Identification of a family of secreted proteins in vascular endothelium

Abstract

The invention relates to SCUBE molecules and generally to gene expression in vascular endothelial cells. The invention specifically relates to the discovery of a novel gene family containing the genes and proteins referred to herein as SCUBE1, SCUBE2 and SCUBE3 which can be expressed in endothelial cells. SCUBE proteins may be involved in the development of cardiovascular disease, hemostasis, thrombosis, inflammatory disease, bone metabolism disorders, urinary bladder disorders and breast disorders.

Description

FIELD OF THE INVENTION

[0002] The invention relates generally to gene expression in vascular endothelial cells. The invention specifically relates to the discovery of a novel gene and protein family referred to herein as SCUBE1, SCUBE2 and SCUBE3 genes and proteins which can be expressed in endothelial cells. These genes and proteins may be involved in a variety of pathophysiological processes, such as cardiovascular disease, hemostasis, thrombosis, inflammatory disease, bone metabolism disorders, urinary bladder disorders and breast disorders.

[0003] The present invention includes novel proteins encoded by a cDNA and/or by genomic DNA and proteins similar to it, namely, new proteins bearing sequence similarity to SCUBE1, SCUBE2 and SCUBE3 proteins, nucleic acids that encode these proteins or fragments thereof, and binding partners, such as antibodies, that bind specifically to a protein of the invention.

BACKGROUND OF THE INVENTION

[0004] Vascular Endothelium

[0005] Endothelium is composed of a single layer of flattened transparent squamous cells, joined edge to edge in such a manner as to form a membrane of cells. This is found on the free surfaces of the serous membranes, as the lining membrane of the heart, blood vessels and lymphatics. Endothelial cells also line the surface of the brain and spinal cord, as well as the anterior surface of the eye. Endothelial tissue originates from the mesoderm of the embryo, while epithelium arises only from the ectoderm or endoderm (Gray, H. in: Gray's Anatomy. Pick and Howden, eds., pp. 1083 and 1154, Bounty Books, New York, 1977).

[0006] Vascular endothelium forms a continuous, single-cell-thick layer which lines the entire circulatory system. Despite its microscopic dimensions (often less than 1 micron in thickness), this living tissue is a multifunctional organ whose health is essential to normal vascular physiology and whose dysfunction can be a critical factor in the pathogenesis of vascular disease. Anatomically, the vascular endothelium forms the physical boundary separating the intravascular compartment from all of the tissues and organs of the body. Biologically, this interface supports a number of vital functions.

[0007] First and foremost, the vascular endothelium comprises a “container” for blood. As long as this cellular layer remains intact and is functioning normally, a non-thrombogenic surface is presented to the circulating blood, thus allowing it to remain fluid and perform its nutritive functions unimpeded by intravascular clotting. Physical disruption of the endothelial lining, even on a microscopic scale, elicits an immediate hemostatic response, involving localized activation of the coagulation cascade and the adherence and aggregation of platelets, an adaptive reaction that serves to limit blood loss at sites of injury. Conversely, acute or chronic impairment of the non-thrombogenic properties of the intact endothelial lining (a form of endothelial dysfunction, see below) can be an important predisposing factor for intravascular thrombosis.

[0008] Because of its unique anatomical location, the vascular endothelium also functions as a selectively permeable barrier. Macromolecules encountering various regional specializations of the endothelium, including cell surface glycocalyx, cell-cell junctional complexes, microvesicles, transcellular channels and subendothelial extracellular matrix, are enhanced or retarded in their movement from (or into) the intravascular space. Selectivity of this barrier function typically reflects the size and/or charge of the permeant molecule, but may also involve active metabolic processing on the part of the endothelial cell. Enhanced permeability to plasma macromolecules, such as albumin, is a hallmark of acute inflammation, and, in the case of lipoproteins, is an important part of atherosclerotic lesion development. Pathophysiologic stimuli, as well as therapeutic drugs, that can modulate this endothelial function thus have potential clinical relevance.

[0009] Another functionally important consequence of the location of the vascular endothelium is its ability to monitor, integrate and transduce blood-borne signals. Through expression of cell surface receptors for various cytokines (IL-1α,β, TNF-α, IFN-γ, TGF-β), growth factors and other hormones (e.g., basic FGF, VEGF/VPF, insulin and insulin-like growth factors), as well as bacterial products, (e.g., Gram-negative endotoxins such as lipopolysaccharides (LPS) and related binding proteins), and their intracellular coupling, via second messenger cascades, to the metabolic and transcriptional generation of other biological effector molecules, endothelial cells function as important tissue response regulators. At every site in the circulatory system they are sensing and responding to the local pathophysiological milieu, and can help propagate these responses transmurally, from the intimal lining into the walls of larger vessels (e.g., coronary arteries), or from the luminal surface of capillaries directly into the interstitium of adjacent tissues (e.g., myocardium). This sensing and transducing function extends beyond classical humoral stimuli to the biotransduction of distinct types of mechanical forces generated by pulsatile blood flow (e.g., fluid shear stresses, circumferential wall stress and transmural pressure).

[0010] Endothelium is capable of generating a diverse array of biologically active substances, including lipid mediators, cytokines, growth factors and other hormone-like substances, many of which serve as important biological effector molecules, influencing the behavior of multiple cells and tissues. Some act directly within their cell of origin in a so-called autocrine mode, whereas others act on adjacent cells (within the vessel wall or in the blood) in a paracrine mode. Still other endothelial-derived mediators, such as hematopoietic colony-stimulating factors (GM-CSF, M-CSF) are secreted into the circulation to act at a distance, analogous to classical hormones. In addition to being the source of cytokines, growth factors and hormones, the endothelium also is an important target of their actions. Indeed, the capacity for the endothelium to undergo, local or systemic, “activation” in response to such stimuli, with resultant dramatic changes in functional status, is an important aspect of its biology and pathobiology. First demonstrated in the case of MHC-II histocompatibility antigen upregulation by T-lymphocyte products, and then extended to the induction of procoagulant tissue factor activity and endothelial-leukocyte adhesion molecules by inflammatory cytokines and bacterial endotoxin, the phenomenon of “endothelial activation” has become an important paradigm for modulation of endothelial phenotype. It provides a conceptual model that encompasses both physiological adaptation and pathophysiological dysregulation.

[0011] Given its interface location, integrating and transducing capability, and the vast repertoire of its biologically active products, the endothelium plays a pivotal role in a series of pathophysiologic events. In each, endothelial-derived agonists and antagonists dynamically interact in the regulation of important processes that can have both local and systemic ramifications, such as hemostasis and thrombosis, vascular tone, vascular growth and remodeling, and inflammatory and immune reactions. At any given time, factors influencing the activation state or functional integrity of the endothelium determine the relative set-points of each of these balances. For example, the intact, unactivated vascular endothelial lining is non-thrombogenic, because the net activity of antithrombotic factors, such as prostacyclin, thrombomodulin, cell surface heparin-like glycosaminoglycans and ecto-ADPases, exceeds that of the various pro-thrombotic factors potentially also generated by the endothelium. The controlled expression of certain of these pro-thrombotic factors in response to local vascular trauma (e.g., thrombin-induced von Willebrand factor release) can function adaptively, as part of a response-to-injury reaction; conversely, decreased production of anti-thrombotic factors (e.g., prostacyclin, tissue plasminogen activator) may contribute to intravascular thrombosis and vital organ damage.

[0012] Similarly, imbalances in endothelial-derived smooth muscle relaxants versus endothelial-derived vasoconstrictors can influence local circulatory dynamics, as well as systemic blood pressure. The vascular endothelium is the source of some of the most potent naturally occurring vasoactive substances known, including nitric oxide and related substances (originally described as an EDRF, or “endothelium-dependent relaxing factor”, by Furchgott and Zawadski) and endothelin-1, a novel peptide that resembles the lethal toxin in the venom of certain vipers whose bite can induce coronary vasospasm. Other factors in this endothelial vasomotor balance include prostacyclin, angiotensin II (generated by angiotensin converting enzyme at the luminal interface) and platelet-derived growth factor. The latter can be generated by endothelial cells and, in addition to its mitogenic properties, also is a potent smooth muscle contractile agonist.

[0013] Under normal conditions, the cells of the vessel wall are essentially growth quiescent, but following experimental endothelial denudation, a burst of medial smooth muscle migration and division is triggered, which then subsides as endothelial regeneration occurs. This well orchestrated wound healing response presumably reflects not only the localized generation or release of growth stimulators but also a transient, relative deficiency in endothelial-derived growth inhibitors. The resultant intimal hyperplasia is very similar to that which occurs in early atherosclerotic lesions. The more complex issues of sustained smooth muscle hyperplasia, secondary to immune-mediated endothelial damage in transplant-associated arteriosclerosis, or in the post-angioplasty setting, as well as the interplay of angiogenic and anti-angiogenic factors in neovascularization phenomena in ischemic myocardium and peripheral tissues may also reflect imbalances in endothelial-derived growth regulators.

[0014] It is now increasingly clear that biomechanical stimuli derived from flowing blood can modulate the phenotype of endothelial cells. An important aspect of this phenomenon is the ability of these forces to alter the patterns of genes expressed by vascular endothelium. A growing body of in vitro experimental data has demonstrated that when cultured endothelial cells are subjected to defined biomechanical stimuli they can manifest alterations in gene expression. Interestingly, many of the genes that have been demonstrated to be regulated by these stimuli have been found to be expressed in vascular endothelium in vivo.

[0015] Vascular diseases including thrombotic complications are a major cause of death in the industrialized world. Examples of these complications include acute myocardial infarction, unstable angina, chronic stable angina, transient ischemic attacks, strokes, peripheral vascular disease, preeclampsia, deep venous thrombosis, embolism, disseminated intravascular coagulation and thrombotic cytopenic purpura, thrombotic disorders, inflammatory disorders, chronic vascular disease, autoimmune disorders, transplant vasculopathy/rejection, atherosclerosis, hypertension, aneurysmal disease, vasospastic syndromes, ischemic coronary syndromes, cerebral vascular disease, angiogenic (both pro and anti) processes, and wound healing. Thrombotic and restenotic complications also occur following invasive procedures, e.g., angioplasty, carotid endarterectomy, post CABG (coronary artery bypass graft) surgery, vascular graft surgery, stent placements and insertion of endovascular devices and prostheses.

SUMMARY OF THE INVENTION

[0016] The present invention is based on the discovery of a new gene family referred to as SCUBE, genes containing a secretory signal region, a chain of EGF-like domains, and a CUB domain, that can be differentially expressed in human endothelial cells compared to other human cell types.

[0017] The invention includes isolated nucleic acid molecules selected from the group consisting of isolated nucleic acid molecules that encode an amino acid sequence of SEQ ID NO: 2, 4, 17 or 19, an isolated nucleic acid molecule that encodes a fragment of at least 10 amino acids of SEQ ID NO: 2, 4, 17 or 19, and an isolated nucleic acid molecule which hybridizes to the complement of a nucleic acid molecule comprising SEQ ID NO: 1, 3, 16 or 18.

[0018] The present invention also includes isolated nucleic acid molecules selected from the group consisting of isolated nucleic acid molecules that encode an amino acid sequence of SEQ ID NO:6 or 8, an isolated nucleic acid molecule that encodes a fragment of at least 10 amino acids of SEQ ID NO:6 or 8 and an isolated nucleic acid molecule which hybridizes to the complement of a nucleic acid molecule comprising SEQ ID NO:5 or 7.

[0019] The present invention also includes isolated nucleic acid molecules selected from the group consisting of isolated nucleic acid molecules that encode an amino acid sequence of SEQ ID NO:6 or 8, an isolated nucleic acid molecule that encodes a fragment of at least 10 amino acids of SEQ ID NO:6 or 8 and an isolated nucleic acid molecule which hybridizes to the complement of a nucleic acid molecule comprising SEQ ID NO:5 or 7.

[0020] Nucleic acid molecules of the invention can encode a protein having at least about 85% amino acid sequence identity to SEQ ID NO: 2, 17, or 19, preferably at least about 86-90% sequence identity, and even more preferably at least about 91-100% sequence identity to SEQ ID NO: 2, 17 or 19. Nucleic acid molecules of the invention also can encode a protein having at least about 92% amino acid sequence identity to SEQ ID NO: 4, preferably at least about 93-95% sequence identity, and even more preferably at least about 96-100% sequence identity to SEQ ID NO: 4. Nucleic acid molecules of the invention also can encode a protein having at least about 85% amino acid sequence identity to SEQ ID NO: 6 or 8, preferably at least about 90-95% sequence identity, and even more preferably at least about 96, 97, 98, 99 or 100% sequence identity to SEQ ID NO: 6 or 8.

[0021] The present invention further includes the nucleic acid molecules operably linked to one or more expression control elements, including vectors comprising the isolated nucleic acid molecules. The invention further includes host cells transformed to contain the nucleic acid molecules of the invention and methods for producing a protein comprising the step of culturing a host cell transformed with a nucleic acid molecule of the invention under conditions in which the protein is expressed.

[0022] The invention further provides an isolated polypeptide selected from the group consisting of an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 2, 4, 17 or 19, an isolated polypeptide comprising a fragment of at least 10 amino acids of SEQ ID NO: 2, 4, 17 or 19, an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 2, 4, 17 or 19, and an isolated polypeptide comprising naturally occurring amino acid sequence variants of SEQ ID NO: 2, 4, 17 or 19. Polypeptides of the invention also include polypeptides with an amino acid sequence having at least about 85% amino acid sequence identity with the sequence set forth in SEQ ID NO: 2, 17 or 19, preferably at least about 90%, more preferably at least about 95%, and most preferably at least about 98% sequence identity with the sequence set forth in SEQ ID NO: 2, 17 or 19. Polypeptides of the invention further include polypeptides with an amino acid sequence having at least about 92% amino acid sequence identity with the sequence set forth in SEQ ID NO: 4, preferably at least about 95%, and even more preferably at least about 98% sequence identity with the sequence set forth in SEQ ID NO: 4.

[0023] The invention further provides an isolated polypeptide selected from the group consisting of an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 6 or 8, an isolated polypeptide comprising a fragment of at least 10 amino acids of SEQ ID NO: 6 or 8, an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 6 or 8, and an isolated polypeptide comprising naturally occurring amino acid sequence variants of SEQ ID NO: 6 or 8. Polypeptides of the invention also include polypeptides with an amino acid sequence having at least about 85% amino acid sequence identity with the sequence set forth in SEQ ID NO: 6 or 8, preferably at least about 90%, more preferably at least about 95%, and most preferably at least about 97%, 98% or 99% sequence identity with the sequence set forth in SEQ ID NO: 6 or 8.

[0024] The invention further provides an isolated antibody or antigen-binding antibody fragment that specifically binds to a SCUBE1, SCUBE2 or SCUBE3 polypeptide of the invention, including monoclonal and polyclonal antibodies. The invention also provides engineered antibodies, such as chimeric antibodies, humanized antibodies, bi- or multispecific antibodies, or antibodies or antigen-binding antibody fragments which have been engineered to include non-immunoglobulin polypeptide sequences.

[0025] The invention further provides methods of identifying an agent which modulates the expression of a nucleic acid molecule encoding a SCUBE protein of the invention, comprising: exposing cells which express the nucleic acid molecule to the agent; and determining whether the agent modulates expression of said nucleic acid molecule, thereby identifying an agent which modulates the expression of a nucleic acid molecule encoding the protein.

[0026] The invention further provides methods of identifying an agent which modulates the level of or at least one activity of a SCUBE protein of the invention, comprising: exposing cells which express the protein to the agent; and determining whether the agent modulates the level of or at least one activity of said protein, thereby identifying an agent which modulates the level of or at least one activity of the protein.

[0027] The invention further provides methods of identifying binding partners for a SCUBE protein of the invention, comprising: exposing said protein to a potential binding partner; and determining if the potential binding partner binds to said protein, thereby identifying binding partners for the protein.

[0028] The present invention further provides methods of modulating the expression of a nucleic acid molecule encoding a SCUBE protein of the invention, comprising: administering an effective amount of an agent which modulates the expression of a nucleic acid molecule encoding the protein. The invention also provides methods of modulating at least one activity of a SCUBE protein of the invention, comprising: administering an effective amount of an agent which modulates at least one activity of the protein.

[0029] The present invention further includes non-human transgenic animals modified to contain the SCUBE nucleic acid molecules of the invention, or non-human transgenic animals modified to contain mutated nucleic acid molecules or deletions of SCUBE such that expression of the encoded SCUBE polypeptides of the invention is prevented.

[0030] The invention further provides methods of diagnosing vascular diseases, comprising: determining the level of expression of a nucleic acid molecule of the invention or polypeptide of the invention.

[0031] The invention further includes compositions comprising a diluent and a polypeptide or protein selected from the group consisting of an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 2, 4, 17 or 19, an isolated polypeptide comprising a fragment of at least 10 amino acids of SEQ ID NO: 2, 4, 17 or 19, an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 2, 4, 17 or 19, naturally occurring amino acid sequence variants of SEQ ID NO: 2, 4, 17 or 19, an isolated polypeptide with an amino acid sequence having at least about 85% amino acid sequence identity with the sequence set forth in SEQ ID NO: 2, 17 or 19, preferably at least about 90%, more preferably at least about 95%, and most preferably at least about 98% sequence identity with the sequence set forth in SEQ ID NO: 2, 17 or 19, and an isolated polypeptide with an amino acid sequence having at least about 92% amino acid sequence identity with the sequence set forth in SEQ ID NO: 4, preferably at least about 95%, and even more preferably at least about 98% sequence identity with the sequence set forth in SEQ ID NO: 4.

[0032] The invention further includes compositions comprising a diluent and a polypeptide or protein selected from the group consisting of an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 6 or 8, an isolated polypeptide comprising a fragment of at least 10 amino acids of SEQ ID NO: 6 or 8, an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 6 or 8, naturally occurring amino acid sequence variants of SEQ ID NO: 6 or 8, an isolated polypeptide with an amino acid sequence having at least about 85% amino acid sequence identity with the sequence set forth in SEQ ID NO: 6 or 8, preferably at least about 90%, more preferably at least about 95%, and most preferably at least about 97%, 98% or 99% sequence identity with the sequence set forth in SEQ ID NO: 6 or 8.

[0033] In another aspect, the invention features a two dimensional array having a plurality of addresses, each address of the plurality being positionally distinguishable from each other address of the plurality, and each address of the plurality having a unique capture probe, e.g., a nucleic acid or peptide sequence. At least one address of the plurality has a capture probe that recognizes a SCUBE1, SCUBE2, or SCUBE3 molecule. In one embodiment, the capture probe is a nucleic acid, e.g., a probe complementary to a SCUBE1, SCUBE2, or SCUBE3 nucleic acid sequence. In another embodiment, the capture probe is a polypeptide, e.g., an antibody specific for SCUBE1, SCUBE2, or SCUBE3 polypeptides. Also featured is a method of analyzing a sample by contacting the sample to the aforementioned array and detecting binding of the sample to the array.

BRIEF DESCRIPTION OF THE DRAWINGS

[0034] FIG. 1 shows the amino acid sequence of human SCUBE1 (SEQ ID NO:2) as determined from a full-length cDNA clone. The signal peptide, EGF-like repeats and CUB domain are marked or underlined. Potential glycosylation sites are indicated by asterisks. The approximate margins of the C-termini of two deletion constructs in this study, D1 (SEQ ID NO:17) and D2 (SEQ ID NO:19), are marked. The estimated mature mass is 105,553 Da, and the pI is 6.7.

