ZA200105990B - Promotion or inhibition of angiogenesis and cardiovascularization. - Google Patents

Description

PROMOTION OR INHIBITION OF ANGIOGENESIS AND

CARDIOVASCULARIZATION

Background of the Invention Field of the Invention

The present invention relates to compositions and methods useful for promoting or inhibiting angiogenesis and/or cardiovascularization in mammals in need of such biological effect. This includes the diagnosis and treatment of cardiovascular disorders as well as oncological disorders.

Description of Background

A. Cardiac Disorders and Factors

Heart failure affects approximately five million Americans, and new cases of heart failure number about 400,000 each year. It is the single most frequent cause of hospitalization for people age 65 and older in the United

States. Recent advances in the management of acute cardiac diseases, including acute myocardial infarction, are resulting in an expanding patient population that will eventually develop chronic heart failure. From 1979 to 1995, hospitalizations for congestive heart failure (CHF) rose from 377,000 to 872,000 (a 130 percent increase) and CHF deaths increased 116 percent.

CHF is a syndrome characterized by left ventricular dysfunction, reduced exercise tolerance, impaired : quality of life, and markedly shortened life expectancy. The sine qua non of heart failure is an inability of the heart to pump blood at a rate sufficient to meet the metabolic needs of the body's tissues (in other words, there is insufficient cardiac output).

At least four major compensatory mechanisms are activated in the setting of heart failure to boost cardiac output, including peripheral vasoconstriction, increased heart rate, increased cardiac contractility, and increased plasma volume. These effects are mediated primarily by the sympathetic nervous system and the renin-angiotensin system. See, Eichhorn, American Journal of Medicine, 104: 163-169 (1998). Increased output from the sympathetic nervous system increases vascular tone, heart rate, and contractility. Angiotensin II elevates blood pressure by 1) directly stimulating vascular smooth muscle contraction, 2) promoting plasma volume expansion by stimulating aldosterone and antidiuretic hormone secretion, 3) stimulating sympathetic-mediated vascular tone, and 4) catalyzing the degradation of bradykinin, which has vasodilatory and natriuretic activity. See, review by Brown and Vaughan, Circulation, 97: 1411-1420(1998). As noted below, angiotensin II may also have directly deleterious effects on the heart by promoting myocyte necrosis (impairing systolic function) and intracardiac fibrosis (impairing diastolic and in some cases systolic function). See, Weber, Circulation, 96: 4065-4082 (1998).

A consistent feature of congestive heart failure (CHF) is cardiac hypertrophy, an enlargement of the heart that is activated by both mechanical and hormonal stimuli and enables the heart to adapt to demands for increased cardiac output. Morgan and Baker, Circulation, 83: 13-25 (1991). This hypertrophic response is frequently associated with a variety of distinct pathological conditions such as hypertension, aortic stenosis, myocardial infarction, cardiomyopathy, valvular regurgitation, and intracardiac shunt, all of which result in chronic ) hemodynamic overload.

Hypertrophy is generally defined as an increase in size of an organ or structure independent of natural

S growth that does not involve tumor formation. Hypertrophy of the heart is due either to an increase in the mass of the individual cells (myocytes), or to an increase in the number of cells making up the tissue (hyperplasia), or both.

While the enlargement of an embryonic heart is largely dependent on an increase in myocyte number (which continues until shortly after birth), post-natal cardiac myocytes lose their proliferative capacity. Further growth occurs through hypertrophy of the individual cells.

Adult myocyte hypertrophy is initially beneficial as a short term response to impaired cardiac function by permitting a decrease in the load on individual muscle fibers. With severe, long-standing overload, however, the hypertrophied cells begin to deteriorate and die. Katz, "Heart Failure”, in: Katz A.M. ed., Physiology of the Heart (New York: Raven Press, 1992) pp. 638-668. Cardiac hypertrophy is a significant risk factor for both mortality and morbidity in the clinical course of heart failure. Katz, Trends Cardiovasc. Med, 5: 37-44 (1995). For further details of the causes and pathology of cardiac hypertrophy see, e.g., Heart Disease, A Textbook of Cardjovascular

Medicine, Braunwald, E. ed. (W.B. Saunders Co., 1988), Chapter 14, "Pathophysiology of Heart Failure."

On a cellular level, the heart is composed of myocytes and surrounding support cells, generically called non-myocytes. While non-myocytes are primarily fibroblast/mesenchymal cells, they also include endothelial and smooth muscle cells. Indeed, although myocytes make up most of the adult myocardial mass, they represent only about 30% of the total cell numbers present in heart. In response to hormonal, physiological, hemodynamic, and pathological stimuli, adult ventricular muscle cells can adapt to increased workloads through the activation of a hypertrophic process. This response is characterized by an increase in myocyte cell size and contractile protein content of individual cardiac muscle cells, without concomitant cell division and activation of embryonic genes, including the gene for atrial natriuretic peptide (ANP). Chien eral, FASEB J., 5: 3037-3046 (1991); Chien ez al.,

Annu. Rev. Physiol. 55: 77-95 (1993). An increment in myocardial mass as a result of an increase in myocyte size that is associated with an accumulation of interstitial collagen within the extracellular matrix and around intramyocardial coronary arteries has been described in left ventricular hypertrophy secondary to pressure overload in humans. Caspari et al., Cardiovasc. Res., 11: 554-558 (1977); Schwarz et dl, Am_J. Cardiol, 42: 895-903 (1978): Hess er al., Circulation, 63: 360-371 (1981); Pearlman et al., Lab. Invest., 46: 158-164 (1982).

It has also been suggested that paracrine factors produced by non-myocyte supporting cells may additionally be involved in the development of cardiac hypertrophy, and various non-myocyte derived hypertrophic factors, such as, leukocyte inhibitory factor (LIF) and endothelin, have been identified. Metcal f, Growth Factors, 7: 169-173 (1992); Kurzrock er al., Endocrine Reviews, 12: 208-217 (1991); Inoue et al., Proc. Natl. Acad. Sci.

USA. 86: 2863-2867 (1989); Yanagisawa and Masaki, Trends Pharm. Sci., 10: 374-378 (1989); U.S. Patent No. 5,573,762 (issued November 12, 1996). Further exemplary factors that have been identified as potential mediators of cardiac hypertrophy include cardiotrophin-1 (CT-1) (Pennica et al., Proc. Nat. Acad. Sci. USA, 92:1 142-1146 (1995)), catecholamines, adrenocorticosteroids, angiotensin, and prostaglandins.

At present, the treatment of cardiac hypertrophy varies depending on the underlying cardiac disease.

Catecholamines, adrenocorticosteroids, angiotensin, prostaglandins, LIF, endothelin (including endothelin-1, -2, . and -3 and big endothelin), and CT-1 are among the factors identified as potential mediators of hypertrophy. For example, beta-adrenergic receptor blocking drugs (beta-blockers, e. &., propranolol, timolol, tertalolol, carteolol, nadolol, betaxolol, penbutolol, acetobutolol, atenolol, metoprolol, carvedilol, etc.) and verapamil have been used extensively in the treatment of hypertrophic cardiomyopathy. The beneficial effects of beta-blockers on symptoms (e.g..chest pain) and exercise tolerance are largely due to a decrease in the heart rate with a consequent prolongation of diastole and increased passive ventricular filling. Thompson etal., Br. Heart J., 44: 488-98 (1980); Harrison et al., Circulation, 29: 84-98 (1964). Verapamil has been described to improve ventricular filling and probably reducing myocardial ischemia. Bonow et al., Circulation, 72: 853-64 (1985).

Nifedipine and diltiazem have also been used occasionally in the treaunem of hypertrophic cardiomyopathy. Lorell et al., Circulation, 65: 499-507 (1982); Betocchi etal., Am. J. Cardiol., 78: 451-457 (1996).

However, because of its potent vasodilating properties, nifedipine may be harmful, especially in patients with outflow obstruction. Disopyramide has been used to relieve symptoms by virtue of its negative inotropic properties.

Pollick, N. Engl. J. Med., 307: 997-999 (1982). In many patients, however, the initial benefits decrease with time.

Wigleetal., Circulation, 92: 1680-1692 (1995). Antihypertensive drug therapy has been reported to have beneficial effects on cardiac hypertrophy associated with elevated blood pressure. Examples of drugs used in antihypertensive therapy, alone or in combination, are calcium antagonists, e.g., nirendipine; adrenergic receptor blocking agents, e.g., those listed above; angiotensin converting cnzyme (ACE) inhibitors such as quinapril, captopril, enalapril, ramipril, benazepril, fosinopril, and lisinopril; diuretics, e.g., chlorothiazide, hydrochlorothiazide, hydroflumethazide, methylchlothiazide, benzthiazide, dichlorphenamide, acetazolamide, and indapamide; and calcium channel blockers, e.g., diltiazem, nifedipine, verapamil, and nicardipine. ’ For example, treatment of hypertension with diltiazem and captopril showed a decrease in left ventricular muscle mass, but the Doppler indices of diastolic function did not normalize. Szlachcic er al., Am. J. Cardiol. 63: 198-201 (1989); Shahi er al., Lancet, 336: 458-461 (1990). These findings were interpreted to indicate that excessive amounts of interstitial collagen may remain after regression of left ventricular hypertrophy. Rossi et al,

Am. Heart J., 124: 700-709 (1992). Rossi et al., supra, investigated the effect of captopril on the prevention and regression of myocardial cell hypertrophy and interstitial fibrosis in pressure overload cardiac hypertrophy, in experimental rats.

Agents that increase cardiac contractility directly (jontropic agents) were initially thought to benefit patients with heart failure because they improved cardiac output in the short term. However, all positive inotropic agents except digoxigenin have been found to resull in increased long-term mortality, in spite of short-term improvements in cardiac performance. Massie, Curr. Op. in Cardiology, 12: 209-217 (1997): Reddy et al., Curr.

Opin. Cardiol., 12: 233-241 (1997). Beta-adrenergic receptor blockers have recently been advocated for use in heart failure. Evidence from clinical trials suggests that improvements in cardiac function can be achieved without increased mortality, though documented improvements patient survival have not yet been demanstrated. See also,

U.S. Pat. Nos. 5,935,924, 5,624,806; 5,661,122; and 5,610,134 and WO 95/28173 regarding the use of cardiotropin-1 or antagonists thereof, or growth hormone and/or insulin-like growth factor-I in the treatment of

CHF. Another treatment modality is heart transplantation, but this is limited by the availability of donor hearts. 3 y

Endothelin is a vasoconstricting peptide comprising 21 amino acids, isolated from swine arterial endothelial culture supernatant and structurally determined. Yanagisawa er al., Nature, 332: 411-415 (1988). .

Endothelin was later found to exhibit various actions, and endothelin antibodies as endothelin antagonists have proven effective in the treatment of myocardial infarction, renal failure, and other diseases. Since endothelin is present in live bodies and exhibits vasoconstricting action, it is expected to be an endogenous factor involved in the regulation of the circulatory system, and may be associated with hypertension, cardiovascular diseases such as myocardial infarction, and renal diseases such as acute renal failure. Endothelin antagonists are described, for example, in U.S. Pat. No. 5,773,414; JP Pat. Publ. 3130299/1991, EP 457,195; EP 460,679; and EP 552,489. A new endothelin B receptor for identifying endothelin receptor antagonists is described in U.S. Pat. No. 5,773,223.

Current therapy for heart failure is primarily directed to using angiotensin-converting enzyme (ACE) inhibitors, such as captopril, and diuretics. These drugs improve hemodynamic profile and exercise tolerance and reduce the incidence of morbidity and mortality in patients with CHF. Kramer er al., Circulation, 67(4): 807-816 (1983); Captopril Muiticenter Research Group, LA.C.C., 2(4): 755-763 (1983); The CONSENSUS Trial Study

Group, N. Engl. J. Med, 3] 6(23): 1429-1435( 1987); The SOLVD Investigators, N. Engi. J. Med., 325(5): 293-302 (1991). Further, they are useful in treating hypertension, left ventricular dysfunction, atherosclerotic vascular disease, and diabetic nephropathy. Brown and Vaughan, supra. However, despite proven efficacy, response to

ACE inhibitors has been limited. For example, while prolonging survival in the setting of heart failure, ACR inhibitors appear to slow the progression towards end-stage heart failure, and substantial numbers of patients on

ACE inhibitors have functional class III heart failure.

Moreover, improvement of functional capacity and exercise time is onl y small and mortality, although reduced, continucs to be high. The CONSENSUS Trial Study Group, N.Cngl. J. Med., 316(23): 1429-1453 (1987);

The SOLVD Investigators, N. Enel. J. Med., 325(5): 293-302 (1991); Cohn er al., N. Engl. J. Med., 325(5): 303-310(1991); The Captopril-Digoxin Multicenter Research Group, JAMA, 259(4): 539-544 (1988). Hence, ACE inhibitors consistently appear unable 10 relieve symptoms in more than 60% of heart failure patients and reduce mortality of heart failure only by approximately 15-20%. For further adverse effects, see Brown and Vaughan, supra.

An alternative to ACE inhibitors is represented by specific ATI receptor antagonists. Clinical studies are planned to compare the efficacy of these two modalities in the treatment of cardiovascular and renal disease.

However, animal model data suggests that the ACE/Ang II pathway, while clearly involved in cardiac hypertrophy, is not the only, or even the primary pathway active in this role. Mouse genetic "knockout" models have been made to fest individual components of the pathway. In one such model, the primary cardiac receptor for Ang Il, AT sub

TA, has been genetically deleted; these mice do not develop hypertrophy when Ang II is given experimentally (confirming the basic success of the model in eliminating hypertrophy secondary to Ang Il). However, when the aorla is constricted in these animals {a model of hypertensive cardiac stress), the hearts still become hypertrophic.

This suggests that alternative signaling pathways, not depending on this receptor (AT sub 1A), are activated in hypertension. ACE inhibitors would presumably not be able to inhibit these pathways. See, Harada et al.,

Circulation, 97: 1952-1959 (1998). See also. Homey, Circulation, 97: 1890-1892 (1998) regarding the enigma associated with the process and mechanism of cardiac hypertrophy.

About 750,000 patients suffer from acute myocardial infarction (AMI) annually, and approximately . one-fourth of all deaths in the United States are due to AMI. In recent years, thrombolytic agents, e.g., streptokinase, urokinase, and in particular tissue plasminogen activator (1-PA) have significantly increased the survival of patients who suffered myocardial infarction. When administered as a continuous intravenous infusion over 1.5 to 4 hours, t-PA produces coronary patency at 90 minutes in 69% to 90% of the trcated patients. Topol etal, Am. J Cardiol., 61: 723-728 (1988); Neuhaus et al., J. Am. Coll. Cardiol., 12: 581-587 (1988); Neuhaus ef al, J. Am. Coll. Cardiol., 14: 1566-1569 (1989). The highest patency rates have been reported with high dose or accelerated dosing regimens. Topol, J. Am. Call. Cardiol., 15: 922-924 (1990). t-PA may also be administered as a single bolus, although due to its relatively short half-life, it is better svited for infusion therapy. Tebbe et al., Am. 1. Cardiol., 64: 448-453 (1989). A t-PA variant, specifically designed to have longer half-life and very high fibrin specificity, TNK t-PA (a TI03N, N117Q, KHRR(296-299)AAAA t-PA variant, Keyt er al., Proc. Natl. Acad. Sci.

USA, 91: 3670-3674 (1994) is particularly suitable for bolus administration. However, despite all these advances, the long-term prognosis of patient survival depends greatly on the post-infarction monitoring and treatment of the patients, which should include monitoring and treatment of cardiac hypertrophy.

B. Growth Factors

Various naturally occurring polypeptides reportedly induce the proliferation of endothelial cells. Among those polypeptides are the basic and acidic fibroblast growth factors (FGF) (Burgess and Maciag, Annual Rev.

Biochem., 58: 575 (1989)), platelet-derived endothelial cell growth factor (PD-ECGF) (Ishikawa ez al., Nature, 338: 557 (1989)), and vascular endothelial growth factor (VEGF). Leung ef al., Science, 246: 1306 (1989); Ferrara and

Henzel, Biochem. Biophys. Res. Commun., 161: 851 (1989); Tischer ef al., Biochem. Biophys. Res. Commun. 165: 1198 (1989); EP 471,754B granted July 31, 1996.

Media conditioned by cells transfected with the human VEGF (WEGF) cDNA promoted the proliferation . of capillary endothelial cells, whereas control cells did not. Leung et al., Science, 246: 1306 (1989). Several additional cDNAs were identified in human cDNA libraries that encode 121-, 189-, and 206-amino acid isoforms of hVEGF (also collectively referred to as hVEGF-related proteins). The 121-amino acid protein differs from hVEGEF by virtue of the deletion of the 44 amino acids between residues 116 and 159 in h VEGF. The 189-amino acid protein differs from hVEGF by virtue of the insertion of 24 amino acids at residue 116 in hVEGF, and apparently is identical to human vascular permeability factor (hVPF). The 206-amino acid protein differs from hVEGEF by virtue of an insertion of 41 amino acids at residuc 116 in hVEGF. Houck et al., Mo). Endocrin., 5: 1806 (1991); Ferrara et al., J. Cell. Biochem., 47: 211 (1991); Ferrara er al., Endocrine Reviews, 13: 18 (1992); Keck etal., Science, 246: 1309 (1989); Connolly er al., J. Biol. Chem., 264: 20017 (1989); EP 370,989 published May 30, 1990.

It is now well cstablishcd that angiogenesis, which involves the formation of new blood vessels from preexisting endothelium, is implicated in the pathogenesis of a variety of disorders. These include solid tumors and metastasis, atherosclerosis, retrolental fibroplasia, hemangiomas, chronic inflammation, intraocular neovascular syndromes such as proliferative retinopathies, e.g., diabelic retinopathy, age-related macular degeneration (AMD), neovascular glaucoma, immune rejection of transplanted corneal tissue and other tissues, rheumatoid arthritis. and psoriasis. Folkman etal.. J. Biol. Chem., 267: 10931-10934 (1992); Klagsbrun et al., Anny, Rev. Physiol, 53: 217- 239(1991); and Garner A., "Vascular diseases”, In: Pathobiology of Ocular Disease. A Dynamic Approach. Garner .

A, Klintworth GK, eds., 2nd Edition (Marcel Dekker, NY, 1994), pp 1625-1710.

In the case of tumor growth, angiogenesis appears to be crucial for the transition from hyperplasia to neoplasia, and for providing nourishment to the growing solid tumor. Folkman etal, Nature, 339: 58 (1989). The neovascularization allows the tumor cells to acquire a growth advantage and proliferative autonomy compared to the normal cells. Accordingly, a correlation has been observed between density of microvessels in tumor sections and patient survival in breast cancer as well as in several other tumors. Weidner es al, N. Eng). J. Med, 324: 1-6 (1991); Horak ez al., Lancet, 340: 1120-1124 (1992); Macchiarini et al., Lancet, 340: 145-146 (1992).

The search for positive regulators of angiogenesis has yielded many candidates, including aFGF, bFGF, TGF- a, TGF-B, HGF, TNF-a, angiogenin, IL-8, etc. Folkman et al, 1.B.C., supra, and Klagsbrun et al., supra. The negative regulators so far identified include thrombospondin (Good et al., Proc. Natl. Acad. Sci. USA. 87: 6624- 6628 (1990)), the 16-kilodaiton N-terminal fragment of prolactin (Clapp et al., Endocrinology, 133: 1292-1299 (1993)), angiostatin (OReilly et al, Cell, 79: 315-328 (1994)), and endostatin. O'Reilly et al., Cell, 88: 277-285 (1996).

Work done over the last several years has established the key role of VEGF, not only in stimulating vascular endothelial cell proliferation, but also in inducing vascular permeability and angiogenesis. Ferrara et al., Endocr.

Rev., 18: 4-25 (1997). The finding that the loss of even a single VEGF allele results in embryonic lethality points to an irreplaceable role played by this factor in the development and differentiation of the vascular system.

Furthermore, VEGF has been shown to be a key mediator of neovascularization associated with tumors and intraocular disorders. Ferrara er al., Endocr. Rev., supra. The VEGF mRNA is overexpressed by the majority of human tumors examined. Berkman et al., J. Clin. Invest. 91: 153-159 (1993); Brown er al, Human Pathol, 26: 86 91 (1995); Brown et al, Cancer Res., 53: 4727-4735 (1993); Mattern et al. Brit. J. Cancer, 73: 931-934 (1996).

Dvorak eral, Am. J. Pathol, 146: 1029-1039 (1995).

Also, the concentration levels of VEGF in eye fluids are highly correlated to the presence of active proliferation of blood vessels in patients with diabetic and other ischemia-related retinopathies. Aiello eral, N.

Encl. J. Med., 331: 1480-1487 (1994). Furthermore, recent studies have demonstrated the localization of VEGF in choroidal neovascular membranes in patients affected by AMD. Lopez et al., Invest. Ophthalmol. Vis. Sci, 37: 855-868 (1996).

Anti-VEGF neutralizing antibodies suppress the growth of a variety of human tumor cell lines in nude mice (Kim ez al., Nature, 362: 841-844 (1993); Warren ef al., J. Clin. Invest., 95: 1789-1797 (1995): Borgstrom er al.,

Cancer Res., 56: 4032-4039 (1996); Melnyk er al., Cancer Res., 56: 921-924 (1996)) and also inhibit intraocular angiogenesis in models of ischemic retinal disorders. Adamis er al., Arch. Ophthalmol., 114: 66-71 (1996).

Therefore, anti-VEGF monoclonal antibodies or other inhibitors of VEGF action are promising candidates for the treatment of solid tumors and various intraocular neovascular disorders. Such antibodics arc described, for example. in EP 817,648 published January 14. 1998 and in PCT/US 98/06724 filed April 3, 1998.

There exist several other growth factors and mitogens, including transforming oncogenes, that are capable of rapidly inducing a complex set of genes to be expressed by certain cells. I.au and Nathans, Molecular Aspects of

Cellular Regulation, 6: 165-202 (1991). These genes, which have been named immediate-early- or early-response . genes, are transcriptionally activated within minutes after contact with a growth factor or mitogen, independent of de novo protein synthesis. A group of these intermediate-early genes encodes secreted, extracellular proteins that are needed for coordination of complex biological processes such as differentiation and proliferation, regeneration, and wound healing. Ryseck er al., Cell Growth Differ., 2: 235-233 (1991).

Highly-related proteins that belong to this group include cef 10 (Simmons et al., Proc. Natl. Acad. Sci. USA, 86: 1178-1182 (1989)), cyr 61, which is rapidly activated by serum- or platelet-derived growth factor (PDGF) (O'Brien et al., Mol. Cell Biol., 10: 3569-3577 (1990), human connective tissue growth factor (CTGF) (Bradham etal, J. Cell. Biol, 114: 1285-1294 (1991)), which is secreted by human vascular endothelial cells in high levels after activation with transforming growth factor beta (TGF-p), exhibits PDGF-like biological and immunological activities, and competes with PDGF for a particular cell surface receptor, fisp-12 (Ryseck et al., Cell Growth

Differ.. 2: 235-233 (1991)), human vascular IBP-like growth factor (VIGF) (WO 96/17931), and nov, normally arrested in adult kidney cells, which was found to be overexpressed in myeloblastosis-associated-virus-type-1- induced nephroblastomas. Joloit et al., Mol. Cell. Biol., 12: 10-21 (1992).

The expression of these immediate-early genes acts as "third messengers" in the cascade of events triggered by growth factors. Itis also thought that they are needed to integrate and coordinate complex biological processes, such as differentiation and wound healing in which cell proliferation is a common event.

As additional mitogens, insulin-like growth factor binding proteins (IGFBPs) have been shown, in complex with insulin-like growth factor (IGF). to stimulate increased binding of IGF to fibroblast and smooth muscle cell surface receptors. Clemmons eral., I. Clin. Invest., 77: 1548 (1986). Inhibitory effects of IGFBP on various IGF actions in vitro include stimulation of glucose transport by adipocytes, sulfate incorporation by chondrocytes, and : thymidine incorporation in fibroblast. Zapf eral.,]. Clin. Invest., 63: 1077 (1979). In addition, inhibitory effects of IGI'BPs on growth factor-mediated mitogen activity in normal cells have been shown.

C. Need for Further Treatments

In view of the role of vascular endothelial cell growth and angiogenesis in many diseases and disorders, it is desirable to have a means of reducing or inhibiting one or more of the biological effects causing these processes.

Itis also desirable to have a means of assaying for the presence of pathogenic polypeptides in normal and discased conditions, and especially cancer. Further, in a specific aspect, as there is no generally applicable therapy for the treatment of cardiac hypertrophy, the identification of factors that can prevent or reduce cardiac myocyte hypertrophy is of primary importance in the development of new therapeutic strategies to inhibit pathophysiological cardiac growth. While there are several treatment modalities for various cardiovascular and oncologic disorders, there is still a need for additional therapeutic approaches.

Suminary of the Invention

A. Embodiments

Accordingly, the present invention concerns compositions and methods for promoting or inhibiting angiogenesis and/or cardiovascularization in mammals. The present invention is based on the identification of

: proteins that test positive in various cardiovascular assays that test promotion or inhibition of certain biological activities. Accordingly, the proteins are believed to be useful drugs for the diagnosis and/or treatment (including ) prevention) of disorders where such effects are desired, such as thc promotion or inhibition of angiogenesis, inhibition or stimulation of vascular endothelial cel} growth, stimulation of growth or proliferation of vascular endothelial cells, inhibition of tumor growth, inhibition of angiogenesis-dependent tissue growth, stimulation of angiogenesis-dependent tissue growth, inhibition of cardiac hypertrophy and stimulation of cardiac hypertrophy, e.g., for the treatment of congestive heart failure.

In one embodiment, the present invention provides a composition comprising a PRO polypeptide in admixture with a pharmaceutically acceptable carrier. In one aspect, the composition comprises a therapeutically effective amount of the polypeptide. In another aspect, the composition comprises a further active ingredient, namely, a cardiovascular, endothelial or angiogenic agent or an angiostatic agent, preferably an angiogenic or angiostatic agent. Preferably, the composition is sterile. The PRO polypeptide may be administered in the form of a liquid pharmaceutical formulation, which may be preserved to achieve extended storage stability. Preserved liquid pharmaceutical formulations might contain multiple doses of PRO polypeptide, and might, therefore, be suitable for repeated use.

In a further embodiment, the present invention provides a method for preparing such a composition useful for the treatment of a cardiovascular, endothelial or angiogenic disorder comprising admixing a therapeutically effective amount of a PRO polypeptide with a pharmaceutically acceptable carrier. - In another embodiment, the present invention provides a composition comprising an agonist or antagonist of a PRO polypeptide in admixture with a pharmaceutically acceptable carrier. In one aspect, the composition : comprises a therapeutically effective amount of the agonist or antagonist. In another aspect, the composition comprises a further active ingredient, namely, a cardiovascular, endothelial or angiogenic agent or an angiostatic agent, preferably an angiogenic or angiostatic agent. Preferably, the composition is sterile. The PRO polypeptide agonist or antagonist may be administered in the form of a liquid pharmaceutical formulation, which may bc } preserved to achieve extended storage stability. Preserved liquid pharmaceutical formulations might contain multiple doses of a PRO polypeptide agonist or antagonist, and might, therefore. be suitable for repeated use.

In a further embodiment, the present invention provides a method for preparing such a composition useful for the treatment of a cardiovascular, endothelial or angiogenic disorder comprising admixing atherapeutically effective amount of a PRO polypeptide agonist or antagonist with a pharmaceutically acceptable carrier.

In yet another embodiment, the present invention concerns a composition comprising an anti-PRO antibody in admixture with a pharmaceutically acceptable carrier. In one aspect, the composition comprises a therapeutically effective amount of the antibody. In another aspect, the composition comprises a further active ingredient, namely, a cardiovascular, endothelial or angiogenic agent or an angiostatic agent, preferably an angiogenic or angiostatic agent. Preferably, the composition is sterile. The composition may be administered in the form of a liquid pharmaceutical formulation, which may be preserved to achieve extended storage stability. Preserved liquid pharmaceutical formulations might contain multiple doses of the anti-PRO antibody, and might, therctore, be suitable for repeated use. In preferred embodiments, the antibody is a monoclonal antibody, an antibody fragment, a humanized antibody, or a single-chain antibody.

In a further embodiment, the present invention provides a method for preparing such a composition useful for . the treatment of a cardiovascular, endothelial or angiogenic disorder comprising admixing a therapeutically effective amount of an anti-PRO antibody with a pharmaceutically acceptable carrier.

In a still further aspect, the present invention provides an article of manufacture comprising: (a) a composition of matter comprising a PRO polypeptide or agonist or antagonist thereof; (b) a container containing said composition; and (c) alabel affixed to said container, or a package insert included in said container referring to the use of said

PRO polypeptide or agonist or antagonist thereof in the treatment of a cardiovascular, endothelial or angiogenic disorder, wherein the agonist or antagonist may be an antibody which binds to the PRO polypeptide. The composition may comprise a therapeutically effective amount of the PRO polypeptide or the agonist or antagonist thereof.

In another embodiment, the present invention provides a method for identifying an agonist of a PRO polypeptide comprising: (a) contacting cells and a test compound to be screened under conditions suitable for the induction of a cellular response normally induced by a PRO polypeptide; and (b) determining the induction of said cellular response to determine if the test compound is an effective agonist, wherein the induction of said cellular response is indicative of said test compound being an effective agonist.

In another embodiment, the present invention provides a method for identifying an agonist of a PRO polypeptide comprising: (a) contacting cells and a test compound to be screened under conditions suitable for the stimulation of cell : proliferation by a PRO polypeptide; and (b) measuring the proliferation of said cells to determine if the test compound js an effective agonist, wherein } the stimulation of ceil proliferation is indicative of said test compound bcing an effcctive agonist.

In another embodiment, the invention provides a method for identifying a compound that inhibits the activity of a PRO polypeptide comprising contacting a test compound with a PRO polypeptide under conditions and for a time sufficient to allow the test compound and polypeptide to interact and determining whether the activity of the

PRO polypeptide is inhibited. In a specific preferred aspect, either the test compound or the PRO polypeptide is immobilized on a solid support. In another preferred aspect, the non-immobilized component carries a detectable label. In a preferred aspect, this method comprises the steps of: (a) contacting cells and a test compound to be screened in the presence of a PRO polypeptide under conditions suitable for the induction of a cellular response normally induced by a PRO polypeptide; and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist.

