxin for use in directing the cellular toxin to a cell (or tissue) that expresses a OPN polypeptide of interested (both in vitro and in vivo).
  • toxin e.g., DM l
  • derivitized monoclonal antibodies may be generated to the human OPN protein.
  • OPN Polypeptides may be purified by a variety of standard techniques in the art of protein purification. For example, pro-OPN polypeptide, mature OPN polypeptide, or pre- OPN polypeptide is purified by immunoaffinity chromatography using antibodies specific for the OPN polypeptide of interest. In general, an immunoaffinity column is constructed by covalently coupling the anti-OPN polypeptide antibody to an activated chromatographic resin.
  • Polyclonal immunoglobulins are prepared from immune sera either by precipitation with ammonium sulfate or by purification on immobilized Protein A (Pharmacia LKB Biotechnology, Piscataway, N.J.). Likewise, monoclonal antibodies are prepared from mouse ascites fluid by ammonium sulfate precipitation or chromatography on immobilized Protein A. Partially purified immunoglobulin is covalently attached to a chromatographic resin such as CnBr-activated SEPHAROSETM (Pharmacia LKB Biotechnology). The antibody is coupled to the resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's instructions.
  • a chromatographic resin such as CnBr-activated SEPHAROSETM (Pharmacia LKB Biotechnology). The antibody is coupled to the resin, the resin is blocked, and the derivative resin is washed according to the manufacturer's instructions.
  • Such an immunoaffinity column is utilized in the purification of OPN polypeptide by preparing a fraction from cells containing OPN polypeptide in a soluble form. This preparation is derived by solubilization of the whole cell or of a subcellular fraction obtained via differential centrifugation by the addition of detergent or by other methods well known in the art. Alternatively, soluble OPN polypeptide containing a signal sequence may be secreted in useful quantity into the medium in which the cells are grown.
  • a soluble OPN polypeptide-containing preparation is passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of OPN polypeptide ⁇ e.g., high ionic strength buffers in the presence of detergent). Then, the column is eluted under conditions that disrupt antibody/OPN polypeptide binding ⁇ e.g., a low pH buffer such as approximately pH 2-3, or a high concentration of a chaotrope such as urea or thiocyanate ion), and OPN polypeptide is collected.
  • a low pH buffer such as approximately pH 2-3
  • a chaotrope such as urea or thiocyanate ion
  • This assay is designed to measure the ability of antibodies to human osteopontin to inhibit cell attachment to human osteopontin.
  • Anti-OPN antibodies testing positive in this assay would be expected to be useful for therapeutic treatment of bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • MDA-MB-435 or IGROV-I cells were detached from the culture dish with 1OmM EDTA and washed and re-suspended in serum free medium.
  • Ninety-six well protein binding plates were coated with 1.5 ⁇ g/ml of 0PN 2() , a N-terminal fragment of OPN, in PBS and incubated overnight at 4°C. The plates were aspirated and washed and coated for 1 hour at room temperature with 1 % BSA in PBS.
  • cell suspension (50,000 cells), either MDA-MB-435 or IGROV-I cells, and 50 ⁇ l of medium containing anti-OPN antibodies (2G2 or 2H2) or control anti ⁇ tumor necros facctor-alpha (anti-TNF- ⁇ ) antibody (TNF-B), or control anti -osteoprotegerin antibody (IClO) and anti- ⁇ v ⁇ 3 antibody (9D4) was added to the appropriate wells. Plates were centrifuged at 1000 RPM for 3 minutes and incubated at 37 0 C for 90 minutes. Plates were gently washed and the number of adherent cells was established using the hexosaminase substrate p-nitrophenyl-N-Acetyl-
  • Beta-D-Glucosaminide (PNAG substrate). Stop solution was added to the wells and an OD reading was taken at 405 nm.
  • anti-OPN antibodies, 2G2 and 2H2 blocked attachment of MDA-MB- 435 cells to OPN 20 while the control antibody, anti-TNF- ⁇ , TNF-B, did not block attachment of MDA- MB-435 cells on plates with 1.5 ⁇ g/ml OPN 20 .