[0035] FIG. 2 shows a hydrophobicity plot and the domain structure of human SCUBE1. The plot was generated according to the methods of Kyte and Doolittle. The region marked with a thick line indicates the putative signal peptide (see FIG. 1). Polypeptides of the invention include fragments which include: all or part of a hydrophobic sequence, e.g., a sequence above the dashed line, e.g., the sequence from about amino acid 424 to 441 and from about 836 to 847 of SEQ ID NO:2; all or part of a hydrophilic sequence, e.g., a sequence below the dashed line, e.g., the sequence from about amino acid 55 to 71, from about 485 to 500, and from about 962 to 971 of SEQ ID NO:2. The lower panel shows the domain structure of SCUBE1 protein. In addition to EGF-like repeats and CUB domain, a spacer region is located between the 9th and 10 th EGF-like repeat. FL=full-length; D1=deletion construct #1; D2 =deletion construct #2; E=EGF-like repeats; CUB=CUB domain.

[0036] FIG. 3 demonstrates that human SCUBE1 is an uncleaved, secreted protein. a) Inclusion of endogenous signal peptide results in a secreted SCUBE1 protein. SCUBE1 tagged with Myc at the C-termius (SCUBE1.Myc) is detected in the culture medium by anti-Myc antibody (WB=Western blot). b) Secreted SCUBE1 is the same size as the cell-associated form. Flag- and Myc-tagged SCUBE1 (at the N- and C-termini, respectively, Flag.SCUBE1.Myc) is detected in the culture medium by Western blotting with anti-Flag M2 or anti-Myc antibody. c) Secreted SCUBE1 is not a proteolytic product. Culture medium from cells transfected with Flag.SCUBE1.Myc was immunoprecipitated with anti-Flag M2 antibody, and then immunoblotted with either anti-Flag M2 or anti-Myc antiserum. (IP=immunoprecipitation). As in a and b, the secreted protein and the cell-associated protein are the same size.

[0037] FIG. 4 shows that human SCUBE1 is a glycosylated protein. When Flag-tagged full-length or deletion versions (D1 and D2) of human SCUBE1 were cultured in the absence (−) or in the presence (+) of tunicamycin, a glycosylation inhibitor, Western blot analysis of cell lysates reveals that smaller molecules are produced in the presence of tunicamycin.

[0038] FIG. 5, upper panel, shows a Northern blot analysis of ploy(A)+mRNA from various human tissues for SCUBE1. mRNA samples were hybridized to a SCUBE1 cDNA radiolabeled probe, which identified an mRNA species of ˜-4.0 kb. The lower panel shows the same blot in which mRNA samples were probed with β-actin as a control.

[0039] FIG. 6 illustrates that a spacer region is critical for the secretion and surface expression of SCUBE1. a) Vector constructs containing full-length SCUBE1, SCUBE1-D1 and SCUBE1-D2 were analyzed by Western blotting and labeling with anti-Flag M2 antibody, showing that the proteins lacking the spacer region were not secreted (SCUBE1-D2 and controls). b) The expression constructs Flag-SCUBE1-FL (top), -D1 (middle), or -D2 (bottom) were singly or co-transfected with SCUBE1.Myc plasmid into cells and the cell surface analyzed by flow cytometry and labeling with anti-Flag M2 antibody. Again, only proteins containing the spacer region (SCUBE1-FL and SCUBE1-D1) were expressed on the cell surface.

[0040] FIG. 7 shows the membrane association of human SCUBE1 protein. Samples of supernatant from homogenized cells transfected with several SCUBE1 constructs show the presence of the protein encoded by the SCUBE1-D2 construct, while proteins encoded by the longer constructs remained in the cell pellets. When the cell membranes were disrupted by sonication and centrifuged, full-length SCUBE1 and SCUBE1-D1 proteins could be detected in the soluble membrane fraction.

[0041] FIG. 8 shows the homo-oligomerization of human SCUBE1 in transfected cells. a) When Flag-SCUBE1 and SCUBE1.Myc were co-transfected, the expressed protein molecules could be precipitated with anti-Myc antibody and detected with anti-Flag M2 antibody, or visa versa. b) When SCUBE1.Myc was co-transfected with Flag.SCUBE1-FL, Flag.SCUBE1-D1, or Flag.SCUBE1-D2, analysis of the cell lysates revealed polymeric proteins that could be immunoprecipitated with anti-Myc antibody and detected by immunoblotting with anti-Flag M2 antibody. Cell lysates were also immunoblotted to examine the protein expression levels. The polymeric proteins indicate that the EGF-like repeats, rather than the spacer or CUB domain, function in SCUBE1 homotypic associations.

[0042] FIG. 9 shows the tissue distribution of the SCUBE gene family as determined by RT-PCR analyses. Human tissue cDNAs were amplified with primers specific for SCUBE1 and SCUBE2. Amplification of GAPDH was performed as a positive control.

[0043] Figures 10a and 10b show the down-regulation of SCUBE1 and SCUBE2 expression in various cell lines and in mouse kidney tissue following exposure to pro-inflammatory cytokines (IL-1β or TNF-α) or to lipopolysaccharides (LPS).

[0044] FIG. 11 illustrates endothelial expression of SCUBE1 in human umbilical vessels and in monkey tissues. In situ hybridization was used to confirm the endothelial expression in human artery and vein, as well as in several monkey tissues including brain, lung and kidney.

[0045] FIG. 12 shows the expression of mouse SCUBE1 in various mouse embryonic tissues: a) heart; b) vena cava and aorta; c) lung; d) thoracic wall; e) small intestine; f) cerebrum.

[0046] FIG. 13 depicts a hydropathy plot of human SCUBE2. Relatively hydrophobic residues are shown above the dashed horizontal line, and relatively hydrophilic residues are below the dashed horizontal line. The cysteine residues (cys) are indicated by short vertical lines just below the hydropathy trace. The numbers corresponding to the amino acid sequence of human SCUBE2 are indicated. Polypeptides of the invention include fragments which include: all or part of a hydrophobic sequence, e.g., a sequence above the dashed line, e.g., the sequence from about amino acid 300 to 314, from about 756 to 772, and from about 876 to 884 of SEQ ID NO:4; all or part of a hydrophilic sequence, e.g., a sequence below the dashed line, e.g., the sequence from about amino acid 43 to 55, from about 80 to 93, from about 534 to 546, and from about 861 to 872 of SEQ ID NO:4; a sequence which includes a Cys, or a glycosylation site.

[0047] FIGS. 14A and 14B depict hydropathy plots of human SCUBE3. FIG. 14A depicts the hydropathy plot of SCUBE3.1 (SEQ ID NO:6) and FIG. 14B depicts the hydropathy plot of SCUBE3.2 (SEQ ID NO:8). Relatively hydrophobic residues are shown above the dashed horizontal line, and relatively hydrophilic residues are below the dashed horizontal line. The cysteine residues (cys) are indicated by short vertical lines just below the hydropathy trace. The numbers corresponding to the amino acid sequence of human SCUBE3 are indicated. Polypeptides of the invention include fragments which include: all or part of a hydrophobic sequence, e.g., a sequence above the dashed line, e.g., the sequence from about amino acid 201 to 211 and from about 763 to 773 of SEQ ID NO:6; all or part of a hydrophilic sequence, e.g., a sequence below the dashed line, e.g., the sequence from about amino acid 28 to 41, from about 497 to 508, and from about 881 to 897 of SEQ ID NO:6; all or part of a hydrophobic sequence, e.g., a sequence above the dashed line, e.g., the sequence from about amino acid 254 to 268 and from about 842 to 852 of SEQ ID NO:8; all or part of a hydrophilic sequence, e.g., a sequence below the dashed line, e.g., the sequence from about amino acid 28 to 41, from about 529 to 540, and from about 960 to 976 of SEQ ID NO:8; and a sequence which includes a Cys, or a glycosylation site.

DETAILED DESCRIPTION OF THE INVENTION

[0048] I. General Description

[0049] Vascular endothelial cells (EC) play a key role in a variety of physiologic and pathophysiologic processes, such as angiogenesis, inflammation, cancer metastasis and the development of vascular diseases. As a part of a strategy to identify genes that are differentially expressed in human EC, large-scale EST sequencing and expression profiling approaches were performed in human vascular EC cultured under various stimuli (flow, cytokine, angiogenic, etc). One full-length cDNA identified by these approaches encodes a secreted protein containing a signal peptide at the N-terminus followed by nine EGF-like domains, a spacer region, a tenth EGF-like domain and one CUB domain at the C-terminus (referred to herein as SCUBE1, Signal peptide-CUB-EGF-like domain-containing protein 1). A second cDNA identified by these approaches encodes SCUBE2, with an N-terminal signal peptide, eight EGF-like domains, a spacer region and a C-terminal CUB domain. A third set of sequences identified by homology, domain structure and expression analysis encodes the 47971 (gene MG44547) polypeptides, 47971-031 or SCUBE3.1, and Fbh47971FL or SCUBE3.2 referred to herein collectively as “SCUBE3,” with an N-terminal signal peptide, nine EGF-like domains, a spacer region and a C-terminal CUB domain.

[0050] Northern and microarray analyses demonstrate that SCUBE1 is expressed in adults in several highly vascularized tissues such as liver, kidney, lung, spleen and brain. The endothelial-selective pattern of expression for SCUBE1 was further confirmed by in situ hybridization to these tissues. We have characterized the SCUBE1 gene product by using a transient expression system in human kidney embryonic (HEK-293) cells. Overproduction in these cells resulted in expression of SCUBE1 protein in the conditioned medium. Flow cytometry and immunofluorescence analyses showed that this protein could bind to and be displayed on the cell surface. Analyses of several deletion mutants of the SCUBE1 protein revealed that the spacer region between the EGF-like and CUB domains is critical for its secretion and cell-surface association. Furthermore, expression of SCUBE1 is decreased in EC after IL-1β and TNF-α treatment, suggesting a possible role for SCUBE1 in the inflammatory response. A second gene encoding a homologue (designated as SCUBE2) was also identified and appears to be expressed in an EC-specific fashion. These results were confirmed by immunohistochemical detection of SCUBE1 and SCUBE2 proteins at endothelial cells in vivo. When overexpressed, SCUBE1 and SCUBE2 can manifest homo- and heterotypic interactions. These results indicate that SCUBE1 and SCUBE2 define an emerging secreted protein family that is highly expressed in human vascular endothelium.

[0051] The SCUBE1 polypeptide was found by immunohistochemistry to be associated with thrombi in vessels. These thrombi were the result of acute bleeding events which did not allow time for new protein synthesis. Thus, during a thrombotic event, cell-associated SCUBE1 can be released into the plasma and recruited into the thrombus. Accordingly, SCUBE1 molecules of the invention can be used for the treatment and/or diagnosis of thrombotic disorders.

[0052] SCUBE2 mRNA was found at high levels in urge urinary incontinence (UUI) bladder and at lower levels in normal bladder. SCUBE2 also has high levels of expression in breast tumor and low levels of expression in normal breast. Accordingly, SCUBE2 molecules of the invention can be used for the treatment and/or diagnosis of urinary bladder disorders and breast disorders, e.g. breast tumor.

[0053] The SCUBE3 mRNA was found at high levels in osteoblasts and normal fetal kidney, at medium levels in normal artery, normal vein, fetal heart, normal adult heart, normal ventricle, umbilical cord and diseased aorta and at medium to low levels in ischemic ventricle. In contrast, SCUBE3 was found at low levels in idiopathic artery, ischemic artery, and coronary diseased artery, to indicate regulated expression of SCUBE3 in some disease processes. Another example of regulated SCUBE3 expression is the medium level of SCUBE3 expression in urge urinary incontinence (UUI) bladder tissue and only a trace level of expression in normal bladder. Accordingly, SCUBE3 molecules of the invention can be used for the treatment and/or diagnosis of cardiovascular diseases, e.g. vessel or heart calcification and ischemia, disorders of bone metabolism and urinary bladder disorders.

[0054] SCUBE3 gene maps to chromosome 6p21. The Paget's disease of bone is mapped to the 6p21 locus. Accordingly, SCUBE3 molecules of the invention can be used for the treatment and/or diagnosis of Paget's disease.

[0055] The present invention is based in part on the identification of a new gene that encodes SCUBE1 or SCUBE2 and that is differentially expressed in human endothelial cells as compared to other human cell types. These genes correspond to the human cDNAs of SEQ ID NO: 1, 16, or 18, hereinafter referred to collectively as “SCUBE1” or specifically as “SCUBE1,” SCUBE1-D1,” or SCUBE1-D2, ” respectively, and SEQ ID NO:3 (SCUBE2). Genes that encode the human SCUBE proteins of SEQ ID NO: 2, 4, 17 or 19 (SCUBE1, SCUBE2, SCUBE1-D1, SCUBE1-D2, respectively) may also be found in other animal species, particularly mammalian species.

[0056] The present invention also is based in part on the identification of a gene which encodes SCUBE3 and which is differentially expressed in cardiovascular tissues. This gene corresponds to the human cDNAs of SEQ ID NO:5 and 7. Genes that encode the human SCUBE3 protein of SEQ ID NO:6 and 8 may also be found in other animal species, particularly mammalian species.

[0057] The genes and proteins of the invention may be used as diagnostic agents or markers to detect or monitor the progression of diseases or conditions with vascular involvement in a subject or sample.

[0058] A. Cardiovascular Disease

[0059] SCUBE proteins may be implicated in cardiovascular disorders, including in atherosclerotic plaque formation. For example, SCUBE1 has been identified in thrombi of vessels (e.g. in kidney and spleen). In another example, SCUBE3 has regulated expression in arteries, with higher expression in normal arteries than in idiopathic diseased arteries and ischemic diseased arteries. Diseases such as cardiovascular disease, including cerebral thrombosis or hemorrhage, ischemic heart or renal disease, peripheral vascular disease, or thrombosis of other major vessel, and other diseases, including diabetes mellitus, hypertension, hypothyroidism, cholesterol ester storage disease, systemic lupus erythematosus, homocysteinemia, and familial protein or lipid processing diseases, and the like, are either directly or indirectly associated with atherosclerosis. Accordingly, therapeutics of the invention, particularly those that modulate (or supply) SCUBE activity or formation may be effective in treating or preventing atherosclerosis-associated diseases or disorders. Therapeutics of the invention (particularly therapeutics that modulate the levels or activity) can be assayed by any method known in the art, including those described below, for efficacy in treating or preventing such diseases and disorders.

[0060] A vast array of animal and cell culture models exist for processes involved in atherosclerosis. A limited and non-exclusive list of animal models includes knockout mice for premature atherosclerosis (Kurabayashi and Yazaki, 1996, Int. Angiol. 15: 187-194), transgenic mouse models of atherosclerosis (Kappel et al., 1994, FASEB J. 8: 583-592), antisense oligonucleotide treatment of animal models (Callow, 1995, Curr. Opin. Cardiol. 10: 569-576), transgenic rabbit models for atherosclerosis (Taylor, 1997, Ann. N.Y. Acad. Sci 811: 146-152), hypercholesterolemic animal models (Rosenfeld, 1996, Diabetes Res. Clin. Pract. 30 Suppl.: 1-11), hyperlipidemic mice (Paigen et al., 1994, Curr. Opin. Lipidol. 5: 258-264), and inhibition of lipoxygenase in animals (Sigal et al., 1994, Ann. N.Y. Acad. Sci. 714: 211-224). In addition, in vitro cell models include but are not limited to monocytes exposed to low-density lipoprotein (Frostegard et al., 1996, Atherosclerosis 121: 93-103), cloned vascular smooth muscle cells (Suttles et al., 1995, Exp. Cell Res. 218: 331-338), endothelial cell-derived chemoattractant exposed T cells (Katz et al., 1994, J. Leukoc. Biol. 55: 567-573), cultured human aortic endothelial cells (Farber et al., 1992, Am. J. Physiol. 262: H1088-1085), and foam cell cultures (Libby et al., 1996, Curr Opin Lipidol 7: 330-335). Potentially effective therapeutics, for example but not by way of limitation, reduce foam cell formation in cell culture models, or reduce atherosclerotic plaque formation in hypercholesterolemic mouse models of atherosclerosis in comparison to controls.

[0061] Accordingly, once an atherosclerosis-associated disease or disorder has been shown to be amenable to treatment by modulation of activity or formation, that disease or disorder can be treated or prevented by administration of a therapeutic that modulates activity.

[0062] Other cardiovascular disorders in which SCUBE molecules of the invention can play a role include, but are not limited to disorders such as arteriosclerosis, cardiac hypertrophy, ischemia reperfusion injury, restenosis, arterial inflammation, vascular wall remodeling, ventricular remodeling, rapid ventricular pacing, coronary microembolism, tachycardia, bradycardia, pressure overload, aortic bending, coronary artery ligation, vascular heart disease, valvular disease, including but not limited to, valvular degeneration caused by calcification, rheumatic heart disease, endocarditis, or complications of artificial valves; atrial fibrillation, long-QT syndrome, congestive heart failure, sinus node dysfunction, angina, heart failure, hypertension, atrial fibrillation, atrial flutter, pericardial disease, including but not limited to, pericardial effusion and pericarditis; cardiomyopathies, e.g., dilated cardiomyopathy or idiopathic cardiomyopathy, myocardial infarction, coronary artery disease, coronary artery spasm, arrhythmia, sudden cardiac death, and cardiovascular developmental disorders.

[0063] B. Hemostatic and Thrombolytic Activity

[0064] A protein or a therapeutic of the invention may also exhibit hemostatic or thrombolytic activity. As a result, such a protein is expected to be useful in treatment of various coagulation disorders (including hereditary disorders, such as hemophilias) or to enhance coagulation and other hemostatic events in treating wounds resulting from trauma, surgery or other causes. A protein of the invention may also be useful for dissolving or inhibiting formation of thromboses and for treatment and prevention of conditions resulting therefrom (such as, for example, infarction of cardiac and central nervous system vessels (e.g., stroke).

[0065] EGF-like domains, such as those found in SCUBE1, SCUBE 2 and SCUBE3, are components of proteins involved in the coagulation process, for example, thrombomodulin, protein C, protein S, protein Z and factors VII, IX, X and XII. Accordingly, SCUBE1 polypeptide can be found in thrombi of vessels. Therefore, SCUBE proteins may play an important role in coagulation and thromobosis formation, as well as in related diseases.

[0066] The activity of a protein of the invention may, among other means, be measured by the following methods. Assays for hemostatic and thrombolytic activity include, without limitation, those described in: Linet et al., J. Clin. Pharmacol. 26:131-140, 1986; Burdick et al., Thrombosis Res. 45:413-419, 1987; Humphrey et al., Fibrinolysis 5:71-79 (1991); and Schaub, Prostaglandins 35:467-474, 1988.