In another preferred aspect, this process comprises the steps of” (a) contacting cells and a test compound to be screened in the presence of a PRO polypeptide under conditions suitable for the stimulation of cell proliferation by a PRO polypeptide; and (b) measuring the proliferation of the cells to determine if the test compound is an effective antagonist.

In another embodiment, the invention provides a method for identifying a compound that inhibits the expression of a PRO polypeptide in cells that normally expresses the polypeptide, wherein the method compriscs contacting the cells with a test compound and determining whether the expression of the PRO polypeptide is inhibited. In a preferred aspect, this method comprises the steps of: (a) contacting cells and a test compound to be screened under conditions suitable for allowing expression of the PRO polypeptide; and (b) determining the inhibition of expression of said polypeptide.

In a still further embodiment, the invention provides a compound that inhibits the expression of a PRO polypeptide, such as a compound that is identified by the methods set forth above.

Another aspect of the present invention is directed to an agonist or an antagonist of a PRO polypeptide which . may optionally be identified by the methods described above.

One type of antagonist of a PRO polypeptide that inhibits one or more of the functions or activities of the PRO polypeptide isan antibody. Hence, in another aspect, the invention provides an isolated antibody that binds a PRO polypeptide. In a preferred aspect, the antibody is a monoclonal antibody, which preferably has non-human complementarity-determining-region (CDR) residues and human framework-region (FR) residues. The antibody may be labeled and may be immobilized on a solid support. In a further aspect, the antibody is an antibody fragment, a single-chain antibody, or a humanized antibody. Preferably, the antibody specifically binds to the polypeptide.

In a still further aspect, the present invention provides a method for diagnosing a disease or susceptibility to a disease which is related to a mutation in a PRO polypeptide-encoding nucleic acid sequence comprising determining the presence or absence of said mutation in the PRO polypeptide nucleic acid sequence, wherein the presence or absence of said mutation is indicative of the presence of said disease or susceptibility to said disease. :

In a still further aspect, the invention provides a method of diagnosing a cardiovascular, endothelial or angiogenic disorder in a mammal which comprises analyzing the level of expression of a gene encoding a PRO polypeptide (a) in a test sample of tissue cells obtained from said mammal, and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher or lower expression level in the test sample as compared to the control sample is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in said mammal. The expression of a gene encoding a PRO polypeptide may optionally be accomplished by measuring the level of MRNA or the polypeptide in the test sample as compared to the control sample.

In a still further aspect, the present invention provides a method of diagnosing a cardiovascular, endothelial or angiogenic disorder in a mammal which comprises detecting the presence or absence of a PRO polypeptide in atest sample of tissue cells obtained from said mammal, wherein the presence or absence of said PRO polypeptide in said test sample is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in said mammal.

In a still further embodiment, the invention provides a method of diagnosing a cardiovascular. endothelial or angiogenic disorder in a mammal comprising (a) contacting an anti-PRO antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between the antibody and the PRO polypeptide in the test sample, wherein the formation of said complex is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in the mammal. The detection may be qualitative or quantitative, . and may be performed in comparison with monitoring the complex formation in a control sample of known normal tissue cells of the same cell type. A larger or smaller quantity of complexes formed in the test sample indicates the presence of a cardiovascular, endothelial or angiogenic dysfunction in the mammal from which the test tissue cells were obtained. The antibody preferably carries a detectable label. Complex formation can be monitored, for example, by light microscopy, flow cytometry, fluorimetry, or other techniques known in the art. The test sample is usually obtained from an individual suspected to have a cardiovascular, endothelial or angiogenic disorder.

In another embodiment, the invention provides a method for determining the presence of a PRO polypeptide in a sample comprising exposing a sample suspected of containing the PRO polypeptide to an anti-PRO antibody and determining binding of said antibody to a component of said sample. In a specific aspect, the sample comprises a cell suspected of containing the PRO polypeptide and the antibody binds to the cell. The antibody is preferably detectably labeled and/or bound to a solid support.

In further aspects, the invention provides a cardiovascular, endothelial or angiogenic disorder diagnostic kit comprising an anti-PRO antibody and a carrier in suitable packaging. Preferably, such kit further comprises instructions for using said antibody to detect the presence of the PRO polypeptide. Preferably, the carrier is a buffer, for example. Preferably, the cardiovascular, endothelial or angiogenic disorder is cancer.

In yet another embodiment, the present invention provides a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal an effective amount of a PRO polypeptide. Preferably, the disorder is cardiac hypertrophy, trauma such as wounds or burns, or a type of cancer.

In a further aspect, the mammal is further exposed to angioplasty or a drug that treats cardiovascular, endothelial or angiogenic disorders such as ACE inhibitors or chemotherapeutic agents if the cardiovascular, endothelial or : angiogenic disorder is a type of cancer. Preferably, the mammal is human, preferably one who is at risk of developing cardiac hypertrophy and more preferably has suffered myocardial infarction.

In another preferred aspect, the cardiac hypertrophy is characterized by the presence of an elevated level of

PGF,,. Alternatively, the cardiac hypertrophy may be induced by myocardial infarction, wherein preferably the administration of the PRO polypeptide is initiated within 48 hours, more preferably within 24 hours, following myocardial infarction.

In another preferred embodiment, the cardiovascular, endothelial or an giogenic disorder is cardiac hypertrophy and said PRO polypeptide is administered together with a cardiovascular. endothelial or angiogenic agent. The preferred cardiovascular, endothelial or angiogenic agent for this purpose is selected from the group consisting of an antihypertensive drug, an ACE inhibitor, an endothelin receptor antagonist and a thrombolytic agent. Ifa thrombolytic agent is administered, preferably the PRO polypeptide is administered following administration of such agent. More preferably, the thrombolvtic agent is recombinant human tissue plasminogen activator.

In another preferred aspect, the cardiovascular, endothelial or angiogenic disorder is cardiac hypertrophy and the PRO polypeptide is administered following primary angioplasty for the treatment of acute myocardial infarction, preferably wherein the mammal is further exposed to angioplasty or a cardiovascular. endothelial, or angiogenic agent.

In another preferred embodiment. the cardiovascular, endothelial or angiogenic disorder is a cancer and the 11

PRO polypeptide is administered in combination with a chemotherapeutic agent, a growth inhibitory agent or a cytotoxic agent. )

In a further embodiment, the invention concerns a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal an effective amount of an agonist of a

PRO polypeptide. Preferably, the cardiovascular, endothelial or angiogenic disorder is cardiac hypertrophy, trauma, a cancer, or age-related macular degeneration. Also preferred is where the mammal is human, and where an effective amount of an angiogenic or angiostatic agent is administered in conjunction with the agonist.

In a further embodiment, the invention concerns a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal an effective amount of an antagonist of a PRO polypeptide. Preferably, the cardiovascular, endothelial or angiogenic disorder is cardiac hypertrophy, trauma, a cancer, or age-related macular degeneration. Also preferred is where the mammal is human, and where an effective amount of an angiogenic or angiostatic agent is administered in conjunction with the antagonist.

In a further embodiment, the invention concerns a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal an effective amount of an anti-PRO antibody. Preferably, the cardiovascular, endothelial or angiogenic disorder is cardiac hypertrophy, trauma, a cancer, or age-related macular degeneration. Also preferred is where the mammal is human, and where an effective amount of an angiogenic or angiostatic agent is administered in conjunction with the antibody. . In still further embodiments, the invention provides a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal that suffers therefrom comprising administering to the mammal a nucleic acid molecule that codes for either (a) a PRO polypeptide, (b) an agonist of a PRO polypeptide or (c) an antagonist of ,. a PRO polypeptide, wherein said agonist or antagonist may be an anti-PRO antibody. In a preferred embodiment. the mammal is human. In another preferred embodiment, the gene is administered via ex vivo gene therapy. Ina : further preferred embodiment, the gene is comprised within a vector, more preferably an adenoviral, adeno-associated viral, lentiviral, or retroviral vector. }

In yet another aspect. the invention provides a recombinant retroviral particle comprising a retroviral vector consisting essentially of a promoter, nucleic acid encoding (a) a PRO polypeptide, (b) an agonist polypeptide of a

PRO polypeptide, or (c) an antagonist polypeptide of a PRO polypeptide, and a signal sequence for cellular secretion of the polypeptide, wherein the retroviral vector is in association with retroviral structural proteins.

Preferably, the signal sequence is from a mammal, such as from a native PRO polypeptide.

In a still further embodiment, the invention supplies an ex vivo producer cell comprising a nucleic acid construct that expresses retroviral structural proteins and also comprises a retroviral vector consisting essentially of a promoter, nucleic acid encoding (a) a PRO polypeptide, (b) an agonist polypeptide of a PRO polypeptide or (c) an antagonist polypeptide of a PRO polypeptide, and a signal sequence for cellular secretion of the polypeptide. wherein said producer cell packages the retroviral vector in association with the structural proteins to produce recombinant retroviral particles.

In yet another embodiment, the invention provides a method for inhibiting endothelial cell growth in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of a PRO polypeptide, or (c) an antagonist of a PRO polypeptide, wherein endothelial cell growth in said mammal is inhibited, and wherein said agonist or antagonist may be an anti-PRO antibody. Preferably, the mammal is human and the endothelial cell . growth is associated with a tumor or a retinal disorder.

In yet another embodiment, the invention provides a method for stimulating endothelial cell growth in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of a PRO polypeptide,

S or (c) an antagonist of a PRO polypeptide, wherein endothelial cell growth in said mammal is stimulated, and wherein said agonist or antagonist may be an anti-PRO antibody. Preferably, the mammal is human.

In yet another embodiment, the invention provides a method for inhibiting cardiac hypertrophy in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of a PRO polypeptide, or (c) an antagonist of a PRO polypeptide, wherein cardiac hypertrophy in said mammal is inhibited, and wherein said agonist or antagonist may be an anti-PRO antibody . Preferably, the mammal is human and the cardiac hypertrophy has been induced by myocardial infarction.

In yet another embodiment, the invention provides a method for stimulating cardiac hypertrophy in a mammal comprising administering to the mammal (a) a PRO polypeptide, (b) an agonist of a PRO polypeptide, or (c) an antagonist of a PRO polypeptide, wherein cardiac hypertrophy in said mammal is stimulated, and wherein said agonist or antagonist may be an anti-PRO antibody. Preferably, the mammal is human who suffers from congestive heart failure.

In yet another embodiment, the invention provides a method for inhibiting angiogenesis induced by a PRO polypeptide in a mammal comprising administering a therapeutically effective amount of an anti-PRO antibody to thc mammal. Preferably, the marnmal is a human, and more preferably the mammal has a tumor or a retinal disorder.

In yet another embodiment, the invention provides a method for stimulating angiogenesis induced by a PRO : polypeptide in a mammal comprising administering a therapeutically effective amount of a PRO polypeptide to the mammal. Preferably, the mammal is a human, and more preferably angiogeneisis would promote tissue regeneration or wound healing.

Tn yetanother embodiment, the invention provides a method forinhibiting endothelial cell growth in a mammal comprising administering to the mammal a PRO333, PRO364, PRO877. PRO879, PRO882 or PRO8S5 polypeptide or agonist thereof, wherein endothelial cell growth in said mammal is inhibited.

In yet another embodiment, the invention provides a method for stimulating endothelial cell growth in a mammal comprising administering to the mammal a PRO179, PRO321, PRO840, PRO844, PRO846, PRO8B7S8 or

PROZ79 polypeptide or agonist thereof, wherein endothelial cell growth in said mammal is stimulated.

In yet another embodiment, the invention provides a method for inhibiting endothelial cell growth in a mammal comprising administering to the mammal an antagonist of a PRO179, PRO321, PRO840, PRO844. PRO846,

PROB78 or PROB79 polypeptide, wherein endothelial cell growth in said mammal is inhibited.

In yet another embodiment, the invention provides a method for stimulating endothelial cell growth in a mammal comprising administering to the mammal an antagonist of a PRO333, PR0O364, PRO877. PRO879,

PRO882 or PRO88S polypeptide, wherein endothelial cell growth in said mammal is stimulated.

In yet another embodiment, the invention provides a method for inducing cardiac hypertrophy in a mammal comprising administering to the mammal a PRO205, PRO882 or PRO887 polypeptide or agonist thereof, wherein 13 4 i cardiac hypertrophy in said mammal is induced.

In yet another embodiment, the invention provides a method for reducing cardiac hypertrophy in a mammal } comprising administering to the mammal a PRO238, PRO878 or PRO1760 polypeptide or agonist thereof, wherein cardiac hypertrophy in said mammal is reduced.

In yet another embodiment, the invention provides a methed for inducing cardiac hypertrophy in 2 mammal comprising administering to the mammal an antagonist of a PR0O238, PRO878 or PRO1760 polypeptide, wherein cardiac hypertrophy in said mammal is induced.

In yet another embodiment, the invention provides a method for reducing cardiac hypertrophy in a mammal comprising administering to the mammal an antagonist of a PRO205, PRO882 or PRO887 polypeptide, wherein cardiac hypertrophy in said mammal is reduced.

In yetanother embodiment, the invention provides a method for inhibiting angiogenesis induced by aPRO179,

PRO321,PR0O840,PRO844, PRO846, PRO878 or PROST9 polypeptide comprising administering a therapeutically effective amount of an anti-PRO179, anti-PRO321, anti-PRO840), anti-PRO844, anti-PROR46, anti-PRO878 or anti-

PRO879 antibody to the mammal, wherein said angiogenesis is inhibited.

In yet another embodiment, the invention provides a method for stimulating angiogenesis induced by a

PRO179, PRO321, PRO840, PRO844, PRO846, PRO8B78 or PRO879 polypeptide comprising administering a therapeutically effective amount of said polypeptide to the mammal, wherein said angiogenesis is stimulated. i B. Additional Embodiments . 20 In other embodiments of the present invention, the invention provides an isolated nucleic acid molecule . comprising a nucleotide sequence that encodes a PRO polypeptide.

In one aspect, the isolated nucleic acid molecuie comprises a nucleotide sequence having at least about 80% : nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity and alternatively at least about 99% nucleic acid sequence identity to (a) a DNA molecule encoding a PRO polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fraginent of the full-length amino acid sequence as disclosed herein, or (b) the complement of the DNA molecule of (a). 14 h

In other aspects, the isolated nucleic acid molecule comprises a nucleotide sequence having at least about 80% . nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid scqucnce identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity and alternatively at least about 99% nucleic acid sequence identity to (a) a DNA molecule comprising the coding sequence of a full-length PRO polypeptide cDNA as disclosed herein, the coding sequence of a PRO polypeptide lacking the signal peptide as disclosed herein, the coding sequence of an extracellular domain of a transmembrane PRO polypeptide, with or without the signal peptide, as disclosed herein or the coding sequence of any other specifically defined fragment of the full-length amino acid sequence as disclosed herein, or (b) the complement of the DNA molecule of (a).

In afurther aspect, the invention concerns an isolated nucleic acid molecule comprising a nucleotide sequence having at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% : nucleic acid sequence identity, alternatively at least about 86% nucleic acid sequence identity, alternatively at least about 87% nucleic acid sequence identity, alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity, alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity, alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nuclcic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity. alternatively at least about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity and alternatively at least about 99% nucleic acid sequence identity to (a) a DNA molecule that encodes the same mature polypeptide encoded by any of the human protcin cDNAs deposited with the ATCC as disclosed herein, or (b) the complement of the DNA molecule of (a).

Another aspect the invention provides an isolated nucleic acid molecule comprising a nucleotide sequence encoding aPRO polypeptide which is either transmembrane domain-deleted or transmembrane domain-inactivated, or is complementary to such encoding nucleotide sequence, wherein the transmembrane domain(s) of such polypeptide are disclosed herein. Therefore. soluble extracellular domains of the herein described PRO polypeptides are contemplated.

Another embodiment is directed to fragments of a PRO polypeptide coding sequence, or the complement thereof, that may find use as, for example, hybridization probes, for encoding fragments of a PRO polypeptide that may optionally encode a polypeptide comprising a binding site for an anti-PRO antibody or as antisense ] oligonucleotide probes. Such nucleic acid fragments are usually at least about 20 nucleotides in length, alternatively at least about 30 nucleotides in length, alternatively at least about 40 nucleotides in length, alternatively at least about 50 nucleotides in length, alternatively at least about 60 nucleotides in length, alternatively at least about 70 nucleotides in length, alternatively at Icast about 80 nucleotides in length, alternatively at least about 90 nucleotides in length, alternatively at least about 100 nucleotides in length, alternatively at least about 110 nucleotides in length, alternatively at least about 120 nucleotides in length, alternatively at least about 130 nucleotides in length, alternatively at least about 140 nucleotides in length, alternatively at least about 150 nucleotides in length, alternatively at least about 160 nucleotides in length, alternatively at least about 170 nucleotides in length, } alternatively at least about 180 nucleotides in length, alternatively at least about 190 nucleotides in length, alternatively at least ahout 200 nucleotides in length, alternatively at least about 250 nucleotides in length, alternatively at least about 300 nucleotides in length, alternatively at least about 350 nucleotides in length, alternatively at least about 400 nucleotides in length, alternatively at least about 450 nucleotides in length, . 15 alternatively at least about 500 nucleotides in length, alternatively at least about 600 nucleotides in length, alternatively at least about 700 nucleotides in length, alternatively at least about 800 nucleotides in length, : alternatively at least about 900 nucleotides in length and alternatively at least about 1000 nucleotides in length, . wherein in this context the term "about" means the referenced nucleotide sequence length plus or minus 10% of that - referenced length. It is noted that novel fragments of a PRO polypeptide-encoding nucleotide sequence may be determined in a routine manner by aligning the PRO polypeptide-encoding nucleotide sequence with other known nucleotide sequences using any of a number of well known sequence alignment programs and determining which

PRO polypeptide-encoding nucleotide sequence fragment(s) are novel. All of such PRO polypeptide-encoding nucleotide sequences are contemplated herein. Also contemplated are the PRO polypeptide fragments encoded by these nucleotide molecule fragments, preferably those PRO polypeptide fragments that comprise a binding site for an anti-PRO antibody.

In another embodiment, the invention provides isolated PRO polypeptide encoded by any of the isolated nucleic acid sequences hereinabove identified.

In a certain aspect, the invention concerns an isolated PRO polypeptide, comprising an amino acid sequence having ar least about 80% amino acid sequence identity, alternatively at least about 81% amino acid sequence identity, alternatively at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity. alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% amino acid sequence identity, alternatively at least about 87% amino acid sequence identity, alternatively at least about 88% amino acid sequence identity. alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity. alternatively at least about 91% amino acid scquence identity, alternatively at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity. alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity and alternatively at least about 99% amino acid sequence identity to a PRO . polypeptide having a full-length amino acid sequence as disclosed herein, an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of the full-length amino acid sequence as disclosed herein.

In a further aspect, the invention concerns an isolated PRO polypeptide comprising an amino acid sequence having at least about 80% amino acid sequence identity. alternatively at least about 81% amino acid sequence identity, alternatively at least about 82% amino acid sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% amino acid sequence identity, alternatively at least about 87% amino acid sequence identity, alternatively at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91% amino acid sequence identity, alternatively at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity. alternatively at least about 94% amino acid sequence identity, alternatively at least about 95% amino acid sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid scquence identity and alternatively at least about 99% amino acid sequence identity to an .. amino acid sequence encoded by any of the human protein cDNAs deposited with the ATCC as disclosed herein.

In a further aspect, the invention concerns an isolated PRO polypeptide comprising an amino acid sequence

LL 20 scoring at least about 80% positives, alternatively at least about 81% positives, alternatively at least about 82% positives, alternatively at least about 83% positives, alternatively at least about 84% positives, alternatively at least : about 85% positives, alternatively at least about 86% positives, alternatively at least about 87% positives, alternatively at least about 88% positives, alternatively at least about 89% posilives, alternatively at least about 90% positives, alternatively at least about 91% positives, alternatively at least about 92% positives, alternatively at least about 93% positives, alternatively at least about 94% positives, alternatively at least about 95% positives, alternatively at least about 96% positives, alternatively at least about 97% positives, alternatively at least about 98% positives and alternatively at least about 99% positives when compared with the amino acid sequence of a PRO polypeptide having a full-length amino acid sequence as disclosed herein. an amino acid sequence lacking the signal peptide as disclosed herein, an extracellular domain of a transmembrane protein, with or without the signal peptide, as disclosed herein or any other specifically defined fragment of the full-length amino acid sequence as disclosed herein.

In a specific aspect, the invention provides an isolated PRO polypeptide without the N-terminal signal sequence and/or the initiating methionine and is encoded by a nucleotide sequence that encodes such an amino acid sequence as hereinbefore described. Processes for producing the same are also herein described, wherein those processcs comprise culturing a host cell comprising a vector which comprises the appropriate encoding nucleicacid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.

Another aspect the invention provides an isolated PRO polypeptide which is either transmembrane domain-deleted or transmembrane domain-inactivated. Processes for producing the same are also herein described, wherein those processes comprise culturing a host cell comprising a vector which comprises the appropriate . encoding nucleic acid molecule under conditions suitable for expression of the PRO polypeptide and recovering the PRO polypeptide from the cell culture.

In yet another embodiment, the invention concerns agonists and antagonists of a native PRO polypeptide as defined herein. In a particular embodiment, the agonist or antagonist is an anti-PRO antibody ur a small molecule.

In a further embodiment, the invention concerns a method of identifying agonists or antagonists to a PRO polypeptide which comprise contacting the PRO polypeptide with a candidate molecule and monitoring a biological activity mediated by said PRO polypeptide. Preferably, the PRO polypeptide is a native PRO polypeptide.

In a stilt further embodiment, the invention concerns a composition of matter comprising a PRO polypeptide, or an agonist or antagonist of a PRO polypeptide as herein described, or an anti-PRO antibody, in combination with a carrier. Optionally, the carrier is a pharmaceutically acceptable carrier.

Another embodiment of the present invention is directed to the use of a PRO polypeptide, or an agonist or antagonist thereof as hereinbefore described, or an anti-PRO antibody, for the preparation of a medicament useful in the treatment of a condition which is responsive to the PRO polypeptide, an agonist or antagonist thereof or an anti-PRO antibody.

In additional embodiments of the present invention, the invention provides vectors comprising DNA encoding any of the herein described polypeptides. Host cell comprising any such vector are also provided. By way of example, the host cells may be CHO cells, E. coli, yeast, or Baculovirus-infected insect cells. A process for producing any of the herein described polypeptides is further provided and comprises culturing host cells under conditions suitable for expression of the desired polypeptide and recovering the desired polypeptide from the cell culture. )

In other embodiments, the invention provides chimeric molecules comprising any of the herein described polypeptides fused to a heterologous polypeptide or amino acid sequence. Example of such chimeric molecules comprise any of the herein described polypeptides fused to an epitope tag sequence or a Fc region of an immunoglobulin.

In yet another embodiment, the invention provides an antibody which specifically binds 10 any of the above or below described polypeptides. Optionally, the antibody is a monocional antibody. humanized antibody, antibody fragment or single-chain antibody.

In yet other embodiments, the invention provides oligonucleotide probes useful for isolating genomic and ¢DNA nucleotide sequences or as antisense probes, wherein those probes may be derived from any of the above or below described nucleotide sequences.

Figure 1 shows a nucleotide sequence (SEQ ID NO:1) of a native sequence PRO179 cDNA. wherein SEQ

ID NO:1 is a clone designated herein as “DNA16451-1388".

Figure 2 shows the amino acid sequence (SEQ ID NO:2) derived from the coding sequence of SEQ ID NO:) shown in Figure 1.

Figure 3 shows a nucleotide sequence (SEQ ID NO:3) of a native sequence PRO238 cDNA, wherein SEQ . ID NO:3 is a clone designated herein as “DNA35600-1162".

Figure 4 shows the amino acid sequence (SEQ ID NO:4) derived from the coding sequence of SEQ TD NO:3 shown in Figure 3.

Figure 5 shows a nucleotide sequence (SEQ ID NO:5) of a native sequence PRO364 cDNA, wherein SEQ

ID NO:5 is a clone designated herein as “DNA47365-1206".

Figure 6 shows the amino acid sequence (SEQ ID NO:6) derived from the coding sequence of SEQ ID NO:5 shown in Figure 5.

Figure 7 shows a nucleotide sequence (SEQ ID NO:7) of a native sequence PRO844 cDNA, wherein SEQ

ID NO:7 is a clone designated herein as “DNAS59838-1462",

Figure 8 shows the amino acid sequence (SEQ ID NO:8) derived from the coding sequence of SEQ ID NO:7 shown in Figure 7.

Figure 9 shows a nucleotide sequence (SEQ ID NO:9) of a native sequence PRO846 cDNA, wherein SEQ

ID NO:9 is a clone designated herein as “DNA44196-1353".

Figure 10 shows the amino acid sequence (SEQ ID NO:10) derived from the coding sequence of SEQ ID

NO:9 shown in Figure 9.

Figure 11 shows a nucleotide sequence (SEQ ID NO: 11) of a native sequence PRO1760cDNA, wherein SEQ

ID NO:11 is a clone designated herein as “DNA76532-1702".

Figure 12 shows the amino acid sequence (SEQ ID NO:12) derived from the coding sequence of SEQ ID

NO:11 shown in Figure 11.

Figure 13 shows a nucleotide sequence (SEQ ID NO: 13) of a native sequence PRO20S5 cDNA, wherein SEQ : ID NO:13 is a clone designated herein as “DNA30868".

Figure 14 shows the amino acid sequence (SEQ ID NO: 14) derived from the coding sequence of SEQ ID } NO:13 shown in Figure 13.

Figure 15 shows a nucleotide sequence (SEQ ID NO: 15) of a native sequence PRO32! cDNA, wherein SEQ

ID NO:15 is a clone designated herein as “DNA34433".

Figure 16 shows the amino acid sequence (SEQ ID NO: 16) derived from the coding sequence of SEQ ID

NO:15 shown in Figure 15.

Figure 17 shows a nucleotide sequence (SEQ ID NO:17) of a native sequence PRO333 cDNA, wherein SEQ

ID NO:17 is a clone designated herein as “DNA41374".

Figure 18 shows the amino acid sequence (SEQ ID NO:18) derived from the coding sequence of SEQ ID

NO:17 shown in Figure 17.

Figure 19 shows a nucleotide sequence (SEQ ID NO: 19) ot a native sequence PRO840 cDNA, wherein SEQ

ID NO:19 is a clone designated herein as “DNAS53987".

Figure 20 shows the amino acid sequence (SEQ ID NO:20) derived from the coding sequence of SEQ ID

NO:19 shown in Figure 19.

Figure 21 shows a nucleotide sequence (SEQ ID NO:21) of a native sequence PRO877 cDNA, wherein SEQ

ID NO:21 is a clone designated herein as “DNAS58120".

Figure 22 shows the amino acid sequence (SEQ ID NO:22) derived from the coding sequence of SEQ ID

NO:21 shown in Figure 21. .

Figure 23 shows 4 nucleotide sequence (SEQ ID NO:23) of a native sequence PRO878 cDNA, wherein SEQ

ID NQ:23 is a clone designated herein as “DNAS8121".

Figure 24 shows the amino acid sequence (SEQ ID NO:24) derived from the coding sequence of SEQ ID

NO:23 shown in Figure 23. - Figure 25 shows a nucleotide sequence (SEQ ID NO:25) of a native sequence PRO879 cDNA, wherein SEQ . ID NO:25 1s a clone designated herein as “DNAS8122". - Figure 26 shows the amino acid sequence (SEQ ID NO:26) derived from the coding sequence of SEQ ID

NO:25 shown in Figure 25.

Figure 27 shows a nucleotide sequence (SEQ ID NO:27) of a native sequence PRO882 cDNA, wherein SEQ

ID NO:27 1s a clone designated herein as “DNAS8125".

Figure 28 shows the amino acid sequence (SEQ ID NO:28) derived from the coding sequence of SEQ ID

NO:27 shown in Figure 27. - Figure 29 shows a nucleotide sequence (SEQ ID NO:29) of a native sequence PRO885 cDNA, wherein SEQ

ID NO:29 is a clone designated herein as “DNAS8128". _ Figure 30 shows the amino acid sequence (SEQ ID NO:30) derived from the coding sequence of SEQ ID - NO:29 shown in Figure 29. - - Figure 3] shows a nucleotide sequence (SEQ ID NO:31) of a native sequence PRO887 cDNA, wherein SEQ

R 20 ID NO:31 is a clone designated herein as “DNAS58130".

Figure 32 shows the amino acid sequence (SEQ ID NO:32) derived from the coding sequence of SEQ ID

NO:31 shown in Figure 31.

Detailed Description of the Invention . 25 I. Definitions

The phrases "cardiovascular, endothelial and angiogenic disorder”, "cardiovascular, endothelial and angiogenic dysfunction”, “cardiovascular, endothelial or angiogenic disorder” and “cardiovascular, endothelial or angiogenic dysfunction” are used interchangeably and refer in part to systemic disorders that affect vessels, such as diabetes mellitus, as well as diseases of the vessels themselves, such as of the arteries, capillaries, veins, and/or 30 lymphatics. This would include indications that stimulate angiogenesis and/or cardiovascularization, and those that inhibit angiogenesis and/or cardiovascularization. Such disorders include. for example, arterial disease, such as atherosclerosis, hypertension, inflammatory vasculitides, Reynaud's disease and Reynaud's phenomenon, aneurysms, and artcrial restenosis; venous and lymphatic disorders such as thrombophlebitis. lymphan gitis, and lymphedema: and other vascular disorders such as peripheral vascular disease, cancer such as vascular tumors, e.8., hemangioma 35 (capillary and cavernous), glomus tumors, telangiectasia, bacillary angiomatosis, hemangioendothelioma, angiosarcoms, haemangiopericytoma, Kaposi's sarcoma, lymphangioma, and lymphangiosarcoma, tumor angiogenesis, trauma such as wounds, burns, and other injured tissue, implant fixation, scarring, ischemia reperfusion injury, rheumatoid arthritis, cercbrovascular discase, renal diseases such as acute renal fatlure, and osteoporosis.

This would also include angina, myocardial infarctions such as acute myocardial infarctions, cardiac . hypertrophy, and heart failure such as CHF.

“Hypertrophy”, as used herein, is defined as an increase in mass of an organ or structure independent of natural growth that does not involve tumor formation.

Hypertrophy of an organ or tissuc is due either to an increase in the mass of the individual cells (true hypertrophy), or to an increase in the number of cells making up the tissue (hyperplasia), or both.

Certain organs, such as the heart, lose the ability to divide shortly after birth.