  • 2G2 inhibited attachment with an IC 50 Of 1.62 ⁇ g/ml
  • 2H2 inhibited attachment with an ICs 0 Of 1.1 ⁇ g/ml.
  • anti-OPN antibodies, 2H2 blocked attachment of IGROV-I cells to
  • EXAMPLE 8 Binding Assay of Purified ⁇ v ⁇ 3 Receptor to Osteopontin This assay is designed to measure the ability of antibodies to human osteopontin to inhibit binding of purified ⁇ v ⁇ 3 receptor to human osteopontin. Anti-OPN antibodies testing positive in this assay would be expected to be useful for therapeutic treatment of bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • avB3 receptor was prepared as previously reported in Chuntharapai et al. ("Blocking Monoclonal Antibodies to alpha-v beta-3 Integrin: A Unique Epitope of alpha-v beta-e Integrin Is Present on Human Osteoclasts", Experimental Cell Research, 205: 345-352 (1993). The assay was performed as described below. Ninety-six well protein binding plates were coated with 5.0 ⁇ g/ml in PBS of OPN 20 and incubated overnight at 4 0 C. The plates were aspirated and washed and coated for 1 hour at room temperature with 1 % BSA in PBS.
  • Antibody, 2G2 or 2H2 anti-OPN antibodies or anti-TNF- ⁇ , TNF-E antibody, and control samples and ⁇ v ⁇ 3 receptor were diluted in TACTS buffer (2OmM Tris pH 7.4, 0.5% BSA, 0.05% Tween-20, 150 mM NaCl, 1 mM MnCl 2 , 50 uM MgCl 2 , and 50 uM CaCl 2 ) were added to the wells and incubated for 1 hour at room temperature. Plates were gently washed and horseradish peroxidase (HRP)-conjugated
  • HRP horseradish peroxidase
  • This assay is designed to measure the ability of antibodies to human osteopontin to inhibit migration of MDA-MB-435 cells on osteopontin.
  • Anti-OPN antibodies testing positive in this assay would be expected to be useful for therapeutic treatment of bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • 2G2 anti-OPN antibodies inhibited migration of MDA-MB-435 cells in the presence of osteopontin.
  • a suspension of MDA-MB-435 cells were plated on plates pre-coated with 10 ⁇ g/ml osteopontin or controls, BSA or human fibronectin (Fn) and incubated for 30 minutes at 37°C.
  • the cells were pretreated with 20 ⁇ g/ml of 2H2 and additional 2H2 at 10 ⁇ g/ml of 2H2 was added into the assay medium during the 30 minute incubation period with the coated plates.
  • the cells were then lysed and 20 ⁇ g of the lysates were loaded per lane on a SDS-polyacrylamide gel.
  • the gel was subjected to Western blotting with anti-phospho397 FAK antibodies.
  • 2H2 anti-OPN antibodies inhibited phosphorylation of FAK at tyrosine-297 when MDA-MB-435 cells were incubated with plates coated with osteopontin, but did not affect phosphorylation of FAK at tyrosine-297 when MDA-MB-435 cells were incubated with plates coated with human fibronectin (Fn).
  • Anti-OPN antibodies testing positive in this assay would be expected to be useful for therapeutic treatment of bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • EXAMPLE 1 1 Xenograft Animal Study
  • Anti-OPN antibodies testing positive in this assay would be expected to be useful for therapeutic treatment of bone tumor, colon tumor, breast tumor, prostate tumor, ovarian tumor, lung tumor, pancreas tumor, metastatic mammary carcinomas, brain tumor, including glioma, tumor of the central nervous system, tumor of the soft tissue and stomach tumors.
  • estrogen pellets (0.36 mg/pellet/mouse) were implanted subcutaneously in the left dorsal flank area about 1-3 days prior to inoculation.
  • the mice were inoculated with IGROV- 1 cells, human ovarian cancer cells, at 5 million cells/mouse, subcutaneously in the right dorsal flank area at a volume of 0.2 ml per mouse.
  • the mice were randomized into 3 groups of 8 mice each. The antibody treatments were begun on the same day as the cell inoculation.
  • the tumor volumes were measured in each of the mice twice a week for 4 weeks.
  • anti-OPN antibodies 2G2
  • anti-OPN antibodies 2G2