[0067] C. Receptor/Ligand Activity

[0068] A protein or a therapeutic of the present invention may also demonstrate activity as receptors, receptor ligands or inhibitors or agonists of receptor/ligand interactions. Examples of such receptors and ligands include, without limitation, cytokine receptors and their ligands, receptor kinases and their ligands, receptor phosphatases and their ligands, receptors involved in cell-cell interactions and their ligands (including without limitation, cellular adhesion molecules (such as selecting, integrins and their ligands) and receptor/ligand pairs involved in antigen presentation, antigen recognition and development of cellular and humoral immune responses). Receptors and ligands are also useful for screening of potential peptide or small molecule inhibitors of the relevant receptor/ligand interaction. A protein of the present invention (including, without limitation, fragments of receptors and ligands) may themselves be useful as inhibitors of receptor/ligand interactions.

[0069] The activity of a protein of the invention may, among other means, be measured by the following methods: Current Protocols in Immunology, Ed by Coligan, et al., Greene Publishing Associates and Wiley-Interscience (Chapter 7.28, Measurement of Cellular Adhesion under static conditions 7.28.1-7.28.22), Takai et al., Proc Natl Acad Sci USA 84:6864-6868, 1987; Bierer et al., J. Exp. Med. 168:1145-1156, 1988; Rosenstein et al., J. Exp. Med. 169:149-160 1989; Stoltenborg et al., J Immunol Methods 175:59-68, 1994; Stitt et al., Cell 80:661-670, 1995.

[0070] D. Anti-Inflammatory Activity

[0071] SCUBE proteins or therapeutics of the present invention may also exhibit anti-inflammatory activity. The anti-inflammatory activity may be achieved by providing a stimulus to cells involved in the inflammatory response, by inhibiting or promoting cell-cell interactions (such as, for example, cell adhesion), by inhibiting or promoting chemotaxis of cells involved in the inflammatory process, inhibiting or promoting cell extravasation, or by stimulating or suppressing production of other factors which more directly inhibit or promote an inflammatory response. Proteins exhibiting such activities can be used to treat inflammatory conditions including chronic or acute conditions, including without limitation inflammation associated with infection (such as septic shock, sepsis or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine-induced lung injury, inflammatory bowel disease, e.g. Crohn's disease and ulcerative colitis, or resulting from over production of cytokines such as TNF or IL-1. Molecules of the invention may also be useful to treat anaphylaxis, hypersensitivity to an antigenic substance or material and respiratory inflammatory disorders, e.g. asthma, allergic asthma, and chronic obstructive pulmonary disease. Further therapeutic uses of SCUBE molecules of the invention include autoimmune diseases (including, for example, diabetes mellitus, arthritis (including rheumatoid arthritis, juvenile rheumatoid arthritis, osteoarthritis, psoriatic arthritis), multiple sclerosis, encephalomyelitis, myasthenia gravis, systemic lupus erythematosis, autoimmune thyroiditis, dermatitis (including atopic dermatitis and eczematous dermatitis), psoriasis, and Sjögren's Syndrome.

[0072] E. Disorders of Bone Metabolism

[0073] Aberrant expression and/or activity of SCUBE molecules, e.g. SCUBE3, can mediate disorders associated with bone metabolism. “Bone metabolism” refers to direct or indirect effects in the formation or degeneration of bone structures, e.g., bone formation, bone resorption, etc., which can ultimately affect the concentrations in serum of calcium and phosphate. This term also includes activities mediated by SCUBE molecules, e.g. SCUBE3, in bone cells, e.g. osteoblasts, that can in turn result in bone formation and degeneration. For example, SCUBE molecules, e.g. SCUBE3, can support different activities of bone resorbing osteoclasts such as the stimulation of differentiation of monocytes and mononuclear phagocytes into osteoclasts. Accordingly, SCUBE molecules, e.g. SCUBE3, that modulate the production of bone cells can influence bone formation and degeneration, and thus can be used to treat bone disorders. Examples of such disorders include, but are not limited to, Paget's disease, osteoporosis, osteodystrophy, osteomalacia, rickets, osteitis fibrosa cystica, renal osteodystrophy, osteosclerosis, anti-convulsant treatment, osteopenia, fibrogenesis-imperfecta ossium, secondary hyperparathyrodism, hypoparathyroidism, hyperparathyroidism, cirrhosis, obstructive jaundice, drug induced metabolism, medullary carcinoma, chronic renal disease, rickets, sarcoidosis, glucocorticoid antagonism, malabsorption syndrome, steatorrhea, tropical sprue, idiopathic hypercalcemia and milk fever.

[0074] F. Urinary Bladder Disorders

[0075] Aberrant expression and/or activity of SCUBE molecules, e.g. SCUBE2 and SCUBE3, can mediate urinary bladder disorders. The activities mediated by SCUBE molecules, e.g. SCUBE2 and SCUBE3, in bladder cells, e.g. epithelial, capillary endothelial cells, and smooth muscle cells, can in turn result in urinary bladder function. Accordingly, SCUBE molecules, e.g. SCUBE2 and SCUBE3, can modulate urinary bladder function, and thus can be used to treat urinary bladder disorders. Examples of bladder disorders include, but are not limited to, urge urinary incontinence (UUI), overactive bladder, cystitis (e.g. tuberculous cystitis, radiation cystitis, ulcerative interstitial cystitis, emphysematous cystitis, malakoplakia lesions, cystitis cystica, and eosinophilic cystitis), diverticula, vesicoureteral reflux, and bladder neoplasms (e.g. transitional cell carcinoma, squamous cell carcinoma and adenocarcinoma).

[0076] G. Breast Disorders

[0077] Aberrant expression and/or activity of SCUBE molecules, e.g. SCUBE2, can mediate breast disorders. Disorders of the breast include, but are not limited to, disorders of development; inflammations, including but not limited to, acute mastitis, periductal mastitis, periductal mastitis (recurrent subareolar abscess, squamous metaplasia of lactiferous ducts), mammary duct ectasia, fat necrosis, granulomatous mastitis, and pathologies associated with silicone breast implants; fibrocystic changes; proliferative breast disease including, but not limited to, epithelial hyperplasia, sclerosing adenosis, and small duct papillomas; tumors including, but not limited to, stromal tumors such as fibroadenoma, phyllodes tumor, and sarcomas, and epithelial tumors such as large duct papilloma; carcinoma of the breast including in situ (noninvasive) carcinoma that includes ductal carcinoma in situ (including Paget's breast disease) and lobular carcinoma in situ, and invasive (infiltrating) carcinoma including, but not limited to, invasive ductal carcinoma, no special type, invasive lobular carcinoma, medullary carcinoma, colloid (mucinous) carcinoma, tubular carcinoma, and invasive papillary carcinoma, and miscellaneous malignant neoplasms.

[0078] II. Specific Embodiments

[0079] A. SCUBE Proteins and Variants Thereof

[0080] The present invention provides isolated SCUBE proteins, allelic variants of the proteins, and conservative amino acid substitutions of the proteins. As used herein, the “protein” or “polypeptide” refers, in part, to a protein that has the human amino acid sequence depicted in SEQ ID NO: 2, 4, 17, 19, 6 or 8 or fragments thereof with or without the secretory signal region or signal peptide and spacer region. The terms also refer to naturally occurring allelic variants and proteins that have a slightly different amino acid sequence than those specifically recited above. Allelic variants, though possessing a slightly different amino acid sequence than those recited above, will still have the same or similar biological functions associated with these proteins.

[0081] As used herein, the SCUBE family of proteins related to the human amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6 or 8 refers in part, to proteins that have been isolated from organisms in addition to humans. A SCUBE family member can include at least one signal peptide, at least one, two, three, four, five, six, seven, preferably eight, nine or ten EGF-like domains, at least one spacer region and at least one CUB domain. The methods used to identify and isolate other members of the family of proteins related to these proteins are described below.

[0082] As used herein, the term “EGF-like domain” includes an amino acid sequence of about 15 to 50 amino acid residues in length and having a bit score for the alignment of the sequence to the EGF-like domain (HMM) of at least 5. (For reference to Pfam and Prosite annotation, see Example 8.) Preferably, an EGF-like domain includes six conserved cysteines involved in disulfide bonding to maintain the structure of the SCUBE EGF-like domain in an extracellular environment. The EGF-like domains typically can be repeated multiple times (nearly tandemly, in a region containing at least one, two, three, four, five, six, seven, preferably eight or nine EGF-like domains) in the N-terminal half of the SCUBE polypeptide. The EGF-like domains of SCUBE polypeptides can mediate binding of SCUBE molecules to polypeptides having a diphtheria toxin catalytic domain (Pfam PF02763), an immunoglobulin domain (Pfam PF00047), such as is found in a variety of proteins, e.g. antibodies, major histocompatibility complex molecules, and receptor tyrosine kinases, or a trypsin domain (Pfam PF00089) such as is found in a variety of serine proteases, e.g. enzymes of the coagulation system such as thrombin and plasminogen activator. Preferably, an EGF-like domain includes at least about 20 to 45 amino acids, more preferably about 25 to 40 amino acid residues, or about 32 to 37 amino acids and has a bit score for the alignment of the sequence to the EGF-like domain (HMM) of at least 5, 9, 14 or greater. An EGF-like domain can include an EGF-like domain signature 2 sequence (PS01186, SEQ ID NO:11) and/or a calcium-binding EGF-like domain signature sequence (PS01187, SEQ ID NO:12). The EGF-like domain (HMM) has been assigned the PFAM Accession Number PF00008 (SEQ ID NO:9).

[0083] As used herein, the term “spacer region” includes an amino acid sequence of about 350 to 475 amino acid residues in length. A spacer region can have asparagines-targeted glycosylation sites (N-glycosylation sites, Prosite PS00001). Preferably, a spacer region can mediate secretion and cell-surface association of a SCUBE polypeptide. A spacer region can interact with lectin-containing molecules. Preferably, a spacer region includes at least about 375 to 450 amino acids, more preferably about 390 to 430 amino acid residues. The spacer region of the SCUBE molecules typically can be found between the multiple repeated EGF-like domains and the CUB domain.

[0084] As used herein, the term “CUB domain” includes an amino acid sequence of about 90 to 130 amino acid residues in length and having a bit score for the alignment of the sequence to the CUB domain (HMM) of at least 50. A CUB domain can be found in developmentally regulated proteins and can have four conserved cysteines to form disulfide bonds and stabilize this domain in an extracellular environment. Preferably, a CUB domain includes at least about 95 to 125 amino acids, more preferably about 100 to 120 amino acid residues, or about 105 to 115 amino acids and has a bit score for the alignment of the sequence to the CUB domain (HMM) of at least 60, 65, 70 or greater. The CUB domain (HMM) has been assigned the PFAM Accession Number PF0043 1, SEQ ID NO: 10.

[0085] The proteins of the present invention are preferably in isolated form. As used herein, a protein is said to be isolated when physical, mechanical or chemical methods are employed to remove the protein from cellular constituents that are normally associated with the protein. In one embodiment, the language “substantially purified” means preparation of SCUBE protein having less than about 30%, 20%, 10% and more preferably 5% (by dry weight), of non-SCUBE protein (also referred to herein as a “contaminating protein”), or of chemical precursors or non-SCUBE chemicals. When the SCUBE protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation. The invention includes isolated or purified preparations of at least 0.01, 0.1, 1.0, and 10 milligrams in dry weight. A skilled artisan can readily employ standard purification methods to obtain an isolated protein.

[0086] The proteins of the present invention further include insertion, deletion or conservative amino acid substitution variants of SEQ ID NO: 2, 4, 17, 19, 6 or 8. As used herein, a conservative variant refers to alterations in the amino acid sequence that do not adversely affect the biological functions of the protein. A substitution, insertion or deletion is said to adversely affect the protein when the altered sequence prevents or disrupts a biological function associated with the protein. For example, the overall charge, structure or hydrophobic/hydrophilic properties of the protein can be altered without adversely affecting a biological activity. Accordingly, the amino acid sequence can be altered, for example to render the peptide more hydrophobic or hydrophilic, without adversely affecting the biological activities of the protein. In another example, a mutation which results in removal or replacement of a cysteine residue in an EGF-like domain or a CUB domain in a SCUBE polypeptide can have an adverse effect on the resulting SCUBE structure, extracellular half-life or activity. In another example, a mutation which results in removal or replacement of an asparagine in an N-glycosylation site in a spacer region of a SCUBE polypeptide can have an adverse effect on the secretion or the cell-surface association of the resulting SCUBE polypeptide.

[0087] A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a SCUBE protein is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a SCUBE coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for SCUBE biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ID NO:1, 16, 18, 3, 5, or 7, the encoded protein can be expressed recombinantly and the activity of the protein can be determined.

[0088] Ordinarily, the allelic variants, the conservative substitution variants, and the members of the protein family, will have an amino acid sequence having at least about 50%, 60%, 65%, 70% or 75% amino acid sequence identity with the sequence set forth in SEQ ID NO: 2, 4, 17 or 19, preferably at least about 80%, more preferably at least about 85%-90%, and most preferably at least about 91-95% sequence identity. A particularly preferred embodiment will have at least about 84% sequence identity to SEQ ID NO: 2, 17 or 19, more preferably at least about 85-90% sequence identity, and most preferably at least about 91-95% or 96 or 99% sequence identity. Another particularly preferred embodiment will have at least about 92% sequence identity to SEQ ID NO: 4, more preferably at least about 93-95% sequence identity, and most preferably at least about 96% or 99% sequence identity. In another preferred embodiment, polypeptides will have an amino acid sequence having at least about 85% amino acid sequence identity with the sequence set forth in SEQ ID NO: 6 or 8, preferably at least about 90%, more preferably at least about 95%, and most preferably at least about 97%, 98% or 99% sequence identity with the sequence set forth in SEQ ID NO: 6 or 8.

[0089] Identity or homology with respect to such sequences is defined herein as the percentage of amino acid residues in the candidate sequence that are identical with the known peptides, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology or alignment, and not considering any conservative substitutions as part of the sequence identity (see section B for the relevant parameters). Fusion proteins, or N-terminal, C-terminal or internal extensions, deletions, or insertions into the peptide sequence shall not be construed as affecting homology.

[0090] Thus, the proteins of the present invention include molecules having the amino acid sequence disclosed in SEQ ID NO: 2, 4, 17, 19, 6 or 8; fragments thereof having a consecutive sequence of at least about 6, 10, 15, 20, 25, 30, 35 or more amino acid residues of these proteins; amino acid sequence variants wherein one or more amino acid residues has been inserted N- or C-terminal to, or within, the disclosed coding sequence; and amino acid sequence variants of the disclosed sequence, or their fragments as defined above, that have been substituted by at least one residue. Such fragments, also referred to as peptides or polypeptides, may contain antigenic regions, functional regions of the protein identified as regions of the amino acid sequence which correspond to known protein domains, as well as regions of pronounced hydrophilicity. For instance, such regions or domains include EGF-like domains, the spacer region, the CUB domain and the like (for SCUBE1, see FIGS. 1 and 2; for SCUBE2, see Example 1 and FIG. 13 and for SCUBE3, see Example 8 and FIGS. 14A and 14B). The regions are all easily identifiable by using commonly available protein sequence analysis software such as MACVECTOR sequence analysis software (available from Accelrys, Inc., San Diego, Calif.).

[0091] Contemplated variants further include those containing predetermined mutations by, e.g., homologous recombination, site-directed or PCR mutagenesis, and the corresponding proteins of other animal species, including but not limited to rabbit, mouse, rat, porcine, bovine, ovine, equine and non-human primate species, and the alleles or other naturally occurring variants of the family of proteins; and derivatives wherein the protein has been covalently modified by substitution, chemical, enzymatic, or other appropriate means with a moiety other than a naturally occurring amino acid (for example a detectable moiety such as an enzyme or radioisotope).

[0092] In another aspect, the invention provides SCUBE chimeric or fusion proteins. As used herein, a SCUBE “chimeric protein” or “fusion protein” includes a SCUBE polypeptide linked to a non-SCUBE polypeptide. A “non-SCUBE polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the SCUBE protein, e.g., a protein which is different from the SCUBE protein and which is derived from the same or a different organism. The SCUBE polypeptide of the fusion protein can correspond to all or a portion e.g., a fragment described herein of a SCUBE amino acid sequence. In a preferred embodiment, a SCUBE fusion protein includes at least one (or two) biologically active portion of a SCUBE protein. The non-SCUBE polypeptide can be fused to the N-terminus or C-terminus of the SCUBE polypeptide. The fusion protein can include a moiety which has a high affinity for a ligand. For example, the fusion protein can be a GST-SCUBE fusion protein in which the SCUBE sequences are fused to the C-terminus of the GST sequences. In other examples, the fusion protein can have a FLAG epitope tag, a myc epitope tag or a polyhistidine (nickel affinity binding) tag. Such fusion proteins can facilitate the purification of recombinant SCUBE.

[0093] As described below, members of the family of proteins can be used: (1) as a diagnostic or cell marker; (2) to identify agents which modulate at least one activity of the protein; (3) to identify binding partners for the protein, (4) as an antigen to raise polyclonal or monoclonal antibodies, and (5) as a therapeutic agent or target.

[0094] B. Nucleic Acid Molecules

[0095] The present invention further provides nucleic acid molecules that encode the protein having SEQ ID NO: 2, 4, 17, 19, 6 or 8 and the related proteins herein described, preferably in isolated form. As used herein, “nucleic acid” is defined as RNA or DNA or related molecules that encodes a protein or peptide as defined above, is complementary to a nucleic acid sequence encoding such peptides, hybridizes to such a nucleic acid and remains stably bound to it under appropriate stringency conditions, or encodes a polypeptide sharing at least about 50%, 60%, 65%, 70% or 75% sequence identity, preferably at least about 80%, more preferably at least about 85%, and even more preferably at least about 90% or 95% or more identity with the peptide sequences. The “nucleic acid molecules” of the invention further include nucleic acid molecules that share at least about 50%, 60%, 65%, 70% or 75% sequence identity, preferably at least about 80%, more preferably at least about 85%, and even more preferably at least about 90% or 95% or more identity with the nucleotide sequence of SEQ ID NO: 1, 16, 18, 3, 5 or 7 or the open reading frames defined therein. A particularly preferred embodiment will have at least about 87% sequence identity to SEQ ID NO: 1, 16 or 18, more preferably at least about 88-90% sequence identity, and most preferably at least about 91-95% or 96 or 99% sequence identity. Another particularly preferred embodiment will have at least about 94% sequence identity to SEQ ID NO: 3, more preferably at least about 95-96% sequence identity, and most preferably at least about 97% or 99% sequence identity. Other particularly preferred embodiments will have at least about 85% sequence identity to SEQ ID NO: 5 or 7, more preferably at least about 90% sequence identity, even more preferably at least about 95-96% sequence identity, and most preferably at least about 97%, 98% or 99% sequence identity.

[0096] Specifically contemplated are genomic DNA, cDNA, mRNA and antisense molecules, as well as nucleic acids based on alternative backbones or including alternative bases whether derived from natural sources or synthesized. Such nucleic acids, however, are defined further as being novel and unobvious over any prior art nucleic acid including that which encodes, hybridizes under appropriate stringency conditions, or is complementary to nucleic acid encoding a protein according to the present invention.