Accordingly,

“cardiac hypertrophy” is defined as an increase in mass of the heart, which, in adults, is characterized by an increase in myocyte cell size and contractile protein content without concomitant cell division.

The character of the stress responsible for inciting the hypertrophy, (e.g., increased preload, increased afterload, loss of myocytes, as in myocardial infarction, or primary depression of contractility), appears to play a critical role in determining the nature of the response.

The early stage of cardiac hypertrophy is usually characterized morphologically by increases in the size of myofibrils and mitochondria, as well as by enlargement of mitochondria and nuclei.

At this stage, while muscle cells are larger than normal, cellular organization is largely preserved.

At amore advanced stage of cardiac hypertrophy, there are preferential increases in the size or number of specific organelles, such as mitochondria, and new contractile elements are added in localized areas of the cells, in an irregular manncr.

Cells subjected to long- standing hypertrophy show more obvious disruptions in cellular organization, including markedly enlarged nuclei with highly lobulated membranes, which displace adjacent myofibrils and cause breakdown of normal Z-band registration.

The phrase “cardiac hypertrophy” is used to include all stages of the progression of this condition, characterized by various degrees of structural damage of the heart muscle, regardless of the underlying cardiac disorder.

Hence, the tern also includes physiological conditions instrumental in the development of cardiac hypertrophy, such as elevated blood pressure, aortic stenosis, or myocardial infarction.

) “Heart failure” refers to an abnormality of cardiac function where the heart does not pump blood at the rate needed for the requirements of metabolizing tissues.

The heart failure can be caused by a number of factors, } including ischemic, congenital, rheumatic, or idiopathic forms.

“Congestive heart failure” (CHF) is a progressive pathologic state where the heart is increasingly unable to supply adequate cardiac output (the volume of blood pumped by the heart over time) to deliver the oxygenated blood to peripheral tissues.

As CHF progresses, structural and hemodynamic damages occur.

While these damages have a variety of manifestations, one characteristic symptom is ventricular hypertrophy.

CHF is a common end result of a number of various cardiac disorders.

“Myocardial infarction” generally results from atherosclerosis of the coronary arteries, often with superimposed coronary thrombosis.

It may be divided into two major types: transmural infarcts, in which myocardial necrosis involves the full thickness of the ventricular wall. and subendocardial (nontransmural) infarcts, in which the necrosis involves the subendocardium, the intramural myocardium, or both, without extending all the way through the ventricular wall to the epicardium.

Myocardial infarction is known to cause both a change in hemodynamic effects and an alteration in structure in the damaged and healthy zones of the heart.

Thus, for example, myocardial infarction reduces the maximum cardiac output and the stroke volume of the heart.

Also associated with myocardial infarction is a stimulation of the DNA synthesis occurring in the interstice as well as an increase in the formation of collagen in the areas of the heart not affected.

21 i

As a result of the increased stress or strain placed on the heart in prolonged hypertension due, for example, to the increased total peripheral resistance, cardiac hypertrophy has long been associated with “hypertension”. A . characteristic of the ventricle that becomes hypertrophic as a result of chronic pressure overload is an impaired diastolic performance. Fouad er al., J. Am. Coll. Cardiol., 4: 1500-1506 (1984); Smith et al.. J. Am. Coll. Cardiol., 2: 869-874 (1985). A prolonged left ventricular relaxation has been detected in early essential hypertension, in spite . of normal or supranormal systolic function. Hartford et al., Hypertension, 6: 329-338 (1984). However, there is - no close parallelism between blood pressure levels and cardiac hyperrophy. Although improvement in left ventricular function in response to antihypertensive therapy has been reported in humans, patients variously treated with a diuretic (hydrochlorothiazide), a -blocker (propranolol), or a calcium channel blocker (diltiazem), have

Rr 10 shown reversal of left ventricular hypertrophy, without improvement in diastolic function. Inouye eral, Am. J. - Cardiol., 53: 1583-7 (1984).

Another complex cardiac disease associated with cardiac hypertrophy is “hypertrophic cardiomyopathy”. This condition is characterized by a great diversity of morphologic, functional, and clinical features (Maron et al., N.

Engl. J. Med, 316: 780-789 (1987); Spirito etal., N. Engl. J. Med., 320: 749-755 (1989); Louie and Edwards, Prog.

Cardiovasc. Dis, 36: 275-308 (1994); Wigle er al., Circulation, 92: 1680-1692 (1995)), the heterogeneity of which is accentuated by the fact that it afflicts patients of all ages. Spirito ez al., N. Engl. J. Med., 336: 775-785 (1997). n The causative factors of hypertrophic cardiomyopathy are also diverse and little understood. In general, mutations : in genes encoding sarcomeric proteins are associated with hypertrophic cardiomyopathy. Recent data suggest that } B-myosin heavy chain mutations may account for approximately 30 to 40 percent of cases of familial hypertrophic ) 20 cardiomyopathy. Watkins etal., N. Engl. J. Med., 326: 1108-1114 (1992); Schwartz et al, Circulation, 91: 532-540 - (1995); Marian and Roberts, Circulation, 92: 1336-1347 (1995); Thierfelder er al., Cell, 77: 701-712 (1994);

Watkins et al, Nat. Gen, 11: 434-437 (1995). Besides B-myosin heavy chain, other locations of genetic mutations : include cardiac troponin T, alpha topomyosin, cardiac myosin binding protein C, essential myosin light chain, and regulatory myosin light chain. See, Malik and Watkins, Curr. Opin. Cardiol., 12: 295-302 (1997).

Supravalvular “aortic stenosis” is an inherited vascular disorder characterized by narrowing of the ascending aorta, but other arteries, including the pulmonary arteries, may also bc affected. Untreated aortic stenosis may lead to increased intracardiac pressure resulting in myocardial hypertrophy and eventually heart failure and death. The pathogenesis of this disorder is not fully understood, but hypertrophy and possibly hyperplasia of medial smooth muscle are prominent features of this disorder. It has been reported that molecular variants of the elastin gene are involved in the development and pathogenesis of aortic stenosis. U.S. Patent No. 5,650,282 issued July 22, 1997. “Valvular regurgitation” occurs as a result of heart diseases resulting in disorders of the cardiac valves.

Various diseases, like rheumatic fever, can cause the shrinking or pulling apart of the valve orifice. while other diseases may result in endocarditis, an inflammation of the endocardium or lining membrane of the atrioventricular orifices and operation of the heart. Defects such as the narrowing of the valve stenosis or the defective closing of the valve result in an accumulation of blood in the heart cavity or regurgitation of blood past the valve. If uncorrected, prolonged vaivular stenosis or insufficiency may result in cardiac hypertrophy and associated damage to the heart muscle, which may eventually necessitate valve replacement.

The treatment of all these, and other cardiovascular, endothelial and angiogenic disorders. which may or may

. . not be accompanied by cardiac hypertrophy, is encompassed by the present invention. . ‘The terms "cancer", "cancerous”, and "malignant" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. Examples of cancer include but are not limited to, carcinoma including adenocarcinoma, lymphoma, blastoma, melanoma, sarcoma, and leukemia. More particular examples of such cancers include squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, gastrointestinal cancer, Hodgkin's and non-Hodgkin's lymphoma, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer such as hepatic carcinoma and hepatoma, bladder cancer, breast cancer, colon cancer, colorectal cancer, endometrial carcinoma, salivary gland carcinoma, kidney cancer such as renal cell carcinoma and

Wilms’ tumors, basal cell carcinoma, melanoma, prostate cancer, vulval cancer, thyroid cancer, testicular cancer, esophageal cancer, and various types of head and neck cancer. The preferred cancers for treatment herein are breast, colon, lung, melanoma, ovarian, and others involving vascular tumors as noted above.

The term "cytotoxic agent” as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., ‘*'I, '*°, *Y, and '*Re), chemotherapeutic agents, and toxins such as enzymatically active toxins of bacterial, fungal, plant, or animal origin, or fragments thereof.

A "chemotherapeutic agent” is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents, folic acid antagonists, anti-metabolites of nucleic acid : metabolism, antibiotics, pyrimidine analogs, 5-fluorouracil, cisplatin, purine nucleosides, amines, amino acids, triazol nucleosides, or corticosteroids. Specific examples include Adriamycin, Doxorubicin, 5-Fluorouracil,

Cytosine arabinoside ("Ara-C"), Cyclophosphamide, Thiotepa, Busulfan, Cytoxin, Taxol, Toxotere, Methotrexate,

Cisplatin, Melphalan, Vinblastine, Bleomycin, Etoposide, Ifosfamide, Mitomycin C. Mitoxantrone, Vincreistine,

Vinorelbine, Carboplatin, Teniposide, Daunomycin, Carminomycin, Aminopterin, Dactinomycin, Mitomycins,

Esperamicins (see U.S. Pat. No. 4,675,187), Melphalan, and other related nitrogen mustards. Also included in this . definition are hormonal agents that act to regulate or inhibit hormone action on tumors, such as tamoxifen and ~ 25 onapristone.

A "growth-inhibitory agent” when used herein refers to a compound or composition that inhibits growth of a cell, such as an Wnt-overexpressing cancer cell, either in vitro or in vivo. Thus, the growth-inhibitory agent is one which significantly reduces the percentage of malignant cells in S phase. Examples of growth-inhibitory agents include agents that block cell cycle progression (at a place other than S phase), such as agents that induce G1 arrest and M-phase arrest. Classical M-phase blockers include the vincas (vincristine and vinblastine), taxol, and topo

II inhibitors such as doxorubicin, daunorubicin, etoposide, and bleomycin. Those agents that arrest G1 also spill over into S-phase arrest, for example, DNA alkylating agents such as tamoxifen, prednisone, dacarbazine, mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C. Further information can be found in The

Molecular Basis of Cancer, Mendelsohn and Israel, eds., Chapter 1, entitled "Cell cycle regulation, oncogenes, and antineoplastic drugs” by Murakami er al. (WB Saunders: Philadelphia, 1995), especially p. 13. Additional examples include wmor necrosis factor (TNF). an antibody capable of inhibiting or neutralizing the angiogenic activity of acidic or basic FGF or hepatocyte growth factor (HGF), an antibody capable of inhibiting or neutralizing the coagulant activities of tissue facior, protein C, or protein S (see, WO 91/01753, published 21 February 1991), or 23

L an antibody capable of binding to HER? receptor (WO 89/06692), such as the 4DS5 antibody (and functional equivalents thereof) (e.g.. WO 92/22653). . “Treatment” is an intervention performed with the intention of preventing the development or altering the pathology of a cardiovascular, endothelial, and angiogenic disorder. The concept of treatment is used in the broadest sense, and specifically includes the prevention (prophylaxis), moderation, reduction, and curing of cardiovascular, endothelial, and angiogenic disorders of any stage. Accordingly, “treatment” refers to both . therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) a cardiovascular, endothelial, and angiogenic disorder such as hypertrophy. Those in need of treatment include those already with the disorder as well as those prone to have the disorder or those in whom the disorder . 10 is to be prevented. The disorder may result from any cause, including idiopathic, cardiotrophic, or myotrophic } causes, or ischemia or ischemic insults, such as myocardial infarction. "Chronic" administration refers to administration of the agent(s) in a continuous mode as opposed to an acute mode, so as to maintain the initial effect, such as an anti-hypertrophic effect, for an extended period of time. "Mammal" for purposes of treatment refers to any animal classified as a mammal, including humans, domestic - 15 and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, sheep, pigs, etc. Preferably, the mammal is human.

Administration “in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.

The phrase “cardiovascular, endothelial or angiogenic agents” refers generically to any drug that acts in - 20 treating cardiovascular, endothelial. and angiogenic disorders. Examples of cardiovascular agents are those that - promote vascular homeostasis by modulating blood pressure, heart rate, heart contractility, and endotheljal and smooth muscle biology, all of which factors have a role in cardiovascular disease. Specific examples of these include angiotensin-II receptor antagonists; endothelin receptor antagonists such as, for example. BOSENTAN™ and MOXONODIN™; interferon-gamma (IFN-y); des-aspartate-angiotensin I; thrombolytic agents, e.g., } streptokinase, urokinase, t-PA, and a t-PA variant specifically designed to have longer half-life and very high fibrin specificity, TNK t-PA (a T103N, N117Q, KHRR(296-299)AAA A t-PA variant, Keyt et al, Proc. Natl. Acad. Sci.

USA, 91: 3670-3674 (1994)); inotropic or hypertensive agents such as digoxigenin and B-adrenergic receptor blocking agents, e.g., propranolol, timolol, tertalolol, carteolol, nadolol, betaxolol, penbutolol, acetobutolol, atenolol, metoprolol, and carvedilol; angiotensin converting enzyme (ACE) inhibitors, e.g., quinapril, captopril, enalapril, ramipril, benazepril, fosinopril, and lisinopril; diuretics, e.¢.. chlorothiazide, hydrochlorothiazide. hydroflumethazide, methylchlothiazide, benzthiazide, dichlorphenamide. acetazolamide, and indapamide; and calcium channel blockers, e.g., diltiazem, nifedipine, verapamil, nicardipine. One preferred category of this type is a therapeutic agent used for the treatment of cardiac hypertrophy or of a physiological condition instrumental in the development of cardiac hypertrophy, such as elevated blood pressure. aortic stenosis, or myocardial infarction. "Angiogenic agents" and "endothelial agents" arc active agents that promote angiogenesis and/or endothelial cell growth, or. if applicable, vasculogenesis. This would include factors that accelerate wound healing, such as growth hormone, insulin-like growth factor-1 (IGF-1), VEGF, VIGF. PDGF. epidermal growth factor (EGF),CTGF and members of its family, FGF, and TGF-a and TGF-f.

"Angiostatic agents” are active agents that inhibit angiogenesis or vasculogenesis or otherwise inhibit or . prevent growth of cancer cells. Examples include antibodies or other antagonists to angiogenic agents as defined above, such as antibodies to VEGF. They additionally include cytotherapeutic agents such as cytotoxic agents, chemotherapeutic agents, growth-inhibitory agents, apoptotic agents, and other agents to treat cancer, such as anti-

HER-2, anti-CD20, and other bioactive and organic chemical agents.

In a pharmacological sense, in the context of the present invention, a "therapeutically effective amount” of an active agent such as a PRO polypeptide or agonist or antagonist thereto or an anti-PRO antibody, refers to an amount effective in the treatment of a cardiovascular, endothelial or angiogenic disorder in a mammal and can be determined empirically.

As used herein, an “effective amount” of an active agent such as a PRO polypeptide or agonist or antagonist thereto or an anti-PRO antibody, refers to an amount effective for carrying out a stated purpose, whercin such amounts may be determined empirically for the desired effect.

The terms "PRO polypeptide” and "PRO" as used herein and when immediately followed by a numerical designation refer to various polypeptides, wherein the complete designation (i.e., PRO/number) refers to specific polypeptide sequences as described herein. The terms "PRO/number polypeptide” and "PRO/number" wherein the term “number” is provided as an actual numerical designation as used herein encompass native sequence polypeptides and polypeptide variants (which are further defined herein). The PRO polypeptides described herein : may be isolated from a varicty of sources, such as from human tissue types or from another source, or prepared by recombinant or synthetic methods.

A "native sequence PRO polypeptide” comprises a polypeptide having the same amino acid sequence as the corresponding PRO polypeptide derived from nature. Such native sequence PRO polypeptides can bc isolated from ) nature or can be produced by recombinant or synthetic means. The term "native sequence PRO polypeptide” specifically encompasses naturally-occurring truncated or secreted forms of the specific PRO polypeptide (e.g.. an extracellular domain sequence), naturally-occurring variant forms (e.g., alternatively spliced forms) and naturally-occurring allelic variants of the polypeptide. In various cmbodiments of the invention, the native sequence

PRO polypeptides disclosed herein are mature or full-length native sequence polypeptides comprising the full-length amino acids sequences shown in the accompanying figures. Start and stop codons are shown in bold font and underlined in the figures. However, while the PRO polypeptide disclosed in the accompanying figures are shown to begin with methionine residues designated herein as amino acid position | in the figures, it is conceivable and possible that other methionine residues located either upstream or downstream from the amino acid position | in the figures may be employed as the starting amino acid residue for the PRO polypeptides.

The PRO polypeptide "extracellular domain" or "ECD" refers to a form of the PRO polypeptide which is essentially free of the transmembrane and cytoplasmic domains. Ordinarily, a PRO polypeptide ECD will have less than 1% of such transmembrane and/or cytoplasmic domains and preferably, will have less than 0.5% of such domains. It will be understood that any transmembrane domains identified for the PRO polypeptides of the present invention are identified pursuant to criteria routinely employed in the art tor identifying that type of hydrophobic domain. The exact boundaries of a transmembrane domain may vary but most likely by no more than about 5 amino acids at either end of the domain as initially identified herein. Optionally, therefore, an extracellular domain of a

PRO polypeptide may contain from about 5 or fewer amino acids on either side of the transmembrane domain/extracellular domain boundary as identified in the Examples or specification and such polypeptides, with . or without the associated signal peptide, and nucleic acid encoding them, are comtemplated by the present invention.

The approximate location of the "signal peptides” of the various PRO polypeptides disclosed herein are shown in the present specification and/or the accompanying figures. It is noted, however, that the C-terminal boundary of a signal peptide may vary, but most likely by no more than about 5 amino acids on either side of the signal peptide C-terminal boundary as initially identified herein, wherein the C-terminal boundary of the signal peptide may be identified pursuant to criteria routinely employed in the art for identifying that type of amino acid sequence element (e.g., Nielsen et al., Prot. Eng., 10:1-6 (1997) and von Heinje et al., Nucl. Acids Res., 14:4683-4690 (1986)). Moreover, it is also recognized that, in some cases, cleavage of a signal sequence from a secreted polypeptide is not entirely uniform, resulting in more than one secreted species. These mature polypeptides, where the signal peptide is cleaved within no more than about 5 amino acids on either side of the C-terminal boundary of the signal peptide as identified herein, and the polynucleotides encoding them, are contemplated by the present invention. "PRO polypeptide variant” means an active PRO polypeptide as defined above or below having at least about 80% amino acid sequence identity with a full-length native sequence PRO polypeptide sequence as disclosed herein, a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein. Such PRO polypeptide variants include, for instance, PRO polypeptides wherein one or more amino acid residues are added, or deleted, at the N- or C-terminus of the full-length native amino acid sequence. Ordinarily, a PRO polypeptide variant will have at least about 80% amino acid sequence identity, alternatively at least about 81% amino acid sequence identity. alternatively at least about 82% amino acid ’ sequence identity, alternatively at least about 83% amino acid sequence identity, alternatively at least about 84% amino acid sequence identity, alternatively at least about 85% amino acid sequence identity, alternatively at least about 86% amino acid sequence identity, alternatively at least about 87% amino acid sequence identity. alternatively at least about 88% amino acid sequence identity, alternatively at least about 89% amino acid sequence identity, alternatively at least about 90% amino acid sequence identity, alternatively at least about 91% amino acid sequence identity, alternatively at least about 92% amino acid sequence identity, alternatively at least about 93% amino acid sequence identity, alternatively at least about 94% amino acid scquence identity, alternatively at least about 95% amino acid sequence identity, alternatively at least about 96% amino acid sequence identity, alternatively at least about 97% amino acid sequence identity, alternatively at least about 98% amino acid sequence identity and alternatively at least about 99% amino acid sequence identity to a full-length native sequence PRO polypeptide sequence as disclosed herein, a PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide. with or without the signal peptide, as disclosed herein or any other specifically defined fragment of a full-length PRO polypeptide sequence as disclosed herein. Ordinarily, PRO variant polypeptides are at least about 10 amino acids in length, alternatively at least about 20 amino acids in length, alternatively at least about 30 amino acids in length, alternatively at least about 40 amino acids in length, alternatively at least about 50 amino acids in length, alternatively at least about 60 amino acids in length, 26 4 : I alternatively at least about 70 amino acids in length, alternatively at least about 80 amino acids in length, . alternatively at least about 90 amino acids in length, alternatively at least about 100 amino acids in length, alternatively at least about 150 amino acids in length, alternatively at least about 200 amino acids in length, alternatively at least about 300 amino acids in length, or more.

As shown below, Table 1 provides the complete source code for the ALIGN-2 sequence comparison computer program. This source code may be routinely compiled for use on a UNIX operating system to provide the ALIGN-2 sequence comparison computer program.

In addition, Tables 2A-2D show hypothetical exemplifications for using the below described method to determine % amino acid sequence identity (Tables 2A-2B) and % nucleic acid sequence identity (Tables 2C-2D) using the ALIGN-2 sequence comparison computer program, wherein “PRO” represents the amino acid sequence of a hypothetical PRO polypeptide of interest, “Comparison Protein” represents the amino acid sequence of a polypeptide against which the “PRO” polypeptide of interest is being compared, “PRO-DNA” represents a hypothetical PRO-encoding nucleic acid sequence of interest, “Comparison DNA” represents the nucleotide sequence of a nucleic acid molecule against which the “PRO-DNA” nucleic acid molecule of interest is being compared, “X", “Y", and “Z” each represent different hypothetical amino acid residues and “N”, “L” and “V” each represent different hypothetical nucleotides.

Table 1 . . * C-C increased from 12 10 15 * Z is average of EQ * B is average of ND * match with stop is _M; stop-stop = 0; J (joker) match = 0 */ #define _M -8 * value of a match with a stop */ int _day[26][26] = { /* ABCDEFGHIJKLMNOPQRSTUVWXYZ¥ *A% {2.0,-2,00,4,1,-1,-1,0,-1,-2,-1, 0,_M,1,0,2,1, 1,0,0,-6, 0,-3, 0}, /*B */ {0.3,4,3,2,-5,0,1,-2,0,0,-3,-2, 2,_ M,-1, 1,0,0,0, 0,-2,-5, 0,-3, 1}, *C* {2,415:-5-5,-4,3,3,2, 0,-5,-6,-5,-4, M,-3,-5,-4, 0,2, 0,-2,-8, 0. 0,-5}, /*D* {0.3,-5,4,3,-6, 1, 1,-2,0,0,4,-3,2, M,-1,2,-1,0,0, 0,-2,-7, 0,4, 2}, [*E* {0,2,-5,3,4,-5,0, 1,-2, 0, 0,-3,-2, 1._M,-1,2,-1,0, 0, 0,-2,-7, 0,-4, 3}, /*F*/ {-4.-5.4,6,-5, 9,-5,-2, 1, 0,5, 2, 0,-4,_M,-5,-5,-4,-3,-3, 0,-1, 0. 0, 7,-5}, *G* {1,03 1,0,-5,5,2,3,0,2,-4,-3, 0, M,-1,-1,-3, 1, 0, 0,-1,-7, 0.-5, 0}, /*H * {-1.1,-3, 1, 1,-2,-2, 6,-2, 0, 0,-2,-2, 2, M,0,3,2,-1,-1,0,-2,-3, 0,0, 2}. *1% {-1,-2,-2,-2,-2, 1,-3,-2, 5, 0,-2, 2, 2,2, M,-2,-2,-2,-1, 0, 0,4,-5, 0,-1,-2}, 1%] * {0,0,0,0,0,0,0,0,0,0,0,0,0,0, M, 0,0,0,0,0,0, 0,0, 0,0, 0}. /*K* {1,050 0-5.-2,0.-2,0,5-3,0,1, M.-L, 1,3,0,0,0,2,-3, 0,-4, 0}.

I*L* {-2,-3,-6,4.-3.2,-4,-2, 2, 0,-3, 6. 4,-3,_ M.-3,-2,-3,-3,-1, 0, 2,2, 0,-1,-2}, *M=* {-1,2,-5,-3,-2,0,-3,-2,2,0,0, 4, 6,2, M,-2,-1, 0,-2,-1, 0, 2,4, 0,-2,-1},

FN* {0,2,4,2,1,4,0,2,:2,0, 1,-3,-2,2, M,-1, 1,0, 1, 0, 0.-2,4, 0,-2, 1}, ros {M,_M,_M _M _M, M _M MMM MMMM, 0M, M, M, M\ M, M, M, M, M, M, M}, *P*f {1,-1,-3,-1,-1,-5,-1, 0,-2, 0,-1,-3,-2,-1, M, 6,0,0, 1,0, 0,-1,-6, 0,-5, 0}, *Q% {0.1,-5,2,2,-5,-1,3,-2,0, 1,22,-1, 1, M,0,4,1,-1,-1, 0,2,-5, 0,-4, 3}, [*R* ~~ {2,0,-4,-1,-1,4,-3,2,-2,0,3.-3,0,0, M, 0, 1, 6,0,-1, 0,2, 2, 0,-4, 0}, 1*S* {1,0,0,0,0,-3,1,-1,-1,0,0,-3,-2, 1, M, 1,-1,0,2, 1, 0,-1,-2, 0,-3, 0}, 1*T* {1,0,-2,0,0,-3,0,-1,0,0,0,-1,-1,0,_M, 0,-1,-1, 1, 3, 0,0.,-5, 0,-3, 0}, ™u=* {0,0,0,0,0,0,0,0,0,0,0,0,0,0,_ M,0,0,0,0,0.0,0, 0, 0, 0, 0}, *V* {0,-2,-2,-2,-2,-1,-1,-2, 4, 0,-2, 2, 2,-2, M,-1,-2,-2,-1, 0, 0,4,-6, 0,-2,-2}, *wW+* {-6,5,8,-7,-7,0,-7,-3,-5, 0.-3,-2,-4,-4, M,-6,-5, 2,-2,-5, 0,-6,17, 0. 0,-6}, . *X* {0,0,0,0,0.0,00,0.0,0,0,0,0, M,0,0,0,0,0.0,0, 0, 0, 0. 0},

I*Y */ {-3,-3.0,4,4, 7.-5, 0,-1, 0,4,-1,-2,-2, M,-5,4,4,-3,-3, 0,-2, 0, 0,10,-4},

I*Z 3% {0,1,-5,2,3,-5,0, 2,-2,0,0,-2,-1, 1, M, 0, 3,0, 0,0, 0.-2,-6, 0,-4, 4} h :

Page 1 of day.h 28 i

. af #include <stdio.h> finclude <ctype.h> #define MAXIMP 16 /* max jumps in a diag */ #define MAXGAP 24 /* don't continue 10 penalize gaps larger than this */ #define JMPS 1024 /* max jmps in an path */ #define MX 4 /* save if there's at least MX-1 bases since last jmp */ fdefine DMAT 3 /* value of matching bases */ #define DMIS 0 /* penalty for mismatched bases */ #define DINSD 8 /* penalty for a gap */ #define DINS1 1 /* penalty per base */ #define PINSO 8 /* penalty for a gap */ fidefine PINSI 4 /* penalty per residue */ struct jmp { short n[MAXIMP]; /* size of jmp (neg for dely) */ unsigned short x[MAXIMP]; /* base no. of jmp in seq x */ 3 /* limits seq to 2°16 -1 */ struct diag { int score; /* score at last jmp */ long offset; /* offset of prev block */ short ijmp; /* current jmp index */ struct jmp jp; /* list of jmps */ struct path { int spc; /* number of leading spaces */ short n(JMPS]); /* size of jmp (gap) */ int x{IMPS]; /* loc of jmp (last elem before gap) */ ] 5 char *ofile; /* output file name */ char *namex([2]; /* seq names: getseqs() */ char *prog; /* prog name for err msgs */ char *seqx[2]; /* segs: getseqs() */ int dmax; /* best diag: nw() */ int dmax0; /* final diag */ int dna; /* set if dna: main() */ int endgaps; /* set if penalizing end gaps */ int £apx, gapy; /* total gaps in segs */ int lenO, lenl; /* seq lens */ int ngapx, ngapy; /* weal size of gaps */ int smax; /* max score: nw() */ int *xbm; /* bitmap for matching */ long offset; I* current offset in jmp file */ struct diag *dx; /* holds diagonals */ struct path pp(2]: /* holds path for seqs */ char *calloc(), *malloc(), *index(). *strcpy(); char *getseq(), *g_calioc();

Page 1 of nw.h 29

/* Needieman-Wunsch alignment program : » * usage: progs filel file2 * where filel and file2 are two dma or two protein sequences. * The sequences can be in upper- or lower-case an may contain ambiguity * Any lines beginning with ';’, ' >' or ' <' are ignored * Max file length is 65535 (limited by unsigned short x in the jmp struct) * A sequence with 1/3 or more of its elements ACGTU is assumed to be DNA * Output is in the file "align.out” * * The program may create a tmp file in /tmp to hold info about traceback. * Original version developed under BSD 4.3 on a vax 8650 */ #include "nw.h" #include "day.h" static ~~ _dbval[26) = { 1,14,2,13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,8,7,9,0,10,0 h static ~~ _pbval[26] = {

L2[(1< <(D-"A)|(1< <(N'-'AY), 4, 8, 16, 32, 64, 128, 256, OXFFFFFFF, 1< <10,1< <1], 1<<12,1<<13, 1<< 14,

I<<15,1<<16,1<<17,1<<18,1< «19, 1<<20, 1 < <2], 1<<22, 1<<23,1<<24, 1<<25|(I << (EA) |< <('Q-'A") h main(ac, av) main int ac; char *av(]; { prog = av[0j: if (ac = 3) { fprintf(stderr, "usage: %s filel file2\n", prog): fprintf(stderr, "where file] and file2 are two dna or two protein sequences.\n"); fprintf(stderr, "The sequences can be in upper- or lower-case\n"); fprintf(stderr,” Any lines beginning with ';’ or *<' are ignored\n”); fprintf(stderr,” Output is in the file \"align.out\"\n"); exit(1); } namex|0] = avfl]; namex([1] = av[2]; seqx[0] = getseq(namex[0], &lenQ); seqx[1] = getseq(namex[1], &lenl); xbm = (dna)? dbval : pbval; endgaps = 0; /* 1 to penalize endgaps */ ofile = "align.out"; /* output file */ nw(); /* fill in the matrix, get the possible jmps */ readjmps(); /* get the actual jmps */ print); /* print stats, alignment */ cleanup(0); /* unlink any tmp files */ } .