  • a proprietary database containing gene expression information (GeneExpress®, Gene Logic Inc., Gaithersburg, MD) was analyzed in an attempt to identify polypeptides (and their encoding nucleic acids) whose expression is significantly upregulated in a particular tumor tissue(s) of interest as compared to other tumor(s) and/or normal tissues.
  • Analysis of the GeneExpress® database was conducted using either software available through Gene Logic Inc., Gaithersburg, MD, for use with the GeneExpress® database or with proprietary software written and developed at Genentech, Inc. for use with the GeneExpress® database.
  • the rating of positive hits in the analysis is based upon several criteria including, for example, tissue specificity, tumor specificity and expression level in normal essential and/or normal proliferating tissues.
  • DNA92980 also herein referred to as DNA83139 (TAT234) is listed below as a molecule whose tissue expression profile as determined from an analysis of the GeneExpress® database evidences high tissue expression and significant upregulation of expression in a specific tumor or tumors as compared to other tumor(s) and/or normal tissues and optionally relatively low expression in normal essential and/or normal proliferating tissues.
  • DNA92980-1 PRO10004 was also identified as being significantly overexpressed in central nervous tissue (CNS) tumor as compared to normal CNS tissue (data not shown). As such, TAT234 as listed below and PRO 10004 are excellent polypeptide targets for the diagnosis and therapy of cancer in mammals.
  • DNA92980 (TAT234) colon tumor normal colon tissue
  • TAT234 rectum tumor normal rectum tissue
  • DNA92980 (TAT234) endometrial tumor normal endometrial tissue
  • DNA92980 liver tumor ' normal liver tissue
  • DNA92980 (TAT234) lung tumor normal lung tissue
  • DNA92980 (TAT234) ovarian tumor normal ovarian tissue
  • DNA92980 pancreatic tumor normal pancreatic tissue
  • DNA92980 (TAT234) skin tumor normal skin tissue
  • DNA92980 (TAT234) soft tissue tumor normal soft tissue DNA92980 (TAT234) stomach tumor normal stomach tissue
  • EXAMPLE 13 Microarrav Analysis to Detect Upregulation of OPN Polypeptides in Cancerous Tumors
  • Nucleic acid microarrays are useful for identifying differentially expressed genes in diseased tissues as compared to their normal counterparts.
  • test and control mRNA samples from test and control tissue samples are reverse transcribed and labeled to generate cDNA probes.
  • the cDNA probes are then hybridized to an array of nucleic acids immobilized on a solid support.
  • the array is configured such that the sequence and position of each member of the array is known. For example, a selection of genes known to be expressed in certain disease states may be arrayed on a solid support. Hybridization of a labeled probe with a particular array member indicates that the sample from which the probe was derived expresses that gene.
  • hybridization signal of a probe from a test (disease tissue) sample is greater than hybridization signal of a probe from a control (normal tissue) sample, the gene or genes overexpressed in the disease tissue are identified.
  • an overexpressed protein in a diseased tissue is useful not only as a diagnostic marker for the presence of the disease condition, but also as a therapeutic target for treatment of the disease condition.
  • cancerous tumors derived from various human tissues may be studied for upregulated gene expression relative to cancerous tumors from different tissue types and/or non- cancerous human tissues in an attempt to identify those polypeptides which are overexpressed in a particular cancerous tumor(s).
  • cancerous human tumor tissue and non ⁇ cancerous human tumor tissue of the same tissue type are obtained and analyzed for TAT polypeptide expression.
  • cancerous human tumor tissue from any of a variety of different human tumors are obtained and compared to a "universal" epithelial control sample which are prepared by pooling non-cancerous human tissues of epithelial origin, including liver, kidney, and lung.
  • mRNA isolated from the pooled tissues represents a mixture of expressed gene products from these different tissues.