[0097] Homology or identity at the nucleotide or amino acid sequence level is determined by BLAST (Basic Local Alignment Search Tool) analysis using the algorithm employed by the programs blastp, blastn, blastx, tblastn and tblastx (Altschul et al., Nucleic Acids Res 25:3389-3402, 1997, and Karlin et al., Proc Natl Acad Sci USA 87:2264-2268, 1990, both fully incorporated by reference) which are tailored for sequence similarity searching. The approach used by the BLAST program is to first consider similar segments, with and without gaps, between a query sequence and a database sequence, then to evaluate the statistical significance of all matches that are identified and finally to summarize only those matches which satisfy a preselected threshold of significance. For a discussion of basic issues in similarity searching of sequence databases, see Altschul et al., Nature Genetics 6:119-129, 1994, which is fully incorporated by reference. The search parameters for histogram, descriptions, alignments, expect (i.e., the statistical significance threshold for reporting matches against database sequences), cutoff, matrix and filter (low complexity) are at the default settings. The default scoring matrix used by blastp, blastx, tblastn, and tblastx is the BLOSUM62 matrix (Henikoff et al., Proc Natl Acad Sci USA 89: 10915-10919, 1992, fully incorporated by reference), recommended for query sequences over 85 in length (nucleotide bases or amino acids).

[0098] For blastn, the scoring matrix is set by the ratios of M (i.e., the reward score for a pair of matching residues) to N (i.e., the penalty score for mismatching residues), wherein the default values for M and N are +5 and −4, respectively. Four blastn parameters were adjusted as follows: Q=10 (gap creation penalty); R=10 (gap extension penalty); wink=1 (generates word hits at every winkth position along the query); and gapw=16 (sets the window width within which gapped alignments are generated). The equivalent Blastp parameter settings were Q=9; R=2; wink=1; and gapw=32. A Bestfit comparison between sequences, available in the GCG package version 10.0, uses DNA parameters GAP=50 (gap creation penalty) and LEN=3 (gap extension penalty) and the equivalent settings in protein comparisons are GAP=8 and LEN=2.

[0099] “Stringent conditions” include those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M NaCl/0.0015 M sodium citrate/0.1% SDS at 50° C., or (2) employ during hybridization a denaturing agent such as formamide, for example, 50% (vol/vol) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42° C. Another example is hybridization in 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC and 0.1% SDS. A skilled artisan can readily determine and vary the stringency conditions appropriately to obtain a clear and detectable hybridization signal. Preferred molecules are those that hybridize under the above conditions to the complement of SEQ ID NO: 1 and which encode a functional protein. Even more preferred hybridizing molecules are those that hybridize under the above conditions to the complement strand of the open reading frame of SEQ ID NO: 1, 16, 18, 3, 5, or 7.

[0100] As used herein, a nucleic acid molecule is said to be “isolated” when the nucleic acid molecule is substantially separated from contaminant nucleic acid molecules encoding other polypeptides.

[0101] The present invention further provides fragments of the encoding nucleic acid molecule. As used herein, a fragment of an encoding nucleic acid molecule refers to a small portion of the entire protein coding sequence. The size of the fragment will be determined by the intended use. For example, if the fragment is chosen so as to encode an active portion of the protein, the fragment will need to be large enough to encode the functional region(s) of the protein. For instance, fragments which encode peptides corresponding to predicted antigenic regions may be prepared. If the fragment is to be used as a nucleic acid probe or PCR primer, then the fragment length is chosen so as to obtain a relatively small number of false positives during probing/priming (see the discussion in Section H).

[0102] Fragments of the encoding nucleic acid molecules of the present invention (i.e., synthetic oligonucleotides) that are used as probes or specific primers for the polymerase chain reaction (PCR), or to synthesize gene sequences encoding proteins of the invention, can easily be synthesized by chemical techniques, for example, the phosphoramidite method of Matteucci et al., (J Am Chem Soc 103:3185-3191, 1981) or using automated synthesis methods. In addition, larger DNA segments can readily be prepared by well-known methods, such as synthesis of a group of oligonucleotides that define various modular segments of the gene, followed by ligation of oligonucleotides to build the complete modified gene.

[0103] A nucleic acid fragment can include a sequence corresponding to a domain, region, or functional site described herein. A nucleic acid fragment can also include one or more domain, region, or functional site described herein. Thus, for example, a SCUBE nucleic acid fragment can include a sequence encoding an EGF-like domain, a spacer region or a CUB domain of a SCUBE polypeptide, as described herein

[0104] The encoding nucleic acid molecules of the present invention may further be modified so as to contain a detectable label for diagnostic and probe purposes. A variety of such labels are known in the art and can readily be employed with the encoding molecules herein described. Suitable labels include, but are not limited to, biotin, radiolabeled nucleotides and the like. A skilled artisan can readily employ any such label to obtain labeled variants of the nucleic acid molecules of the invention.

[0105] Modifications to the primary structure of the nucleic acid molecules by deletion, addition, or alteration of the nucleotide sequence can be made without destroying the activity of the encoded proteins. Such substitutions or other alterations result in proteins having an amino acid sequence falling within the contemplated scope of the present invention.

[0106] C. Isolation of other Related Nucleic Acid Molecules

[0107] As described above, the identification and characterization of the nucleic acid molecule having SEQ ID NO: 1, 16, 18, 3, 5, or 7 allows a skilled artisan to isolate nucleic acid molecules that encode other members of the protein family in addition to the sequences herein described.

[0108] For instance, a skilled artisan can readily use the amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8 to generate antibody probes to screen expression libraries prepared from appropriate cells. Typically, polyclonal antiserum from mammals such as rabbits immunized with the purified protein (as described below) or monoclonal antibodies can be used to probe a mammalian cDNA or genomic expression library, such as lambda gtll library, to obtain the appropriate coding sequence for other members of the protein family. The cloned cDNA sequence can be expressed as a fusion protein, expressed directly using its own control sequences, or expressed by constructions using control sequences appropriate to the particular host used for expression of the enzyme.

[0109] Alternatively, a portion of the coding sequence herein described can be synthesized and used as a probe to retrieve DNA encoding a member of the protein family from any mammalian organism. Oligomers containing approximately 18-20 nucleotides (encoding about a 6-7 amino acid stretch) are prepared and used to screen genomic DNA or cDNA libraries to obtain hybridization under stringent conditions or conditions of sufficient stringency to eliminate an undue level of false positives.

[0110] Additionally, pairs of oligonucleotide primers can be prepared for use in a polymerase chain reaction (PCR) to selectively clone an encoding nucleic acid molecule. A PCR denature/anneal/extend cycle for using such PCR primers is well known in the art and can readily be adapted for use in isolating other encoding nucleic acid molecules.

[0111] Nucleic acid molecules encoding other members of the protein family may also be identified in existing genomic or other sequence information using any available computational method, including but not limited to: PSI-BLAST (Altschul, et al., Nucleic Acids Res 25:3389-3402, 1997); PHI-BLAST (Zhang, et al., Nucleic Acids Res 26:3986-3990, 1998), 3D-PSSM (Kelly et al., J Mol Biol 299(2): 499-520, 2000); and other computational analysis methods (Shi et al., Biochem Biophys Res Commun 262(1):132-138, 1999 and Matsunami et al., Nature 404(6778):601-604, 2000).

[0112] D. rDNA molecules Containing a Nucleic Acid Molecule

[0113] The present invention further provides recombinant DNA molecules (rDNAs) that contain a coding sequence. As used herein, a rDNA molecule is a DNA molecule that has been subjected to molecular manipulation in situ. Methods for generating rDNA molecules are well known in the art, for example, see Sambrook et al., Molecular Cloning—A Laboratory Manual, 3d Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001. In the preferred rDNA molecules, a coding DNA sequence is operably linked to expression control sequences and/or vector sequences.

[0114] The choice of vector and/or expression control sequences to which one of the protein family encoding sequences of the present invention is operably linked depends directly, as is well known in the art, on the functional properties desired, e.g., protein expression, and the host cell to be transformed. A vector contemplated by the present invention is at least capable of directing the replication or insertion into the host chromosome, and preferably also expression, of the structural gene included in the rDNA molecule.

[0115] Expression control elements that are used for regulating the expression of an operably linked protein encoding sequence are known in the art and include, but are not limited to, inducible promoters, constitutive promoters, secretion signals, and other regulatory elements. Preferably, the inducible promoter is readily controlled, such as being responsive to a nutrient in the host cell's medium.

[0116] In one embodiment, the vector containing a coding nucleic acid molecule will include a prokaryotic replicon, i.e., a DNA sequence having the ability to direct autonomous replication and maintenance of the recombinant DNA molecule extrachromosomally in a prokaryotic host cell, such as a bacterial host cell, transformed therewith. Such replicons are well known in the art. In addition, vectors that include a prokaryotic replicon may also include a gene whose expression confers a detectable marker such as a drug resistance. Typical bacterial drug resistance genes are those that confer resistance to ampicillin or tetracycline.

[0117] Vectors that include a prokaryotic replicon can further include a prokaryotic or bacteriophage promoter capable of directing the expression (transcription and translation) of the coding gene sequences in a bacterial host cell, such as E. coli. A promoter is an expression control element formed by a DNA sequence that permits binding of RNA polymerase and transcription to occur. Promoter sequences compatible with bacterial hosts are typically provided in plasmid vectors containing convenient restriction sites for insertion of a DNA segment of the present invention. Typical of such vector plasmids are pUC8, pUC9, pBR322 and pBR329 available from BioRad Laboratories, (Richmond, Calif.), pPL and pKK223 available from Pharmacia (Piscataway, N.J.).

[0118] Expression vectors compatible with eukaryotic cells, preferably those compatible with vertebrate cells, can also be used to form rDNA molecules that contain a coding sequence. Eukaryotic cell expression vectors, including viral vectors, are well known in the art and are available from several commercial sources. Typically, such vectors are provided containing convenient restriction sites for insertion of the desired DNA segment. Typical of such vectors are pSVL and pKSV-10 (Pharmacia), pBPV-1/pML2d (International Biotechnologies, Inc.), pTDT1 (ATCC, #31255), the vector pCDM8 described herein, and the like eukaryotic expression vectors.

[0119] Eukaryotic cell expression vectors used to construct the rDNA molecules of the present invention may further include a selectable marker that is effective in an eukaryotic cell, preferably a drug resistance selection marker. A preferred drug resistance marker is the gene whose expression results in neomycin resistance, i.e., the neomycin phosphotransferase (neo) gene. (Southern et al., J Mol Anal Genet 1, 327-341, 1982) Alternatively, the selectable marker can be present on a separate plasmid, and the two vectors are introduced by co-transfection of the host cell, and selected by culturing in the appropriate drug for the selectable marker.

[0120] E. Host Cells Containing an Exogenously Supplied Coding Nucleic Acid Molecule

[0121] The present invention further provides host cells transformed with a nucleic acid molecule that encodes a protein of the present invention. The host cell can be either prokaryotic or eukaryotic. Eukaryotic cells useful for expression of a protein of the invention are not limited, so long as the cell line is compatible with cell culture methods and compatible with the propagation of the expression vector and expression of the gene product. Preferred eukaryotic host cells include, but are not limited to, yeast, insect and mammalian cells, preferably vertebrate cells such as those from a mouse, rat, monkey or human cell line. Preferred eukaryotic host cells include Chinese hamster ovary (CHO) cells available from the ATCC as CCL61, NIH Swiss mouse embryo cells (NIH/3T3) available from the ATCC as CRL 1658, baby hamster kidney cells (BHK), and the like eukaryotic tissue culture cell lines.

[0122] Any prokaryotic host can be used to express a rDNA molecule encoding a protein of the invention. The preferred prokaryotic host is E. coli.

[0123] Transformation of appropriate cell hosts with a rDNA molecule of the present invention is accomplished by well-known methods that typically depend on the type of vector used and host system employed. With regard to transformation of prokaryotic host cells, electroporation and salt treatment methods are typically employed, see, for example, Cohen et al., Proc Natl Acad Sci USA 69:2110, 1972; and Sambrook et al. (supra). With regard to transformation of vertebrate cells with vectors containing rDNAs, electroporation, cationic lipid or salt treatment methods are typically employed, see, for example, Graham et al., Virol 52:456, 1973; or Wigler et al., Proc Natl Acad Sci USA 76:1373-1376, 1979.

[0124] Successfully transformed cells, i.e., cells that contain a rDNA molecule of the present invention, can be identified by well known techniques including the selection for a selectable marker. For example, cells resulting from the introduction of an rDNA of the present invention can be cloned to produce single colonies. Cells from those colonies can be harvested, lysed and their DNA content examined for the presence of the rDNA using a method such as that described by Southern, J Mol Bio. 98:503, 1975, or Berent et al., Biotech 3:208, 1985, or the proteins produced from the cell assayed via an immunological method.

[0125] F. Production of Recombinant Proteins Using a rDNA Molecule

[0126] The present invention further provides methods for producing a protein of the invention using nucleic acid molecules herein described. In general terms, the production of a recombinant form of a protein typically involves the following steps:

[0127] A nucleic acid molecule is first obtained that encodes a protein of the invention, such as but not limited to a nucleic acid molecule comprising, consisting essentially of or consisting of SEQ ID NO: 1, 16, 18, 3, 5, or 7, or the open reading frame defined by nucleotides 21-2984 (2987 with the stop codon) of SEQ ID NO: 1, the open reading frame defined by nucleotides 81-2837 (or 2840 with the stop codon) of SEQ ID NO: 3, the open reading frame defined by nucleotides 449-3190 (or 3193 with the stop codon) of SEQ ID NO:5, or the open reading frame defined by nucleotides 443-3421 (or 3424 with the stop codon) of SEQ ID NO:7. If the encoding sequence is uninterrupted by introns, as are these open reading frames, it is directly suitable for expression in any host.

[0128] The nucleic acid molecule is then preferably placed in operable linkage with suitable control sequences, as described above, to form an expression unit containing the protein open reading frame. The expression unit is used to transform a suitable host and the transformed host is cultured under conditions that allow the production of the recombinant protein. Optionally the recombinant protein is isolated from the medium or from the cells; recovery and purification of the protein may not be necessary in some instances where some impurities may be tolerated.

[0129] Each of the foregoing steps can be done in a variety of ways. For example, the desired coding sequences may be obtained from genomic fragments and used directly in appropriate hosts. The construction of expression vectors that are operable in a variety of hosts is accomplished using appropriate replicons and control sequences, as set forth above. The control sequences, expression vectors, and transformation methods are dependent on the type of host cell used to express the gene and were discussed in detail earlier. Suitable restriction sites can, if not normally available, be added to the ends of the coding sequence so as to provide an excisable gene to insert into these vectors. A skilled artisan can readily adapt any host/expression system known in the art for use with the nucleic acid molecules of the invention to produce recombinant protein.

[0130] G. Methods to Identify Binding Partners

[0131] Another embodiment of the present invention provides methods of isolating and identifying binding partners of proteins of the invention. In general, a protein of the invention is mixed with a potential binding partner or an extract or fraction of a cell under conditions that allow the association of potential binding partners with the protein of the invention. After mixing, peptides, polypeptides, proteins or other molecules that have become associated with a protein of the invention are separated from the mixture. The binding partner that bound to the protein of the invention can then be removed and further analyzed. To identify and isolate a binding partner, the entire protein, for instance a protein comprising the entire amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8 can be used. Alternatively, a fragment of the protein can be used.

[0132] As used herein, a cellular extract refers to a preparation or fraction which is made from a lysed or disrupted cell. The preferred source of cellular extracts will be cells derived from human endothelial tissue or from a human organ that is highly vascularized, such as kidney, liver or lung. Alternatively, cellular extracts may be prepared from normal tissue or available cell lines, particularly endothelial cell lines.

[0133] A variety of methods can be used to obtain an extract of a cell. Cells can be disrupted using either physical or chemical disruption methods. Examples of physical disruption methods include, but are not limited to, sonication and mechanical shearing. Examples of chemical lysis methods include, but are not limited to, detergent lysis and enzyme lysis. A skilled artisan can readily adapt methods for preparing cellular extracts in order to obtain extracts for use in the present methods.

[0134] Once an extract of a cell is prepared, the extract is mixed with the protein of the invention under conditions in which association of the protein with the binding partner can occur. A variety of conditions can be used, the most preferred being conditions that closely resemble conditions found in the cytoplasm of a human cell. Features such as osmolarity, pH, temperature, and the concentration of cellular extract used, can be varied to optimize the association of the protein with the binding partner.

[0135] After mixing under appropriate conditions, the bound complex is separated from the mixture. A variety of techniques can be utilized to separate the mixture. For example, antibodies specific to a protein of the invention can be used to immunoprecipitate the binding partner complex. Alternatively, standard chemical separation techniques such as chromatography and density/sediment centrifugation can be used.

[0136] After removal of non-associated cellular constituents found in the extract, the binding partner can be dissociated from the complex using conventional methods. For example, dissociation can be accomplished by altering the salt concentration or pH of the mixture.

[0137] To aid in separating associated binding partner pairs from the mixed extract, the protein of the invention can be immobilized on a solid support. For example, the protein can be attached to a nitrocellulose matrix or acrylic beads. Attachment of the protein to a solid support aids in separating peptide/binding partner pairs from other constituents found in the extract. The identified binding partners can be either a single protein or a complex made up of two or more proteins. Alternatively, binding partners may be identified using a Far-Western assay according to the procedures of Takayama et al., Methods Mol Biol 69:171-184, 1997, or Sauder et al., J GenVirol 77:991-996, 1996, or identified through the use of epitope tagged proteins or GST fusion proteins.

[0138] Alternatively, the nucleic acid molecules of the invention can be used in a yeast two-hybrid system. The yeast two-hybrid system has been used to identify other protein partner pairs and can readily be adapted to employ the nucleic acid molecules herein described.

[0139] H. Methods to Identify Agents that Modulate the Expression of a Nucleic Acid Encoding the Gene Associated with Vascular Disease

[0140] Another embodiment of the present invention provides methods for identifying agents that modulate the expression of a nucleic acid encoding a protein of the invention such as a protein having the amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8. Such assays may utilize any available means of monitoring for changes in the expression level of the nucleic acids of the invention. As used herein, an agent is said to modulate the expression of a nucleic acid of the invention if it is capable of up- or down-regulating expression of the nucleic acid in a cell.

[0141] In one assay format, cell lines that contain reporter gene fusions between SEQ ID NO:16, SEQ ID NO:18, the open reading frame defined by nucleotides 21-2984 of SEQ ID NO: 1, 81-2837 of SEQ ID NO:3, 449-3190 of SEQ ID NO:5, or the open reading frame defined by nucleotides 443-3421 of SEQ ID NO:7, and/or the 5′ and/or 3′ regulatory elements and any assayable fusion partner may be prepared. Numerous assayable fusion partners are known and readily available including the firefly luciferase gene and the gene encoding chloramphenicol acetyltransferase (Alam et al., Anal Biochem 188:245-254, 1990). Cell lines containing the reporter gene fusions are then exposed to the agent to be tested under appropriate conditions and time. Differential expression of the reporter gene between samples exposed to the agent and control samples identifies agents which modulate the expression of a nucleic acid of the invention.

[0142] Additional assay formats may be used to monitor the ability of the agent to modulate the expression of a nucleic acid encoding a protein of the invention, such as the protein having SEQ ID NO: 2, 4, 17, 19, 6, or 8. For instance, mRNA expression may be monitored directly by hybridization to the nucleic acids of the invention. Cell lines are exposed to the agent to be tested under appropriate conditions and time and total RNA or mRNA is isolated by standard procedures such those disclosed in Sambrook et al., Molecular Cloning—A Laboratory Manual, 3d Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001.