Page 1 of nw.c i } LL

. /* do the alignment, return best score: main() * dna: values in Fitch and Smith, PNAS, 80, 1382-1386, 1983 * pro: PAM 250 values * When scores are equal, we prefer mismatches to any gap, prefer * a new gap to extending an ongoing gap, and prefer a gap in seqx *toagapinseqy. */ nw() nw { char *pX, *py; /* seqs and prs */ int *ndely, *dely. /* keep track of dely */ int ndelx, deix; /* keep track of delx */ int *tmp; I* for swapping row0, row] */ int mis; /* score for each type */ int ins0, insl; /* insertion penalties */ register id; /* diagonal index */ register ij; /* jmp index */ register *col0, *coll: /* score for curr, last row */ register XX. YY: /* index into seqs */ dx = (struct diag *)g_calloc("to get diags”, len0+lenl + 1, sizeof(struct diag)); ndely = (int *)g_calloc("to get ndely”, lenl +1, sizeof(int)); dely = (int *)g_calloc("to get dely™, lenl +1, sizeof(int)); col0 = (int *)g_calloc(“to get col0™, lenl +1, sizeof(int)); coll = (int *)g_calloc("10 get coll”, lenl +1, sizeof(int)); insO = (dna)? DINSO : PINSO; ins] = (dna)? DINS] : PINS]; smax = -10000; if (endgaps) { for (colO[0] = dely[0] = -insD, yy = 1; yy <= len]; yy+ +) { : colO(yy] = delylyy] = colO[yy-1] - ins]; ndely[yy] = vy; 3 col0[0] = 0; /* Waterman Bull Math Biol 84 */ : } else for (yy = 1: yy <= lenl; yv+ +) dely[yy) = -ins0; /* fill in match matrix */ for (px = seqx[0], xx = 1; xx < = len0; px+ +, xx+ +) { /* initialize first entry in col */ if (endgaps) { f(xx ==1) collf0] = delx = -(insO+insl); else coll0] = delx = col0[0] - insl; ndelx = xx; 3 else { coli{0) = 0; delx = -ins0; ndelx = 0; }

Page 2 of nw.c ee IW for (py = seqx[1], yy = 1; yy <= lenl; py++, yy+ +) { mis = colQlyy-11]; if (dna) mis + = (xbm[*px-'A’']&xbm[*py-'A'])? DMAT : DMIS; else mis += _day[*px-'A’'][*py-'A’]; /* update penalty for del in x scq; * favor new del over ongong del * ignore MAXGAP if weighting endgaps */ if (endgaps | | ndely[yy] < MAXGAP) { if (col0fyy] - insO > = dely[yy}) { dely[yy] = colO[yy] - (insO+ins1); ndelylyy] = 1; } else { dely[yy] -= ins; ndely[yy]+ +;

H

} else { if (colOlyy] - (insO+insl) > = dely(yy]) { dely[yy}l = colO[yy] - (insO +insl); ndely[yy] = 1; } else ndely[yy) + +; } /* update penalty for del in y seq: * favor new del over ongong del */ if (endgaps || ndelx < MAXGAP) § if (collfyy-1] - insO > = delx) { delx = coll{yy-1] - (insO+insl); ndelx = 1; } else { delx -= insi; ndelx + +; } } else { if (coll[yy-1) - (insO+insl) > = delx) { delx = coll[yy-1] - (ins0+insl); ndelx = 1; } else ndeix+ +; } /* pick the maximum score; we're favoring : * mis over any del and delx over dely x!

Page 3 of nw.c 32 y Ce ve oIW id =xx-yy + len} - I; . if (mis > = delx && mis > = dely|yy]) coll[yy] = mis; else if (delx > = dely[yy)) { collfyy] = deix; ij = dx(id}.ijmp; if (dx[id].jp.n[0) && (!dna || (ndelx >= MAXIMP && xx > dxfid).jp.x{ij}+MX) | | mis > dx[id).score + DINSO)) { dx[id).ijmp+ +; if (+ +ij >= MAXIMP) { writejmps(id); ij = dx[id].ijmp = O; dx[id).offset = offset; offser + = sizeof(struct jmp) + sizeof(offset); } } dx[id].jp-nlij| = ndelx; dx[id}.jp.x[ij] = xx; dx[id].score = delx; } else { collfyy] = delylyy]: ij = dx[id].ijmp; if (dx[id}.jp.n[0} && (!dna || (ndely[yy] > = MAXJMP && xx > dx[id].jp.x[ij} + MX) || mis > dx][id).score +DINSO0)) { dxfid}.ijmp+ +; if (+ +ij >= MAXIMP) { writejmps(id); ij = dx[id].ijmp = 0; dx[id].offset = offset; offset + = sizeof(struct jmp) + sizeof(offset); } } dx{id).jp.nlij] = -ndelylyy}: dx[id].jp.x[ij] = xx; dxfid}.score = delyfyyl: } if (xx == lend && yy < lenl) { /* last col * if (endgaps) coll[yy] -= insO+insl*(lenl-yvi; if (coll{yy] > smax) { smax = colllyyl]; dmax = id; } } } if (endgaps && xx < len0) collfyy-1] - = insO + ins] *(Jen0-xx); if (collfyy-1} > smax) { smax = collyy-1]; dmax = id; } np = ¢ol0; cold = coll; coll = wmp; } (void) free((char *)ndely); (void) frec((char *)dely); (void) free((char *)col0); (void) free{{char *)coll);

H Page 4 of nw.c 33

PR

I” . * * print() -- only routine visible outside this module * * static: * getmat() -- trace back best path, count matches: print() * pr_align() -- print alignment of described in array pf): print() * dumpblock() - dump a block of lines with numbers, stars: pr_align() * nums() ~ put out & number line: dumpblock() * putline() -- put out a line (name, [num], seq, (num]): dumpblock() * stars() - -put a line of stars: dumpblock() * stripname() -- strip any path and prefix from a seqname */ #include “nw.h" #define SPC 3 #define P_ LINE 256 /* maximum output line */ #define P SPC 3 /* space between name or num and seq */ extern _day{26][26); int olen; /* set output line length */

FILE *fx; /* output file */ print() print { int Ix, ly, firstgap, lastgap; /* overlap */ if (fx = fopen(ofile, "w")) == 0) { fprintf(stderr,” %s: can't write %s\n", prog, ofile); cleanup(l); } fprintf(fx, " < first sequence: %s (length = %d)\n”, namex[0], len0); fprintf(fx, " <second sequence: %s (length = %d)\n", namex(1], len); olen = 60;

Ix = len0; ly = lenl; firstgap = lastgap = 0; if (dmax < lent - 1) { {* leading gap in x */ pplOl.spc = firstgap = len! - dmax - 1; , ly -= ppl{0].spc; else if (dmax > lenl - 1) { /* leading gap in y */ ppl1].spc = firstgap = dmax - (leni - 1);

Ix -= pp[1].spc; } if {dmax0 < len0 - 1) { /* traifing gap in x */ lastgap = len0 - dmax0 -1;

Ix -= lastgap; } else if (dmax0 > fenO - 1) { /* trailing gap in y */ lasigap = dmax0 - (len0 - 1); ly -= lastgap; } geumat(ix, ly, firstgap, lastgap); pr_align(); }

Page 1 of nwprint.c

] v . * trace back the best path, count matches */ static getmat(ix, ly, firstgap, lastgap) getmat int Ix, ly; /* "core" (minus endgaps) */ { int firstgap, lastgap; /* leading trailing overlap */ int nm, i0, il, siz0, sizl; char outx[32]; double pet; register n0, nl; register char *p0, *pl; /* get total matches, score */ i0 = il = siz0 = sizl = (; pO = seqx[0] + ppil]).spc; pl = seqx[1] + pp[0].spc; nO = pp[l}.spc + 1; nt = pp{0).spc + 1; nm = 0; while ( *p0 && *pl) { if (siz0) { pl+ +; nl+ +; siz0--; } else if (sizl) { pO+ +; n0+ +; sizl--; : } else { if (xbm{*p0-'A’]&xbm{*pl-'A']) nm+ 4; if (n0+ + = = pp[0].x[i0]) siz0 = pp[0}.n(i0+ +]; if (n1+ + == pp[1}).x[i1}) sizl = pp{1].n[il + +]; pO+ +; pl+ +: } } /* pct homology: * if penalizing endgaps, base is the shorter seq * else, knock off overhangs and wake shorter core */ if (endgaps)

Ix = (lenQ < lenl)? len0 : lent; else

Ix = (Ix < ly)? Ix: ly; pct = 100.*(double)nm/(double)ix: fprintf(fx, "\n"); fprintf(fx, “ < %d match%s in an overlap of %d: %.2f percent similarity\n", nm, (nm == 1)? "" : "es", |x, pct);

Page 2 of nwprint.c

T { fprintf(fx, " < gaps in first sequence: %d", gapx); ...getmat if (gapx) { : (void) sprintf(outx, " (%d %s%s)", ngapx, (dna)? "base": “residue”, (ngapx == 1)? "":"s"); fprintf(fx,” %s”, outx); fprintf(fx, ", gaps in second sequence: %d", gapy); if (gapy) { (void) sprintf(outx, " (%d %s%s)", ngapy. (dna)? "base": "residue", (ngapy == 1)? "":"s"); fprintf(fx,” %s”, outx); } if (dna) fprintf(fx, "\n<score: %d (match = %d, mismatch = %d, gap penalty = %d + %d per base)\n", smax, DMAT, DMIS, DINSO, DINSI); else fprintf(fx, "\n< score: %d (Dayhoff PAM 250 matrix, gap penalty = %d + %d per residue)\n”, smax, PINSO, PINS1); if (endgaps) fprintf(fx, " < endgaps penalized. lcft endgap: %d %s%s, right cndgap: %d %s%s\n”, firstgap, (dna)? "base" : “residue”, (firstgap == 1)? "" : "s", lastgap, (dna)? "base" : “residue”, (lastgap == 1)? "" : "s"); else fprintf(fx, " <endgaps not penalized\n™); } static nm; /* matches in core -- for checking */ static Imax; /* lengths of stripped file names */ static ij[2]; /* jmp index for a path */ static nc(2); /* number at start of current line */ static ni(2]; /* current elem number -- for gapping */ static siz[2); static char *ps(2]: /* ptr to current element */ static char *pof2]; /* ptr to next output char slot */ static char out[2][P_LINE}; /* output line */ static char star[P_LINE]; /* set by stars() */ * * print alignment of described in struct path pp[} */ static pr_align() pr_align { int nn; /* char count */ int more; register it for i = 0, Imax =0:i <2;i++){ nn = stripname(namex[i]); if (nn > Imax)

Imax = nn: ncfi] = 1: nifi} = 1; siz[i] = iii] = 0; psli} = seqx(i); poli} = out{i): }

Page 3 of nwprint.c 36

» ‘ ’ for (nn = nm = 0, more = 1; more; ) { ...pr_align for (i = more = 0; i < 2; i++) { * * do we have more of this sequence? */ if (!*psli]) continue; more+ +; if (ppli}-spe) { /* leading space */ *pofij++ ="; ; pplil.spe--; elseif (sizi]){ /*inagap®*/ *poli}++ = '-'; siz[i]--; } else { /* we're putting a seq element */ *poli) = *psfi; if (islower(*pslil)) *ps[i] = toupper(*ps|i}); polil+ +; pslil ++;

Ad * are we at next gap for this seq? */ if (nif) == ppli).x(ij(i})) { /* * we need to merge all gaps . * at this location * siz[i} = ppli]-n(ijli] + +]; while (nili] == ppli).x[ij{i]}) : sizfi] + = pplil.nfij[i)+ +]; } nifij + +; } } if (+ +nn == olen || 'more && nn) { dumpblock(); for(i=0;i<2;i++) poli] = out[i); nn = 0; } } } 1¥ * dump a block of lines, including numbers, stars: pr_alignt) */ static dumpblock() dumpblock { register i; for (i=0;i <2;i+ +) *poli}-- = "\0';

Page 4 of nwprint.c i ' < ...dumpblock . (void) putc('\n', fx); for (i =0;i < 2; i++) { if (*outfi} && (*out[i} !="" || *poli]) t=") { if (i==0) nums(i); if (i == 0&& *out|1]) starsQ; putline(i); if i == 0 && *out{1]) fprintf(fx, star); ifi==1 nums(i); } } } /* * put out a number line: dumpblock() */ static nums(ix) nums int ix; /* index in out[] holding seq line */ { char nline{P_LINE]; register i, J; register char *pn, *px, *py; for (pn = nline, i = 0; i < Imax+P_SPC; i++, pn++) *pn =""; for (i = nc[ix], py — out[ix|; *py; py+ +, pn+ +) { if(*py ==""1|*py =="-) *pn=""; : else { if(i%10 ==0 || 0 == 1 && ncfix] I= 1)) {

Jj=0< 0d; for (px = pn; j; j /= 10, px--) . *x = j%10 + '0’; if(i <0) px = } else n=" i++; } } *pn = '\0'; . ncfix] = i; for (pn = nline; *pn; pn+ +) (void) putc(*pn, fx); (void) putc("\n’, fx); } 1% * put out a line (name, [num), seq, [num}): dumpblock() *f static putline(ix) putline int ix: {

Page 5 of nwprint.c

» . : ...putlinc int i; register char *px; for (px = namex[ix], i = 0; *px && *px !'= ":"; px+ +, i++) (void) putc(*px, fx); for (; i < Imax+P_SPC:; i++) (void) putc(' *, fx); /* these count from 1: * nif] is current element (from 1) * nc(] is number at start of current line */ for (px = out(ix); *px; px+ +) (void) putc(*px&0x7F, fx); (void) putc('\n', fx); } 1* * put a line of stars (segs always in out{0], out[1]): dumpblock() =/ static stars() stars { int i; register char *p0, *pl, cx, *px; if (**out[0] || (*out(0] =="" && *(po[0]) == "") { ¥out[1] || (*out[1] == '' && *(po[l}) == "")) return; px = star; : for (i = lmax+P_SPC; j; i--) px++ ="; for (p0 = out[0}, p! = out[1]); *p0 && *pl; pO0+ +, pl++) { . if (isalpha(*p0) && isalpha(*p1)) { if (xbm[*p0-"A‘J&xbm{*pl-'A"}) { cx = "* nm+ +;

H else if (dna && _day[*p0-'A’|{*pl-'A’| > 0) cx = ".% else cx ="7 } else cx =""; *px+ + = cx; } *x++ = "\n'; m= "\0'; }

Page 6 of nwprint.c

. [] * strip path or prefix from pn, return len: pr_align() . */ static stripname(pn) stripname char *pn; /* file name (may be path) */ { register char *px, *py; py =0; for (px = pn; *px; px+ +) if (px =="1") py =px +L; if (py) (void) strcpy(pn, py); return(strien(pn));

Page 7 of nwprint.c

. * cleanup() -- cleanup any tmp file * getseq() -- read in seq, set dna, len, maxlen * g_calloc() -- calioc() with error checkin * readjmps() -- get the good jmps, from tmp file if necessary * writejmps() -- write a filled array of jmps to a tmp filc: nw() */ #include “nw.h" #include <sys/file.h> char *jname = "/tmp/homgXXXXXX"; /* mp file for jmps */

FILE *fj; int cleanup(); /* cleanup tmp file */ long lIseek(); 1* * remove any tmp file if we blow */ cleanup(i) cleanup int i: { if (f)) (void) unlink(jname); exit(i); } /* * read, return ptr to seq, set dna, len, maxlen * skip lines starting with *;', '<’, or ' >" * seq in upper or lower case */ char * getseq(file, len) getseq char *file; /* file name */ int *len; /* seq len */ { char linef1024], *pseq; register char *px, *py. int natgc, tien;

FILE *fp; if ((fp = fopen(file,"r")) == 0) { fprintf(stderr,” %s: can't read %s\n”, prog, file); exit(1); } tlen = natgc = 0; while (fgets(line, 1024, fp)) { if (*line == ';' || Hine == '<' || *ine == '>") continue; for (px = line; *px !="\n'; px-++)

If (isupper(*px) || islower(*px)) tlen+ +; } if ((pscq = malloc((unsigned)(tien+6))) == 0) { fprimfistderr," %s: malloc() failed to get %d bytes for %s\n”, prog. tlen+6, fic); : exit(l); } pseq[0] = pseq[1] = pseq(2] = pseq(3] = "\0';

Page 1 of nwsubr.c

. ] ...getseq py = pseq + 4; - *len = tlen; rewind(fp); while (fgets(line, 1024, fp)) { if (*line == "';" |] *line == '<' [| *line == '>") continue; for (px = line; *px !'= "\n'; px+ +) { if (isupper(*px)) py ++ = px else if (islower(*px)) *py + + = toupper(*px); if (index("ATGCU",*(py-1))) natgc+ +; } } *oy++ = "0; *py = "\0%; (void) fclose(fp); dna = natgc > (tlen/3); return(pseq +4); } ) char * g_calloc(msg, nx, sz) g calloc char *msg; /* program, calling routine */ int nx, sz; /* number and size of elements */ { char *px, *calloc(); if (px = calloc((unsigned)nx, (unsigned)sz)) == 0) { if (*msg) { fprintf(stderr, “%s: g_calloc() failed %s (n= %d, sz= %d)\n", prog, msg, nx, sz); exit(1); } } return(px); } 1* * get final jmps from dx[] or unp file, set pp[], reset dmax: main() *f readjmps() readjmps { int fd =-1; int siz, i0, il; register i, J, XX; i (f) { (void) fclose(fj); if (fd = open(jname, O_RDONLY, 0)) < 0) { fprintf(stderr, " %s: can't open() %s\n", prog, jname); cleanup(1); } } for (i = i0 = il = 0, dmax0 = dmax, xx = len0; ; i++) { while (1) { for (j = dx[dmax].ijmp; j > = 0 && dx[dmax}.jp.x[i| > = xX; j--)

Page 2 of nwsubr.c

...readjmps if § < 0 && dx[dmax].offset && fj) { : (void) iseek(fd, dx[dmax].offsct, 0); (void) read(fd, (char *)&dx[dmax].jp, sizeof(struct jmp)); (void) read(fd, (char *)&dx[dmax].offset, sizeof(dx{dmax]}.offset)); dx[dmax].ijmp = MAXJMP-1; } else break; } if (i >= IMPS) { fprintf(stderr, "%s: too many gaps in alignment\n”, prog); cleanup(l); } if j >=0){ siz = dx[dmax].jp.n[j]; xx = dx[dmax].jp.x[j}: dmax + = siz; if (siz < 0) { /* gap in second seq */ ppl1).n(il] = -siz;

XX + = siz; /*id = xx - yy + lenl - 1 */ ppl1].x{il] = xx - dmax + len! - 1; gapy+ +; ngapy -= siz; /* ignore MAXGAP when doing endgaps */ siz = (-siz < MAXGAP || endgaps)? -siz : MAXGAP; il++; } else if (siz > 0) { /* gap in first seq */ ppl0].nli0] = siz; ppl0}.x[i0] = xx; gapx+ +; ngapx + = siz; /* ignore MAXGAP when doing endgaps */ siz = (siz < MAXGAP || endgaps)? siz : MAXGAP; . 0+ +: } } else break; } /* reverse the order of jmps */ for j =0,i0--;j < 0; j++, i0--) { i = ppl0].n[j}; pp(0}.n[j] = pp(0).nfi0}; pp(0).n[i0] = i; , i = pplO].x[j}; pp(0).x(i] = pp(0}.x[i0); pp[0).x[i0} = i; for = 0,il--;j < il; j++,i1-){ i = ppl1).n{il; ppl1}.n(i] = pp(i).nfil]; pp{1).nlil] = i; t = ppl1].x[j}: ppl1].x[) = ppl(1).x[il}; pp{l).x[i1] = i; } if (fd >= 0) (void) close(fd); if (f) { (void) unlink(jname); fi=0 offset = 0; } } Page 3 of nwsubr.c

* . * write a filled jmp struct offset of the prev one (if any): nw() */ writejmps(ix) writejmps int ix; { char *mktemp(); if (3) { if (mktemp(jname) < 0) { fprintf(stderr, "%s: can't mktemp() %s\n", prog, jname); cleanup(1); } if (ff = fopen(jname, "w")) == 0) { fprintf(stderr, "%s: can't write %s\n", prog, jname); exit(1); } } (void) fwrite((char *)&dx{ix).jp, sizeof(struct jmp), 1, fj); (void) fwrite((char *)&dx{ix]. offset, sizeof(dx[ix).offset), 1, fi) }

Page 4 of nwsubr.c

Table 2A

PRO XXXXXXXXXXXXXXX {Length = 15 amino acids)

Comparison Protein XXXXXYYYYYYY (Length = 12 amino acids) % amino acid sequence identity = (the number of identically matching amino acid residues between the two polypeptide sequences as determined by ALIGN-2) divided by (the total number of amino acid residues of thc PRO polypeptide) = divided by 15 = 33.3%

Table 2B

PRO XXXXXXXXXX (Length = 10 amino acids)

Comparison Protein XXXXXYYYYYYZZYZ (Length = 15 amino acids) % amino acid sequence identity = (the number of identically matching amino acid residues between the two polypeptide sequences as determined by ALIGN-2) divided by (the total number of amino acid residues of the PRO polypeptide) = divided by 10 = 50%

Table 2C

PRO-DNA NNNNNNNNNNNNNN (Length = 14 nucleotides)

Comparison DNA NNNNNNLLLLLLLLLL (Length = 16 nucleotides) % nucleic acid sequence identity = (the number of identically matching nucleotides between the two nucleic acid sequences as determined by

ALIGN-2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid sequence) = 6 divided by 14 = 42.9%

Table 2D

PRO-DNA NNNNNNNNNNNN (Length = 12 nucleotides)

Comparison DNA NNNNLLLVV (Length = 9 nucleotides) % nucleic acid sequence identity = (the number of identically matching nucleotides between the two nucleic acid sequences as determined by

ALIGN-2) divided by (the total number of nucleotides of the PRO-DNA nucleic acid sequence) = 4 divided by 12 = 33.3%

"Percent (%) amino acid sequence identity” with respect to the PRO polypeptide sequences identified herein : is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a PRO sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST,

BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are obtained as described below by using the sequence comparison computer program ALIGN-2, wherein the complete source code for the ALIGN-2 program is provided in Table 1. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code shown in Table | has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under

U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available through Genentech,

Inc., South San Francisco, California or may be compiled from the source code provided in Table 1. The ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.

For purposes herein, the % amino acid sequence identity of a given amino acid sequence A to, with. or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X/Y where X is the number of amino acid residues scored as identical matches by the scquence alignment program

ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B.

It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the 5 amino acid sequence identity of B 10 A. As examples of % amino acid sequence identity calculations, Tables 2A-2B demonstrate how to calculate the % amino acid sequence identity of the amino acid sequence designated “Comparison Protein” to the amino acid sequence designated “PRO”.

Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program. However, % amino acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST?2 (Altschul er al.. Nucleic

Acids Res., 25:3389-3402 (1997)). The NCBI-BLAST?2 sequence comparison program may be downloaded from http:/iwww,ncbi.plm nih.gov. or otherwise obtained from the National Institute of Health, Bethesda, MD. NCBI-

BLAST uses several search parameters, wherein all of those scarch parameters are set to default values including, for example, unmask = yes, strand = all, expected occurrences = 10, minimum low complexity length = 15/5, multi- pass e-value = 0.01, constant for multi-pass = 25, dropoff for final gapped alignment = 25 and scoring matrix =

EE —ES i ————————.

BLOSUMS62.

In situations where NCBI-BLAST? is employed for amino acid sequence comparisons, the % amino acid . scquence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X/Y where X is the number of amino acid residues scored as identical matches by the sequence alignment program

NCBI-BLAST? in that program’s alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.

In addition, % amino acid sequence identity may also be determined using the WU-BLAST-2 computer program (Altschul et al, Methods in Enzymology, 266:460-480 (1996)). Most of the WU-BLAST-2 search parameters are set to the default values. Those not set to default values, i.e., the adjustable parameters, are set with the following values: overlap span = 1, averlap fraction = 0.125, word threshold (T) = 11, and scoring matrix =

BLOSUMS62. For purposes herein, a % amino acid sequence identity value is determined by dividing (a) the number of matching identical amino acids residues between the amino acid sequence of the PRO polypeptide of interest having a sequence derived from the native PRO polypeptide and the comparison amino acid sequence of interest (i.e., the sequence against which the PRO polypeptide of interest is being compared which may be a PRO variant polypeptide) as determined by WU-BLAST-2 by (b) the total number of amino acid residues of the PRO polypeptide of interest. For example, in the statement “a polypeptide comprising an amino acid sequence A which has or having at least 80% amino acid sequence identity to the amino acid sequence B’". the amino acid sequence

A is the comparison amino acid sequence of interest and the amino acid sequence B is the amino acid sequence of the PRO polypeptide of interest. "PRO variant polynucleotide" or "PRO variant nucleic acid sequence” means a nucleic acid molecule which encodes an active PRO polypeptide as defined below and which has at least about 80% nucleic acid sequence identity with a nucleotide acid sequence encoding a full-length native sequence PRO polypeptide sequence as disclosed herein, a full-length native sequence PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO pol vpeptide, with or without the signal peptide, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein. Ordinarily. a PRO variant polynucleotide will have at least about 80% nucleic acid sequence identity, alternatively at least about 81% nucleic acid sequence identity, alternatively at least about 82% nucleic acid sequence identity, alternatively at least about 83% nucleic acid sequence identity, alternatively at least about 84% nucleic acid sequence identity, alternatively at least about 85% nucleic acid sequence identity, alternatively at least about 86% nucleic acid scquence identity, alternatively at least about 87% nucleic acid sequence identity. alternatively at least about 88% nucleic acid sequence identity, alternatively at least about 89% nucleic acid sequence identity. alternatively at least about 90% nucleic acid sequence identity, alternatively at least about 91% nucleic acid sequence identity. alternatively at least about 92% nucleic acid sequence identity, alternatively at least about 93% nucleic acid sequence identity, alternatively at least about 94% nucleic acid sequence identity, alternatively at least about 95% nucleic acid sequence identity, alternatively at least about 96% nucleic acid sequence identity, alternatively at feast about 97% nucleic acid sequence identity, alternatively at least about 98% nucleic acid sequence identity and alternatively at least about 99% nucleic acid sequence identity with a nucleic acid sequence encoding a full-length native sequence

PRO polypeptide sequence as disclosed herein, a full-length native sequence PRO polypeptide sequence lacking the signal peptide as disclosed herein, an extracellular domain of a PRO polypeptide, with or without the signal sequence, as disclosed herein or any other fragment of a full-length PRO polypeptide sequence as disclosed herein.

Variants do not encompass the native nucleotide sequence.

Ordinarily, PRO variant polynucleotides are at least about 30 nucleotides in length, alternatively at Jeast about 60 nucleotides in length, alternatively at least about 90 nucleotides in length, alternatively at least about 120 nucleotides in length, alternatively at least about 150 nucleotides in length, alternatively at least about 180 nucleotides in length, alternatively at least about 210 nucleotides in length, alternatively at least about 240 nucleotides in length, alternatively at least about 270 nucleotides in length, alternatively at least about 300 nucleotides in length, alternatively at least about 450 nucleotides in length, alternatively at least about 600 nucleotides in length, alternatively at least about 900 nucleotides in length, or more. "Percent (%) nucleic acid sequence identity” with respect to the PRO polypeptide-encoding nucleic acid sequences identified herein is defined as the percentage of nucleotides in a candidate sequence that are identical with the nucleotides in a PRO polypeptide-encoding nucleic acid sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. Alignment for purposes of determining percent nucleic acid scquence identity can be achieved in various ways that are within the skill in the . : art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or

Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared. For purposes herein, however, % nucleic acid sequence identity values are obtained as described below by using the sequence comparison computer program ALIGN-2, wherein the complete source code for the

ALIGN-2 program is provided in Table 1. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code shown in Table 1 has been filed with user documentation in the U.S.

Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No.

TXU510087. The ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco,

California or may be compiled from the source code provided in Table 1. The ALIGN-2 program should be compiled for use on a UNIX operating system, preferably digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary.

For purposes herein, the 9% nucleic acid sequence identity of a given nucleic acid sequence C to, with, or againsta given nucleic acid sequence D (which can alternatively be phrased as a given nucleic acid sequence C that has or comprises a certain % nucleic acid sequence identity to, with, or against a given nucleic acid sequence D) is calculated as follows: 100 times the fraction W/Z 51 y where W is the number of nucleotides scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of C and D, and where Z is the total sumber of nucleotides in D. Twill be appreciated that where the length of nucleic acid sequence Cis not equal to the length of nucleic acid sequence D, the % nucleic acid sequence identity of C to D will not equal the % nucleic acid sequence identity of D to C. As examples of % nucleic acid sequence identity calculations, Tables 2C-2D demonstrate how to calculate the % nucleic acid sequence identity of the nucleic acid sequence designated “Comparison DNA” 10 the nucleic acid sequence desi gnated “PRO-

DNA”.

Unless specifically stated otherwise, all % nucleic acid sequence identity values used herein are obtained as described above using the ALIGN-2 sequence comparison computer program. However, % nucleic acid sequence identity may also be determined using the sequence comparison program NCBI-BLAST?2 (Altschul et al., Nucleic

Acids Res, 25:3389-3402 (1997))- The NCBI-BLAST?2 sequence comparison program may be downloaded from http://www .ncbi.nlm.nih.gov. or otherwise obtained from the National Institute of Health, Bethesda, MD. NCBI-

BLAST? uses several search parameters, wherein all of those search parameters are set to default values incl uding, for example, unmask = yes, strand = all, expected occurrences = 10, minimum low complexity length = 15/5, multi- pass e-value= 0.01, constant for multi-pass = 25, dropoff for final gapped alignment = 25 and scoring matrix =

BLOSUMG62.

In situations where NCBI-BLAST? is employed for sequence comparisons, the % nucleic acid sequence identity of a given pucleic acid sequence C to, with, or against a given nucleic acid sequence D (which can alternatively be phrased as a given nucleic acid sequence C that has or comprises a certain 9% nucleic acid sequence identity to, with, or against a given nucleic acid sequence D) is calculated as follows: 100 times the fraction W/Z where W is the number of nucleotides scored as identical matches by the sequence alignment program NCBI-

BLAST? in that program's alignment of C and D, and where Z is the total number of nucleotides in D. It will be appreciated that where the length of nucleic acid sequence C is not equal to the length of nucleic acid sequence D. the % nucleic acid sequence identity of C to D will not equal the % nucleic acid sequence identity of Do C.