  • Microarray hybridization experiments using the pooled control samples generate a linear plot in a 2-color analysis.
  • the slope of the line generated in a 2-color analysis is then used to normalize the ratios of (testxontrol detection) within each experiment.
  • the normalized ratios from various experiments are then compared and used to identify clustering of gene expression.
  • the pooled "universal control" sample not only allows effective relative gene expression determinations in a simple 2-sample comparison, it also allows multi-sample comparisons across several experiments.
  • nucleic acid probes derived from the herein described OPN polypeptide-encoding nucleic acid sequence are used in the creation of the microarray and RNA from various tumor tissues are used for the hybridization thereto.
  • OPN polypeptides of the present invention may significantly overexpressed in various human tumor tissues as compared to their normal counterpart tissue(s).
  • OPN may be significantly overexpressed in their specific tumor tissue(s) as compared to in the "universal" epithelial control.
  • this data may demonstrate that the OPN polypeptides of the present invention may be useful not only as diagnostic markers for the presence of one or more cancerous tumors, but also may serve as therapeutic targets for the treatment of those tumors.
  • a 5' nuclease assay for example, TaqMan®
  • real-time quantitative PCR for example, ABI Prizm 7700 Sequence Detection System® (Perkin Elmer, Applied Biosystems Division, Foster City, CA)
  • the 5' nuclease assay reaction is a fluorescent PCR-based technique which makes use of the 5' exonuclease activity of Taq DNA polymerase enzyme to monitor gene expression in real time.
  • oligonucleotide primers (whose sequences are based upon the gene or EST sequence of interest) are used to generate an amplicon typical of a PCR reaction.
  • a third oligonucleotide, or probe is designed to detect nucleotide sequence located between the two PCR primers.
  • the probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser- induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe.
  • the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner.
  • the resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore.
  • One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.
  • the 5' nuclease procedure is run on a real-time quantitative PCR device such as the ABI Prism 7700TM Sequence Detection.
  • the system consists of a thermocycler, laser, charge-coupled device (CCD) camera and computer.
  • the system amplifies samples in a 96-well format on a thermocycler. During amplification, laser-induced fluorescent signal is collected in real-time through fiber optics cables for all 96 wells, and detected at the CCD.
  • the system includes software for running the instrument and for analyzing the data.
  • the starting material for the screen was mRNA isolated from a variety of different cancerous tissues.
  • the mRNA is quantitated precisely, e.g., fluorometrically.
  • RNA was isolated from various normal tissues of the same tissue type as the cancerous tissues being tested.
  • 5' nuclease assay data are initially expressed as Ct, or the threshold cycle. This is defined as the cycle at which the reporter signal accumulates above the background level of fluorescence.
  • the ⁇ Ct values are used as quantitative measurement of the relative number of starting copies of a particular target sequence in a nucleic acid sample when comparing cancer mRNA results to normal human mRNA results.
  • DNA92980 also herein referred as DNA83139 (TAT234) molecule listed below has been identified as being significantly overexpressed in a particular tumor(s) as compared to their normal non-cancerous counterpart tissue(s) (from both the same and different tissue donors) and thus, TAT234 represents an excellent polypeptide target for the diagnosis and therapy of cancer in mammals.
  • DNA92980-1 PRO10004 was also identified as being significantly overexpressed in lung tumor as compared to normal lung tissue (data not shown) and thus, PRO1004 represents an excellent polypeptide target for the diagnosis and therapy of cancer in mammals.