[0143] Probes to detect differences in RNA expression levels between cells exposed to the agent and control cells may be prepared from the nucleic acids of the invention. It is preferable, but not necessary, to design probes which hybridize only with target nucleic acids under conditions of high stringency. Only highly complementary nucleic acid hybrids form under conditions of high stringency. Accordingly, the stringency of the assay conditions determines the amount of complementarity which should exist between two nucleic acid strands in order to form a hybrid. Stringency should be chosen to maximize the difference in stability between the probe:target hybrid and probe:non-target hybrids.

[0144] Probes may be designed from the nucleic acids of the invention through methods known in the art. For instance, the G+C content of the probe and the probe length can affect probe binding to its target sequence. Methods to optimize probe specificity are commonly available in Sambrook et al., (supra) or Ausubel et al., Short Protocols in Molecular Biology, 4th Ed., John Wiley & Sons, Inc., New York, 1999.

[0145] Hybridization conditions are modified using known methods, such as those described by Sambrook et al. and Ausubel et al. as required for each probe. Hybridization of total cellular RNA or RNA enriched for polyA RNA can be accomplished in any available format. For instance, total cellular RNA or RNA enriched for polyA RNA can be affixed to a solid support and the solid support exposed to at least one probe comprising at least one, or part of one of the sequences of the invention under conditions in which the probe will specifically hybridize. Alternatively, nucleic acid fragments comprising at least one, or part of one of the sequences of the invention can be affixed to a solid support, such as a silicon chip or a porous glass wafer. The wafer can then be exposed to total cellular RNA or polyA RNA from a sample under conditions in which the affixed sequences will specifically hybridize. Such solid supports and hybridization methods are widely available, for example, those disclosed by Beattie, (1995) WO 95/11755. By examining for the ability of a given probe to specifically hybridize to an RNA sample from an untreated cell population and from a cell population exposed to the agent, agents which up or down regulate the expression of a nucleic acid encoding the protein having the sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8 are identified.

[0146] Hybridization for qualitative and quantitative analysis of mRNAs may also be carried out by using an RNase Protection Assay (i.e., RPA, see Ma et al. Methods 10:273-238, 1996). Briefly, an expression vehicle comprising cDNA encoding the gene product and a phage specific DNA dependent RNA polymerase promoter (e.g., T7, T3 or SP6 RNA polymerase) is linearized at the 3′ end of the cDNA molecule, downstream from the phage promoter, wherein such a linearized molecule is subsequently used as a template for synthesis of a labeled antisense transcript of the cDNA by in vitro transcription. The labeled transcript is then hybridized to a mixture of isolated RNA (i.e., total or fractionated mRNA) by incubation at 45° C. overnight in a buffer comprising 80% formamide, 40 mM Pipes, pH 6.4, 0.4 M NaCl and 1 mM EDTA. The resulting hybrids are then digested in a buffer comprising 40 μg/ml ribonuclease A and 2 μg/ml ribonuclease. After deactivation and extraction of extraneous proteins, the samples are loaded onto urea/polyacrylamide gels for analysis.

[0147] In another assay format, cells or cell lines are first identified which express the gene products of the invention physiologically. Cell and/or cell lines so identified would be expected to comprise the necessary cellular machinery such that the fidelity of modulation of the transcriptional apparatus is maintained with regard to exogenous contact of agent with appropriate surface transduction mechanisms and/or the cytosolic cascades. Further, such cells or cell lines would be transduced or transfected with an expression vehicle (e.g., a plasmid or viral vector) construct comprising an operable non-translated 5′-promoter containing end of the structural gene encoding the instant gene products fused to one or more antigenic fragments, which are peculiar to the instant gene products, wherein said fragments are under the transcriptional control of said promoter and are expressed as polypeptides whose molecular weight can be distinguished from the naturally occurring polypeptides or may further comprise an immunologically distinct tag or other detectable marker. Such a process is well known in the art (see Sambrook et al., supra).

[0148] Cells or cell lines transduced or transfected as outlined above are then contacted with agents under appropriate conditions; for example, the agent in a pharmaceutically acceptable excipient is contacted with cells in an aqueous physiological buffer such as phosphate buffered saline (PBS) at physiological pH, Eagles balanced salt solution (BSS) at physiological pH, PBS or BSS comprising serum or conditioned media comprising PBS or BSS and/or serum incubated at 37° C. Said conditions may be modulated as deemed necessary by one of skill in the art. Subsequent to contacting the cells with the agent, said cells will be disrupted and the polypeptides of the lysate are fractionated such that a polypeptide fraction is pooled and contacted with an antibody to be further processed by immunological assay (e.g., ELISA, immunoprecipitation or Western blot). The pool of proteins isolated from the “agent-contacted” sample will be compared with a control sample where only the excipient is contacted with the cells and an increase or decrease in the immunologically generated signal from the “agent-contacted” sample compared to the control will be used to distinguish the effectiveness of the agent.

[0149] I. Methods to Identify Agents that Modulate the Level of or at Least One Activity of SCUBE Proteins and Production of Antibodies

[0150] Another embodiment of the present invention provides methods for identifying agents that modulate at least one activity of a protein of the invention such as the protein having the amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8. Such methods or assays may utilize any means of monitoring or detecting the desired activity.

[0151] The term “antibody” as used herein refers to an immunoglobulin molecule or immunologically active portion thereof, i.e., an antigen-binding portion. Examples of immunologically active portions of immunoglobulin molecules include scFV and dcFV fragments, Fab and F(ab′)2 fragments which can be generated by treating the antibody with an enzyme such as papain or pepsin, respectively.

[0152] A full-length SCUBE protein or, antigenic peptide fragment of SCUBE can be used as an immunogen or can be used to identify anti-SCUBE antibodies made with other immunogens, e.g., cells, membrane preparations, and the like. The antigenic peptide of SCUBE should include at least 8 amino acid residues of the amino acid sequence shown in SEQ ID NO:2, 4, 17, 19, 6, or 8 and encompasses an epitope of a SCUBE polypeptide. Preferably, the antigenic peptide includes at least 10 amino acid residues, more preferably at least 15 amino acid residues, even more preferably at least 20 amino acid residues, and most preferably at least 30 amino acid residues.

[0153] Fragments of SCUBE1 which include residues about 55 to 71, from about 485 to 500, and from about 962 to 971 of SEQ ID NO:2 can be used to make, e.g., used as immunogens or used to characterize the specificity of an antibody, antibodies against hydrophilic regions of the SCUBE1 protein (see FIG. 2). Similarly, fragments of SCUBE1 which include residues about 424 to 441 and from about 836 to 847 of SEQ ID NO:2 can be used to make an antibody against a hydrophobic region of the SCUBE protein. A fragment of SCUBE1 which includes residues about 37 to 401, or a subset thereof, e.g. about residues 37 to 120, about residues 121 to 241 or about residues 242 to 401 of SEQ ID NO:2, 17 or 19 can be used to make an antibody against the N-terminal EGF-repeat region of the SCUBE1 protein; a fragment of SCUBE1 which includes residues about 36 to 50 of SEQ ID NO:2, 17 or 19 (SEQ ID NO:20) can be used to make an antibody against the first EGF-like repeat of the SCUBE1 protein; a fragment of SCUBE1 which includes residues about 415 to 789, or a subset thereof, e.g. about residues 415 to 480, about 481 to 640, about 641 to 789 of SEQ ID NO:2 or 17, or about 487 to 503 of SEQ ID NO:2 or 17 (SEQ ID NO:21) can be used to make an antibody against the spacer region of the SCUBE1 protein; or a fragment of SCUBE1 which includes residues about 798 to 907, or a subset thereof, e.g. about residues 798 to 840, about residues 841 to 870 or about residues 871 to 907 of SEQ ID NO:2 can be used to make an antibody against the CUB domain of the SCUBE1 protein.

[0154] Fragments of SCUBE2 which include residues about 43 to 55, from about 80 to 93, from about 534 to 546, and from about 861 to 872 of SEQ ID NO:4 can be used to make, e.g., used as immunogens or used to characterize the specificity of an antibody, antibodies against hydrophilic regions of the SCUBE2 protein (see FIG. 13). Similarly, fragments of SCUBE2 which include residues about 300 to 314, from about 756 to 772, and from about 876 to 884 of SEQ ID NO:4 can be used to make an antibody against a hydrophobic region of the SCUBE2 protein. A fragment of SCUBE2 which includes residues about 49 to 401, or a subset thereof, e.g. about residues 49 to 126, about residues 127 to 252 or about residues 253 to 401 of SEQ ID NO:4 can be used to make an antibody against the N-terminal EGF-repeat region of the SCUBE2 protein; a fragment of SCUBE2 which includes residues about 185 to 200 of SEQ ID NO:4 (SEQ ID NO:22) can be used to make an antibody against the fourth EGF-like repeat of the SCUBE2 protein; a fragment of SCUBE2 which includes residues about 402 to 728, or a subset thereof, e.g. about residues 402 to 480, about 481 to 640, about 641 to 728 of SEQ ID NO:4, or about 471 to 489 of SEQ ID NO:14 (SEQ ID NO:23, which includes residues 403 to 409 of SEQ ID NO:4) can be used to make an antibody against the spacer region of the SCUBE2 protein; or a fragment of SCUBE2 which includes residues about 729 to 838, or a subset thereof, e.g. about residues 729 to 770, about residues 771 to 800 or about residues 801 to 838 of SEQ ID NO:4 can be used to make an antibody against the CUB domain of the SCUBE2 protein.

[0155] Fragments of SCUBE3 which include residues about 28 to 41, from about 497 to 508, and from about 881 to 897 of SEQ ID NO:6 or about 28 to 41, from about 529 to 540, and from about 960 to 976 of SEQ ID NO:8 can be used to make, e.g., used as immunogens or used to characterize the specificity of an antibody, antibodies against a hydrophilic region of the SCUBE3 protein (see FIGS. 14A and 14B). Similarly, fragments of SCUBE3 which include residues about 201 to 211 and from about 763 to 773 of SEQ ID NO:6 or residues about 254 to 268 and from about 842 to 852 of SEQ ID NO:8 can be used to make an antibody against a hydrophobic region of the SCUBE3 protein. A fragment of SCUBE3 which includes residues about 33 to 404, or a subset thereof, e.g. about residues 33 to 110, about residues 111 to 243 or about residues 244 to 404 of SEQ ID NO:6 or about 33 to 397, or a subset thereof, e.g. about residues 33 to 110, about residues 111 to 236 or about residues 237 to 397 of SEQ ID NO:8 can be used to make an antibody against the N-terminal EGF-repeat region of the SCUBE3 protein; a fragment of SCUBE3 which includes residues about 405 to 724, or a subset thereof, e.g. about residues 405 to 480, about 481 to 640, or about 641 to 724 of SEQ ID NO:6 or about 398 to 803, or a subset thereof, e.g. about residues about residues 398 to 500, about 501 to 640, or about 641 to 803 of SEQ ID NO:8 can be used to make an antibody against the spacer region of the SCUBE3 protein; or a fragment of SCUBE3 which includes residues about 725 to 834, or a subset thereof, e.g. about residues 725 to 770, about residues 771 to 800 or about residues 801 to 834 of SEQ ID NO:6 or about 804 to 913, or a subset thereof, e.g. about residues 804 to 850, about residues 851 to 880 or about residues 881 to 913 of SEQ ID NO:8 can be used to make an antibody against the CUB domain of the SCUBE3 protein.

[0156] In one format, the relative amounts of a protein of the invention between a cell population that has been exposed to the agent to be tested compared to an unexposed control cell population may be assayed. In this format, probes such as specific antibodies are used to monitor the differential expression of the protein in the different cell populations. Cell lines or populations are exposed to the agent to be tested under appropriate conditions and time. Cellular lysates may be prepared from the exposed cell line or population and a control, unexposed cell line or population. The cellular lysates are then analyzed with the probe.

[0157] Antibody probes are prepared by immunizing suitable mammalian hosts in appropriate immunization protocols using the peptides, polypeptides or proteins of the invention if they are of sufficient length, or, if desired, or if required to enhance immunogenicity, conjugated to suitable carriers. Methods for preparing immunogenic conjugates with carriers such as bovine serum albumin (BSA), keyhole limpet hemocyanin (KLH), or other carrier proteins are well known in the art. In some circumstances, direct conjugation using, for example, carbodiimide reagents may be effective; in other instances linking reagents such as those supplied by Pierce Chemical Co. (Rockford, Ill.), may be desirable to provide accessibility to the hapten. The hapten peptides can be extended at either the amino or carboxy terminus with a cysteine residue or interspersed with cysteine residues, for example, to facilitate linking to a carrier. Administration of the immunogens is conducted generally by injection over a suitable time period and with use of suitable adjuvants, as is generally understood in the art. During the immunization schedule, titers of antibodies are taken to determine adequacy of antibody formation.

[0158] While the polyclonal antisera produced in this way may be satisfactory for some applications, for pharmaceutical compositions, use of monoclonal preparations is preferred. Immortalized cell lines which secrete the desired monoclonal antibodies may be prepared using the standard method of Kohler and Milstein (Nature 256:495-497, 1975) or modifications which effect immortalization of lymphocytes or spleen cells, as is generally known. The immortalized cell lines secreting the desired antibodies are screened by immunoassay in which the antigen is the peptide hapten, polypeptide or protein. When the appropriate immortalized cell culture secreting the desired antibody is identified, the cells can be cultured either in vitro or by production in ascites fluid.

[0159] For therapeutic purposes, the antibody can be a polyclonal, monoclonal, recombinant, e.g., a chimeric or humanized, fully human, non-human, e.g., murine, or single chain antibody. Chimeric, humanized, but most preferably, completely human antibodies are desirable for applications which include repeated administration, e.g., therapeutic treatment of human patients, and some diagnostic applications. In a preferred embodiment it has effector function and can fix complement. The antibody can be coupled to a toxin or imaging agent.

[0160] The desired monoclonal antibodies are then recovered from the culture supernatant or from the ascites supernatant. Fragments of the monoclonal antibodies or the polyclonal antisera which contain the immunologically significant portion can be used as antagonists, as well as the intact antibodies. Use of immunologically reactive antibody fragments, such as the Fab, Fab′, or F(ab′)2 fragments is often preferable, especially in a therapeutic context, as these fragments are generally less immunogenic than the whole immunoglobulin.

[0161] The antibodies or fragments may also be produced, using current technology, by recombinant means. Antibody regions that bind specifically to the desired regions of the protein can also be produced in the context of chimeras with multiple species origin, such as humanized antibodies. The antibodies may be used in any of the methods described herein, may be used as diagnostic agents or may be used as therapeutic agents.

[0162] Chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, can be made using standard recombinant DNA techniques. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, European Patent Application 171,496; Morrison et al. European Patent Application 173,494; Neuberger et al. PCT International Publication No. WO 86/01533; Cabilly et al. U.S. Pat. No. 4,816,567; Cabilly et al. European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al. (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Canc. Res. 47:999-1005; Wood et al. (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559).

[0163] A humanized or complementarity determining region (CDR)-grafted antibody will have at least one or two, but generally all three recipient CDR's (of heavy and or light immuoglobulin chains) replaced with a donor CDR. The antibody may be replaced with at least a portion of a non-human CDR or only some of the CDR's may be replaced with non-human CDR's. It is only necessary to replace the number of CDR's required for binding of the humanized antibody to a SCUBE or a fragment thereof. Preferably, the donor will be a rodent antibody, e.g., a rat or mouse antibody, and the recipient will be a human framework or a human consensus framework. Typically, the immunoglobulin providing the CDR's is called the “donor” and the immunoglobulin providing the framework is called the “acceptor.” In one embodiment, the donor immunoglobulin is a non-human (e.g., rodent). The acceptor framework is a naturally-occurring (e.g., a human) framework or a consensus framework, or a sequence about 85% or higher, preferably 90%, 95%, 99% or higher identical thereto.

[0164] As used herein, the term “consensus sequence” refers to the sequence formed from the most frequently occurring amino acids (or nucleotides) in a family of related sequences (See e.g., Winnaker, (1987) From Genes to Clones (Verlagsgesellschaft, Weinheim, Germany). In a family of proteins, each position in the consensus sequence is occupied by the amino acid occurring most frequently at that position in the family. If two amino acids occur equally frequently, either can be included in the consensus sequence. A “consensus framework” refers to the framework region in the consensus immunoglobulin sequence.

[0165] An antibody can be humanized by methods known in the art. Humanized antibodies can be generated by replacing sequences of the Fv variable region which are not directly involved in antigen binding with equivalent sequences from human Fv variable regions. General methods for generating humanized antibodies are provided by Morrison (1985) Science 229:1202-1207, by Oi et al. (1986) BioTechniques 4:214, and by Queen et al. U.S. Pat. Nos. 5,585,089, 5,693,761 and 5,693,762, the contents of all of which are hereby incorporated by reference. Those methods include isolating, manipulating, and expressing the nucleic acid sequences that encode all or part of immunoglobulin Fv variable regions from at least one of a heavy or light chain. Sources of such nucleic acid are well known to those skilled in the art and, for example, may be obtained from a hybridoma producing an antibody against a SCUBE polypeptide or fragment thereof. The recombinant DNA encoding the humanized antibody, or fragment thereof, can then be cloned into an appropriate expression vector.

[0166] Humanized or CDR-grafted antibodies can be produced by CDR-grafting or CDR substitution, wherein one, two, or all CDR's of an immunoglobulin chain can be replaced. See e.g., U.S. Pat. No. 5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; Beidler et al. (1988) J. Immunol. 141:4053-4060; Winter U.S. Pat. No. 5,225,539, the contents of all of which are hereby expressly incorporated by reference. Winter describes a CDR-grafting method which may be used to prepare the humanized antibodies of the present invention (UK Patent Application GB 2188638A, filed on Mar. 26, 1987; Winter U.S. Pat. No. 5,225,539), the contents of which is expressly incorporated by reference.

[0167] Also within the scope of the invention are humanized antibodies in which specific amino acids have been substituted, deleted or added. Preferred humanized antibodies have amino acid substitutions in the framework region, such as to improve binding to the antigen. For example, a humanized antibody will have framework residues identical to the donor framework residue or to another amino acid other than the recipient framework residue. To generate such antibodies, a selected, small number of acceptor framework residues of the humanized immunoglobulin chain can be replaced by the corresponding donor amino acids. Preferred locations of the substitutions include amino acid residues adjacent to the CDR, or which are capable of interacting with a CDR (see e.g., U.S. Pat. No. 5,585,089). Criteria for selecting amino acids from the donor are described in U.S. Pat. No. 5,585,089, e.g., columns 12-16 of U.S. Pat. No. 5,585,089, the e.g., columns 12-16 of U.S. Pat. No. 5,585,089, the contents of which are hereby incorporated by reference. Other techniques for humanizing antibodies are described in Padlan et al. EP 519596 A1, published on Dec. 23, 1992.

[0168] Completely human antibodies are particularly desirable for therapeutic treatment of human patients. Such antibodies can be produced using transgenic mice that are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes. See, for example, Lonberg and Huszar (1995) Int. Rev. Immunol. 13:65-93); and U.S. Pat. Nos. 5,625,126; 5,633,425; 5,569,825; 5,661,016; and 5,545,806. In addition, companies such as Abgenix, Inc. (Fremont, Calif.) and Medarex, Inc. (Princeton, N.J.), can be engaged to provide human antibodies directed against a selected antigen using technology similar to that described above.