In addition, % nucleic acid sequence identity values may also be generated using the WU-BLAST-2 computer program (Altschul er al, Methods in Enzymology, 266:460-480 (1996)). Most of the WU-BLAST-2 search parameters are set to the default values. Those not set to default values, Lé., the adjustable parameters, are set with the following values: overlap span = 1, overlap fraction = 0.125, word threshold (T) = 11, and scoring matrix =BLOSUMG62. For purposes herein, a % nucleic acid sequence identity valuc is determined by dividing (a) the number of matching identical nucleotides between the nucleic acid sequence of the PRO pol ypeptide-encoding nucleic acid molecule of interest having a sequence derived from the native sequence PRO polypeptide-encoding nucleic acid and the comparison nucleic acid molecule of interest (i.e., the sequence against which the PRO polypeptide-encading nucleic acid molecule of interest is being compared which may be a variant PRO polynucleotide) as determined by WU-BLAST-2 by (b) the total number of nucleotides of the PRO polypeptide- encoding nucleic acid molecule of interest. For example, in the statement «an isolated nucleic acid molecule comprising a nucleic acid sequence A which has or having at least 80% nucleic acid sequence identity 10 the nucleic acid sequence B”, the nucleic acid sequence A is the comparison nucleic acid molecule of interest and the nucleic acid sequence B is the nucleic acid sequence of the PRO polypeptide-encoding nucleic acid molecule of interest.

In other embodiments, PRO variant polynucleotides are nucleic acid molecules that encode an active PRO polypeptide and which are capabie of hybridizing, preferably under stringent hybridization and wash conditions, to nucleotide sequences encoding the full-length PRO polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ

ID NO:12), Figure 14 (SEQ ID NO:14), Figure 16 (SEQ ID NO:16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ

ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ

ID NO:28), Figure 30 (SEQ ID NO:30), and Figure 32 (SEQ ID NO:32), respectively. PRO variant polypeptides may be those that are encoded by a PRO variant polynucleotide.

The term "positives", in the context of the amino acid sequence identity comparisons performed as described above, includes amino acid residues in the sequences compared that are not only identical, but also those that have similar properties. Amino acid residues that score a positive value to an amino acid residue of interest are those that are either identical to the amino acid residue of interest or are a preferred substitution (as defined in Table 3 below) of the amino acid residue of interest.

For purposes herein, the % value of positives of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrascd as a given amino acid sequence A that has or comprises . a certain % positives to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X/Y } 20 where X is the number of amino acid residues scoring a positive value by the sequence alignment program ALIGN- 2 in that program’s alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, . the % positives of A to B will not equal the % positives of B to A. “Isolated”, when used to describe the various polypeptides disclosed herein, means a polypeptide that has been identified and separated and/or recovered from a component of its natural environment. Preferably, the isolated polypeptide is free of association with all components with which it is naturally associated. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes. In preferred embodiments, the polypeptide will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain.

Isolated polypeptide includes polypeptide in situ within recombinant cells, since at least one component of the PRO natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least once purification step.

An "isolated" nucleic acid molecule encoding a PRO polypeptide or an “isolated” nucleic acid molecule encoding an anti-PRO antibody is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the PRO-encoding nucleic acid or the natural source of the anti-PRO-encading nucleic acid. Preferably, the isolated nucleic acid is free of association with all components with which it is naturally associated. An isolated PRO-encoding nucleic acid molecule or an isolated anti-PRO-encoding nucleic acid molecule is other than in the form or setting in which itis found in nature. Isolated nucleic acid molecules therefore are distinguished from the PRO-encoding nucleic acid molecule or from the anti-PRO-encoding nucleic acid molecule as it exists in natural cells. However, an isolated nucleic acid molecule encoding a PRO polypeptide or an isolated nucleic acid molecule encoding an anti-

PRO antibody includes PRO-nucleic acid molecules or anti-PRO-nucleic acid molecules contained in cells that ordinarily express PRO polypeptides or anti-PRO antibodies where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.

The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.

Nucleic acid is "operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a PRO polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, "operably linked" means that the DN A sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice. "Stringency” of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures.

Hybridization generally depends on the ability of denatured DNA to reanneal when complementary strands are present in an environment below their melting temperaturc. The higher the degree of desired homology between the probe and hybridizable sequence, the higher the relative temperature that can be used. As a result, it follows that higher relative temperatures would tend to make the reaction conditions more stringent, while lower temperatures less so. For additional details and explanation of stringency of hybridization reactions, see, Ausubel et al., Current Protocols in Molecular Biology (Wiley Interscience Publishers, 1995). "Stringent conditions" or "high-stringency conditions", as defined herein, may be identified by those that: (1) employ low ionic strength and high temperature for washing, for example, 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50°C; (2) employ during hybridization a denaturing agent, such as formamide, for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0. 1% Ficoll/0.1% polyvinylpyrrolidone/SOmM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride. 75 mM sodium citrate at 42°C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCl, 0.075 M sodium citrate). 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 pg/ml), 0.1% SDS. and 10% dextran sulfate at 42°C, with washes a142°C in 0.2 x SSC (sodium chloride/sodium citrate) and 50% formamide at 55°C, followed by a high-stringency wash consisting of 0.1 x SSC containing EDTA at 55°C. "Moderately-stringent conditions" may be identified as described by Sambrook et al., Molecular Cloning: A

Laboratory Manual (New York: Cold Spring Harbor Press, 1989), and include the use of washing solution and hybridization conditions (e.g., temperature, ionic strength, and % SDS) less stringent than those described above.

An example of moderately stringent conditions is overnight incubation at 37°C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), SO mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-50°C. The skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.

The modifier “epitope-tagged” when used herein refers to a chimeric polypeptide comprising a PRO polypeptide fused to a "tag polypeptide”. The tag polypeptide has enough residues to provide an epitope against which an antibody can be made, yet is short enough such that it does not interfere with activity of the polypeptide to which itis fused. The tag polypeptide preferably also is fairly unique so that the antibody does not substantially cross-react with other epitopes. Suitable tag polypeptides generally have at least six amino acid residues and usually between about 8 and 50 amino acid residues (preferably, between about 10 and 20 amino acid residues). "Active" or "activity" in the context of PRO variants refers to form(s) of PRO proteins that retain the biologic - and/or immunologic activities of a native or naturally-occurring PRO polypeptide. “Biological activity” in the context of a molecule that antagonizes a PRO polypeptide that can be identified by the screening assays disclosed herein (e.g., an organic or inorganic small molecule, peptide, etc.) is used to refer to the ability of such molecules to bind or complex with the PRO polypeptide identified herein, or otherwise : interfere with the interaction of the PRO polypeptides with other cellular proteins or otherwise inhibits the : transcription or translation of the PRO polypeptide. Particularly preferred biological activity includes cardiac hypertrophy, activity that acts on systemic disorders that affect vessels, such as diabetes mellitus, as well as diseases of the arteries, capillaries, veins, and/or lymphatics, and cancer.

The term "antagonist" is used in the broadest sense, and includes any molecule that partially or fully blocks, inhibits, or neutralizes one or more of the biological activitics of a native PRO polypeptide disclosed herein, for example, if applicable, its mitogenic or angiogenic activity. Antagonists of a PRO polypeptide may act by interfering with the binding of a PRO polypeptide to a cellular receptor, by incapacitating or killing cells that have been activated by a PRO polypeptide, or by interfering with vascular endothelial cell activation after binding of a

PRO polypeptide to a cellular receptor. All such points of intervention by a PRO polypeptide antagonist shall be considered equivalent for purposes of this invention. The antagonists inhibit the mitogenic, angiogenic, or other biological activity of PRO polypeptides. and thus are useful for the treatment of diseases or disorders characterized by undesirable excessive neovascularization, including by way of example tumors. and especially solid malignant tumors, rheumatoid arthritis, psoriasis, atherosclerosis, diabetic and other retinopathies. retrolental fibroplasia, age- related macular degeneration, neovascular glaucoma, hemangiomas, thyroid hyperplasias (including Grave's disease), corneal and other tissue transplantation, and chronic inflammation. The antagonists also are useful for the treatment of diseases or disorders characterized by undesirable excessive vascular permeability, such as edema associated with brain tumors, ascites associated with malignancies, Meigs' syndrome. lung inflammation, nephrotic 55 aR syndrome, pericardial effusion (such as that associated with pericarditis), and pleural effusion. In a similar manner, the term “agonist” is used in the broadest sense and includes any molecule that mimics a biological activity of a } native PRO polypeptide disclosed herein. Suitable agonist or antagonist molecules specifically include agonist or antagonist antibodies or antibody fragments, fragments, or amino acid sequence variants of native PRO polypeptides, peptides, small organic molecules, etc.

A "small molecule” is defined herein to have a molecular weight below about 500 daltons.

The term "PRO polypeptide receptor” as used herein refers to a cellular receptor tor a PRO polypeptide, ordinarily a celi-surface receptor found on vascular endothelial cells, as well as variants thereof that retain the ability to bind a PRO polypeptide. "Antibodies" (Abs) and "immunoglobulins" (Igs) are glycoproteins having the same structural characteristics.

While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules that lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas. The term "antibody" is used in the broadest sense and specifically covers, without limitation, intact monoclonal antibodics, polyclonal antibodies, mulispecific antibodies (e.g., bispecific antibodies) formed from at least two intact antibodies, and antibody fragments, so long as they exhibit the desired biological activity. "Native antibodies" and "native immunoglobulins" are usually heterotetrameric glycoproteins of about 150,000 daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each light chain is linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages varies among the heavy chains of different immunoglobulin isotypes. Each heavy and light chain also has regularly spaced intrachain disulfide bridges. Each heavy chain has at one end a variable domain (Vy) followed by a number of constant domains. Each light chain has a variable domain at one end (V, ) and a constant domain at its other end; the constant . domain of the light chain is aligned with the first constant domain of the heavy chain, and the light-chain variable domain is aligned with the variable domain of the heavy chain. Particular amino acid residues are believed to form an interface between the light- and heavy-chain variable domains.

The term "variable" refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody to and for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies.

It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework regions (FR). The variable domains of native heavy and light chains cach comprise four FR regions, largely adopting a -sheet configuration. connected by three CDRs, which form loops connecting, and in some cases forming part of, the B-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies. See, Kabat er al., NIH Publ. N0.91-3242, Vol. 1, pages 647-669 (1991). The constant domains are not involved directly in binding an antibody to an antigen. but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity. "Antibody fragments” comprise a portion of an intact antibody. preferably the antigen-binding or variable region of the intact antibody. Examples of antibody fragments include Fab, Fab’, F(ab'),, and Fv fragments;

diabodies; linear antibodies (Zapata ez al., Protein Eng., 8(10): 1057-1062 (1995)); single-chain antibody molecules: and multispecific antibodies formed from antibody fragments.

Papain digestion of antibodics produces two identical antigen-binding fragments, called "Fab" fragments, each with a single antigen-binding site, and a residual "Fc" fragment, whose name reflects its ability to crystallize readily.

Pepsintreatment yields an F(ab"), fragment that has two antigen-combining sites and is still capable of cross-linking antigen. "Fv" is the minimum antibody tragment that contains a complete antigen-recognition and -binding site. This region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association.

It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the Vy-V, dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody.

However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.

The Fab fragment also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. Fab’ fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CH1 domain including one or more cysteines from the antibody hinge region. Fab'-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.

F(ab’), antibody fragments originally were produced as pairs of Fab’ fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.

The "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearlydistinct types, called kappa (x) and lambda (1), based on the amino acid sequences of their constant domains.

Depending on the amino acid sequence of the constant domain of their heavy chains, immunoglobulins can ’ be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM; and several of these may be further divided into subclasses (isotypes), e.g., IeG1,12G2,1gG3, 1gG4, IgA, and IgA2. ) The heavy-chain constant domains that correspond to the different classes of immunoglobulins are called a, 9, €, vy, and yu. respectively. The subunit structures and three-dimensional confi gurations of different classes of immunoglobulins are well known.

The term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific. being directed against a single antigenic site. Furthermore, in contrast to conventional (polyclonal) antibody preparations that typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity. the monoctonal antibodies are advantageous in that they are synthesized by the hybridoma culture, uncontaminated by other immunoglobulins. The modifier “monoclonal” indicates the character of the antibody as being obtained froma substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al., Nature, 256: 495 (1975), or may be made by recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567). The "monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature, 352:

624-628 (1991) and Marks er al, 1. Mol. Biol., 222: 581-597 (1991), for example.

The monoclonal antibodies herein specifically include "chimeric" antibodies (immunoglobulins) in which a portion of the heavy and/or fight chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging toa particular antibody class or subclass, while the remainder of the § chain(s)is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity. U.S. Patent No. 4,816,567; Morrison ez al. Proc. Natl, Acad. Sci. USA, 81: 6831 -6855 (1984). "Humanized" forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains, or fragments thereof (such as Fv, Fab, Fab’, F(ab), or other antigen-binding subsequences of antibodies) that contain minimal sequence derived from non-human immunoglobulin. For the most part, humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a CDR of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as touse, rat or rabbit having the desired specificity, affinity, and capacity. In some instances, Fv FR residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications are made to further refine and maximize antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or substantially ai} of the FR regions are those of a human immunoglobulin sequence. The humanized antibody preferably also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see

Jones ef al., Nature, 321: 522-525 (1986); Reichmann et al., Nature, 332: 323-329 (1988); and Presta, Curr. Op. :

Struct. Biol, 2: 593-596 (1992). The humanized antibody includes a PRIMATIZED™ antibody wherein the antigen-binding region of the antibody is derived froman antibody produced by immunizing macaque monkeys with ) the antigen of interest. "Single-chain Fv" or "sFv" antibody fragments comprise the Vand V, domains of an antibody, wherein these domains arc present in a single polypeptide chain. Preferably, the Fv polypeptide further comprises a polypeptide linker between the V,, and V; domains that enables the sFv to form the desired structure for antigen binding. For a review of SFV see, Pluckthun in The Pharmacology of Monoclonal Antibodies, Vol. 113, Rosenburg and Moore, eds. (Springer-Verlag: New York, 1994), pp. 269-31 5.

The term “diabodies" refers to small antibody fragments with two antigen-binding sites. which fragments comprise a heavy-chain variable domain (Vy) connected to a light-chain variable domain (V,) in the same polypeptide chain (Vy - Vy). Byusinga linker that is too short to allow pairing between the 1wo domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create TWO antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and

Hollinger ef al., Proc. Natl. Acad. Sci. USA, Y0: 6444-6448 (1993).

An “isolated” antibody is one that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proieinaceous ot nonproteinaceous solutes. In preferred embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody as determined by the Lowry method, and most preferably more than 99% by weight, (2) 10 a ’ degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blueor, preferably, silver stain. Isolated antibody includes thc antibody in site within recombinant cells, since at least one component of the antibody’s natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.

The word “label” when used herein refers to a detectable compound or other composition that is conjugated directly or indirectly to the antibody so as to generate a “labeled” antibody. The label may be detectable by itself (eg. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition that is detectable. Radionuclides that can serve as detectable labels include, for example, 1-131, 1-123, 1-125, Y-90, Re-188, At-211, Cu-67, Bi-212, and Pd-109. The label may also be a non- detectable entity such as a toxin.

By "solid phase” is meant a non-aqueous matrix to which an antibody of the present invention can adhere.

Examples of solid phases encompassed herein include those formed partially or entirely of glass (e.g., controlled pore glass), polysaccharides (e.g., agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones. In certain embodiments, depending on the context, the solid phase can comprise the well of an assay plate; in others - itis a purification column (e.g., an affinity chromatography column). This term also includes a discontinuous solid phase of discrete particles, such as those described in U.S. Patent No. 4,275,149. : 20 A "liposome" is a small vesicle composed of various types of lipids, phospholipids and/or surfactant that is useful for delivery of a drug (such as the PRO polypeptide or antibodies thereto disclosed herein) to a mammal. : The components of the liposome are commonly arranged in a bilayer formation, similar to the lipid arrangement of biological membranes. ; As used herein, the term "immunoadhesin” designates antibody-like molecules that combine the binding specificity of a heterologous protein (an "adhesin”) with the effector functions of immunoglobulin constant domains. Structurally, the immunoadhesins comprise a fusion of an amino acid sequence with the desired binding specificity that is other than the antigen recognition and binding site of an antibody (i.e., is "heterologous”), and an immunoglobulin constant domain sequence. The adhesin part of an immunoadhesin molecule typically is a contiguous amino acid sequence comprising at least the binding site of a receptor or a ligand. The immunoglobulin constantdomain sequence in the immunoadhesin may be obtained from any immunoglobulin, such as IgG- 1, 1gG-2, 1gG-3, or 1gG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE, 1gD, or IgM.

II. Compositions and Methods of the Invention

A. PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S. PRO321. PRO333, PRO840

PRO877, PRO878. PRO879, PRO882, PRO885 and PRO8BR7 Variants

In addition to the full-length native sequence PRO179, PRO238, PRO364. PRO844, PRO846, PRO1760,

PRO205,PR0O321,PR0O333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 and PRO887 polypeptides described herein, it is contemplated that PRO179, PRO238, PRO364, PROS. PRO846, PRO1760, PRO20S,

PRO321, PRO333, PRO840, PRO877. PRO878, PRO879, PRO882, PRO885 and PRO887 variants can be prepared. PRO}79, PRO238, PRO364, PROY44, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840,

PRO877,PRO878, PRO879, PRO882, PRO88S and PRO887 variants can be prepared by introducing appropriate nucleotide changes into the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 DNA, and/or by synthesis of the 5S desired PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PROS40,

PRO877, PRO878, PRO879, PRO882, PRO88S or PRO8S7 polypeptide. Those skilled in the art will appreciate that amino acid changes may alter post-translational processes of the PRO179, PR0O238, PRO364, PRO844,

PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PROB78, PRO879, PRO882, PRO8SS or

PRO887, such as changing the number or position of glycosylation sites or altering the membrane anchoring characteristics.

Variations in the native full-length sequence PRO179, PR0O238, PRO364, PRO844, PRO846, PRO1760,

PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 or PRO887, or in various domains of the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840,

PRO877,PR0O878, PRO879, PRO882, PRO885 or PRO887 described herein, can be made, for example, using any of the techniques and guidelines for conservative and non-conservative mutations set forth, for instance, in U.S.

Patent No. 5,364,934. Variations may be a substitution, deletion or insertion of one or more codons encoding the

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PROBSS or PROSS7 that results in a change in the amino acid sequence of the

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO88S or PRO887 as compared with the native sequence PRO179, PRO2338,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PR0O333, PRO840, PRO877, PRO878, PROBTY,

PRO882, PRO88S or PRO887. Optionally the variation is by substitution of at least one amino acid with any other : amino acid in one or more of the domains of the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 or PRO887. Guidance in 2S determining which amino acid residue may be inserted, substituted or deleted without adversely affecting the desired activity may be found by comparing the sequence of the PRO179, PR0O238. PRO364, PRO844, PRO846, PRO 1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 with that of homologous known protein molecules and minimizing the number of amino acid sequence changes made in regions of high homology. Amino acid substitutions can be the result of replacing one amino acid with another amino acid having similar structural and/or chemical properties, such as the replacement of a leucine with a serine, i.c., conservative amino acid replacements. Insertions or deletions may optionally be in the range of about 1 to 5 amino acids. The variation allowed may be determined by systematically making insertions, deletions or substitutions of amino acids in the sequence and testing the resulting variants for activity exhibited by the full-length or mature native sequence.

In particular embodiments, conservative substitutions of interest are shown in Table 3 under the heading of preferred substitutions. If such substitutions result in a change in biological activity, then more substantial changes, denominated exemplary substitutions in Table 3, or as further described below in reference to amino acid classes, are introduced and the products screened.

Table 3 : Original Exemplary Preferred

Residue Substitutions Substitutions

Ala (A) val; leu; ile val

ArgR) lys; gln; asn lys

Asn (N) gin; his; lys; arg gin

Asp (D) glu glu

Cys (C) ser ser

Gln (Q) asn asn

Gu@E) asp asp

Gly (G) pro; ala ala

His (H) asn; gin; lys; arg arg

Ile (I) leu; val; met; ala; phe; norleucine leu

Leu() norleucine; ile; val; met; ala; phe ile

Lys (K) arg; gin; asn arg

Met (M) leu; phe; ile feu

Phe (F) leu; val; ile; ala; tyr leu

Pro(P) ala ala

Ser (S) thr thr

Thr (T) ser ser

Trp (W) tyr; phe tyr

Tyr (Y) trp; phe; thr; ser phe wval(v) ile; leu; met; phe; - ala; norleucine leu

Substantial modifications in function or immunological identity of the PRO179, PRO238, PRO364, PRO844,

PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or

PRO887 polypeptide are accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side : chain. Naturally occurring residues are divided into groups based on common side-chain properties: uw (1) hydrophobic: norleucine, met, ala, val, leu, ile; (2) neutral hydrophilic: cys, ser, thr; (3) acidic: asp, glu; (4) basic: asn, gin, his, lys, arg; (5) residues that influence chain orientation: gly, pro; and (6) aromatic: trp, tyr, phe.

Non-conservative substitutions will entail exchanging a member of one of these classes for another class. 40 Such substituted residues also may be introduced into the conservative substitution sites or, more preferably, into the remaining (non-conserved) sites.

The variations can be made using methods known in the art such as oligonucleotide-mediated (site-directed) . mutagenesis. alanine scanning, and PCR mutagenesis. Site-directed mutagenesis [Carter et al., Nucl. Acids Res. 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)], cassette mutagenesis [Wells ef al., Gene, 34:315 45 (1985)), restriction selection mutagenesis [Wells er al., Philos. Trans. R. Soc. London SerA, 317:415 (1986)] or other known techniques can be performed on the cloned DNA to produce the PRO179, PRO238, PR0O364,

PRO844, PRO846, PRO1760, PRO20S5, PRO321, PRO333. PRO840, PRO877, PRO878, PRO879, PR0O8S2, 61

Ci

PRO885 or PRO887 variant DNA.

Scanning amino acid analysis can also be employed to identify one or more amino acids along a contiguous ) sequence. Among the preferred scanning amino acids are relatively small, neutral amino acids. Such amino acids include alanine, glycine, serine, and cysteine. Alanine is typically a preferred scanning amino acid among this group because it eliminates the side-chain beyond the beta-carbon and is less likely to alter the main-chain conformation of the variant [Cunningham and Wells, Science, 244: 1081-1085 (1989)]. Alanine is also typically preferred because it is the most common amino acid. Further, it is frequently found in both buried and exposed positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.); Chathia, I. Mol. Biol., 150:1 (1976)]. If alanine substitution docs not yicld adequate amounts of variant, an isoteric amino acid can be used.

B. Modifications of PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 and PRO887

Covalent modifications of PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 and PRO887 are included within the scope of this invention. One type of covalent modification includes reacting targeted amino acid residues of a PRO179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO8TS,

PRO879, PRO882, PRO88S or PRO887 polypeptide with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues of the PRO179, PRO238, PRO364, PRO844, PRO846,

PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887.

Derivatization with bifunctional agents is useful, for instance, for crosslinking PRO179, PRO238, PRO364,

PROS844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PRO885 or PRO8S87 10 a water-insoluble support matrix or surface for use in the method for purifying anti- :

PRO179, anti-PR0O238, anti-PRO364, anti-PRO844, anti-PR0O846, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PR0O333, anti-PRO840, anti-PRO877, anti-PRO8B78, anti-PR0O879, anti-PRO882, anti-PRO8RS or anti-PROBRT antibodies, and vice-versa. Cornmonly used crosslinking agents include, e.g., 1, 1-bis(diazoacetyl)-2-phenylethanc, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3"-dithiobis(succinimidylpropionate). bifunctional maleimides such as bis-N-maleimido-1,8-octane and agents such as methyl-3-{(p-azidophenyl)dithio]propioimidate.

Other modifications include deamidation of glutaminyl and asparaginyl residues to the corresponding elutamy! and asparty! residucs, respectively, hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the a-amino groups of lysine, arginine. and histidine side chains [T.E. Creighton, Proteins: Structure and Molecular Properties, W H. Freeman & Co.. San Francisco, pp. 79-86 (1983)), acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.

Another type of covalent modification of the PRO179, PRO238, PRO364. PROB, PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRORS2, PRO885 or PRO887 polypeptide included within the scope of this invention comprises altering the native glycosylation pattern of the polypeptide. "Altering the native glycosylation pattern” is intended for purposes herein to mean deleting one or more carbohydrate moieties found in native sequence PRO179, PRO238, PRO364, PROS. PROS846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or PRO887 (either by removing the underlying glycosylation site or by deleting the glycosylation by chemical and/or enzymatic means), . and/or adding one or more glycosylation sites that are not present in the native sequence PRO179, PR0O238,

PRO364, PRO844, PRO846, PRO1760, PRO20S, PR0O321, PRO333. PRO840, PRO877, PRO878, PRO879,

PRO882, PRO88S or PRO887. In addition, the phrase includes qualitative changes in the glycosylation of the

S native proteins, involving a change in the nature and proportions of the various carbohydrate moieties present.

Addition of glycosylation sites to the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205,

PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROBS or PRO887 polypeptide may be accomplished by altering the amino acid sequence. The alteration may be made, for example, by the addition of, or substitution by, ore or more serine or threonine residues to the native sequence PRO179, PRO238, PRO364,

PROB44, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PROSS2,

PRO885 or PRO887 (for O-linked glycosylation sites). The PRO179, PRO238, PRO364, PRO844, PRO846,

PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 amino acid sequence may optionally be altered through changes at the DNA level, particularly by mutating the DNA encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840,

PRO877,PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.

Another means of increasing the number of carbohydrate moieties on the PRO179, PRO238, PRO364, y PROR44, PRO846, PRO1760, PRO20S5, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO382, : PRO885 or PRO887 polypeptide is by chemical or enzymatic coupling of glycosides to the polypeptide. Such methods are described in the art, e.g., in WO 87/05330 published 11 September 1987, and in Aplin and Wriston,

CRC Crit. Rev. Biochem., pp. 259-306 (1981). : Removal of carbohydrate moieties present on the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO20S. PRO321, PR0O333, PRO840, PROR77, PRO878, PRO879, PRO882, PRO885 or PRO8S7 polypeptide may be accomplished chemically or enzymatically or by mutational substitution of codons encoding for amino acid . 25 residues that serve as targets for glycosylation. Chemical deglycosylation techniques are known in the art and described, for instance, by Hakitnuddin, ez al., Arch. Biochem. Biophys., 259:52 (1987) and by Edge er al., Anal.

Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura er al., Meth. Enzvmol.. 138:350 (1987).

Another type of covalent modification of PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO20S. PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 comprises linking the PRO17Y, PR0O238, PRO364, PRO844, PRO846, PRO 1760, PRO205. PRO321, PRO333. PRO840,

PRO877, PRO878, PRO879, PRO882, PRO885 or PROS? polypeptide to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the manner set forth in

U.S. Patent Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179.337.

The PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321. PRO333, PRO840,

PRO877,PRO878,PRO879,PRO882, PRO8SS or PRO887 of the present invention may also be modified in a way to form a chimeric molecule comprising PRO179, PR0O238, PRO364, PRO844, PRO846. PRO1760, PRO205,

PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 fused to another, heterologous polypeptide or amino acid sequence.

In one embodiment, such a chimeric molecule comprises 2 fusion of the PRO179, PRO238, PRO364,

PROBA4, PROBA, PRO1760, PRO205, PRO321, PRO333, PROS40, PRO8T7, PRO878, PROS79, PROSS2, }

PRO¥SS or PROBST with atag polypeptide which provides an epitope 10 which an anti-tag antibody can selectively bind. The epitope tag is generally placed at the amino- or carboxyl- terminus of the PRO179, PRO238, PRO364, pRO844, PROBA4S, PRO1760, PRO20S, PRO32}, PRO333, PROS40, PRO8TT, PRO878, PROBS, PROS882,

PROS88S or PROBST. The presence of such epitope-tagged forms of the PRO179, PRO238, PRO364, PRO3844,

PRO846, PRO1760, PRO20S. PRO321, PRO333, PRO84U, PROS77, PROSTS, PRO879, PROBS2, PROSBS or

PRO8S7 can be detected using an antibody against the tag polypeptide. Also, provision of the epitope tag enables the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PROB40, PROS77,

PROS878, PROS79, PROBS82, PRO8SS or PROSST to be readily purified by affinity purification using an anti-tag antibody or another type of affinity matrix that binds to the epitope tag. Various tag polypeptides and their respective antibodies are well known in the art. Examples include poly-histidine (poly-His) or poly-histidine- glycine (poly-His-gly) tags; the flu HA tag polypeptide and its antibody 12CAS (Field er al., Mol. Cell. Biol, 8:2159-2165 ( 1988)]: the c-myc tag and the 8F9, 3C7, 6E10. G4. B7 and 9E10 antibodies thereto [Evan et al.

Molecular and Cellular Biology, 5:3610-361 6 (1985)}; and the Herpes Simplex virus glycoprotein D (gD) tag and its antibody {Paborsky ef al., Protein Engineering, 3(6):547-553 (1990). Othertag polypeptides include the Flag- peptide {Hopp €t al., BioTechnology, 6:1204-1210 (1988)}; the KT3 epitope peptide {Martin ef al., Science, 255:192-194 (1992)}; an «-tubulin epitope peptide {Skinner ef al., J. Biol. Chem. 266:15163-1 5166 (1991)); and the T7 gene 10 protein peptide tag {Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA, 87. 16393-6397 (1990)].

In an alternative embodiment, the chimeric molecule may comprise a fusion of the PRO179, PRO238,

PRO364, PROS44, PRO846, PRO1760, PRO205, PRO321, PRO333, PROB40, PROSTT, PROB78, PROB879,

PROS8S2, PRO83S or PRO887 withan immunoglobulinor a particular region of an immunoglobulin. Fora bivalent : form of the chimeric molecule (also referred to as an «jmmunoadhesin™), such a fusion could be to the Fc region of an 1gG molecule. The Ig fusions preferably include the substitution of asoluble (transmembrane domain deleted 75 orinactivated) form of aPRO179,PRO23E, PRO364, PROB44, PROS846, PRO1760. PRO205,PRO32L, PRO333,

PROR40, PROT, PRO378, PROBT9, PRO8S2, PROB8S or PROSE polypeptide in place of at leastone variable region within an Ig molecule. Ina particularly preferred embodiment, the immunoglobulin fusion includes the hinge, CH2 and CH3, or the hinge. CH1, CH2 and CH3 regions of an 1gG} molecule. For the production of jmmunoglobulin fusions see also, Us Patent No. 5,428,130 issued June 27, 1995.

C. a IT FROZE, PROS, PROS. PROB POI EROS EEE

PRO333. PROBAO, PRORTT, PROBYS. pROBTY, PROBED, PRORSKS and PROBE]

The present invention provides newly identified and isolated nucleotide sequences encoding polypeptides referred to in the present application as PRO179, PRO238, PRO364, PRO844, PROR46, PRO1760. PRO205.