  • DNA92980 (TAT234) ovarian tumor normal ovarian tissue
  • EXAMPLE 15 In situ Hybridization In situ hybridization is a powerful and versatile technique for the detection and localization of nucleic acid sequences within cell or tissue preparations. It may be useful, for example, to identify sites of gene expression, analyze the tissue distribution of transcription, identify and localize viral infection, follow changes in specific mRNA synthesis and aid in chromosome mapping.
  • In situ hybridization was performed following an optimized version of the protocol by Lu and Gillett, Cell Vision 1 :169-176 (1994), using PCR-generated 33 P-labeled riboprobes. Briefly, formalin- fixed, paraffin-embedded human tissues were sectioned, deparaffinized, deproteinated in proteinase K (20 g/ml) for 15 minutes at 37 0 C, and further processed for in situ hybridization as described by Lu and Gillett, supra. A [ -P] UTP-labeled antisense riboprobe was generated from a PCR product and hybridized at 55 0 C overnight. The slides were dipped in Kodak NTB2 nuclear track emulsion and exposed for 4 weeks. P-Riboprobe synthesis
  • the tubes were incubated at 37 0 C for one hour.
  • 1.0 ⁇ l RQl DNase were added, followed by incubation at 37°C for 15 minutes.
  • 90 ⁇ l TE (10 mM Tris pH 7.6/ImM EDTA pH 8.0) were added, and the mixture was pipetted onto DE81 paper.
  • the remaining solution was loaded in a Microcon-50 ultrafiltration unit, and spun using program 10 (6 minutes).
  • the filtration unit was inverted over a second tube and spun using program 2 (3 minutes).
  • 100 ⁇ l TE were added. 1 ⁇ l of the final product was pipetted on DE81 paper and counted in 6 ml of Biofluor II.
  • the probe was run on a TBE/urea gel. 1 -3 ⁇ l of the probe or 5 ⁇ l of RNA Mrk III were added to 3 ⁇ l of loading buffer. After heating on a 95 °C heat block for three minutes, the probe was immediately placed on ice. The wells of gel were flushed, the sample loaded, and run at 180-250 volts for 45 minutes. The gel was wrapped in saran wrap and exposed to XAR film with an intensifying screen in -70 0 C freezer one hour to overnight. P-Hvbridization
  • the slides were deparaffinized, placed in SQ H 2 O, and rinsed twice in 2 x SSC at room temperature, for 5 minutes each time.
  • the sections were deproteinated in 20 ⁇ g/ml proteinase K (500 ⁇ l of 10 mg/ml in 250 ml RNase-free RNase buffer; 37 0 C, 15 minutes) - human embryo, or 8 x proteinase K (100 ⁇ l in 250 ml Rnase buffer, 37°C, 30 minutes) - formalin tissues. Subsequent rinsing in 0.5 x SSC and dehydration were performed as described above.
  • EXAMPLE 16 Verification and Analysis of Differential TAT234 Polypeptide Expression by GEPIS TAT polypeptides which may have been identified as a tumor antigen as described in one or more of the above Examples were analyzed and verified as follows.
  • An expressed sequence tag (EST) DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, CA) was searched and interesting EST sequences were identified by GEPIS.
  • Gene expression profiling in silico (GEPIS) is a bioinformatics tool developed at Genentech, Inc. that characterizes genes of interest for new cancer therapeutic targets. GEPIS takes advantage of large amounts of EST sequence and library information to determine gene expression profiles.
  • GEPIS is capable of determining the expression profile of a gene based upon its proportional correlation with the number of its occurrences in EST databases, and it works by integrating the LIFESEQ® EST relational database and Genentech proprietary information in a stringent and statistically meaningful way.
  • GEPIS is used to identify and cross- validate novel tumor antigens, although GEPIS can be configured to perform either very specific analyses or broad screening tasks.
  • GEPIS is used to identify EST sequences from the LIFESEQ® database that correlate to expression in a particular tissue or tissues of interest (often a tumor tissue of interest).