[0169] Completely human antibodies that recognize a selected epitope can be generated using a technique referred to as “guided selection.” In this approach a selected non-human monoclonal antibody, e.g., a murine antibody, is used to guide the selection of a completely human antibody recognizing the same epitope. This technology is described by Jespers et al. (1994) Bio/Technology 12:899-903).

[0170] The anti-SCUBE antibody can be a single chain antibody. A single-chain antibody (scFV) can be engineered as described in, for example, Colcher et al. (1999) Ann. N Y Acad. Sci. 880:263-80; and Reiter (1996) Clin. Cancer Res. 2:245-52. The single chain antibody can be dimerized or multimerized to generate multivalent antibodies having specificities for different epitopes of the same target SCUBE protein.

[0171] In a preferred embodiment, the antibody has reduced or no ability to bind an Fe receptor. For example, it is an isotype or subtype, fragment or other mutant, which does not support binding to an Fe receptor, e.g., it has a mutagenized or deleted Fe receptor binding region.

[0172] An antibody (or fragment thereof) may be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent or a radioactive ion. A cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, puromycin, maytansinoids, e.g., maytansinol (see U.S. Pat. No. 5,208,020), CC-1065 (see U.S. Pat. Nos. 5,475,092, 5,585,499, 5,846,545) and analogs or homologs thereof. Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, CC-1065, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (II) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g., dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g., vincristine, vinblastine, taxol and maytansinoids). Radioactive ions include, but are not limited to iodine, yttrium and praseodymium.

[0173] The conjugates of the invention can be used for modifying a given biological response, the therapeutic moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the therapeutic moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, α-interferon, β-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator; or, biological response modifiers such as, for example, lymphokines, interleukin-1 (“IL-1”), interleukin-2 (“IL-2”), interleukin-6 (“IL-6”), granulocyte macrophase colony stimulating factor (“GM-CSF”), granulocyte colony stimulating factor (“G-CSF”), or other growth factors.

[0174] Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Pat. No. 4,676,980.

[0175] An anti-SCUBE antibody (e.g., monoclonal antibody) can be used to isolate SCUBE by standard techniques, such as affinity chromatography or immunoprecipitation. Moreover, an anti-SCUBE antibody can be used to detect SCUBE protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the protein. Anti-SCUBE antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance (i.e., antibody labelling). Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, β-galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125I, 131I, 35S or 3H.

[0176] Antibodies which bind only a native SCUBE protein, only denatured or otherwise non-native SCUBE protein, or which bind both, are within the invention. Antibodies with linear or conformational epitopes are within the invention. Conformational epitopes sometimes can be identified by identifying antibodies which bind to native but not denatured SCUBE protein.

[0177] Agents that are assayed in the method which measures the relative amounts of a protein of the invention between a cell population that has been exposed to the agent and a control cell population can be randomly selected or rationally selected or designed. As used herein, an agent is said to be randomly selected when the agent is chosen randomly without considering the specific sequences involved in the association of a protein of the invention alone or with its associated substrates, binding partners, etc. An example of randomly selected agents is the use a chemical library or a peptide combinatorial library, or a growth broth of an organism.

[0178] As used herein, an agent is said to be rationally selected or designed when the agent is chosen on a nonrandom basis which takes into account the sequence of the target site and/or its conformation in connection with the agents action. Agents can be rationally selected or rationally designed by utilizing the peptide sequences that make up these sites. For example, a rationally selected peptide agent can be a peptide whose amino acid sequence is identical to or a derivative of any functional consensus site.

[0179] The agents of the present invention can be, as examples, peptides, small molecules, vitamin derivatives, as well as carbohydrates. Dominant negative proteins, DNAs encoding these proteins, antibodies to these proteins, peptide fragments of these proteins or mimics of these proteins may be introduced into cells to affect function. “Mimic” used herein refers to the modification of a region or several regions of a peptide molecule to provide a structure chemically different from the parent peptide but topographically and functionally similar to the parent peptide (see Grant GA. in: Molecular Biology and Biotechnology, Myers, ed., pp. 659-664, VCH Publishers, New York, 1995). A skilled artisan can readily recognize that there is no limit as to the structural nature of the agents of the present invention.

[0180] The peptide agents of the invention can be prepared using standard solid phase (or solution phase) peptide synthesis methods, as is known in the art. In addition, the DNA encoding these peptides may be synthesized using commercially available oligonucleotide synthesis instrumentation and produced recombinantly using standard recombinant production systems. The production using solid phase peptide synthesis is necessitated if non-gene-encoded amino acids are to be included.

[0181] Another class of agents of the present invention are antibodies immunoreactive with critical positions of proteins of the invention. Antibody agents are obtained by immunization of suitable mammalian subjects with peptides, containing as antigenic regions, those portions of the protein intended to be targeted by the antibodies.

[0182] J. Uses for Agents that Modulate at Least One Activity of SCUBE Proteins.

[0183] As provided in the Examples, the proteins and nucleic acids of the invention, such as the protein having the amino acid sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8, are differentially expressed in normal vascular endothelial tissue compared to other normal tissues and in normal endothelial tissue compared to endothelial tissue in vascular and other disease states. Agents that modulate or up-or-down-regulate the expression of the protein, or agents, such as agonists or antagonists of at least one activity of the protein, may be used to modulate biological and pathologic processes associated with the proteins function and activity, e.g. binding to a binding partner. As described above, the agents of the present invention can be, as examples, antibodies, peptides, small molecules, vitamin derivatives, as well as carbohydrates.

[0184] As used herein, a subject can be any mammal, so long as the mammal is in need of modulation of a pathological or biological process mediated by a protein of the invention. The term mammal is defined as an individual belonging to the class Mammalia. The invention is particularly useful in the treatment of human subjects.

[0185] As used herein, an “effective amount” is an amount of a substance, compound or agent which is effective to inhibit, reduce, ameliorate, modulate or control at least one symptom or effect of a disease, condition or another administered substance, compound or agent either in vivo, ex vivo, or in vitro.

[0186] Pathological processes refer to a category of biological processes which produce a deleterious effect. For example, expression of a protein of the invention may be associated with vascular disease. As used herein, an agent is said to modulate a pathological process when the agent reduces the degree or severity of the process. For instance, vascular disease may be prevented or disease progression modulated by the administration of agents which up- or down-regulate or modulate in some way the expression or at least one activity of a protein of the invention.

[0187] The agents of the present invention can be provided alone, or in combination with other agents that modulate a particular pathological process. For example, an agent of the present invention can be administered in combination with other known drugs. As used herein, two agents are said to be administered in combination when the two agents are administered simultaneously or are administered independently in a fashion such that the agents will act at the same time.

[0188] The agents of the present invention can be administered via parenteral, subcutaneous, intravenous, intramuscular, intraperitoneal, transdermal, or site specific routes. Alternatively, or concurrently, administration may be by the oral route. The dosage administered will be dependent upon the age, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired.

[0189] The present invention further provides compositions containing one or more agents which modulate expression or at least one activity of a protein of the invention. While individual needs vary, determination of optimal ranges of effective amounts of each component is within the skill of the art. Typical dosages comprise 0.1 to 100 μg/kg body wt. The preferred dosages comprise 0.1 to 10 μg/kg body wt. The most preferred dosages comprise 0.1 to 1 μg/kg body wt.

[0190] In addition to the pharmacologically active agent, the compositions of the present invention may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically for delivery to the site of action. Suitable formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form, for example, water-soluble salts. In addition, suspensions of the active compounds as appropriate oily injection suspensions may be administered. Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, ethyl oleate or triglycerides. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension include, for example, sodium carboxymethyl cellulose, sorbitol, and/or dextran. Optionally, the suspension may also contain stabilizers. Liposomes can also be used to encapsulate the agent for delivery into the cell.

[0191] The pharmaceutical formulation for systemic administration according to the invention may be formulated for enteral, parenteral or topical administration. Indeed, all three types of formulations may be used simultaneously to achieve systemic administration of the active ingredient.

[0192] Suitable formulations for oral administration include hard or soft gelatin capsules, pills, tablets, including coated tablets, elixirs, suspensions, syrups or inhalations and controlled release forms thereof.

[0193] In practicing the methods of this invention, the compounds of this invention may be used alone or in combination, or in combination with other therapeutic or diagnostic agents. In certain preferred embodiments, the compounds of this invention may be coadministered along with other compounds typically prescribed for these conditions according to generally accepted medical practice such as antihistamines. The compounds of this invention can be utilized in vivo, ordinarily in mammals, such as humans, sheep, goats, horses, cattle, pigs, dogs, cats, rats and mice, or in vitro.

[0194] K. Transgenic Animals

[0195] Transgenic animals containing mutant, knock-out, knock-in or modified genes corresponding to the cDNA sequence of SEQ ID NO: 1, 16, 18, 3, 5, or 7, or the open reading frame encoding the polypeptide sequence of SEQ ID NO: 2, 4, 17, 19, 6, or 8, or fragments thereof having a consecutive sequence of at least about 10, 15, 20, 25, 30, 35, 40, 45, 50 or more amino acid residues, are also included in the invention. Transgenic animals are genetically modified animals into which recombinant, exogenous or cloned genetic material has been experimentally transferred. Such genetic material is often referred to as a “transgene.” The nucleic acid sequence of the transgene, in this case a form of SEQ ID NO: 1, 16, 18, 3, 5, or 7 may be integrated either at a locus of a genome where that particular nucleic acid sequence is not otherwise normally found or at the normal locus for the transgene. The transgene may consist of nucleic acid sequences derived from the genome of the same species or of a different species than the species of the target animal.

[0196] In some embodiments, transgenic animals in which all or a portion of a gene comprising SEQ ID NO: 1, 16, 18, 3, 5, or 7 is deleted may be constructed. In those cases where the gene corresponding to SEQ ID NO: 1, 16, 18, 3, 5, or 7 contains one or more introns, the entire gene- all exons, introns and the regulatory sequences- may be deleted. Alternatively, less than the entire gene may be deleted. For example, a single exon and/or intron may be deleted, so as to create an animal expressing a modified version of a protein of the invention.

[0197] The term “germ cell line transgenic animal” refers to a transgenic animal in which the genetic alteration or genetic information was introduced into a germ line cell, thereby conferring the ability of the transgenic animal to transfer the genetic information to offspring. If such offspring in fact possess some or all of that alteration or genetic information, then they too are transgenic animals.

[0198] The alteration or genetic information may be foreign to the species of animal to which the recipient belongs, foreign only to the particular individual recipient, or may be genetic information already possessed by the recipient. In the last case, the altered or introduced gene may be expressed differently than the native gene.

[0199] Transgenic animals can be produced by a variety of different methods including transfection, electroporation, microinjection, gene targeting in embryonic stem cells and recombinant viral and retroviral infection (see, e.g., U.S. Pat. No. 4,736,866; U.S. Pat. No. 5,602,307; Mullins et al., Hypertension 22:630-633, 1993; Brenin et al., Surg Oncol 6:99-110, 1997; Tuan, Recombinant Gene Expression Protocols (Methods in Molecular Biology, Vol. 62), Humana Press, Totowa, N.J., 1997).

[0200] A number of recombinant or transgenic mice have been produced, including those which express an activated oncogene sequence (U.S. Pat. No. 4,736,866); express simian SV40 T-antigen (U.S. Pat. No. 5,728,915); lack the expression of interferon regulatory factor 1 (IRF-1) (U.S. Pat. No. 5,731,490); exhibit dopaminergic dysfunction (U.S. Pat. No. 5,723,719); express at least one human gene which participates in blood pressure control (U.S. Pat. No. 5,731,489); display greater similarity to the conditions existing in naturally occurring Alzheimer's disease (U.S. Pat. No. 5,720,936); have a reduced capacity to mediate cellular adhesion (U.S. Pat. No. 5,602,307); possess a bovine growth hormone gene (Clutter et al., Genetics 143:1753-1760, 1996); or, are capable of generating a fully human antibody response (McCarthy, Lancet 349:405, 1997).

[0201] While mice and rats remain the animals of choice for most transgenic experimentation, in some instances it is preferable or even necessary to use alternative animal species. Transgenic procedures have been successfully utilized in a variety of non-murine animals, including sheep, goats, pigs, dogs, cats, monkeys, chimpanzees, hamsters, rabbits, cows and guinea pigs (see, e.g., Kim et al., Mol Reprod Dev 46:515-526, 1997; Houdebine, Reprod Nutr Dev 35:609-617, 1995; Petters, Reprod Fertil Dev 6:643-645, 1994; Schnieke et al., Science 278:2130-2133, 1997; and Amoah, J Animal Science 75:578-585, 1997).

[0202] The method of introduction of nucleic acid fragments into recombination competent mammalian cells can be by any method which favors co-transformation of multiple nucleic acid molecules. Detailed procedures for producing transgenic animals are readily available to one skilled in the art, including the disclosures in U.S. Pat. No. 5,489,743 and U.S. Pat. No. 5,602,307.

[0203] L. Diagnostic Methods and Agents

[0204] The genes and proteins of the invention may be used to detect SCUBE expressing cells in vivo or ex vivo in a cell suspension or a tissue sample, for example. The genes and proteins of the invention may further be used to diagnose or monitor diseases or conditions with vascular involvement in a subject or sample, or to track disease progression. Such diseases or conditions include, but are not limited to cardiovascular diseases, such as angiogenesis, cardiomyopathy, atherosclerosis, hypertension, congenital heart defects, aortic stenosis, atrial septal defect (ASD), atrioventricular (A-V) canal defect, ductus arteriosus, pulmonary stenosis, subaortic stenosis, ventricular septal defect (VSD), valve diseases, tuberous sclerosis and renal artery stenosis; scleroderma, obesity, inflammatory diseases, such as those following transplantation, systemic lupus erythematosus, autoimmune disease, asthma, emphysema, allergy, diabetes, interstitial nephritis, glomerulonephritis, polycystic kidney disease, and IgA nephropathy; renal tubular acidosis, hypercalceimia, Lesch-Nyhan syndrome, diabetes, cancer metastasis, and other diseases, disorders and conditions of the like.

[0205] The use of molecular biological tools has become routine in forensic technology. For example, nucleic acid probes may be used to determine the expression of a nucleic acid molecule comprising all or at least part of the sequences of SEQ ID NO: 1, 16, 18, 3, 5, or 7 in forensic/pathology specimens. Further, nucleic acid assays may be carried out by any means of conducting a transcriptional profiling analysis. In addition to nucleic acid analysis, forensic methods of the invention may target the proteins of the invention, particularly a protein comprising SEQ ID NO: 2, 4, 17, 19, 6, or 8, to determine up or down regulation of the genes (Shiverick et al., Biochim Biophys Acta 393:124-133, 1975).

[0206] Methods of the invention may involve treatment of tissues with collagenases or other proteases to make the tissue amenable to cell lysis (Semenov et al., Biull Eksp Biol Med 104:113-116, 1987). Further, it is possible to obtain biopsy samples from different regions of blood vessels or of the kidney, liver, lungs or other highly vascularized organs for analysis.

[0207] Assays to detect nucleic acid or protein molecules of the invention may be in any available format. Typical assays for nucleic acid molecules include hybridization or PCR based formats. Typical assays for the detection of proteins, polypeptides or peptides of the invention include the use of antibody probes in any available format such as in situ binding assays, etc. See Harlow & Lane, Antibodies—A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1988. In preferred embodiments, assays are carried out with appropriate controls.

[0208] The above methods may also be used in other diagnostic protocols, including protocols and methods to detect disease states in other tissues or organs, for example the tissues in which gene expression is detected.

[0209] M. Detection Assays

[0210] Portions or fragments of the cDNA sequences identified herein, their complements and the corresponding complete gene sequences can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample.

[0211] The SCUBE sequences of the present invention can be used to identify individuals from minute biological samples. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification. The sequences of the present invention are useful as additional DNA markers for RFLP (“restriction fragment length polymorphisms,” described in U.S. Pat. No. 5,272,057).

[0212] Furthermore, the sequences of the present invention can be used to provide an alternative technique that determines the actual base-by-base DNA sequence of selected portions of an individual's genome. Thus, the SCUBE sequences described herein can be used to prepare two PCR primers from the 5′ and 3′ ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.

[0213] Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences. The sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue. The SCUBE sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases. Much of the allelic variation is due to single nucleotide polymorphisms (SNPs), which include restriction fragment length polymorphisms (RFLPs).

[0214] Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes. Because greater numbers of polymorphisms occur in the noncoding regions, fewer sequences are necessary to differentiate individuals. The noncoding sequences of SEQ ID NO: 1, 16, 18, 3, 5, or 7, as described above, can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers that each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences are used, a more appropriate number of primers for positive individual identification would be 500-2,000.

[0215] N. Use of SCUBE Sequences in Forensic Biology

[0216] DNA-based identification techniques can also be used in forensic biology. Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a perpetrator of a crime. To make such an identification, PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample.

[0217] The sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, that can enhance the reliability of DNA-based forensic identifications by, for example, providing another “identification marker” (i.e. another DNA sequence that is unique to a particular individual). As mentioned above, actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments. Sequences targeted to noncoding regions of SEQ ID NO: 1, 3, 5, or 7 are particularly appropriate for this use as greater numbers of polymorphisms occur in the noncoding regions, making it easier to differentiate individuals using this technique. Examples of polynucleotide reagents include the SCUBE sequences or portions thereof, e.g., fragments derived from the noncoding regions of SEQ ID NO: 1, 3, 5, or 7 having a length of at least 20 bases, preferably at least 30 bases.

[0218] The SCUBE sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or label-able probes that can be used, for example, in an in situ hybridization technique, to identify a specific tissue, e.g., liver, etc. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such SCUBE probes can be used to identify tissue by species and/or by organ type.

[0219] In a similar fashion, these reagents, e.g., SCUBE primers or probes can be used to screen tissue culture for contamination (i.e. screen for the presence of a mixture of different types of cells in a culture).

[0220] O. Predictive Medicine

[0221] The present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trials are used for prognostic (predictive) purposes to thereby treat an individual prophylactically. Accordingly, one aspect of the present invention relates to diagnostic assays for determining a SCUBE protein and/or nucleic acid expression as well as SCUBE protein activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant SCUBE expression or activity. The invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with a SCUBE protein, nucleic acid expression or activity. For example, mutations in a SCUBE gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with SCUBE protein or nucleic acid expression or activity.

[0222] Another aspect of the invention provides methods for determining SCUBE protein or nucleic acid expression or SCUBE protein activity in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (referred to herein as “Pharmacogenomics”). Pharmacogenomics allows for the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g., the genotype of the individual examined to determine the ability of the individual to respond to a particular agent.)

[0223] Yet another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of a SCUBE protein in clinical trials.

[0224] P. Diagnostic Assays

[0225] A SCUBE polypeptide may be used to identify an interacting polypeptide in a sample or tissue. The method comprises contacting the sample or tissue with a SCUBE protein, allowing formation of a complex between the SCUBE polypeptide and the interacting polypeptide, and detecting the complex, if present.