PRO321,PRO333, PRO&40, PRO877. PRO8T8, PROSTY, PROBR?, PRO8SS or PROS37. In particular. cDNAs encoding PRO179, PRO238, PRO364. PROg44, PROB4S, PRO1760, PRO205. PRO321, PRO333. PRO840,

PROR77, PROB78, PROB79, PRO8E2. PROSSS or PROBST polypeptides have been identified and isolated, as disclosed in further detail in the Examples pelow. Itis noted that proteins produced in separate expression rounds may be given dif ferent PRO numbers but the UNQ number is unique for any given DNA and the encoded protein,

and will not be changed. However, for sake of simplicity, in the present specification the protein encoded by

DNA16451-1388, DNA35600-1162, DNA47365-1206, DNA59838-1462, DNA44196-1353, DNA 76532-1702,

DNA30868, DNA34433, DNA41374, DNA53987, DNA58120, DNAS58121, DNAS8122, DNA58125, DNAS8128, or DNA58130, as well as all further native homologues and variants included in the foregoing definition of

PROI179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO88S or PRO887, will be referred to as “PRO179", “PRO238", “PRO364", “PRO844", “PRO846", “PRO1760", “PR0O205", “PRO321", “PRO333", “PRO840", “PRO877", “PRO878", “PRO879", “PRO882", “PRO885" or “PROBS7", respectively, regardless of their origin or mode of preparation.

The description below relates primarily to production of PRO179, PRO238, PRO364, PRO844, PR0O846,

PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PROS? polypeptides by culturing cells transformed or transfected with a vector containing nucleic acid encoding PRO179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PROS78,

PRO879, PRO882, PRO885 or PRO887 polypeptides. It is, of course, contemplated that alternative methods that are well known in the art may be employed to prepare PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO20S,PRO321, PRO333, PRO840, PRO877, PRO878. PROS79, PRO882, PRO88S or PRO887. For instance, the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide sequence, or portions thereof, may be produced by direct peptide synthesis using solid-phase techniques. See, e.g., Stewart et al., Solid-Phase Peptide Synthesis (W.H.

Freeman Co.: San Francisco, CA, 1969); Merrifield, J. Am. Chem. Soc., 85: 2149-2154 (1963). In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be accomplished, for instance, with an Applied Biosystems Peptide Synthesizer (Foster City. CA) using manufacturcr's instructions. : Various portions of PRO179, PR0O238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333,

PRO840. PRO877, PRO878, PRO879, PRO882, PR0O885 or PRO887 may be chemically synthesized separately and combined using chemical or enzymatic methods to produce the full-length PRO179, PRO238, PRO364, - 25 PROB844, PRO846, PRO1760, PRO205, PRO321, PRO333. PRO840, PRO877, PRO878, PRO879, PROSS2,

PRO885 or PRO887 polypeptide. i. Isolation of DNA Encoding PRO179, PR0O238, PRO364, PROB44, PRO846, PRO1760, PRO20S

PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8]2, PRO88S or PRO887

DNA encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333,

PRO840,PRO877, PRO878, PRO879, PRO882, PRO8SS or PRO887 polypeptide may be obtained from a cDNA library prepared from tissue believed to possess the mRNA encoding PRO179, PRO238, PRO364, PRO844,

PROB46, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877. PRO878, PRO879, PRO882, PROSSS or

PRO887 and to express it at a detectable level. Accordingly, DNAs encoding human PRO179, human PRO238, human PRO364, human PRO844, human PRO846, human PRO1760, human PRO205, human PRO321. human

PRO333, human PRO840, human PRO877, human PRO878, human PRO879, human PRO882, human PRO8S5 or human PRO887 can be conveniently obtained from cDNA libraries prepared from human tissues, such as described in the Examples. The gene encoding PRO179, PRO238, PRO364, PRO844, PRO846, PROI760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879. PRO882, PRO885 or PRO8S87 polypeptide ray also be obtained from a genomic library of by oligonucleotide synthesis.

Libraries can be screened with probes (such as antibodies to the PRO179, PRO238, PRO364, PROR44,

PROB46, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO8T77, PRO878, PRO879, PRO882, PRO83S or

PRO887 polypeptide or oligonucleotides of at least about 20-80 bases) designed to identify the gene of interest or the protein encoded by it. Screening the cDNA or genomic library with the selected probe may be conducted using standard procedures, such as described in Sambrook ef al. supra. An alternative means to isolate the gene encoding

PRO179, PRO238, PRO364, PROB44, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PROS77,

PRO878. PRO879, PRO882, PROBS or PROS887 is to use PCR methodology. Sambrook ef al., supra,

Dieffenbach ef al., PCR Primer: A Laboratory Manual (New York: Cold Spring Harbor Laboratory Press, 1995).

The Examples below describe techniques for screening a cDNA library. The oligonucleotide sequences selected as probes should be of sufficient length and sufficiently unambiguous that false positives are minimized.

The oligonucleotide is preferably labeled such that it can be detected upon hybridization to DNA in the library being screened. Methods of labeling are well known in the art, and include the use of radiolabels like 3p.labeled ATP, biotinylation, or enzyme labeling. Hybridization conditions, including moderate stringency and high stringency. are provided in Sambrook ef al., supra.

Sequences identified in such library screening methods can be compared and aligned to other known . sequences deposited and available in public databases such as GenBank or other private sequence databases.

Sequence identity (at either the amino acid or nucleotide level) within defined regions of the molecule or across the full-length sequence can be determined through sequence alignment using computer software programs such as

ALIGN, DNAstar, and INHERIT, which employ various algorithms to measure homology.

Nucleic acid having protein coding sequence may be obtained by screening selected cDNA or genomic libraries using the deduced amino acid sequence disclosed herein for the first time, and, if necessary, using conventional primer extension procedures as described in Sambrook er al., supra, 1© detect precursors and processing intermediates of mRNA that may not have been reverse-transcribed into cDNA. ii. Selection and Transformation of Host Cells

Host cells are transfected or transformed with expression or cloning vectors described herein for PRO179,

PRO238. PRO364, PROB44, PROB46, PRO1760, PRO20S, PRO321, PRO333, PRO840. PROB77. PROS878.

PRO879. PRO882, PRO88S or PRO887 production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, of amplifying the genes encoding the desired sequences. The culwre conditions, such as media, temperature, pH, and the like, can be selected by the skilled artisan without undue experimentation. In general, principles, protocols, and practical techniques for maximizing the productivity of cell cultures can be found in Mammalian Cell Biatechnalogy: A Practical Approach, M. Butler, ed. (IRL Press, 1991) and Sambrook ef al.. supra.

Methods of transfection are known to the ordinarily skilled artisan, for example, CaPO; treatment and electroporation. Depending on the host cell used, transformation is performed using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride, as described in Sambrook ef al., supra, OF electroporation js generally used for prokaryotes or other cells that contain substantial cell-wall barriers.

Infection with Agrobacterium tumefaciens is used for transformation of certain plant cells. as described by Shaw et al., Gene, 23: 315 (1983) and WO 89/05859 published 29 June 1989. For mammalian cells without such cell ] walls, the calcium phosphate precipitation method of Graham and van der Eb, Virology, 52:456-457 (1978) can be employed. General aspects of mammalian cell host system transformations have been described in U.S. Patent No. 4,399,216. Transformations into yeast are typically carried out according to the method of Van Solingen et al., J.

Bact., 130: 946 (1977) and Hsiao et al., Proc. Natl. Acad. Sci. (USA), 76: 3829 (1979). However, other methods for introducing DNA into cells, such as by nuclear microinjection, electroporation, bacterial protoplast fusion with intact cells, or polycations, e.g., polybrene or polyornithine, may also be used. For various techniques for transforming mammalian cells, see, Keown er al., Methods in Enzymology, 185: 527-537 (1990) and Mansour ef al., Nature, 336: 348-352 (1988).

Suitable host cells for cloning or expressing the DNA in the vectors herein include prokaryote, yeast, or higher eukaryote cells. Suitable prokaryotes include, but are not limited to, eubacteria, such as Gram-negative or Gram- positive organisms, for example, Enterobacteriaceae such as E. coli. Various E. coli strains are publicly available, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776 (ATCC 31,537); E. coli strain W3110 (ATCC 27,325); and KS 772 (ATCC 53,635). Other suitable prokaryotic host cells include Enterobacteriaceae such as

Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e. 8. Salmonella typhimurium,

Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. licheniformis (e.g.,

B. licheniformis 41P disclosed in DD 266,710 published 12 April 1989), Pseudomonas such as P. aeruginosa, and

Streptomyces. These examples are illustrative rather than limiting. Strain W3110 is one particularly preferred host or parent host because it is a common host strain for recombinant DNA product fermentations. Preferably, the host cell secretes minimal amounts of proteolytic enzymes. For example, strain W3110 may be modified to cffect a genetic mutation in the genes encoding proteins endogenous to the host, with examples of such hosts including E. : coli W3110 strain 1A2, which has the complete genotype tonA ; E. coli W3110 strain 9E4, which has the complete genotype tonA ptr3; E. coliW3110 strain 27C7 (ATCC 55,244), which has the complete genotype tonA ptr3 phoA

E15 (argF-lac)i69 degP ompTkan'; E. coli W3110 strain 37D6, which has the complete genotype tonA ptr3 phoA

EIS (argF-lac)i69 degP ompT rbs7 ilvG kan"; E. coli W3110 strain 40B4, which is strain 37D6 with a non- kanamycin resistant deg P deletion mutation; and an E. coli strain having mutant periplasmic protease disclosed in

U.S. Patent No. 4,946,783 issued 7 August 1990. Alternatively, in vitro methods of cloning, e.g., PCR or other nucleic acid polymerase reactions, are suitable.

In addition to prokaryotes, eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for vectors encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205,

PRO321, PRO333, PRO840, PRO877. PRO878, PRO879, PRO882, PRO88S or PRO887. Saccharomyces cerevisiae is a commonly used lower eukaryotic host microorganism. Others include Schizosaccharomyces pombe (Beach and Nurse, Nature, 290: 140 [1981]; EP 139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Patent

No. 4,943,529; Fleer et al., Bio/Technology, 9: 968-975 (1991)) such as, e.g., K. lactis (MW98-8C, CBS683,

CBS4574; Louvencourtetal., J, Bacteriol, 737 [1983)), K. fragilis (ATCC 12,424). K. bulgaricus (ATCC 16,045),

K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al.,

Bio/Technology, 8: 135 (1990), K . thermotolerans, and K. marxianus; yarrowia (EP 402,226): Pichia pastoris (EP 183,070; Sreckrishna ef al., J. Basic Microbiol. 28: 265-278 [1988)); Candida: Trichoderma reesia (EP 244,234). Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA, 76: 5259-5263 [1979]): Schwanniomyces 67 suchas Schwanniomyces occidentalis (EP 394,538 published 31 October 1990); and filamentous fungisuchas,e.g.,

Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10 January 1991), and Aspergillus hosts such } as A. nidulans (Ballance er al., Biochem. Biophys. Res. Commun., 112: 284-289 [1983]; Tilbum ez al., Gene, 26: 205-221 [1983); Yelton et al., Proc. Natl. Acad. Sci. USA, 81: 1470-1474 [1984]) and A. niger (Kelly and Hynes,

S EMBO, 4: 475-479 [1985)). Methylotropic yeasts are suitable herein and include, but are not limited to, yeast capable of growth on methanol selected from the genera consisting of Hansenula, Candida, Kloeckera, Pichia,

Saccharomyces, Torulopsis, and Rhodotorula. A list of specific species that are exemplary of this class of yeasts may be found in C. Anthony, The Biochemistry of Methylotrophs, 269 (1982).

Suitable host cells for the expression of nucleic acid encoding glycosylated PRO179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO87Y9, PROSS2,

PROB85 or PRO887 are derived from multicellular organisms. Examples of invertebrate cells include insect cells such as Drosophila S2 and Spodoptera Sf9, as well as plant cells. Examples of useful mammalian host cell lines include Chinese hamster ovary (CHO) and COS cells. More specific examples include monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, Graham er al, I. Gen. Virol, 36: 59 (1977)); Chinese hamster ovary cells/-DHFR (CHO, Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 17:4216 (1980)); mouse sertoli cells (TM4, Mather, Biol.

Reprod., 23:243-251 (1980)); human lung cells (W138, ATCC CCL 75); human liver cclls (Hep G2, HB 8065); and mouse mammary tumor (MMT 060562, ATCC CCLS51). The selection of the appropriate host cell is deemed to be within the skill in the art. iii. Selection and Use of a Replicabie Vector

The nucleic acid (e.g., cDNA or genomic DNA) encoding PRO 179, PRO238, PRO364, PRO844, PRO846, :

PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PROS78, PRO879, PRO8S2, PRO885 or PRO887 may be inserted into a replicable vector for cloning (amplification of the DNA) or for expression. Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage.

The appropriate nucleic acid sequence may be inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence if the sequence is to be secreted, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniqucs that are known to the skilled artisan.

The PRO179, PRO238, PRO364, PRO844, PRO846, PROI760, PRO205. PRO321, PRO333. PRO840.

PRO877,PRO878, PRO879, PRO882, PRO88S or PRO8S7 may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific clcavage site at the N-terminus of the mature protein or polypeptide. In general, the signal sequencemaybea component of the vector, or it may be a part of the DNA encoding PRO 179, PRO238, PRO364,

PROB844, PROB46, PRO1760, PRO205, PRO32}, PRO333, PRO840. PRO877. PRO878, PRO879, PRO8S2,

PRORRS or PRO887 that is inserted into the vector. The signal sequence nay be a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, Ipp. or heat-stable enterotoxin If leaders. For yeast secretion the signal sequence may be, e.g., the yeast invertase leader, alpha factor leader . (including Saccharomyces and Kluyveromyces a-factor leaders, the latter described in U.S. Patent No. 5,010,182), or acid phosphatase leader, the C. albicans glucoamylase leader (EP 362,179 published 4 April 1990), or the signal described in WO 90/13646 published 15 November 1990. In mammalian cell expression, mammalian signal sequences may be used to direct secretion of the protein, such as signal sequences from secreted polypeptides of the same or related species, as well as viral secretory leaders.

Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells. Such sequences are well known for a variety of bacteria, yeast, and viruses. The origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2u plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV, or BPV) are useful for cloning vectors in mammalian cells.

Expression and cloning vectors will typically contain a selection gene, also termed a selectable marker.

Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (¢) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.

An example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the nucleic acid encoding PRO179, PRO238, PR0O364, PRO844, PRO846, PRO} 760,

PRO205,PR0O321,PRO333,PRO840, PRO877, PRO878, PRO879,PRO882, PROSSS or PRO887, such as DHFR or thymidine kinase. An appropriate host cell when wild-type DHFR is employed is the CHO cell line deficient in DHFR activity, prepared and propagated as described by Urlaub ef al., Proc. Natl. Acad. Sci. USA, 77: 4216 (1980). A suitable selection gene for usc in yeast is the trp] genc present in the yeast plasmid YRp7. Stinchcomb eral. Nature, 282: 39 (1979); Kingsman et al., Gene, 7: 141 (1979); Tschemper et al., Gene, 10: 157 (1980). The trp] gene provides a selection marker for a mutant strain of yeast lacking the ability to grow in tryptophan, for example, ATCC No. 44076 or PEP4-1. Jones, Genetics, 85: 12 (1977).

Expression and cloning vectors usually contain a promoter operably linked to the nucleic acid sequence encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840,

PRO877, PROB78. PRO879, PRO882, PRO885 or PRO8S7 to direct mRNA synthesis. Promoters recognized by a variety of potential host cells arc well known. Promoters suitable for use with prokaryotic hosts include the p- lactamase and lactose promoter systems (Chang et al., Nature, 275: 615 (1978); Goeddel er al., Nature, 281: 544 (1979). alkaline phosphatase, a tryptophan (trp) promoter system (Goeddel, Nucleic Acids Res., 8: 4057 (1980):

EP 36,776), and hybrid promoters such as the tac promoter. deBoer er al.. Proc. Natl. Acad, Sci. USA, 80: 21-25 (1983). Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding PRO179, PRO238, PRO364, PRO844, PRO346, PRO1760, PRO205, PRO321, PRO333,

PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PROS87.

Examples of suitable promoting sequences for use with yeast hosts include the promoters for 3- phosphoglycerate kinase (Hitzeman ez al., J. Biol. Chem, 255: 2073 (1980)) or other glycolytic enzymes (Hess er al.,J. Adv. Enzyme Reg., 7: 149 (1968); Holland, Biochemistry, [7: 4900(1978)), such as enolase, glyceraldehyde- 3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase. and 69 j glucokinase.

Other yeast promoters that are inducible promoters having the additional advantage of transcription controlled by growth conditions are the promoter regions for alcohol dehydrogenase 2, isocytochrome C, acid phosphatase, degradative enzymes associated with nitrogen metabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase, and enzymes responsible for maltose and galactose utilization. Suitable vectors and promoters for usc in yeast expression are further described in EP 73,657.

PRO179,PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PROS77,

PRO878, PRO879, PRO882, PRO88S or PRO887 nucleic acid transcription from vectors in mammalian host cells is controlled, for example, by promoters obtained fromthe genomes of viruses such as polyoma virus, fowlpox virus (UK 2,211,504 published 51 uly 1989), adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus, and Simian Virus 40 (SV40); by heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter; and by heat-shock promoters, provided such promoters are compatible with the host cell systems.

Transcription of a DNA encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205,

PRO321,PRO333,PRO840, PRO877, PRO878, PRO879, PRO8S2, PROSSS or PROSS7 by higher eukaryotes may be increased by inserting an enhancer sequence into the vector. Enhancers are cis-acting elements of DNA, usually about from 10 to 300 bp, that act on a promoter to increase its transcription. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, a-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. The enhancer may be spliced into the vector at a position §' or 3' to the sequence coding for PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SSS or PROSR7, but is preferably located at a site §' from the promoter.

Expression vectors used in eukaryotic host cells (yeast. fungi, insect, plant, animal, human, or nucleated cells from other multicellular organisms) will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5’ and. occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding PRO179, PRO238, PRO364. PRO844,

PROB846, PRO1760, PRO20S, PRO321, PRO333, PRO840. PRO877, PRO878, PRO879, PRO8S2. PRO8SS or

PROS887.

Still other methods, vectors, and host cells suitable for adaptation to the synthesis of PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO32], PRO333, PRO840. PRO877, PRO878. PRO879,

PROB8B2. PROSRS or PRO887 in recombinant vertebrate cell culture are described in Gething er al., Nature, 293: 620-625 (1981); Mantei et al., Nature, 281: 40-46 (1979): LP 117.060; and EP 117.058. iv. Detecting Gene Amplification/Expression

Gene amplification and/or expression may be measured in a sample directly, for example, by conventional

Southern blotting, Northern blotting to quantitate the transcription of mRNA (Thomas, Proc. Natl. Acad. Sci. USA,

77:5201-5205 (1980)), dot blotting (DNA analysis), or in situ hybridization, using an appropriately labeled probe, . based on the sequences provided herein. Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes.

The antibodies in turn may be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon the formation of duplex on the surface, the presence of antibody bound 10 the duplex can he detected.

Gene expression, alternatively, may be measured by immunological methods, such as immunohistochemical staining of cells or tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared againstanative-sequence PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333,

PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to DNA encoding PRO179,

PRO238, PRO364, PRO844, PROB46, PRO176(), PRO205, PRO321, PRO333, PRO840, PRO877, PRO878,

PRO879, PRO882, PRO885 or PRO887 and encoding a specific antibody epitope. v. Purification of Polypeptide

Forms of PRO179, PR0O238, PRO364, PRO844, PR0846, PRO 1760, PRO205, PRO321,PR0O333, PRO840,

PRO877, PRO878, PRO879, PRO882, PRO88S5 or PRO887 polypeptides may be recovered from culture medium or from host cell lysates. If membrane-bound, it can be released from the membrane using a suitable detergent solution (e.g., TRITON-X™ 100) or by enzymatic cleavage. Cells employed in expression of nucleic acid encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, : PRO878, PRO879, PRO882, PROS8S or PRO887 polypeptide can be disrupted by various physical or chemical means, such as freeze-thaw cycling, sonication, mechanical disruption, or cell-lysing agents. It may be desired to purify the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S. PRO321, PRO333, PRO840, i PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide from recombinant cell proteins or polypeptides. The following procedures are exemplary of suitable purification procedures: by fractionation on an ion-exchange column; ethanol precipitation: reverse phase HPLC; chromatography on silica or on a cation-exchange resin such as DEAE; chromatofocusing; SDS-PAGE; ammonium sulfate precipitation: gel filtration using, for example, Sephadex G-75; protein A Sepharose columns 10 remove contaminants such as IgG; and metal chelating columns to bind epitope-tagged forins of the PRO179, PR0238, PRO364, PRO844, PRO846, PRO 1760, PRO20S,

PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide. Various methods of protein purification may be employed and such methods are known in the art and described, for example, in Deutscher, Methods in Enzymology, 182 (1990); Scopes, Protein Purification: Principles and Practice (Springer-Verlag: New York, 1982). The purification step(s) selected will depend. for example. on the nature of the production process used and the particular PRO179, PRO238, PRO364, PRO844. PRO846. PRO1760.

PRO205, PRO321, PRO333, PRO840. PRO877, PRO878, PRO879, PRO882, PRO8S3 or PRO887 produced. 71

A

D. Uses of the PRO179, PRO238. PRO364, PRO844, PRO846, PRO1760, PRQ205, PRO321, PRO333,

PRO840, PRO877, PRQ878, PRO879, PRO882, PRO88S or PRO887 polypeptides i. Assays for Cardiovascular, Endothelial, and Angiogenic Activity

Various assays can be used to test the polypeptide herein for cardiovascular, endothelial, and angiogenic activity. Such assays include those provided in the Examples below.

Assays for testing for endothelin antagonist activity, as disclosed in U.S. Pat. No. 5,773,414, include aratheart ventricle binding assay where the polypeptide is tested for its ability to inhibit iodinized endothelin-1 binding in a receptor assay, an endothelin receptor binding assay testing for intact cel! binding of radiolabeled endothelin- 1 using rabbit renal artery vascular smooth muscle cells, an inositol phosphate accumulation assay where functional activity is determined in Rat-1 cells by measuring intra-cellular levels of second messengers, an arachidonic acid relcase assay that measures the ability of added compounds to reduce endothelin-stimulated arachidonic acid release in cultured vascular smooth muscles, in vitro (isolated vessel) studies using endothelium from male New Zealand rabbits, and in vivo studies using male Sprague-Dawley rats.

Assays for tissue generation activity include, without limitation, those described in WO 95/16035 (bone, cartilage, tendon): WO 95/05846 (nerve, neuronal), and WO 91/07491 (skin, endothelium).

Assays for wound-healing activity include, for example, those described in Winter, Epidermal Wound Healing,

Maibach, HI and Rovee, DT, eds. (Year Book Medical Publishers, Inc., Chicago), pp. 71 -112, as modified by the article of Eaglstein and Mertz, J. Invest. Dermatol, 71: 382-384 (1978).

An assay to screen for a test molecule relating to a PRO polypeptide that binds an endothelin B, (ETB,) receptor polypeptide and modulates signal transduction activity involves providing a host cell transformed with a

DNA encoding endothelin B, receptor polypeptide, exposing the cells to the test candidate, and measuring endothelin B, receptor signal transduction activity, as described, e.g., in U.S. Pat. No. 5,773,223. .

There are several cardiac hypertrophy assays. In vitro assays include induction of spreading of adult rat cardiac myocytes. In this assay, ventricular myocytes are isolated from a single (male Sprague-Dawley) rat, essentially following a modification of the procedure described in detail by Piper er al.. “Adult ventricular rat heart muscle cells” in Cell Culture Techniques in Heart and Vessel Research, H.M. Piper, ed. (Berlin: Springer-Verlag, 1990), pp. 36-60. This procedure permits the isolation of adult ventricular myocytes and the long-term culture of these cells in the rod-shaped phenotype. Phenylephrine and Prostaglandin F,, (PGF,,) have becn shown to induce a spreading response in these adult cells. The inhibition of myocyte spreading induced by PGF, or PGF», analogs (ez. fluprostenol) and phenylephrine by various potential inhibitors of cardiac hypertrophy is then tested.

One example of an in vivo assay is a test for inhibiting cardiac hypertrophy induced by fluprostenol in vivo.

This pharmacological model tests the ability of the PRO polypeptide to inhibit cardiac hypertrophy induced in rats (e.g., male Wistar or Sprague-Dawley) by subcutaneous injection of fluprostenol (an agonist analog of PGF,,). It , is known that rats with pathologic cardiac hypertrophy induced by myocardial infarction have chronically elevated ) 35 levels of extractable PGF,, in their myocardium. Lai etal, Am. J. Phvsiol. (Heart Circ, Physiol), 271: H2197-

H2208 (1996). Accordingly. factors that can inhibit the effects of fluprostenol on myocardial growth in vivo are potentially useful for treating cardiac hypertrophy. The effects of the PRO polypeptide on cardiac hypertrophy are determined by measuring the weight of heart, ventricles, and left ventricle (normalized by body weight) relative to fluprostenol-treated rats not receiving the PRO polypeptide.

Another example of an in vivo assay is the pressure-overload cardiac hypertrophy assay. For in vivo testing } itis common to induce pressure-overload cardiac hypertrophy by constriction of the abdominal aorta of test animals.

In a typical protocol, rats (e.g., male Wistar or Sprague-Dawley) are treated under anesthesia, and the abdominal aorta of each rat is narrowed down just below the diaphragm. Beznak M., Can. J. Biochem. Physiol., 33: 985-94 (1955). The aorta is exposed through a surgical incision, and a blunted needle is placed next to the vessel. The aorta is constricted with a ligature of silk thread around the needle, which is immediately removed and which reduces the lumen of the aorta to the diameter of the needle. This approach is described, for example, in Rossi ef al, Am. Heart J., 124: 700-709 (1992) and O’Rourke and Reibel, P.S.E.M.B., 200: 95-100 (1992).

In yet another in vivo assay, the effect on cardiac hypertrophy following experimentally induced myocardial infarction (MI) is measured. Acute MI is induced in rats by lcft coronary artery ligation and confirmed by electrocardiographic examination. A sham-operated group of animals is also prepared as control animals. Earlier data have shown that cardiac hypertrophy is present in the group of animals with MI, as evidenced by an 18% increase in heart weight-to-body weightratio. Lai etal, supra. Treatment of these animals with candidate blockers of cardiac hypertrophy, e.g., PRO polypeptide, provides valuable information about the therapeutic potential of the candidates tested. One further such assay test for induction of cardiac hypertrophy is disclosed in U.S. Pat. No. 5,773,415, using Sprague-Dawley rats.

For cancer, a variety of well-known animal models can be used to further understand the role of the genes identified herein in the development and pathogenesis of tumors, and to test the efficacy of candidate therapeutic agents, including antibodies and other antagonists of the native PRO polypeptides, such as small-molecule antagonists. The in vivo nature of such models makes them particularly predictive of responses in human patients.

Animal models of tumors and cancers (e.g., breast cancer, colon cancer, prostate cancer, lung cancer, etc.) include : both non-recombinant and recombinant (transgenic) animals. Non-recombinant animal models include, for example, rodent, e.g., murine models. Such models can be generated by introducing tumor cells into syngeneic mice using standard techniques, e.g., subcutancous injection, tail vein injection, spleen implantation, intraperitoneal implantation, implantation under the renal capsule, or orthopin implantation, e.g., colon cancer cells implanted in colonic tissue. See, e.g., PCT publication No. WO 97/33551. published September 18, 1997. Probably the most often used animal species in oncological studies are immunodeficient mice and, in particular, nude mice. The observation that the nude mouse with thymic hypo/aplasia could successfully act as a host for human wmor xenografts has lead to its widespread use for this purpose. The autosomal recessive nu gene has been introduced into a very large number of distinct congenic strains of nude mouse. including, for example, ASW, A/He, AKR,

BALB/c, B10.LP, C17, C3H, CS7BL, C57, CBA, DBA. DDD, I/st. NC, NFR, NFS, NFS/N, NZB, NZC, NZW,

P, RII], and SJL. In addition, a wide variety of other animals with inherited immunological defects other than the nude mouse have been bred and used as recipients of tumor xenografts. For further details see, e.g., The Nude

Mouse in Oncology Research, E. Boven and B. Winograd. eds. (CRC Press, Inc., 1991).

The cells introduced into such animals can be derived from known tumor/cancer cell lines, such as any of the above-listed tumor cell lines, and, for cxample, the B104-1-1 cell line (stable NIH-3T3 cell line wranstected with the nen protooncogene); ras-transfected NIH-3T3 cells: Caco-2 (ATCC HTB-37), or a moderately well- differentiated grade Il human colon adenocarcinoma cell line. HT-29 (ATCC HTB- 38); or from tumors and cancers.

Samples of tumor or cancer cells can be obtained from patients undergoing surgery, using standard conditions involving freezing and storing in liquid nitrogen. Karmali er al., Br. J. Cancer, 48: 689-696 (1983).

Tumor cells can be introduced into animals such as nude mice by a variety of procedures. The subcutaneous (s.c.) space in mice is very suitable for tumor implantation. Tumors can be transplanted s.c. as solid blacks, as needle biopsies by use of a trochar, or as cell suspensions. For solid-block or trochar implantation, tumor tissue fragments of suitable size are introduced into the s.c. space. Cell suspensions are freshly prepared from primary tumors or stabic tumor cell lines, and injected subcutaneously. Tumor cells can also be injected as subdermal implants. In this location, the inoculum is deposited between the lower part of the dermal connective tissue and the s.c. tissue.

Animal models of breast cancer can be generated, for example, by implanting rat neuroblastoma cells (from which the neu oncogene was initially isolated), or neu-transformed NIH-3T3 cells into nude mice, essentially as described by Drebin ef al. Proc. Nat. Acad. Sci. USA, 83: 9129-9133 (1986).

Similarly, animal models of colon cancer can be generated by passaging colon cancer cells in animals, e.g., nude mice, leading to the appearance of tumors in these animals. An orthotopic transplant model of human colon cancer in nude mice has been described, for example, by Wang er al., Cancer Research, 54: 4726-4728 (1994) and

Too eral, Cancer Research, 55: 681-684 (1995). This model is based on the so-called “METAMOUSE™" sold by AntiCancer, Inc., (San Diego, California).