  • TAT234 polypeptide (and its encoding nucleic acid molecule) was identified as being significantly overexpressed in a particular type of cancer or certain cancers as compared to other cancers and/or normal non-cancerous tissues.
  • TAT234 is listed below as a molecule whose tissue expression profile as determined by GEPIS evidences high tissue expression and significant upregulation of expression in a specific tumor or tumors as compared to other tumor(s) and/or normal tissues and optionally relatively low expression in normal essential and/or normal proliferating tissues. As such, TAT234 as listed below is an excellent polypeptide target for the diagnosis and therapy of cancer in mammals. Molecule upregulation of expression in: as compared to:
  • DNA92980 (TAT234) cervical tumor normal cervical tissue
  • DNA92980 (TAT234) colon tumor normal colon tissue
  • DNA92980 (TAT234) rectum tumor normal rectum tissue
  • DNA92980 (TAT234) endometrial tumor normal endometrial tissue
  • DNA92980 liver tumor normal liver tissue
  • DNA92980 lung tumor normal lung tissue
  • DNA92980 (TAT234) ovarian tumor normal ovarian tissue
  • DNA92980 pancreatic tumor normal pancreatic tissue
  • DNA92980 skin tumor normal skin tissue DNA92980 (TAT234) soft tissue tumor normal soft tissue
  • DNA92980 (TAT234) esophagus tumor normal esophagus tissue
  • DNA92980 (TAT234) testis tumor normal testis tissue
  • EXAMPLE 17 Use of TAT234 or OPN as a hybridization probe
  • the following method describes use of a nucleotide sequence encoding TAT234 or OPN as a hybridization probe for, i.e., diagnosis of the presence of a tumor in a mammal.
  • DNA comprising the coding sequence of full-length or mature TAT234 or OPN as disclosed herein can also be employed as a probe to screen for homologous DNAs (such as those encoding naturally-occurring variants of TAT234 or OPN) in human tissue cDNA libraries or human tissue genomic libraries. Hybridization and washing of filters containing either library DNAs is performed under the following high stringency conditions.
  • Hybridization of radiolabeled TAT234- or OPN-derived probe to the filters is performed in a solution of 50% formamide, 5x SSC, 0.1 % SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2x Denhardt's solution, and 10% dextran sulfate at 42°C for 20 hours. Washing of the filters is performed in an aqueous solution of 0.1 x SSC and 0.1% SDS at 42°C.
  • DNAs having a desired sequence identity with the DNA encoding full-length native sequence TAT234 or OPN can then be identified using standard techniques known in the art.
  • EXAMPLE 18 In Vitro Tumor Cell Killing Assay
  • Mammalian cells expressing the TAT234 or OPN polypeptide of interest may be obtained using standard expression vector and cloning techniques. Alternatively, many tumor cell lines expressing TAT polypeptides of interest are publicly available, for example, through the ATCC and can be routinely identified using standard ELISA or FACS analysis. Anti-TAT234 or anti-OPN polypeptide monoclonal antibodies (and toxin conjugated derivatives thereof) may then be employed in assays to determine the ability of the antibody to kill TAT234 or OPN polypeptide expressing cells in vitro.
  • cells expressing the TAT234 or OPN polypeptide of interest are obtained as described above and plated into 96 well dishes.
  • the antibody/toxin conjugate (or naked antibody) is included throughout the cell incubation for a period of 4 days.
  • the cells are incubated for 1 hour with the antibody/toxin conjugate (or naked antibody) and then washed and incubated in the absence of antibody/toxin conjugate for a period of 4 days.
  • Cell viability is then measured using the CellTiter-Glo Luminescent Cell Viability Assay from Promega (Cat# G7571 ). Untreated cells serve as a negative control.
  • a hybridoma clone expressing 2G2 anti-osteopontin antibody was deposited with the ATCC on October 8, 2004.
  • a hybridoma clone expressing 2H2 anti-osteopontin antibody was deposited with the ATCC on October 8, 2004. The deposit was made under the provisions of the Budapest Treaty on the International