[0226] The proteins of the invention may be used to stimulate production of antibodies specifically binding the proteins. Such antibodies may be used in immunodiagnostic procedures to detect the occurrence of the protein in a sample. The proteins of the invention may be used to stimulate cell growth and cell proliferation in conditions in which such growth would be favorable. An example would be to counteract toxic side effects of chemotherapeutic agents on, for example, vascular endothelium or other endothelial linings of the body, such as those of the brain, spinal cord or eye, for example. They may also be used to stimulate new cell growth in vascular diseases. Alternatively, antagonistic treatments may be administered in which an antibody specifically binding a SCUBE protein of the invention would abrogate the specific growth-inducing effects of the proteins. Such antibodies may be useful, for example, in the treatment of proliferative disorders including various tumors and benign hyperplasias.

[0227] Polynucleotides or oligonucleotides corresponding to any one portion of the SCUBE nucleic acid of SEQ ID NO: 1, 16, 18, 3, 5, or 7 may be used to detect DNA containing a corresponding ORF gene, or to detect the expression of a corresponding SCUBE gene. For example, a SCUBE nucleic acid expressed in a particular cell or tissue can be used to identify the presence of that particular cell type.

[0228] An exemplary method for detecting the presence or absence of a SCUBE in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting a SCUBE protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes a SCUBE protein such that the presence of a SCUBE molecule is detected in the biological sample. An agent for detecting SCUBE mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to a SCUBE mRNA or genomic DNA. The nucleic acid probe can be, for example, a full-length SCUBE nucleic acid, such as the nucleic acid of SEQ ID NO: 1, 16, 18, 3, 5, or 7, or a portion thereof, such as an oligonucleotide of at least about 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to a SCUBE mRNA or genomic DNA, as described above. Other suitable probes for use in the diagnostic assays of the invention are described herein.

[0229] An agent for detecting a SCUBE protein is an antibody capable of binding to a SCUBE protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab′)2) can be used. The term labeled, with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin. The term biological sample is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect a SCUBE mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of a SCUBE mRNA include Northern hybridizations and in situ hybridizations, as described above. In vitro techniques for detection of a SCUBE protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence, i.a., the Western blotting and immunoprecipitation methods described above. In vitro techniques for detection of SCUBE genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of a SCUBE protein include introducing into a subject a labeled anti-SCUBE protein antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.

[0230] In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.

[0231] In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting a SCUBE protein, mRNA, or genomic DNA, such that the presence of a SCUBE protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of a SCUBE protein, mRNA or genomic DNA in the control sample with the presence of a SCUBE protein, mRNA or genomic DNA in the test sample.

[0232] The invention also encompasses kits for detecting the presence of a SCUBE molecule in a biological sample. For example, the kit can comprise: a labeled compound or agent capable of detecting a SCUBE protein or mRNA in a biological sample; means for determining the amount of a SCUBE molecule in the sample; and means for comparing the amount of a SCUBE molecule in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect a SCUBE protein or nucleic acid.

[0233] Without further description, it is believed that one of ordinary skill in the art can, using the preceding description and the following illustrative examples, make and utilize the compounds of the present invention and practice the claimed methods. The following working examples therefore, specifically point out preferred embodiments of the present invention, and are not to be construed as limiting in any way the remainder of the disclosure.

EXAMPLES

Example 1

[0234] Cloning of SCUBE1 and SCUBE 2

[0235] The SCUBE1 gene was found to reside on human chromosome 22q13 and is comprised of multiple exons. Cloning and sequencing of the SCUBE1 gene was accomplished by screening a mixed tissue human cDNA library. A pair of primers flanking the ORF of SCUBE1 were used in standard PCR amplification techniques. The resultant PCR product was cloned into pCDNA3.1 and sequenced to confirm that a full-length clone of SCUBE1 had been obtained.

[0236] The SCUBE1 nucleic acid sequence is disclosed herein as SEQ ID NO: 1. SCUBE1 is 2992 nucleotides in length and has an open reading frame encoding a protein of 988 amino acids (SEQ ID NO: 2). The ORF spans nucleotides 21-2987 (21-2984 without the TAA stop codon) of SEQ ID NO: 1. A signal peptide is found at amino acids 1-22 of SEQ ID NO: 2 (FIG. 1), and 10 EGF-like domains are found at amino acids 37-72; 78-115; 121-156; 166-202; 206-241; 245-280; 286-321; 327-360; 366-401; and 737-773. A CUB domain is located at amino acids 798-907. Deletion mutants of SCUBE1, D1 and D2, were constructed in a pFLAG-CMV vector (Sigma-Aldrich, St. Louis, Mo., see FIG. 1 for approximate C-terminal boundaries), which supplied the signal sequence for secretion of the mutant polypeptide. The deletion 1 construct (SCUBE1-D1, SEQ ID NO:16) encodes amino acids 26-789 of SEQ ID NO:2 (SEQ ID NO:17, deleting the CUB domain) and the deletion 2 construct (SCUBE1-D2, SEQ ID NO:18) encodes amino acids 26-411 of SEQ ID NO:2 (SEQ ID NO:19, deleting the spacer, the 10th EGF-like domain and the CUB domain).

[0237] Human SCUBE1 shows sequence similarity to the mouse SCUBE1 gene (GenBank Accession No. NM—022723, GenPept Accession No. NP—073560, SEQ ID NO:13), approximately 84% identity at the protein level and 87% identity at the nucleic acid level. The mouse protein (961 amino acids in length) is not homologous to the human after 911 amino acids. The human and mouse proteins, therefore, have different C-termini, the significance of which may be that different molecules function as agonists, antagonists and biochemical signals in each animal.

[0238] The top portion of FIG. 2 displays the results of a hydrophobicity analysis of the amino acid sequence of SEQ ID NO: 2 (SCUBE1 ). The protein appears to be largely hydrophilic, particularly in the EGF-like and CUB regions.

[0239] The SCUBE2 gene, which has some homology to SCUBE1 and which is located on chromosome 11p15, was discovered by screening commercially available clones (e.g., from OriGene Technologies, Inc., Rockville, Md.) using sequence information from human SCUBE1 and using standard methods such as those described above and in Sambrook et al., supra. The SCUBE2 nucleic acid sequence (SEQ ID NO:3) is 3497 nucleotides in length and contains and open reading frame from nucleotides 81-2837, followed by a TGA stop codon. The encoded protein, 919 amino acids in length includes the secretion signal sequence, 9 EGF-like domains and a CUB domain. FIG. 13 displays the results of a hydrophobicity analysis of the amino acid sequence of SEQ ID NO: 4 (SCUBE2).

[0240] In greater detail, the SCUBE2 amino acid sequence is disclosed herein as SEQ ID NO: 4. A signal peptide is found at amino acids 1-37 of SEQ ID NO: 4, and 8 EGF-like domains (Pfam PF00008, SEQ ID NO:9) are found at amino acids 49-84, 90-126, 132-167, 177-213, 217-252, 286-321, 327-362, and 368-401 of SEQ ID NO:4. The spacer region is between amino acids 402-728 of SEQ ID NO:4 and the CUB domain (Pfam PF00431, SEQ ID NO:10) is between amino acids 729-838 of SEQ ID NO:4. SCUBE2 has some Prosite signature sequences: 7 EGF-like domain signature 2 sequences (Prosite PS01186, SEQ ID NO:11) located at about amino acids 71 to 84, 111 to 126, 152 to 167, 198 to 213, 306 to 321, 347 to 362, and 387 to 401 of SEQ If) NO:4; 5 calcium-binding EGF-like domain pattern signatures (Prosite PS01187, SEQ ID NO:12) located at about amino acids 45 to 71, 86 to 111, 128 to 152, 323 to 347, and 364 to 387 of SEQ ID NO:4; and 7 N-glycosylation sites (Prosite PS00001, see FIG. 13) located mostly in the spacer region at about amino acids 266 to 269, 451 to 454, 579 to 582, 610 to 613, 681 to 681, 710 to 713, and 720 to 723 of SEQ ID NO:4. (For reference to Pfam and Prosite annotation, see Example 8.)

[0241] Human SCUBE2 shows sequence similarity to a human genome sequencing clone (GenBank Accession No. NM—020974, GenPept Accession No. NP—066025, SEQ ID NO: 14), approximately 94% identity at the nucleic acid level and approximately 92% identity compared to the protein predicted from the genomic clone. An alignment of SCUBE2 with the NM—020974 protein suggests that they are splice variants, with NM—020974 having an insert of about 80 amino acids at about amino acid residue 403 of SEQ ID NO:4 (from about 404 to 483 of SEQ ID NO:14).

Example 2

[0242] SCUBE mRNA Expression in Vascular Endothelium

[0243] SCUBE cDNA, or portions or fragments thereof, can be used to detect the presence of SCUBE mRNA in human tissues, as well as to probe for SCUBE-related gene products in other species.

[0244] Differential expression of SCUBE in human tissues was determined using by Northern blotting and by RT-PCR.

[0245] The tissue distribution of RNA encoding the protein of SEQ ID NO: 2 was analyzed by Northern blot (FIG. 5), as well as by RT-PCR expression analysis (FIG. 9). For Northern blotting, RNA was isolated from the following human tissues using standard protocols: human brain, heart, skeletal muscle, colon, thymus, spleen, kidney, liver, small intestine, placenta, lung and peripheral blood lymphocytes. Northern blots were prepared using a probe derived from SEQ ID NO: 1, with hybridization conditions as described by Sambrook et al. Expression of SCUBE1 is strong in the liver, kidney, lung, and small intestine.

[0246] RT-PCR expression analysis was also performed on the samples listed above, as well as on samples prepared from pancreas, prostate, testis and ovary tissue, using primers derived from SEQ ID NO: 1 or 3 and using AmpliTaq PCR® amplification kits (Perkin Elmer). Again, SCUBE1 is strongly expressed in the liver, kidney and lung, while SCUBE2 has a broader tissue distribution. It is expressed at relatively higher levels in the lung, placenta, pancreas, prostate and heart, and at lower levels in the liver, kidney, small intestine, brain and skeletal muscle.

[0247] SCUBE1 cDNA was used as a probe for the detection of SCUBE1 mRNA expression in tissue sections. Human umblical vein and artery samples and several tissue samples from Cynomolgus macaque monkeys (brain, lung and kidney samples) were probed using standard in situ hybridization techniques. Both samples display highly specific expression of SCUBE1 in the vascular endothelium (see FIG. 11). Further, the results show clearly that SCUBE1 cDNA can be used to probe or generate probes for related genes in other species. In contrast, FIG. 12 shows that the mouse SCUBE1 gene has a broad range of expression in fetal mouse tissues. It is expressed in embryonic cardiac muscle, cardiac blood vessels, lung, thoracic wall, small intestine and brain, although no expression was found in adult tissues- heart, brain, spleen, lung, liver, skeletal muscle, kidney or testis (Grimmond et al., Genomics 70:74-81, 2000).

Example 3

[0248] SCUBE1 is a Secreted Protein.

[0249] As predicted by the signal sequence and EGF-like motifs, the SCUBE1 protein is secreted (see FIG. 3). HEK-293 cells were transfected with the expression vector encoding Myc-tagged human SCUBE1 at the C-termius (SCUBE1.Myc) and the endogenous signal peptide. Forty-eight hours after transfection, conditioned medium was collected and cells were detached with PBS. Extracellular matrix on the culture dish was extracted with Laemmli sample buffer. Samples from conditioned culture medium (Medium), cell lysates (Cell) and the extracellular matrix (Matrix) were separated by 4-20% SDS-polyacrylamide gel electrophoresis and transferred to PVDF membranes. Recombinant SCUBE1 proteins were detected in the culture medium and in the cell lysate by Western blotting with anti-Myc antibody (FIG. 3a).

[0250] HEK-293 cells were also transfected with the expression vector encoding both Flag- and Myc-tagged SCUBE1 at the N- and C-termini (Flag.SCUBE1.Myc). Two days after transfection, samples from conditioned culture medium (Medium), cell lysates (Cell) and the extracellular matrix (Matrix) were separated by 4-20% SDS-polyacrylamide gel electrophoresis and transferred to PVDF membranes. Recombinant SCUBE1 proteins were detected by Western blotting with anti-Flag M2 or anti-Myc antibody. Again, the blots show that SCUBE1 is secreted into the culture medium and that the secreted protein is the same size as the protein that remains associated with the cells, i.e., the whole protein is secreted, rather than a cleaved product (FIG. 3b).

[0251] Conditioned culture medium from cells transfected with Flag.SCUBE1.Myc was also immunoprecipitated with anti-Flag M2 antibody, and the precipitate then was immunoblotted with indicated antisera (FIG. 3c). This experiment confirms that secreted SCUBE1 is not a proteolytic product.

[0252] SCUBE1 is also a glycosylated protein (FIG. 4). HEK-293 cells were transfected with the expression vector encoding Flag-tagged full-length or deletion versions (D1 and D2) of human SCUBE1. Transfected cells were cultured in the absence (−) or in the presence (+) of tunicamycin, a potent inhibitor of glycosylation of asparagine residues, for twenty-four hours. Cell lysates from each culture were analyzed by Western blotting with anti-Flag M2 antibody. For each construct tested, glycosylation of the expressed protein was inhibited by tunicamycin, producing a smaller glycoprotein molecule, as shown by each pair of samples in the Western blot.

[0253] A spacer region is critical for the secretion and surface expression of SCUBE1 (FIG. 6). As shown in FIG. 6a, HEK-293 cells were transfected with the expression plasmids encoding Flag-tagged full-length SCUBE1, Flag-tagged SCUBE1-D1, Flag-tagged SCUBE1-D2, Flag-tagged IL-1R1 or Flag-tagged JNK1. Two days after transfection, conditioned culture medium was concentrated and separated on SDS-PAGE and Western blotted with anti-Flag M2 antibody. Only the constructs containing the spacer sequence could encode proteins that were secreted into the cell medium, i.e., full-length and D1 SCUBE. FIG. 6b shows that the spacer region is essential for cell-surface expression of recombinant SCUBE1. The expression constructs Flag-SCUBE1-FL (top), -D1 (middle), or -D2 (bottom) were singly or co-transfected with SCUBE1.Myc plasmid in HEK-293 cells. Twenty-four hours after transfection, cells were detached, stained with anti-Flag M2 antibody and analyzed by flow cytometry. Cell number in the flow channel was plotted as a function of fluorescence intensity, using fluorescently labeled SCUBE1 proteins as a cell surface marker. The graphs show that cells containing Flag-SCUBE1-FL or Flag-SCUBE1-FL and SCUBE1.Myc have the same surface properties when Flag is detected; Flag-SCUBE1-FL is externalized to the same degree in the two preparations. Cell surface properties are almost the same when the same constructs with SCUBE-D1 are transfected instead of SCUBE-FL (almost as much Flag-SCUBE-D1 protein is on the cell surface in co-transfected cells as in cells transfected with one vector). When these constructs containing SCUBE-D2 are used, however, two Flag-containing peaks are detected, indicating that the Flag-SCUBE1-D2 proteins remain internalized in the cells, while protein complexes composed of Flag-SCUBE1-D2 linked to SCUBE1.Myc are found on the cell surface, externalization enabled by the spacer region in the SCUBE1.Myc portion.

[0254] FIG. 7 shows the membrane association of human SCUBE1 protein. HEK-293 cells were transfected with expression plasmids encoding Flag-tagged full-length SCUBE1, SCUBE1-D1, SCUBE1-D2 and TLR2 (control) proteins, and, two days after transfection, cells were collected and homogenized. Samples of supernatant (S10) were centrifuged at 100,000×g for 30 min to give soluble fractions (S100) and pellets (P100 membrane fraction). Pellets were resuspended in original volumes of homogenization buffer with 0.1 M Na2CO3 (pH 12), sonicated briefly, and then incubated on ice for 30 min. Samples were centrifuged again at 100,000×g for 30 min. to give washed fractions S100′ and pellets P100′. Each fraction was subjected to SDS-PAGE and immunoblot analysis using anti-Flag M2 antibody. The results show that only the protein encoded by the D2 construct is present in appreciable amounts in the first soluble fraction, while the full-length and D1 construct proteins remain associated with the membrane. Upon disruption by sonication, however, they are released from the membrane and can be detected in the soluble membrane fraction. The ability of SCUBE1 to form homo-oligomers in transfected HEK-293 cells is shown in FIG. 8. FIG. 8a shows the homomeric interaction of SCUBE1 proteins. Flag-SCUBE1 and SCUBE1.Myc were singly or co-transfected in 293T cells. As a control, SCUBE1.Myc was expressed together with Flag-tagged IL-1β receptor (Flag.IL-1R1). Immunoprecipitation (IP) and Western blot (WB) were performed using antisera as indicated. The bands indicate the presence of protein complexes that can be precipitated by one antibody and detected by another. FIG. 8b shows that EGF-like repeats are sufficient for SCUBE1 homotypic associations. The spacer and CUB sequences are not required. SCUBE1.Myc was expressed together with Flag.SCUBE1-FL, -D1, or -D2 by transient transfection. Detergent lysates were immunoprecipitated with anti-Myc antibody and then immunoblotted with anti-Flag M2 antibody to determine the associated proteins. Cell lysates were also immunoblotted to examine the protein expression levels. In each case, a protein complex that could be precipitated with anti-Myc antibody was detected with anti-Flag M2 antibody.

Example 4

[0255] Down-regulation of SCUBE Expression by Cellular Signaling Factors (IL-1β, TNF-α) or by Toxins (LPS)

[0256] SCUBE1 and SCUBE2 messages were down-regulated following treatment with pro-inflammatory cytokines or lipopolysaccharides (LPS) in vitro and in vivo (see FIG. 10). As shown in a), pro-inflammatory cytokines decreased expression of the SCUBE gene family in vitro. Several human primary cell lines and HUVEC treated with IL-1β or TNF-α for 6 and 24 hrs were analyzed by RT-PCR. b) shows the inhibition of SCUBE gene expression in the kidney after intraperitoneal injection of LPS. C57/B16 mice were sacrificed at the indicated times after i.p. injection of either LPS at 5 mg/kg or PBS vehicle. Kidneys were collected and submitted for TaqMan analyses. Down-regulation of SCUBE1 was strongest 3 hours after exposure to LPS, while down-regulation of SCUBE2 was most marked 3 and 6 hours after exposure to LPS, both returning to normal levels in 48 hours.

Example 5

[0257] Interaction of SCUBE1 with Growth Factors

[0258] SCUBE1 was co-transfected into HEK-293 cells using the methods of Example 3, above, along with an expression vector containing the gene for PDGF-C or PDGF-D (platelet-derived growth factor C or D). Analysis of proteins in cell lysates antibody preparations showed the presence of protein complexes containing SCUBE1 and PDGF-C or SCUBE1 and PDGF-D. These results indicate that the binding of SCUBE may serve to modulate growth factor activity. These findings also suggest that SCUBE proteins can be used as therapeutic compounds to regulate the activity of growth factors, such as PDGF-C or PDGF-D.

Example 6

[0259] Antibodies to SCUBE1 and SCUBE2

[0260] Monoclonal Antibodies to SCUBE1. A GST-fusion protein with the CUB domain of human SCUBE1 as antigen was generated for monoclonal antibody production. After immunization and fusion, three clones showed specificity for human SCUBE1 by immunoprecipitation (IP), fluorescent antibody cell sorting (FACS) analyses and/or western blot (WB). The results of characterizing the antibodies are shown in Table 1.