Tumors that arise in animals can be removed and cultured in vitro. Cells from the in vitro cultures can then be passaged to animals. Such tumors can serve as targets for further testing or drug screening. Alternatively, the tumors resulting from the passage can be isolated and RNA from pre-passage cells and cells isolated after one or more rounds of passage analyzed for differential expression of genes of interest. Such passaging techniques can be performed with any known tumor or cancer cell lines.

For example, Meth A, CMS4, CMS5, CMS21, and WEHI-164 are chemically induced fibrosarcomas of

BALB/c female mice (DcLeo ef al, J. Exp. Med., 146: 720 (1977)), which provide a highly controllable model system for studying the anti-tumor activitics of various agents. Palladino et al. I. Immunol., 138: 4023-4032 (1987). Briefly, tumor cells are propagated in vitro in cell culture. Prior to injection into the animals. the cell lines are washed and suspended in buffer, at a cell density of about 10x10° to 10x10 cells/ml. The animals are then infected subcutaneously with 10 to 100 1 of the cell suspension, allowing one to three weeks for a tumor to appear.

In addition, the Lewis lung (BLL) carcinoma of mice, which is one of the most thoroughly studied experimental tumors, can be used as an investigational tumor model. Efficacy in this tumor model has been correlated with beneficial effects in the treatment of human patients diagnosed with small-cell carcinoma of the lung (SCCL). This tumor can be introduced in normal mice upon injection of tumor fragments from an affected mouse or of cells maintained in culture. Zupi etal., Br. J. Cancer, 41: suppl. 4, 30 (1980). Evidence indicates that tumors can he started from injection of even a single cell and that a very high proportion of infected tumor cells survive.

For further information about this tumor model see, Zacharski, Haemostasis, 16: 300-320 (1986).

One way of evaluating the efficacy of a test compound in an animal model with an implanted twmor is to measure the size of the tumor before and after trcatment. Traditional) y. the size of implanted tumors has been measured with a slide caliper in two or three dimensions. The measure limited to two dimensions does not accurately reflect the size of the tumor; therefore, it is usually converted into the corresponding volume by using a mathematical formula. However, the measurement of wumor size is very inaccurate. The therapeutic effects of a drug candidate can be better described as treatment-induced growth delay and specific growth delay. Another . important variable in the description of tumor growth is the tumor volume doubling time. Computer programs for the calculation and description of tumor growth are also available, such as the program reported by Rygaard and

Spang-Thomsen, Proc. 6th Int. Workshop on Immune-Deficient Animals. Wu and Sheng eds. (Basel, 1989), p. 301. Itisnoted, however, that necrosis and inflammatory responses following treatment may actually result in an increase in tumor size, at least initially. Therefore, these changes need to be carefully monitored, by a combination of a morphometric method and flow cytometric analysis.

Further, recombinant (transgenic) animal models can be engineered by introducing the coding portion of the

PRO gene identified herein into the genome of animals of interest, using standard techniques for producing transgenic animals. Animals thatcan serve as atarget for transgenic manipulation include, without limitation, mice, rats, rabbits, guinea pigs, sheep, goats, pigs, and non-human primates, e.g., baboons, chimpanzees and monkeys.

Techniques known in the ast to introduce a transgene into such animals include pronucleic microinjection (U.S.

Patent No. 4,873,191); retrovirus-mediated gene transfer into germ lines (e.g., Van der Putten ez al., Proc. Natl,

Acad. Sci. USA, 82: 6148-615 (1985)); gene targeting in embryonic stem cells (Thompson et al., Cell, 56: 313-321 (1989): electroporation of embryos (Lo, Mol. Cell. Biol., 3: 1803-1814 (1983)); and sperm-mediated genc transfer.

Lavitrano et al., Cell, 57: 717-73 (1989). For a review, see for example, U.S. Patent No. 4,736,866.

For the purpose of the present invention, transgenic animals include those that carry the transgene only in part of their cells (“mosaic animals”). The transgene can be integrated cither as a single transgene, or in concatamers, e.g., head-to-head or head-to-tail tandems. Selective introduction of a transgene into a particular cell type is also possible by following, for example, the technique of Lasko et al., Proc. Natl. Acad. Sci. USA, 89: 6232-636 (1992).

The expression of the transgene in transgenic animals can be monitored by standard techniques. For cxample,

Southern blot analysis or PCR amplification can be used to verify the integration of the transgene. The level of mRNA expression can then be analyzed using techniques such as in situ hybridization, Northern blot analysis, PCR, or immunocytochemistry. The animals are further examined for signs of tumor ar cancer developinent.

Alternatively, "knock-out" animals can be constructed that have a defective or altered gene encoding a PRO polypeptide identified herein, as a result of homologous recombination between the endogenous gene encoding the

PRO polypeptide and altered genomic DNA encoding the same polypeptide introduced into an embryonic cell of the animal. For example, cDNA encoding a particular PRO polypeptide can be used to clone genomic DNA encoding that polypeptide in accordance with established techniques. A portion of the genomic DNA encoding a particular PRO polypeptide can be deleted or replaced with another gene, such as a gene encoding a selectable marker that can be used to monitor integration. Typically, several kilobases of unaltered flanking DNA (both at the 5’ and 3" ends) are included in the vector. See, e.g., Thomas and Capecchi, Cell. 51: 503 (1987) for a description of homologous recombination vectors. The vector is introduced into an embryonic stem cell line (e.g., by clectroporation) and cells in which the introduced DNA has homologously recombined with the endogenous DNA areselected. See, e.g. Lietal., Cell, 69: 915 (1992). The selected cells are then injected into a blastocyst of an animal (e.g., a mouse or rat) to form aggregation chimeras. See, e.g., Bradley, in Teratocarcinomas and Embryonic

Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL: Oxford, 1987), pp. 113-152. A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term to create a “knock-out” animal. Progeny harboring the homologously recombined DNA in their germ cells can be identified by standard techniques and used to breed animals in which all cells of the animal contain the homologously recombined DNA. Knockout animals can be characterized, for instance, by their ability to defend against certain : pathological conditions and by their development of pathological conditions due to absence of the PRO polypeptide.

The efficacy of antibodies specifically binding the PRO polypeptides identified herein, and other drug candidates, can be tested also in the treatment of spontaneous animal tumors. A suitable target for such studies is the feline oral squamous cell carcinoma (SCC). Feline oral SCC is a highly invasive, malignant tumor that is the most common oral malignancy of cats, accounting for over 60% of the oral tumors reported in this species. Itrarely metastasizes to distant sites, although this low incidence of metastasis may mercly be a reflection of the short survival times for cats with this tumor. These tumors are usually not amenable to surgery, primarily because of the anatomy of the feline oral cavity. At present, there is no effective treatment for this tumor. Prior to entry into the study, each cat undergoes complete clinical examination and biopsy, and is scanned by computed tomography (CT).

Cats diagnosed with sublingual oral squamous cell tumors are excluded from the study. The tongue can become paralyzed as a result of such tumor, and even if the treatment kills the tumor, the animals may not be able to feed themselves. Each cat is treated repeatedly, over a longer period of time. Photographs of the tumors will be taken daily during the treatment period, and at each subsequent recheck. After trcatment, each cat undergocs another CT scan. CT scans and thoracic radiograms are evaluated every 8 weeks thereafter. The data are evaluated for differences in survival, response, and toxicity as compared to control groups. Positive response may require evidence of tumor regression, preferably with improvement of quality of life and/or increased life span.

Inaddition, other spontaneous animal tumors, such as fibrosarcoma, adenocarcinoma, lymphoma, chondroma, or leiomyosarcoma of dogs, cats, and baboons can also be tested. Of these, mammary adenocarcinoma in dogs and cats is a preferred model as its appearance and behavior are very similar to those in humans. However, the use of this model is limited by the rare occurrence of this type of tumor in animals.

Other in vitro and in vive cardiovascular, endothelial, and angiogenic tests known in the art are also suitable herein. ii. Tissue Distribution

The results of the cardiovascular, endothelial, and angiogenic assays herein can be verified by further studies, such as by determining mRNA expression in various human tissues.

As noted before, gene amplification and/or gene expression in various tissues may be measured by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA (Thomas, Proc. Natl.

Acad. Sci. USA, 77:5201-5205 (1980)), dot blotting (DNA analysis). or in sir hybridization, using an appropriately labeled probe, based on the sequences provided herein. Alternatively. antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes. and DNA-RNA hybrid duplexes or

DNA-protein duplexes.

Gene expression in various tissues, alternatively, may be measured by immunological methods, such as immunohistochemical staining of tissue sections and assay of cell culture or body fluids, to quantitate directly the expression of gene product. Antibodies useful for immunohistochemical staining and/or assay of sample fluids may be either monoclonal or polyclonal, and may be prepared in any mammal. Conveniently, the antibodies may be prepared against a native-sequence PRO polypeptide or against a synthetic peptide based on the DNA sequences provided herein or against exogenous sequence fused to PRO DNA and encoding a specific antibody epitope. . General techniques for generating antibodies, and special protocols for in situ hybridization are provided hereinbelow. iii. Antibody Binding Studies

The results of the cardiovascular, endothelial, and angiogenic study can be further verified by antibody binding studies, in which the ability of anti-PRO antibodies to inhibit the effect of the PRO polypeptides on endothelial cells or other cells used in the cardiovascular, endothelial, and angiogenic assays is tested. Exemplary antibodies include polyclonal, monoclonal, humanized, bispecific, and heteroconjugate antibodies, the preparation of which will be described hereinbelow.

Antibody binding studies may be carried out in any known assay method, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays. Zola, Monaclonal Antibodies: A Manual of

Techniques (CRC Press, Inc., 1987), pp.147-158.

Competitive binding assays rely on the ability of a labeled standard to compete with the test sample analyte for binding with a limited amount of antibody. The amount of target protein in the test sample is inversely proportional to the amount of standard that becomes bound to the antibodies. To facilitate determining the amount of standard that becomes bound, the antibodies preferably are insolubilized before or after the competition, so that the standard and analyte that are bound to the antibodies may conveniently be separated from the standard and analyte that remain unbound. . Sandwich assays involve the use of two antibodies, each capable of binding to a different immunogenic portion, or epitope, of the protein to be detected. In a sandwich assay, the test sample analyte is bound by a first antibody that is immobilized on a solid support, and thereafter a second antibody binds to the analyte, thus forming an insoluble three-part complex. See, e.g., US Pat No. 4,376,110. The second antibody may itself be labeled with a detectable moiety (direct sandwich assays) or may be measured using an anti-immunoglobulin antibody that is labeled with a detectable moiety (indirect sandwich assay). For example, one type of sandwich assay is an ELISA assay, in which case the detectable moiety is an enzyme.

For immunohistochemistry, the tissue sample may be fresh or frozen or may be embedded in paraffin and fixed with a preservative such as formalin, for example. iv. Cell-Based Tumor Assays

Cell-based assays and animal models for cardiovascular, endothelial, and angiogenic disorders, such as tumors, can be used to verify the findings of a cardiovascular, endothelial, and angiogenic assay herein. and further to understand the relationship between the genes identified herein and the devclopment and pathogenesis of undesirable cardiovascular. endothelial, and angiogenic cell growth. The role of gene products identified herein in the development and pathology of undesirable cardiovascular, endothelial, and angiogenic cell growth, .£., tumor cells, can be tested by using cells or cells lines that have been identified as being stimulated or inhibited by the PRO polypeptide herein. Such cells include, for example, those set forth in the Examples below.

In a different approach, cclis of a cell type known to be involved in a particular cardiovascular, endothelial, and angiogenic disorder are transfected with the cDNAs herein, and the ability of these cDNAs to induce excessive growth or inhibit growth is analyzed. If the cardiovascular, endothelial, and angiogenic disorder is cancer, suitable tumor cells include, for example, stable tumor cells lines such as the B104-1-1 cell line (stable NIH-3T3 cell line ] transfected with the neu protooncogene) and ras-transfected NIH-3T3 cells, which can be transfected with the desired gene and monitored for tumorigenic growth. Such transfected cell lines can then be used to test the ability of poly-ormonoclonal antibodies or antibody compositions to inhibit tumorigenic cell growth by exerting cytostatic or cytotoxic activity on the growth of the transformed cells, or by mediating antibody-dependent cellular cytotoxicity (ADCC). Cells transfected with the coding sequences of the genes identified herein can further be used to identify drug candidates for the treatment of cardiovascular, endothelial, and angiogenic disorders such as cancer.

In addition, primary cultures derived from tumors in transgenic animals (as described above) can be used in thecell-based assays herein, although stable cell lines are preferred. Techniques to derive continuous cell lines from transgenic animals are well known in the art. See, e.g., Small et al., Mol. Cell. Biol, 5: 642-648 (1985). v. Gene Therapy

The PROI79, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO8S40,

PRO877, PRO878, PRO879, PRO882, PRO88S5 or PROS87 polypeptide herein and polypeptidyl agonists and antagonists may be employed in accordance with the present invention by expression of such polypeptides in viva, which is often referred to as gene therapy.

There are two major approaches to getting the nucleic acid (optionally contained in a vector) into the patient's cells: in vivo and ex vivo. For in vivo delivery the nucleic acid is injected directly into the patient, usually at the sites where the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PROS40,

PRO877. PRO878, PRO8T9. PRO882, PRO8S5 or PROSS7 polypeptide is required, i.e., the site of synthesis of the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, :

PROB878, PRO879, PRO882, PRO8SSS or PRO887 polypeptide, if known, and the site (e.g., wound) where biological activity of PRO179, PRO238, PRO364, PRO844. PRO846, PRO1760, PRO205, PRO321, PR0O333,

PRO840.PROR77,PRO878, PRO879. PRO882. PRO88S5 or PRO8S? polypeptide is needed. For ex vivo treatment, the patient's cells are removed, the nucleic acid is introduced into these isolated cells, and the modified cells are administered to the patient either directly or, for example, encapsulated within porous membranes that are implanted into the paticnt (see, e.g., U.S. Pat. Nos. 4,892,538 and 5,283,187). There are a variety of techniques available for introducing nucleic acids into viable cells. The techniques vary depending upon whether the nucleic acid is transferred into cultured cells in vitro, or transferred én vivo in the cells of the intended host. Techniques suitable for the transfer of nucleic acid into mammalian cells in vitro include the use of liposomes, electroporation, microinjection, transduction, cell fusion, DEAE-dextran. the calcium phosphate precipitation method, etc.

Transduction involves the association of a replication-defective, recombinant viral (preferably retroviral) particle with a cellular receptor, followed by introduction of the nucleic acids contained by the particle into the cell. A commonly used vector for ex vivo delivery of the gene is a retrovirus.

The currently preferred in vivo nucleic acid transfer techniques include transfection with viral or non-viral vectors (such as adenovirus, lentivirus, Herpes simplex I virus, or adeno-associated virus (AAV)) and lipid-based systems (useful lipids for lipid-mediated transfer of the gene are, for example, DOTMA, DOPE, and DC-Chol; see, e.g., Tonkinson er al., Cancer Investigation, 14(1): 54-65 (1996). The most preferred vectors for use in gene therapy are viruses, most preferably adenoviruses, AAV, lentiviruses, or retroviruses. A viral vector such as a . retroviral vector includes at least one transcriptional promoter/enhancer or locus-defining element(s), or other elements that control gene expression by other means such as altemnate splicing, nuclear RNA export, or post-translational modification of messenger. In addition, a viral vector such as aretroviral vector includes a nucleic acid molecule that, when transcribed in the presence of a gene encoding PRO179, PRO238, PRO364, PRO844,

PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROBSS or

PRO887 polypeptide, is operably linked thereto and acts as a translation initiation sequence. Such vector constructs also include a packaging signal, long terminal repeats (LTRs) or portions thereof, and positive and negative strand primer binding sites appropriate to the virus used (if these are not already present in the viral vector). In addition, such vector typically includes a signal sequence for secretion of the PRO179, PRO238, PRO364, PRO844,

PROB46, PRO1760, PRO205, PR0O321, PR0O333, PRO840, PRO877, PRO878, PRO879, PRO882, PROSSS or

PROB887 polypeptide from a host cell in which it is placed. Preferably the signal sequence for this purpose is a mammalian signal sequence, most preferably the native signal sequence for the PRO179, PRO238, PRO364,

PROBg44, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PROS88S5 or PRO887 polypeptide. Optionally, the vector construct may also include a signal that directs polyadenylation, as well as one or more restriction sites and a translation termination sequence. By way of example, such vectors will typically include a 5' LTR, a tRNA binding site, a packaging signal, an origin of second-strand

DNA synthesis, and a 3' LTR or a portion thercof. Other vectors can be used that are non-viral, such as cationic lipids, polylysine, and dendrimers.

In some situations, it is desirable to provide the nucleic acid source with an agent that targets the target cells, such as an antibody specific for a cell-surface membrane protein or the target cell, a lizand for a receptor on the : target cell, etc. Where liposomes are employed, proteins that bind to a cell-surface membrane protein associated with endocytosis may be used for targeting and/or to facilitate uptake, e.g., capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins that undergo internalization in cycling. and proteins that targetintracellular localization and enhance intracellular half-life. The technique of receptor-mediated endocytosis is described, for example, by Wuer al., J. Biol. Chem, 262: 4429-4432 (1987); and Wagner er al.. Proc, Natl. Acad.

Sci. USA, 87: 3410-3414 (1990). For areview of the currently known gene marking and gene therapy protocols, see, Anderson et al., Science, 256: 808-813 (1992). See also WO 93/25673 and the references cited therein.

Suitable gene therapy and methods for making retroviral particles and structural proteins can be found in. e.g.,

U.S. Pat. No. 5,681,746. vi. Use of Gene as Diagnostic

This invention is also related to the use of the gene encoding the PRO179. PRO238. PRO364, PRO844,

PROB46, PRO1760, PR0O205, PRO321, PR0O333, PRO840, PRO877, PRO878. PRO879, PRO882, PROSS5 or

PRO887 polypeptide as a diagnostic. Detection of a mutated form of the PRO179. PRO238. PRO364, PROB44,

PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878. PRO879, PRO882, PROSSS or

PRORRT polypeptide will allow a diagnosis of a cardiovascular, endothelial. and angiogenic disease or a susceptibility to a cardiovascular, endothelial, and angiogenic disease, such as a tumor, since mutations in the

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321. PRO333, PRO840, PROS877,

PRO878, PRO§79, PRO882, PRO885 or PRO8S87 polypeptide may cause tumors.

Individuals carrying mutations in the genes encoding a human PRO179, human PRO238, human PRO364, . human PRO844, human PRO846, human PRO1760, human PRO205, human PRO321, human PRO333, human

PROB40, human PRO877, human PRO878, human PRO879, human PRO882, human PRO885 or human PRO8S7 polypeptide may be detected at the DNA level by a variety of techniques. Nucleic acids for diagnosis may be obtained from a patient's cells, such as from blood, urine, saliva, tissue biopsy, and autopsy material. The genomic

DNA may be used directly for detection or may be amplified enzymatically by using PCR (Saiki er al., Nature, 324: 163-166 (1986)) prior to analysis. RNA or cDNA may also be used for the same purpose. As an example, PCR primers complementary tothe nucleic acid encoding the PRO 179, PRO238, PRO364, PRO844, PRO846, PRO] 760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide canbe used to identify and analyze PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321 ,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO%82. PRO88S or PRO8S7 polypeptide mutations. For example, deletions and insertions can be detected by a change in size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to radiolabeled RNA encoding the PRO179, PRO238, PRO364, PROS44, PROB846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide, or alternatively, radiolabeled antisense DNA sequences encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333,

PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide. Perfectly matched sequences can be distinguished from mismatched duplexes by RNase A digestion or by differences in melting temperatures.

Genetic testing based on DNA sequence differences may be achieved by detection of alteration in electrophoretic mobility of DNA fragments in gels with or without denaturing agents. Sinall sequence deletions and insertions can be visualized by high resolution gel electrophoresis. DNA fragments of different sequences may be distinguished on denaturing formamidine gradient gels in which the mobilities of different DNA fragments are retarded in the gel at different positions according to their specific melting or partial melting temperatures. See, e.g.,

Myers ezal., Science, 230: 1242 (1985).

Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and S1 protection or the chemical cleavage method, for example, Cotton et al., Proc. Natl. Acad. Sci. USA, 85: 43974401 (1985).

Thus, the detection of a specific DNA sequence may be achieved by methods such as hybridization, RNase protection, chemical cleavage, direct DNA sequencing, or the use of restriction enzymes, ¢.g., restriction fragment length polymorphisms (RFLP). and Southern blotting of genomic DNA. vii. Use to Detect PRO Polypeptide Levels

In addition to more conventional gel-electrophoresis and DNA sequencing, mutations can also be detected by in situ analysis.

Expression of nucleic acid encoding the PRO polypeptide may be linked to vascular disease or neovascularization associated with tumor formation. If the PRO polypeptide has a signal sequence and the mRNA is highly expressed in endothelial cells and to a lesser extent in smooth muscle cells, this indicates that the PRO polypeptide is present in serum. Accordingly, an anti-PRO polypeptide antibody could be used to diagnose vascular

B wo 00/53757 } PCT/US00/05004 disease or neovascularization associated with tumor formation, since an altercd level of this PRO polypeptide may . be indicative of such disorders.

A competition assay may be employed wherein antibodies specific to the PRO polypeptide are attached to a solid support and the labeled PRO polypeptide and a sample derived from the host are passed over the solid support andtheamount of label detected attached to the solid support can be correlated to a quantity of the PRO polypeptide in the sample. viii. Chromosome Mapping

The sequences of the present invention are also valuable for chromosome identification. The sequence is specifically targeted to and can hybridize with a particular location on an individual human chromosome.

Moreover, there is a current need for identifying particular sites on the chromosome. Few chromosome marking reagents based on actual sequence data (repeat polymorphisms) are presently available for marking chromosomal location. The mapping of DNAs to chromosomes according to the present invention is an important first step in correlating those sequences with genes associated with disease.

Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp) from the cDNA. Computer analysis for the 3'- untranslated region is used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers are then used for

PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the primer will yield an amplified fragment.

PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular DNA to a particular chromosome. Using the present invention with the same oligonucleotide primers, sublocalization can be achieved : with panels of fragments from specific chromosomes or pools of large genomic clones in an analogous manner.

Other mapping strategies that can similarly be used to map to its chromosome include in sine hybridization, prescreening with labeled flow-sorted chromosomes, and preselection by hybridization to construct chromosome- specific cDNA libraries.

Fluorescence in situ hybridization (FISH) of a cDNA clone to a metaphase chromosomal spread can be used to provide a precise chromosomal location in one step. This technique can be used with cDNA as short as 500 or 600 bases; however, clones larger than 2,000 bp have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. FISH requires use of the clones from which the gene encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO 1760, PRO205, PRO321, PRO333, PRO840,

PROS877,PRO878, PRO879, PRO882, PRO8SS or PRO887 was derived, and the longer the better. For example, 2,000 bp is good, 4,000 bp is better, and more than 4,000 is probably not necessary to get good results a reasonable percentage of the time. For areview of this technique, see, Verma er al., Human Chromosomes: a Manual of Basic

Techniques (Pergamon Press, New York, 1988).

Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found, for example, in V. McKusick,

Mendelian Inheritance jn Man (available online through Johns Hopkins University Welch Medical Library). The relationship between genes and discases that have been mapped to the same chromosomal region is then identified through linkage analysis (coinheritance of physically adjacent genes).

Next, it is necessary to determine the differences in the cDNA or genomic sequence between affected and unaffected individuals. If a mutation is observed in some or al} of the affected individuals but not in any normal individuals, then the mutation is likely to be the causative agent of the disease.

With current resolution of physical mapping and genetic mapping techniques, a cDNA precisely localized to achromosomal region associated with the disease could be one of between 50 and 500 potential causative genes. (This assumes | megabase mapping resolution and one gene per 20 kb). ix. Screening Assays for Drug Candidates

This invention encompasses methods of screening compounds 10 identify those that mimic the PRO179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PROBS,

PRO879, PRO882, PRO88S or PROSS7 polypeptide (agonists) or prevent the effect of the PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879,

PRO882, PRO88S or PRO887 polypeptide (antagonists). Screening assays for antagonist drug candidates are designed to identify compounds that bind or complex with the PRO179, PRO238, PRO364, PRO844, PRO846,

PROI1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide encoded by the genes identified herein, or otherwise interfere with the interaction of the encoded polypeptides with other cellular proteins. Such screening assays will include assays amenable to high-throughput screening of chemical libraries, making them particularly suitable for identifying small molecule drug candidates.

The assays can be performed in a variety of formats, including protein-protein binding assays, biochemical screening assays, immunoassays, and cell-based assays, which are well characterized in the art.

All assays for antagonists are common in that they call for contacting the drug candidate with a PRO179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PROS77, PROS878,

PROB79, PRO882, PRO88S5 or PRO887 polypeptide encoded by a nucleic acid identified herein under conditions and for a time sufficient to allow these two components to interact.

In binding assays, the interaction is binding and the complex formed can be isolated or detected in the reaction mixture. Ina particular embodiment, the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760. PRO205,

PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or PRO8S7 polypeptide encoded by the gene identified herein or the drug candidate is immobilized on a solid phase, e.g.. on a microtiter plate, by covalent or non-covalent attachments. Non-covalent attachment generally is accomplished by coating the solid surface with a solution of the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760. PRO205. PRO321,

PRO333. PRO840, PRO877, PROg78, PRO879, PRO882, PRO88S or PRO88/7 polypeptide and drying.

Alternatively, an immobilized antibody, e.g., a monoclonal antibody, specific for the PRO179. PRO238, PRO364,

PRO844. PRO846, PRO1760, PRO20S5. PRO321, PRO333, PRO840, PRO877, PRO878. PRO879. PRO8S2,

PRO885 or PROBST polypeptide to be immobilized can be used to anchor it to a solid surface. The assay is performed by adding the non-immobilized component, which may be labeled by a detectable label. to the immobilized component, e.g.. the coated surface containing the anchored component. When the reaction is complete, the non-reacted components are removed, e.g., by washing, and complexes anchored on the solid surface arc detected. When the originally non-immobilized component carries a detectable label, the detection of label immobilized on the surface indicates that complexing occurred. Where the originally non-immobilized component does not carry a label, complexing can be detected, for example, by using a labeled antibody specifically binding } the immobilized complex.

If the candidate compound interacts with but does not bind to a particular PRO 179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PROS885 or PRO887 polypeptide encoded by a gene identified herein, its interaction with that polypeptide can be assayed by methods well known for detecting protein-protein interactions. Such assays include traditional approaches, such as, e.g., cross-linking, co-immunoprecipitation, and co-purification through gradients or chromatographic columns. In addition, protein-protein interactions can be monitored by using a yeast-based genetic system described by Fields and co-workers (Fields and Song, Nature {I_ondon), 340: 245-246 (1989); Chien et al.,

Proc. Natl. Acad. Sci. USA, 88: 9578-9582 (1991)) as disclosed by Chevray and Nathans, Proc. Natl. Acad. Sci.

USA, 89: 5789-5793 (1991). Many transcriptional activators, such as yeast GALA, consist of two physically discrete modular domains, one acting as the DNA-binding domain, the other one functioning as the transcription- activation domain. The yeast expression system described in the foregoing publications (generally referred to as the "two-hybrid system™) takes advantage of this property, and employs two hybrid proteins, one in which the target proteinis fused to the DNA-binding domain of GALA, and another, in which candidate activating proteins are fused to the activation domain. The expression of a GAL1-lacZ reporter gene under control of a GAL4-activated promoter depends on reconstitution of GALA activity via protein-protein interaction. Colonies containing interacting polypeptides are detected with a chromogenic substrate for f-galactosidase. A complete kit (MATCHMAKER™) for identifying protein-protein interactions between two specific proteins using the two- hybrid technique is commercially available from Clontech. This system can also be extended to map protein domains involved in specific protein interactions as well as to pinpoint amino acid residues that are crucial for these interactions.

Compounds that interfere with the interaction of a gene encoding a PRO179, PRO238, PRO364, PRO844,

PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROSSS or PRO8R7 polypeptide identified herein and other intra- or extracellular components can be tested as follows: usually a reaction mixture is prepared containing the product of the gene and the intra- or extracellular component under conditions and for a time allowing for the interaction and binding of the two products. To tcst the ability of a candidate compound to inhibit binding, the reaction is run in the absence and in the presence of the test compound.

In addition, a placebo may be added 10 a third reaction mixture, to serve as positive control. The binding (complex formation) between the test compound and the intra- or extracellular component present in the mixture is monitored as described hereinabove. The formation of a complex in the control reaction(s) but not in the reaction mixture containing the test compound indicates that the test compound interferes with the interaction of the test compound and its reaction partner.

If the PRO polypeptide has the ability to stimulate the proliferation of endothelial cells in the presence of the co-mitogen ConA, then one example of a screening method takes advantage of this ability. Specifically, in the proliferation assay, human umbilical vein endothelial cells are obtained and cultured in 96-well flat-bottomed culture plates (Costar, Cambridge, MA) and supplemented with a reaction mixture appropriate for facilitating prolifcration of the cells, the mixture containing Con-A (Calbiochem, La Jolla, CA). Con-A and the compound to be screened are added and after incubation at 37 °C, cultures are pulsed with >H-thymidine and harvested onto glass fiber filters (phD; Cambridge Technology, Watertown, MA). Mean “H- thymidine incorporation (cpm) of triplicate cultures is determined using a Jiquid scintillation counter (Beckman Instruments, Irvine, CA). Significant *(H)- ) thymidine incorporation indicates stimulation of endothelial cell proliferation.

To assay for antagonists, the assay described above is performed; however, in this assay the PRO polypeptide 5S is added along with the compound to be screened and the ability of the compound to inhibit *(H)thymidine incorporation in the presence of the PRO polypeptide indicates that the compound is an antagonist to the PRO polypeptide. Alternatively, antagonists may be detected by combining the PRO polypeptide and a potential antagonist with membrane-bound PRO polypeptide receptors or recombinant receptors under appropriate conditions for a competitive inhibition assay. The PRO polypeptide can be labeled, such as by radioactivity, such that the number of PRO polypeptide molecules bound to the receptor can be used to determine the effectiveness of the potential antagonist. The gene encoding the receptor can be identified by numerous methods known to those of skill in the art, for example, ligand panning and FACS sorting. Coligan et al., Current Protocols in Immun., 1(2):

Chapter 5(1991). Preferably, expression cloning is employed wherein polyadenylated RNA is prepared from a cell responsive to the PRO polypeptide and a cDNA library created from this RNA is divided into pools and used to transfect COS cells or other cells that are not responsive to the PRO polypeptide. Transfected cells that are grown on glass slides are exposed to the labeled PRO polypeptide. The PRO polypeptide can be labeled by a variety of means including iodination or inclusion of a recognition site for a site-specific protein kinase. Following fixation and incubation, the slides are subjected to autoradiographic analysis. Positive pools are identified and sub-pools are prepared and re-transf{ected using an interactive sub-pooling and re-screening process, eventually yielding a single clone that encodes the putative receptor.