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  • Genetics & Genomics (AREA)
  • Public Health (AREA)
  • Cell Biology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Veterinary Medicine (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Animal Behavior & Ethology (AREA)
  • Medicines Containing Antibodies Or Antigens For Use As Internal Diagnostic Agents (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)
  • Peptides Or Proteins (AREA)

Abstract

L'invention concerne des compositions permettant de traiter une tumeur chez des mammifères et des méthodes utilisant lesdites compositions.
PCT/US2004/034878 2001-11-20 2004-10-13 Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine WO2006043954A1 (fr)

Priority Applications (5)

Application Number Priority Date Filing Date Title
CA002584028A CA2584028A1 (fr) 2004-10-13 2004-10-13 Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine
PCT/US2004/034878 WO2006043954A1 (fr) 2004-10-13 2004-10-13 Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine
AU2004324192A AU2004324192A1 (en) 2004-10-13 2004-10-13 Method for treating tumors using anti-osteopontin antibodies
EP04795965A EP1805220A1 (fr) 2004-10-13 2004-10-13 Méthode permettant de traiter les tumeurs à l'aide d'anticorps anti-ostéopontine
US11/536,489 US20070041983A1 (en) 2001-11-20 2006-09-28 Method for treating tumors using anti-osteopontin antibodies

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/US2004/034878 WO2006043954A1 (fr) 2004-10-13 2004-10-13 Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine

Related Parent Applications (2)

Application Number Title Priority Date Filing Date
US10/241,220 Continuation-In-Part US20030148408A1 (en) 2001-06-20 2002-09-11 Compositions and methods for the diagnosis and treatment of tumor
PCT/US2002/028859 Continuation-In-Part WO2003024392A2 (fr) 2001-09-18 2002-09-11 Compositions et procedes pour le diagnostic et le traitement des tumeurs

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US11/536,489 Continuation US20070041983A1 (en) 2001-11-20 2006-09-28 Method for treating tumors using anti-osteopontin antibodies

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WO2006043954A1 true WO2006043954A1 (fr) 2006-04-27

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PCT/US2004/034878 WO2006043954A1 (fr) 2001-11-20 2004-10-13 Methode permettant de traiter les tumeurs a l'aide d'anticorps anti-osteopontine

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Country Link
EP (1) EP1805220A1 (fr)
AU (1) AU2004324192A1 (fr)
CA (1) CA2584028A1 (fr)
WO (1) WO2006043954A1 (fr)

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007139164A1 (fr) 2006-05-31 2007-12-06 Astellas Pharma Inc. Anticorps d'ostéopontine anti-humains humanisés
WO2007149948A2 (fr) * 2006-06-20 2007-12-27 The Gov. Of The Usa As Represented By The Secretary Of The Department Of Health And Human Services Compositions et procédés de diagnostic et de traitement des tumeurs
WO2008128455A1 (fr) * 2007-04-24 2008-10-30 Shanghai Cp Guojian Pharmaceutical Co. Ltd Épitopes fonctionnels d'ostéopontine, anticorps monoclonaux contre ces épitopes et leurs utilisations
WO2011021146A1 (fr) * 2009-08-20 2011-02-24 Pfizer Inc. Anticorps contre l'ostéopontine
EP4010369A4 (fr) * 2019-08-09 2023-11-22 The Board of Trustees of the Leland Stanford Junior University Anticorps thérapeutiques dirigés contre l'ostéopontine

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1375518A1 (fr) * 2001-04-05 2004-01-02 Immuno-Biological Laboratories Co., Ltd. Anticorps dirig contre l'ost opontine, et son utilisation

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1375518A1 (fr) * 2001-04-05 2004-01-02 Immuno-Biological Laboratories Co., Ltd. Anticorps dirig contre l'ost opontine, et son utilisation