TABLE 1
Characterization of SCUBE1 Monoclonal Antibody Clones
Clone #	Isotype	IP	FACS	WB
33	IgG3	+	+	+
701	IgG1	+	+	+
712	IgG1	+		+

[0261] Polyclonal Antibodies to SCUBE1 and SCUBE2. Polyclonal antibodies to peptides from SCUBE1 and SCUBE2 were elicited in chickens. The peptides used as immunogens are listed in Table 2:

TABLE 2
SCUBE1 and SCUBE2 Peptides For Raising Chicken Antibodies
			Location in
Peptide Sequence	SEQ ID NO:	Region of Protein	Protein
ECSEGTDDCHIDAIC	SEQ ID NO:20	first EGF-like	from about amino
		domain of	acid residues 36
		SCUBE1	through 50 of SEQ
			ID NO:2
KARFKIRDAKCHLRPHS	SEQ ID NO:21	spacer region of	from about amino
		SCUBE1	acid residues 487
			through 503 of
			SEQ ID NO:2
SHICKEAPRGSVACEC	SEQ ID NO:22	fourth EGF-like	from about amino
		domain of	acid residues 185
		SCUBE2	through 200 of
			SEQ ID NO:4
FLRCHSGIHLSSDVTTIRT	SEQ ID NO:23	spacer region of	from about amino
		SCUBE2 in splice	acid residues 471
		region of overlap	through 489 of
		with NM_020974	SEQ ID NO: 14
			(partial overlap in
			residues 403 to
			409 of SEQ ID
			NO:4)

[0262] The chicken antibodies were prepared from these sequences by Washington Biotechnology, Inc. (Baltimore, Md.). Briefly, peptides were synthesized and linked to keyhole limpet hemocyanin for immunization of chickens. The immunized chickens then produced Y′EGGS (immune eggs), from which the yolks yielded IgY antibodies, with specific antibodies present at about 5% of total IgY. Purification of specific SCUBE antibodies yielded solutions with about >90% specific IgY antibodies. The antibodies demonstrated specificity for SCUBE1 or SCUBE2 on western blots of recombinantly expressed SCUBE1 or SCUBE2 or of lysates of human umbilical cord endothelial cells. In addition, use of the antibodies in immunohistochemistry confirmed that both SCUBE1 and SCUBE2 proteins are expressed in endothelial cells in vivo.

Example 7

[0263] SCUBE1 is Found in Thrombi

[0264] Monkey tissues were collected from exsanguinated animals in which thrombi were allowed to form in the bleeding process. Tissues were prepared for immunochemistry and examined after reaction with SCUBE1 monoclonal antibodies from clones 33 and 701. Both antibody clones yielded the same result. SCUBE1 was detected in thrombi in many tissues, including in kidney and spleen.

Example 8

[0265] Isolation of SCUBE3

[0266] SCUBE3 (gene MG44547) was first identified as 47971-031 (SCUBE3.1) in a search for polynucleotides homologous to sequences in various receptor classes. The 47971-031 nucleic acid sequences of the present invention were classified by means of one or more HMM motifs and/or TBLASTN set. The HMM motif included a consensus sequence for a receptor protein domain. The TBLASTN set included a set of protein sequence probes corresponding to amino acid sequence motifs that are conserved in various receptor classes/families. The novel sequences were derived from usually random cDNA library sequencing. The HMM/TBLASTN motifs were used to “hunt” for specific receptor classes among the novel sequences. The 47971 nucleic acid sequence was identified in the hunt using tumor necrosis factor receptor (TNFR)/nerve growth factor receptor (NGFR) motifs from the cysteine-rich regions of those molecules. A number of proteins, some of which are known to be receptors for growth factors, were found to contain a cysteine-rich domain of about 110 to 160 amino acids in their N-terminal part, that can be subdivided into four (or in some cases, three) modules of about 40 residues containing 6 conserved cysteines. The HMM Probes for TNF Receptor/NGF Receptor domain were Pfam identifier: PF00020 and Prosite identifier: PDOC00561. (For general information regarding PFAM identifiers and PF prefix domain identification numbers, refer to Sonnhammer et al. (1997) Protein 28:405-420 and the Pfam database, release 2.1, and the Pfam website maintained in several locations, e.g. by the Sanger Institute (pfam.sanger.ac.uk), Washington University (pfam.wustl.edu), the Karolinska Institute (pfam.cgr.kr.se) or Institut de la National Recherche Agronomique (pfam.jouy.inra.fr); for general information regarding Prosite identification numbers, refer to Sonnhammer et al. (1997) Protein 28:405-420 and the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland.)

[0267] The 47971-031 (SCUBE3.1) nucleic acid sequence (SEQ ID NO:5) is 3193 nucleotides in length and contains and open reading frame from nucleotides 449-3190, followed by a TAG stop codon. The encoded protein, 914 amino acids in length includes the secretion signal sequence, 9 EGF-like domains and a CUB domain. FIG. 14A displays the results of a hydrophobicity analysis of the amino acid sequence of SEQ ID NO: 6 (SCUBE3.1).

[0268] The second example of isolation of the SCUBE3 (gene MG44547) sequence yielded the Fbh47971FL clone (SCUBE3.2). This process began from searching for sequences with homology to the 47971-031 sequences. Clones containing 47971 sequences were walked to produce a full length clone which was inserted into a pFLAGCMV1 vector with a FLAG epitope tag (Sigma Pharmaceuticals, St. Louis, Mo.) or a pSecTag vector with a myc epitope tag (Invitrogen Corp., Carlsbad, Calif.). This clone, named Fbh47971FL has 99% identity to the nucleic acid and protein sequences found in GenBank Accession No. AF452494, GenPept Accession No. AAN76808 (SEQ ID NO:15).

[0269] The Fbh47971FL (SCUBE3.2) nucleic acid sequence (SEQ ID NO:7) is 3947 nucleotides in length and contains and open reading frame from nucleotides 443-3421, followed by a TAG stop codon. The encoded protein, 993 amino acids in length includes the secretion signal sequence, 9 EGF-like domains and a CUB domain. FIG. 14B displays the results of a hydrophobicity analysis of the amino acid sequence of SEQ ID NO: 8 (SCUBE3.2).

[0270] 47971 (gene MG44547) (SCUBE3) is located on human chromosome 6p21.

[0271] In greater detail, the SCUBE3 amino acid sequences are disclosed herein as SEQ ID NO: 6 (SCUBE3.1) and SEQ ID NO:8 (SCUBE3.2). A signal peptide is found at amino acids 1-21 of SEQ ID NO: 6 and 8, and 9 EGF-like domains (Pfam PF00008, SEQ ID NO:9) are found at amino acids 33 to 68, 74 to 110, 116 to 151, 161 to 197, 208 to 243, 247 to 282, 288 to 323, 329 to 362, and 368 to 404 of SEQ ID NO:6; and at amino acids 33 to 68, 74 to 110, 116 to 151, 161 to 197, 201 to 236, 240 to 275, 281 to 316, 322 to 355, and 361 to 397 of SEQ ID NO:8. The spacer region is found at about amino acids 405-724 of SEQ ID NO:6 and 398 to 803 of SEQ ID NO:8 and the CUB domain (Pfam PF00431, SEQ ID NO:10) is found at about amino acids 725 to 834 of SEQ ID NO:6 and 804 to 913 of SEQ ID NO:8. SCUBE3 polypeptides have some Prosite signature sequences: 7 EGF-like domain signature 2 sequences (Prosite PS01186, SEQ ID NO:11) located at about amino acids 55 to 68, 95 to 110, 136 to 151, 182 to 197, 267 to 282, 308 to 323, and 348 to 362 SEQ ID NO:6 and at about amino acids 55 to 68, 95 to 110, 136 to 151, 182 to 197, 260 to 275, 301 to 316, and 341 to 355 of SEQ ID NO:8; 6 calcium-binding EGF-like domain pattern signatures (Prosite PS01187, SEQ ID NO:12) located at about amino acids 29 to 55, 70 to 95, 112 to 136, 284 to 308, 325 to 348, and 364 to 388 of SEQ ID NO:6 and 29 to 55, 70 to 95, 112 to 136, 277to 301, 318to 341, and 357 to 381 of SEQ ID NO:8; and 5 N-glycosylation sites (Prosite PS00001, see FIG. 13) located in the spacer region at about amino acids 424 to 427, 471 to 474, 606 to 609, 677 to 680, and 706 to 709 of SEQ ID NO:6 and at about amino acids 417 to 420, 464 to 467, 685 to 688, 756 to 759 and 785 to 788 of SEQ ID NO:8. (For reference to Pfam and Prosite annotation, see Example 8.)

Example 9

[0272] Expression Analysis of SCUBE2 and SCUBE3

[0273] Total RNA was prepared from various human tissues by a single step extraction method using RNA STAT-60 according to the manufacturer's instructions (TelTest, Inc). Each RNA preparation was treated with DNase I (Ambion) at 37° C. for 1 hour. DNAse I treatment was determined to be complete if the sample required at least 38 PCR amplification cycles to reach a threshold level of fluorescence using β-2 microglobulin as an internal amplicon reference. The integrity of the RNA samples following DNase I treatment was confirmed by agarose gel electrophoresis and ethidium bromide staining. After phenol extraction cDNA was prepared from the sample using the SUPERSCRIPT™ Choice System following the manufacturer's instructions (GibcoBRL). A negative control of RNA without reverse transcriptase was mock reverse transcribed for each RNA sample.

[0274] Human SCUBE expression was measured by TaqMan® quantitative PCR (Perkin Elmer Applied Biosystems) in cDNA prepared from a variety of normal and diseased (e.g., cancerous) human tissues or cell lines.

[0275] Probes were designed by PrimerExpress software (PE Biosystems) based on the sequence of the human SCUBE2 and SCUBE3 genes. Each human SCUBE probe was labeled using FAM (6-carboxyfluorescein), and the β2-microglobulin reference probe was labeled with a different fluorescent dye, VIC. The differential labeling of the target gene and internal reference gene thus enabled measurement in same well. Forward and reverse primers and the probes for both β2-microglobulin and target gene were added to the TaqMan® Universal PCR Master Mix (PE Applied Biosystems). Although the final concentration of primer and probe could vary, each was internally consistent within a given experiment. A typical experiment contained 200 nM of forward and reverse primers plus 100 nM probe for β-2 microglobulin and 600 nM forward and reverse primers plus 200 nM probe for the target gene. TaqMan matrix experiments were carried out on an ABI PRISM 7700 Sequence Detection System (PE Applied Biosystems). The thermal cycler conditions were as follows: hold for 2 min at 50° C. and 10 min at 95° C., followed by two-step PCR for 40 cycles of 95° C. for 15 sec followed by 60° C. for 1 min.

[0276] The following method was used to quantitatively calculate human SCUBE gene expression in the various tissues relative to β-2 microglobulin expression in the same tissue. The threshold cycle (Ct) value is defined as the cycle at which a statistically significant increase in fluorescence is detected. A lower Ct value is indicative of a higher mRNA concentration. The Ct value of the human SCUBE3 gene is normalized by subtracting the Ct value of the β-2 microglobulin gene to obtain a ΔCt value using the following formula: ΔCt=Cthuman 59914 and 59921−Ct β-2 microglobulin. Expression is then calibrated against a cDNA sample showing a comparatively low level of expression of the human SCUBE3 gene. The ΔCt value for the calibrator sample is then subtracted from ΔCt for each tissue sample according to the following formula: ΔΔCt=ΔCt−sample−ΔCt−calibrator. Relative expression is then calculated using the arithmetic formula given by 2−ΔΔCt. Expression of the target human SCUBE gene in each of the tissues tested is then graphically represented as discussed in more detail below.

[0277] In addition to the SCUBE2 expression found in Example 2, the analysis found some regulated expression of SCUBE2 in some disease conditions. For example, these results indicate that SCUBE2 has high levels of expression in urge urinary incontinence (UUI) bladder and lower levels of expression in normal bladder. SCUBE2 also has high levels of expression in breast tumor and low levels of expression in normal breast.

[0278] The results indicate that SCUBE3 has high levels of expression in osteoblasts and normal fetal kidney, medium levels of expression in normal artery, normal vein, fetal heart, normal adult heart, normal ventricle, umbilical cord, and diseased aorta and medium to low levels in ischemic ventricle. In contrast, SCUBE3 expression is low in idiopathic artery, ischemic artery, and coronary diseased artery, to indicate regulated expression of SCUBE3 in some disease processes. Another example of regulated SCUBE3 expression is the medium level of SCUBE3 expression in urge urinary incontinence (UUI) bladder and only a trace level of expression in normal bladder.

[0279] Although the present invention has been described in detail with reference to examples above, it is understood that various modifications can be made without departing from the spirit of the invention. Accordingly, the invention is limited only by the following claims. All cited patents, patent applications and publications referred to in this application are herein incorporated by reference in their entirety.

Claims

1. An isolated nucleic acid molecule selected from the group consisting of: (a) an isolated nucleic acid molecule comprising SEQ ID NO: 16, 18, 3, 5, or 7; (b) an isolated nucleic acid molecule that encodes the amino acid sequence of SEQ ID NO: 17, 19, 4, 6 or 8; (c) an isolated nucleic acid molecule which hybridizes to the complement of a nucleic acid molecule comprising SEQ ID NO: 16, 18, 3, 5, or 7 and which encodes a human SCUBE protein; (d) an isolated nucleic acid molecule which hybridizes to the complement of a nucleic acid molecule that encodes the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8 and which encodes a human SCUBE protein; (e) an isolated nucleic acid molecule that encodes a protein that exhibits at least about 92% amino acid sequence identity to SEQ ID NO: 4; (f) an isolated nucleic acid molecule that encodes a protein that exhibits at least about 95% amino acid sequence identity to SEQ ID NO: 6; (g) an isolated nucleic acid molecule that encodes a protein that exhibits at least about 95% amino acid sequence identity to SEQ ID NO: 8; (h) a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8, wherein the fragment comprises at least 10 contiguous amino acids of SEQ ID NO: 17, 19, 4, 6, or 8; and (i) an isolated nucleic acid molecule that encodes the amino acid sequences of SEQ ID NO: 4, 6 or 8 without a signal peptide sequence.

2. An isolated nucleic acid molecule of claim 1, which is selected from the group consisting of: (a) a nucleic acid molecule comprising nucleotides 81-2837 of SEQ ID NO: 3; (b) a nucleic acid molecule comprises nucleotides 449-3190 of SEQ ID NO: 5; (c) a nucleic acid molecule comprises nucleotides 443-3421 of SEQ ID NO: 7; (d) a nucleic acid molecule consisting of SEQ ID NO:16; (e) a nucleic acid molecule consisting of SEQ ID NO:18; and (d) a nucleic acid molecule which encodes the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8.

3. An isolated nucleic acid molecule of claim 1, wherein the nucleic acid molecule is operably linked to one or more expression control elements.

4. A vector comprising an isolated nucleic acid molecule of claim 1.

5. A host cell transformed to contain the nucleic acid molecule of claim 1.

6. The nucleic acid molecule of claim 1 further comprising nucleic acid sequences encoding a heterologous polypeptide.

7. A method for producing a polypeptide, comprising culturing a host cell transformed with the nucleic acid molecule of any one of claim 1 under conditions in which the protein encoded by said nucleic acid molecule is expressed.

8. An isolated polypeptide produced by the method of claim 7.

9. An isolated polypeptide molecule selected from the group consisting of: (a) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8; (b) an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 17, 19, 4, 6, or 8; (c) a naturally occurring amino acid sequence variant of SEQ ID NO: 17, 19, 4, 6, or 8; (d) an isolated polypeptide exhibiting at least 92% amino acid sequence identity with SEQ ID NO: 4; (e) an isolated polypeptide exhibiting at least 95% amino acid sequence identity with SEQ ID NO: 6; (f) an isolated polypeptide exhibiting at least 95% amino acid sequence identity with SEQ ID NO: 8; (g) a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8, wherein the fragment comprises at least 10 contiguous amino acids of SEQ ID NO: 17, 19, 4, 6, or 8; and (i) an isolated polypeptide comprising SEQ ID NO: 4, 6, or 8 without a signal peptide.

10. The polypeptide of claim 9 further comprising heterologous amino acid sequences.

11. An isolated antibody that binds to a polypeptide of claim 9.

12. A method of identifying an agent which modulates the expression of a nucleic acid encoding a polypeptide of claim 9, comprising: (a) exposing a cell which expresses the nucleic acid to the agent; and (b) determining whether the agent modulates expression of the nucleic acid, thereby identifying an agent which modulates the expression of a nucleic acid encoding the polypeptide.

13. A method for detecting the presence of a polypeptide of claim 9 in a sample, comprising: a) contacting the sample with a compound which selectively binds to a polypeptide of claim 9; and b) determining whether the compound binds to the polypeptide in the sample.

14. A method of identifying an agent which modulates at least one activity of a polypeptide of claim 9, comprising: contacting a polypeptide or a cell expressing a polypeptide of claim 9 with the agent; and determining whether the agent modulates at least one activity of the protein, thereby identifying an agent which modulates at least one activity of the protein.

15. A method of identifying binding partners for a polypeptide of claim 9, comprising: exposing said polypeptide to a potential binding partner; and determining if the potential binding partner binds to said polypeptide, thereby identifying binding partners for the polypeptide.

16. A method of modulating the expression of a nucleic acid encoding a polypeptide of claim 9, comprising: administering an effective amount of an agent which modulates the expression of a nucleic acid encoding the polypeptide.

17. A method of modulating at least one activity of a polypeptide of claim 9, comprising: administering an effective amount of an agent which modulates at least one activity of the polypeptide.

18. A kit comprising a compound which selectively binds to a polypeptide of claim 9 and instructions for use.

19. A method of diagnosing a disease state in a subject, comprising determining the level of expression of a nucleic acid molecule of claim 1.

20. A composition comprising a protein of claim 9 and an aqueous carrier.

21. A method of treating a disorder from the group consisting of: atherosclerosis, ischemia, a coagulation disorder or thrombosis; in a subject by administering to the subject a compound which modulates the function of a polypeptide selected from the group consisting of: (a) an isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8; (b) an isolated polypeptide comprising conservative amino acid substitutions of SEQ ID NO: 17, 19, 4, 6, or 8; (c) a naturally occurring amino acid sequence variant of SEQ ID NO: 17, 19, 4, 6, or 8; (d) an isolated polypeptide exhibiting at least 92% amino acid sequence identity with SEQ I) NO: 4; (e) an isolated polypeptide exhibiting at least 95% amino acid sequence identity with SEQ ID NO: 6; (f) an isolated polypeptide exhibiting at least 95% amino acid sequence identity with SEQ ID NO: 8; (g) a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8, wherein the fragment comprises at least 10 contiguous amino acids of SEQ ID NO: 17, 19, 4, 6, or 8; (h) an isolated polypeptide comprising SEQ ID NO: 4, 6, or 8 without a signal peptide; (i) a polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence comprising the nucleotide sequence of SEQ ID NO: 16, 18, 3, 5, or 7, or a complement thereof; (j) a fragment of a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8, wherein the fragment comprises at least 10 contiguous amino acids of SEQ ID NO: 17, 19, 4, 6, or 8, further comprising heterologous amino acid sequences; and (k) a polypeptide comprising the amino acid sequence of SEQ ID NO: 17, 19, 4, 6, or 8, further comprising heterologous amino acid sequences.