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
BAUTISTA D S ET AL: "INHIBITION OF ARG-GLY-ASP (RGD)-MEDIATED CELL ADHESION TO OSTEOPONTIN BY A MONOCLONAL ANTIBODY AGAINST OSTEOPONTIN", JOURNAL OF BIOLOGICAL CHEMISTRY, AMERICAN SOCIETY OF BIOLOCHEMICAL BIOLOGISTS, BIRMINGHAM,, US, vol. 269, no. 37, 16 September 1994 (1994-09-16), pages 23280 - 23285, XP002953832, ISSN: 0021-9258 *
LIAW L ET AL: "Neutralizing antibodies directed against osteopontin inhibit rat carotid neointimal thickening after endothelial denudation", ARTERIOSCLEROSIS, THROMBOSIS, AND VASCULAR BIOLOGY, vol. 17, no. 1, January 1997 (1997-01-01), pages 188 - 193, XP002100970, ISSN: 1079-5642 *
SODEK J ET AL: "OSTEOPONTIN", CRITICAL REVIEWS IN ORAL BIOLOGY AND MEDICINE, CRC PRESS, BOCA RATON, FL, US, vol. 11, no. 3, 2000, pages 279 - 303, XP001022167, ISSN: 1045-4411 *
THALMANN G N ET AL: "Osteopontin: possible role in prostate cancer progression.", CLINICAL CANCER RESEARCH : AN OFFICIAL JOURNAL OF THE AMERICAN ASSOCIATION FOR CANCER RESEARCH. AUG 1999, vol. 5, no. 8, August 1999 (1999-08-01), pages 2271 - 2277, XP002348201, ISSN: 1078-0432 *
WEBER G F: "The metastasis gene osteopontin: a candidate target for cancer therapy", BBA - REVIEWS ON CANCER, ELSEVIER SCIENCE BV, AMSTERDAM, NL, vol. 1552, no. 2, 28 December 2001 (2001-12-28), pages 61 - 85, XP004334757, ISSN: 0304-419X *

Cited By (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007139164A1 (fr) 2006-05-31 2007-12-06 Astellas Pharma Inc. Anticorps d'ostéopontine anti-humains humanisés
US7807161B2 (en) 2006-05-31 2010-10-05 Astellas Pharma Inc. Humanized anti-human osteopontin antibody
WO2007149948A2 (fr) * 2006-06-20 2007-12-27 The Gov. Of The Usa As Represented By The Secretary Of The Department Of Health And Human Services Compositions et procédés de diagnostic et de traitement des tumeurs
WO2007149948A3 (fr) * 2006-06-20 2008-09-18 Gov Of The Usa As Represented Compositions et procédés de diagnostic et de traitement des tumeurs
US7803380B2 (en) 2006-06-20 2010-09-28 The United States Of America As Represented By The Department Of Health And Human Services Compositions and methods for diagnosis and treatment of tumors
US8247183B2 (en) 2006-06-20 2012-08-21 The United States of America, as represented by the Secretary of the Departmant of Health and Human Services Compositions and methods for diagnosis and treatment of tumors
US8568977B2 (en) 2006-06-20 2013-10-29 The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services Compositions and methods for diagnosis and treatment of tumors
WO2008128455A1 (fr) * 2007-04-24 2008-10-30 Shanghai Cp Guojian Pharmaceutical Co. Ltd Épitopes fonctionnels d'ostéopontine, anticorps monoclonaux contre ces épitopes et leurs utilisations
WO2011021146A1 (fr) * 2009-08-20 2011-02-24 Pfizer Inc. Anticorps contre l'ostéopontine
EP4010369A4 (fr) * 2019-08-09 2023-11-22 The Board of Trustees of the Leland Stanford Junior University Anticorps thérapeutiques dirigés contre l'ostéopontine

Also Published As

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CA2584028A1 (fr) 2006-04-27
EP1805220A1 (fr) 2007-07-11
AU2004324192A1 (en) 2006-04-27
AU2004324192A2 (en) 2006-04-27

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