As an alternative approach for receptor identification, the labeled PRO polypeptide can be photoaffinity- linked with cell membrane or extract preparations that express the receptor molecule. Cross-linked material is resolved by PAGE and cxposed to X-ray film. The labeled complex containing the receptor can be excised, resolved into peptide fragments, and subjected to protein micro-sequencing. The amino acid sequence obtained from micro-sequencing would be used to design a set of degenerate oligonucleotide probes to screen a cDNA library to identify the gene encoding the putative receptor.

In another assay for antagonists, mammalian cells or a membrane preparation expressing the receptor would be incubated with the labeled PRO polypeptide in the presence of the candidate compound. The ability of the compound to enhance or block this interaction could then be measured.

The compositions useful in the treatment of cardiovascular, endothelial, and angiogenic disorders include, without limitation. antibodies, small organic and inorganic molecules, peptides, phosphopeptides, antisense and ribozyme molecules, triple-helix molecules, etc., that inhibit the expression and/or activity of the target gene product.

More specific examples of potential antagonists include an oligonucleotide that binds to the fusions of immunoglobulin with a PRO polypeptide, and, in particular, antibodies including, without limitation, poly- and monoclonal antibodies and antibody fragments, single-chain antibodics. anti-idiotypic antibodics, and chimeric or humanized versions of such antibodies or fragments, as well as human antibodies and antibody fragments.

Alternatively, a potential antagonist may be a closely related protein, for example, a mutated form of the PRO polypeptide that recognizes the receptor but imparts no effect, thereby competitively inhibiting the action of the

PRO polypeptide. . Another potential PRO polypeptide antagonist or agonist is an antisense RNA or DNA construct prepared using antisense technology, where, e.g., an antisense RNA or DNA molecule acts to block directly the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. Antisense technology can be used to control gene expression through triple-helix formation or antisense DNA or RNA, both of which methods are based on binding of a polynucleotide to DNA or RNA. For example, the 5' coding portion of the polynucleotide sequence, which encodes the mature PRO polypeptides herein, is used to design an antisense RNA oligonucleotide of from about 10 to 40 base pairs in length. A DNA oligonucleotide is designed to be complementary to a region of the gene involved in transcription (triple helix - see, Lee er al., Nucl, Acids Res., 6:3073 (1979); Cooney ef al.,

Science, 241: 456 (1988); Dervan er al., Science, 251:1360 (1991), thereby preventing transcription and the production of the PRO polypeptide. The antisense RNA oligonucleotide hybridizes to the mRNA in vive and blocks translation of the mRNA molecule into the PRO polypeptide (antisense - Okano, Neurochem. 56:560 (1991);

Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression (CRC Press: Boca Raton, FL, 1988). The oligonucleotides described above can also be delivered to cells such that the antisense RNA or DNA may be expressed in vivo to inhibit production of the PRO polypeptide. When antisense DNA is used, oligodeoxyribonucleotides derived from the translation-initiation site, e.g., between about -10 and +10 positions of the target gene nucleotide sequence, are preferred.

Autisense RNA or DNA molecules are generally at least about S bases in length, about 10 bases in length, about 15 bases in length, about 20 bases in length, about 25 bases in length, about 30 bases in length, about 35 bases in length, about 40 bases in length, about 45 bases in length, about 50 bases in length, about 55 bases in length, about 60 bases in length, about 65 bases in length, about 70 bases in length, about 75 bases in length, about 80 bases in length, about 85 bases in length, about 90 bases in length, about 95 bases in length, about 100 bases in length, or more.

Potential antagonists include small molecules that bind to the active site, the receptor binding site, or growth factor or other relevant binding site of the PRO polypeptide, thereby blocking the normal biological activity of the

PRO polypeptide. Examples of small molecules include, but are not limited to, small peptides or peptide-like molecules, preferably soluble peptides, and synthetic non-peptidyl organic or inorganic compounds.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. Ribozymes act by sequence-specific hybridization to the complementary target RNA, followed by endonucleolytic cleavage.

Specific ribozyme cleavage sites within a potential RNA target can be identified by known techniques. For further details see. e.g. Rossi, Current Biology, 4: 469-471 (1994), and PCT publication No. WO 97/33551 (published

September 18, 1997).

Nucleic acid molecules in triple-helix formation used to inhibit transcription should be single-stranded and composed of deoxynucleotides. The base composition of these oligonucleotides is designed such that it promotes triple-helix formation via Hoogsteen base-pairing rules, which generally require sizeable stretches of purines or pyrimidines on one strand of a duplex. For further details see, e.g.. PCT publication No. WO 97/3355]. supra.

These small molecules can be identified by any one or more of the screening assays discussed hereinabove and/or by any other screening techniques well known for those skilled in the art. 8S

Cd

X. Types of Cardiovascular. Endothelial, and Angiogenic Disorders to be Treated

The PRO polypeptides, or agonists or antagonists thereto, that have activity in the cardiovascular, angiogenic, ) and endothelial assays described herein, and/or whose gene product has been found to be localized to the cardiovascular system, are likely to have therapeutic uses in a variety of cardiovascular, endothelial, and angiogenic disorders, including systemic disorders that affect vessels, such as diabetes mellitus. Their therapeutic utility could include diseases of the arteries, capillaries, veins, and/or lymphatics. Examples of treatments hereunder include treating muscle wasting disease, treating osteoporosis, aiding in implant fixation to stimulate the growth of cells around the implant and therefore facilitate its attachment to its intended site, increasing IGF stability in tissues or in serum, if applicable, and increasing binding to the IGF receptor (since IGF has been shown in vitro to enhance human marrow erythroid and granulocytic progenitor cell growth).

The PRO polypeptides or agonists or antagonists thereto may also be employed to stimulate erythropoiesis or granulopoiesis, to stimulate wound healing or tissue regeneration and associated therapies concerned with re- growth of tissue, such as connective tissue, skin, bone, cartilage, muscle, lung, or kidney, to promote angiogenesis, to stimulate or inhibit migration of endothelial cells, and to proliferate the growth of vascular smooth muscle and endothelial cell production. The increase in angiogenesis mediated by the PRO polypeptide or antagonist would be beneficial to ischemic tissues and to collateral coronary development in the heart subsequent to coronary stenosis.

Antagonists are used to inhibit the action of such polypeptides, for example, to limit the production of excess connective tissue during wound healing or pulmonary fibrosis if the PRO polypeptide promotes such production.

This would include treatment of acute myocardial infarction and heart failure.

Moreover, the present invention concerns the treatment of cardiac hypertrophy, regardless of the underlying cause, by administering a therapeutically effective dose of the PRO polypeptide, or agonist or antagonist thereto.

If the objective is the treatment of human patients, the PRO polypeptide preferably is recombinant human PRO polypeptide (rhPRO polypeptide). The treatment for cardiac hypertrophy can be performed at any of its various stages, which may result from a variety of diverse pathologic conditions, including myocardial infarction, } hypertension, hypertrophic cardiomyopathy, and valvular regurgitation. The treatment extends to all stages of the progression of cardiac hypertrophy, with or without structural damage of the heart muscle. regardless of the underlying cardiac disorder.

The decision of whether to use the molecule itself or an agonist thereof for any particular indication, as opposed 10 an antagonist to the molecule, would depend mainly on whether the molecule herein promotes cardiovascularization, genesis of endothelial cells, or angiogenesis or inhibits these conditions. For example, if the molecule promotes angiogenesis, an antagonist thereof would be useful for treatment of disorders where itis desired to limit or prevent angiogenesis. Examples of such disorders include vascular tumors such as haemangioma, tumor angiogenesis, neovascularization in the retina. choroid. or cornea, associated with diabetic retinopathy or premature infant retinopathy ormacular degeneration and proliferative vilreoretinopathy, rheumatoid arthritis, Crohn's disease, atherosclerosis, ovarian hyperstimulation, psoriasis, endometriosis associated with neovascularization, restenosis subsequent to balloon angioplasty, scar tissuc overproduction, for example, that seen in a keloid that forms after surgery, fibrosis after myocardial infarction, or fibrotic lesions associated with pulmonary fibrosis.

If, however, the molecule inhibits angiogenesis, it would be expected to be used directly for treatment of the abovc conditions.

On the other hand, if the molecule stimulates angiogenesis it would be used itself (or an agonist thereof) for ] indications where angiogenesis is desired such as peripheral vascular disease, hypertension, inflammatory vasculitides, Reynaud's disease and Reynaud's phenomenon, aneurysms, arterial restenosis, thrombophlebitis, lymphangitis, lymphedema, wound healing and tissue repair, ischemia reperfusion injury, angina, myocardial infarctions such as acute myocardial infarctions, chronic heart conditions, heart failure such as congestive heart failure, and osteoporosis.

If, however, the molecule inhibits angiogenesis, an antagonist thereof would be used for treatment of those conditions where angiogenesis is desired.

Specific types of diseases are described below, where the PRO polypeptide herein or antagonists thereof may serve as useful for vascular-related drug targeting or as therapeutic targets for the treatment or prevention of the disorders. Atherosclerosis is a disease characterized by accumulation of plaques of intimal thickening in arteries, due to accumulation of lipids, proliferation of smooth muscle cells, and formation of fibrous tissue within the arterial wall. The disease can atfect large, medium, and small arteries in any organ. Changes in endothelial and vascular smooth muscle cell function are known to play an important role in modulating the accumulation and regression of these plaques.

Hypertension is characterized by raised vascular pressure in the systemic arterial, pulmonary arterial, or portal venous systems. Elevated pressure may result from or result in impaired endothelial function and/or vascular disease.

Intlammatory vasculitides include giant cell arteritis, Takayasu's arteritis, polyarteritis nodosa (including the microangiopathic form), Kawasaki's disease, microscopic polyangiitis, Wegener's granulomatosis, and a variety of infectious-related vascular disorders (including Henoch-Schonlein prupura). Altered endothelial cell function has : been shown to be important in these diseases.

Reynaud's disease and Reynaud's phenomenon are characterized by intermittent abnormal impairment of the circulation through the extremities on exposure to cold. Altered endothelial cell function has been shown to be : important in this disease.

Aneurysms are saccular or fusiform dilatations of the arterial or venous tree that are associated with altered endothelial cell and/or vascular smooth muscle cells.

Arterial restenosis (restenosis of the arterial wall) may occur following angioplasty as a result of alteration in the function and proliferation of endothelial and vascular smooth muscle cells.

Thrombophlebitis and lymphangitis are inflammatory disorders of veins and lymphatics. respectively, that may result from, and/or in, altered endothelial cell function. Similarly, lymphedema is a condition involving impaired lymphatic vessels resulting from endothelial cell function.

The family of benign and malignant vascular tumors are characterized by abnormal proliferation and growth of cellular elements of the vascular system. For example, lymphangiomas are benign tumors of the lymphatic system that are congenital, often cystic, malformations of the lymphatics that usually occur in newborns. Cystic tumors tend 10 grow into the adjacent tissue. Cystic tumors usually occur in the cervical and axillary region. They can also occur in the soft tissue of the extremities. The main symptoms are dilated. sometimes reticular, structured lymphatics and lymphocysts surrounded by connective tissue. Lymphangiomas are assumed to be caused by improperly connected cmbryonic lymphatics or their deficiency. The result is impaired local lymph drainage.

2 a

Griener et al., Lymphology, 4: 140-144 (1971).

Another use for the PRO polypeptides herein or antagonists thereto is in the prevention of tumor angiogenesis, . which involves vascularization of a tumor to enable it to growth and/or metastasize. This process is dependent on the growth of new blood vessels. Examples of neoplasms and related conditions that involve tumor angiogenesis include breast carcinomas, lung carcinomas, gastric carcinomas, esophageal carcinomas, colorectal carcinomas, liver carcinomas, ovarian carcinomas, thecomas, arrhenoblastomas, cervical carcinomas, endometrial carcinoma, endometrial hyperplasia, endometriosis, fibrosarcomas, choriocarcinoma, head and neck cancer, nasopharyngeal! carcinoma, laryngeal carcinomas, hepatohlastoma, Kaposi's sarcoma, melanoma, skin carcinomas, hemangioma, cavernous hemangioma, hemangioblastoma, pancreas carcinomas, retinoblastoma, astrocytoma, glioblastoma,

Schwannoma, oligodendroglioma, medulloblastoma, neuroblastomas, rhabdomyosarcoma, osteogenic sarcoma, leiomyosarcomas, urinary tract carcinomas, thyroid carcinomas, Wilm's tumor, renal cell carcinoma, prostate carcinoma, abnormal vascular proliferation associated with phakomatoses, edema (such as that associated with brain tumors), and Meigs’ syndrome.

Age-related macular degeneration (AMD) is a leading cause of severe visual loss in the elderly population.

The exudative form of AMD is characterized by choroidal neovascularization and retinal pigment epithelial cell detachment. Because choroidal neovascularization is associated with a dramatic worsening in prognosis, the PRO polypeptide or antagonist thereto is expected to be useful in reducing the severity of AMD.

Healing of trauma such as wound healing and tissue repair is also 4 targeted use for the PRO polypeptides herein or their antagonists. Formation and regression of new blood vessels is essential for tissue healing and repair.

This category includes bone, cartilage, tendon, ligament, and/or nerve tissue growth or regeneration, as well as wound healing and tissue repair and replacement, and in the treatment of burns, incisions, and ulcers. A PRO polypeptide or antagonist thereof that induces cartilage and/or bone growth in circumstances where bane is not : normally formed has application in the healing of bone fractures and cartilage damage or defects in humans and other animals. Such a preparation employing a PRO polypeptide or antagonist thereof may have prophylactic use in closed as well as open fracture reduction and also in the improved fixation of artificial joints. De novo bone formation induced by an ostcogenic agent contributes to the repair of congenital, trauma-induced, or oncologic, resection-induced craniofacial defects, and also is useful in cosmetic plastic surgery.

PRO polypeptides or antagonists thereto may also be useful to promote better or faster closure of non-healing wounds, including without limitation pressure ulcers, ulcers associated with vascular insufficiency, surgical and traumatic wounds, and the like.

It is expected that a PRO polypeptide or antagonist thereto may also exhibit activity for generation or regeneration of other tissues, such as organs (including, for example, pancreas, liver. intestine, kidney, skin, or endothelium), muscle (smooth, skeletal, or cardiac), and vascular (including vascular endothelium} tissue, or for promoting the growth of cells comprising such tissucs. Part of the desired effects may be by inhibition or modulation of fibrotic scarring to allow normal tissue to regenerate.

A PRO polypeptide herein or antagonist thereto may also be useful for gut protection or regeneration and treatment of lung or liver fibrosis, reperfusion injury in various tissues, and conditions resulting from systemic cytokine damage. Also, the PRO polypeptide or antagonist thereto may be useful for promoting or inhibiting differentiation of tissues described above from precursor tissues or cells, or for inhibiting the growth of tissues described above.

A PRO polypeptide or antagonist thereto may also be used in the treatment of periodontal diseases and in other tooth-repair processes. Such agents may provide an environment to attract bone-forming cells, stimulate growth of bone-forming cells, or induce differentiation of progenitors of bone-forming cells. A PRO polypeptide herein 3 or an antagonist thereto may also be useful in the treatment of osteoporosis or osteoarthritis, such as through stimulation of bone and/or cartilage repair or by blocking inflammation or processes of tissue destruction (collagenase activity, osteoclast activity, etc.) mediated by inflammatory processes, since blood vessels play an important role in the regulation of bone turnover and growth.

Another category of tissue regeneration activity that may be attributable to the PRO polypeptide herein or antagonist thereto is tendon/ti gament formation. A protein that induccs tcndon/ligament-like tissue or other tissue formation in circumstances where such tissue is not normally formed has application in the healing of tendon or ligament tears, deformities, and other tendon or ligament defects in humans and other animals. Such a preparation may have prophylactic use in preventing damage to tendon or ligament tissue, as well as use in the improved fixation of tendon or ligament to bone or other tissues, and in repairing defects to tendon or ligament tissue. De novo tendonfligament-like tissue formation induced by a composition of the PRO polypeptide herein or antagonist thereto contributes to the repair of congenital, trauma-induced, or other tendon or ligament defects of other origin, and is also useful in cosmetic plastic surgery for attachment or repair of tendons or ligaments. The compositions herein may provide an environment to attract tendon- or ligament-forming cells, stimulate growth of tendon- or ligament-forming cells, induce differentiation of progenitors of tendon- or ligament-forming cells, or induce growth of tendon/ligament cells or progenitors ex vivo for return in vivo to effect tissue repair. The compositions herein may also be useful in the treatment of tendinitis, carpal tunnel syndrome. and other tendon or ligament defects. The . compositions may also include an appropriate matrix and/or sequestering agent as a carrier as is well known in the art.

The PRO polypeptide or its antagonist may also be useful for proliferation of neural cells and for regeneration of nerve and brain tissue, i.e., for the treatment of central and peripheral nervous system disease and neuropathies. as well as mechanical and traumatic disorders, that involve degeneration, death, or trauma to neural cells or nerve tissue. More specifically, a PRO polypeptide or its antagonist may be used in the treatment of discascs of the peripheral nervous system, such as peripheral nerve injuries, peripheral neuropathy and localized neuropathies, and central nervous system diseases, such as Alzheimer's, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome. Further conditions that may be treated in accordance with the present invention include mechanical and traumatic disorders, such as spinal cord disorders, head trauma, and cerebrovascular diseases such as stroke. Peripheral neuropathies resulting from chemotherapy or other medical therapies may also be treatable using a PRO polypeptide herein or antagonist thereto.

Ischemia-reperfusion injury is another indication. Endothelial cell dysfunction may be important in both the initiation of, and in regulation of the sequelae of cvents that occur following ischemia-reperfusion injury.

Rheumatoid arthritis is a further indication. Blood vessel growth and targeting of inflammatory cells through the vasculature is an important component in the pathogenesis of rheumatoid and sero-negative forms of arthritis.

A PRO polypeptide or its antagonist may also be administered prophylactically to patients with cardiac hypertrophy, to prevent the progression of the condition, and avoid sudden death, including death of asymptomatic patients. Such preventative therapy is particularly warranted in the case of patients diagnosed with massive left ventricular cardiac hypertrophy (a maximal wall thickness of 35 mm or more in adults, or a comparable value in children), or in instances when the hemodynamic burden on the heart is particularly strong.

A PRO polypeptide or its antagonist may also be useful in the management of atrial fibrillation, which develops in a substantial portion of patients diagnosed with hypertrophic cardiomyopathy.

Further indications include angina, myocardial infarctions such as acute myocardial infarctions, and heart failure such as congestive heart failure. Additional non-neoplastic conditions include psoriasis, diabetic and other proliferative retinopathies including retinopathy of prematurity, retrolental fibroplasia, neovascular glaucoma, thyroid hyperplasias (including Grave's disease), corneal and other tissue transplantation, chronic inflammation, lung inflammation, nephrotic syndrome, preeclampsia, ascites, pericardial effusion (such as that associated with pericarditis), and pleural effusion.

In view of the above, the PRO polypeptides or agonists or antagonists thereof described herein, which are shown to alter or impact endothelial celt function, proliferation, and/or form, are likely to play an important role in the etiology and pathogenesis of many or all of the disorders noted above, and as such can serve as therapeutic targetsto augment or inhibit these processes or for vascular-related drug targeting in these disorders. xi. Administration Protocols, Schedules, Doses, and Formulations

The molecules herein and agonists and antagonists thereto are pharmaceutically useful as a prophylactic and therapeutic agent for various disorders and diseases as set forth above,

Therapeutic compositions of the PRO polypeptides or agonists or antagonists are prepared for storage by mixing the desired molecule having the appropriate degree of purity with optional pharmaceutically acceptable carriers, excipients, or stabilizers (Remington's Pharmaceutical Sciences, 16th edition, Osol, A. ed. (1980)), in the - form of lyophilized formulations or aqueous solutions. Acceptable carriers, exci pients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate. citrate. and other } organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecvidimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride: phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol: 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides: proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone: amino acids such as glycine, glutamine, asparagine, histidine. arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes): and/or non- ionic surfactants such as TWEEN™, PI.URONICS™ or polyethylene glycol (PEG).

Additional examples of such carriers include ion exchangers, alumina, aluminum stearate. lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid. potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts, or electrolytes such as protamine sulfate. disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts. colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, celiulnse-based substances. and polyethylene glvcol. Carriers for topical or gel-based forms of antagonist include polysaccharides such as sodium carboxymethylceliulose or methylcellulose, polyvinylpyrrolidone, polyacrylates, polyoxyethylene-polyoxypropylene-block polymers, . polyethylene glycol, and wood wax alcohols. For all administrations, conventional depot forms are suitably uscd.

Such forms include, for example, microcapsules, nano-capsules, liposomes, plasters, inhalation forms, nose sprays, sublingual tablets, and sustained-release preparations. The PRO polypeptides or agonists or antagonists will typically be formulated in such vehicles at a concentration of about 0.1 mg/ml to 100 mg/ml.

Another formulation comprises incorporating a PRO polypeptide or antagonist thereof into formed articles.

Such articles can be used in modulating endothelial cell growth and angiogenesis. In addition, tumor invasion and metastasis may be modulated with these articles.

PRO polypeptide or antagonist to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution. PRO polypeptide ordinarily will be stored in lyophilized form or in solution if administered systemically. If in lyophilized form, PRO polypeptide or antagonist thereto is typically formulated in combination with other ingredients for reconstitution with an appropriate diluent at the time for use. An example of a liquid formulation of PRO polypeptide or antagonist is a sterile, clear, colorless unpreserved solution filled in a single- dose vial for subcutaneous injection. Preserved pharmaceutical compositions suitable for repeated use may contain, for example, depending mainly on the indication and type of polypeptide: a) PRO polypeptide or agonist or antagonist thereto; b) a buffer capable of maintaining the pH in a range of maximum stability of the polypeptide or other molecule in solution, preferably about 4-8; ¢) a detergent/surfactant primarily to stabilize the polypeptide or molecule against agitation-induced aggregation, - d) an isotonifier; e) aprescrvative selected from the group of phenol, benzyl alcohol and a benzethonium halide, e.g., chloride; and f) water.

If the detergent employed is non-ionic, it may, for example, be polysorbates (e.g., POLYSORBATE'™ (TWEEN™) 20, 80, etc.) or poloxamers (e.g.. POLOXAMER™ 188). The use of non-ionic surfactants permits the formulation to be exposed to shear surface stresses without causing denaturation of the polypeptide. Further, such surfactant-containing formulations may be employed in aerosol devices such as those used in a pulmonary dosing. and needleless jet injector guns (see, e.g., EP 257,956).

An isotonifier may be present to ensure isotonicity of a liquid composition of the PRO polypeptide or antagonist thereto, and includes polyhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol. sorbitol, and mannitol. These sugar alcohols can be used alone or in combination. Alternatively, sodiumchloride or other appropriate inorganic salts may be used to render the solutions isotonic.

The buffer may, for example, be an acetate, citrate, succinate, or phosphate buffer depending on the pH desired. The pH of one type of liquid formulation of this invention is buffered in the range of about 4 to 8, preferably about physiological pH.

The preservatives phenol, benzyl alcohol and benzethonium halides, e.g., chioride. are known antimicrobial agents that may be employed.

Therapeutic PRO polypeptide compositions generally are placed into a container having a sterile access pon, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle. The formulations are preferably administered as repeated intravenous (i.v.), subcutaneous (s.c.), or intramuscular (i.m.) injections, or as acrosol formulations suitable for intranasal or intrapulmonary delivery (for intrapulmonary delivery see, e.g., EP 257,956).

PRO polypeptide can also be administered in the form of sustained-released preparations. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the protein, which matrices arc in the form of shaped articles, e.g., films, or microcapsules. Examples of sustained- release matrices include polyesters, hydrogels (e.g., poly(2-hydroxyethyl-methacrylate) as described by Langer er al). Biomed. Mater. Res., 15: 167-277 (1981 )and Langer, Chem. Tech., 12: 98-105 (1982) or poly(vinylalcohol)), polylactides (U.S. Patent No. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman er al, Biopolymers, 22: 547-556 (1983)), non-degradabic ethylene-vinyl acetate (Langer et al., supra), degradable lactic acid-glycolic acid copolymers such as the Lupron Depot™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3-hydroxybutyric acid (EP 133,988).

While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated proteins remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in aloss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for protein stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, Iyophilizing from acidic solutions, controlling moisture content, using appropriate . additives, and developing specific polymer matrix compositions.

Sustained-release PRO polypeptide compositions also include liposomally entrapped PRO polypeptides.

Liposomes containing the PRO polypeptide are prepared by methods known per se: DE 3,218,121; Epstein er al..

Proc. Natl. Acad. Sci. USA, 82: 3688-3692 (1985); Hwang ef al., Proc. Natl. Acad. Sci. USA, 77: 4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP 142.64]; Japanese patent application 83-118008; U.S.

Patent Nos. 4,485,045 and 4,544,545: and EP 102,324. Ordinarily the liposomes are of the small (about 200-800

Angstroms) unilamellar type in which the lipid content is greater than about 30 mol. % cholesterol, the selected proportion being adjusted for the optimal therapy.

The therapeutically effective dose of PRO polypeptide or antagonist thereto will, of course, vary depending on such factors as the pathological condition to be treated (including prevention), the method of administration, the type of compound being used for treatment, any co-therapy involved. the patient's age, weight, general medical condition, medical history, etc.. and its determination is well within the skill of a practicing physician. Accordingly, irwillbe necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the maximal therapeutic effect. If the PRO polypeptide has a narrow host range, for the treatment of human patients formulations comprising human PRO polypeptide, more preferably native-sequence human PRO polypeptide, are preferred. The clinician will administer PRO polypeptide until a dosage is reached that achieves the desired cffect for treatment of the condition in question. For cxample, if the objective is the treatment of CHF, the amount would be one that inhibits the progressive cardiac hypertrophy associated with this condition. The progress of this therapy } is easily monitored by echo cardiography. Similarly, in patients with hypertrophic cardiomyopathy, PRO polypeptide can be administered on an empirical basis.

With the above guidelines, the effective dose generally is within the range of from about 0.001 to about 1.0 mg/kg, more preferably about 0.01-1.0 mg/kg, most preferably about 0.01-0.1 mg/kg.

For non-oral use in treating human adult hypertension, it is advantageous to administer PRO polypeptide in the form of an injection at about 0.01 to 50 mg, preferably about 0.05 to 20 mg, most preferably 1 to 20 mg, per kg body weight, 1 to 3 times daily by intravenous injection. For oral administration, a molecule based on the PRO polypeptide is preferably administered at about 5 mg to 1 g, preferably about 10 to 100 mg, per kg body weight, 1 103 times daily. It should be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less than 0.5 ng/mg protein. Moreover, for human administration, the formulations preferably meet sterility, pyrogenicity, general safety, and purity as required by FDA Office and Biologics standards.

The dosage regimen of a pharmaceutical composition containing PRO polypeptide to be used in tissue regeneration will be determined by the attending physician considering various factors that modify the action of the polypeptides, e.g., amount of tissue weight desired to be formed, the site of damage, the condition of the damaged tissue, the size of a wound, type of damaged tissue (e.g., bone), the patient's age, sex, and diet, the severity of any infection, time of administration, and other clinical factors. The dosage may vary with the type of matrix used in the reconstitution and with inclusion of other proteins in the pharmaceutical composition. For example, the addition of other known growth factors, such as IGF-I, to the final composition may also affect the dosage. Progress can be monitored by periodic assessment of tissue/bone growth and/or repair, for example, X-rays, histomorphometric determinations, and tetracycline labeling. - The route of PRO polypeptide or antagonist or agonist administration is in accord with known methods, e.g., by injection or infusion by intravenous, intramuscular, intracerebral, intraperitoneal, intracerobrospinal, subcutaneous, intraocular, intraarticular, intrasynovial, intrathecal, oral, topical, or inhalation routes, or by sustained-release systems as noted below. The PRO polypeptide or antagonists thereof also are suitably administered by intratumoral, peritumoral, intralesional, or perilesional routes, 10 exert local as well as systemic therapeutic effects. The intraperitoneal route is expected to be particularly useful, for example, in the treatment of ovarian tumors.

If a peptide or small nolecule is employed as an antagonist or agonist, it is preferably administered orally or non-orally in the form of a liquid or solid to mammals.

Examples of pharmacologically acceptable salts of molecules that form salts and are useful hereunder include alkali metal salts (e.g., sodium salt, potassium salt), alkaline earth metal salts (e.g., calcium salt, magnesium salt), ammonium salts. organic base salts (e.g., pyridine salt, triethylamine salt), inorganic acid salts (e.g., hydrochloride, sulfate, nitrate), and salts of organic acid (e.g., acetate, oxalate, p-toluenesulfonate).

For compositions herein that are useful for bone, cartilage, tendon, or ligament regeneration. the therapeutic method includes administering the composition topicaliy, systemically, or locally as an implant or device. When administered, the therapeutic composition for use is in a pyrogen-free, physiologically acceptable form. Further, the composition may desirably be encapsulated or injected in a viscous form for delivery to the site of bone, cartilage, or tissue damage. Topical administration may be suitable for wound healing and tissue repair. Preferably,

for bone and/or cartilage formation, the composition would include a matrix capable of delivering the protein- containing composition to the site of bone and/or cartilage damage, providing a structure for the developing bone . and cartilage and preferably capable of being resorbed into the body. Such matrices may be formed of materials presently in use for other implanted medical applications.

S The choice of matrix material is based on biocompatibility, biodegradability, mechanical properties, cosmetic appearance, and interface properties. The particular application of the compositions will define the appropriate formulation. Potential matrices for the compositions may be biodegradable and chemically defined calcium sulfate, tricaicium phosphate, hydroxyapatite, polylactic acid, polyglycolic acid, and polyanhydrides. Other potential materials are biodegradable and biologically well-defined, such as bone or dermal collagen. Further matrices are comprised of pure proteins or extracellular matrix components. Other potential matrices are nonbiodegradable and chemically defined, such as sintered hydroxyapatite, bioglass, aluminates, or other ceramics. Matrices may be comprised of combinations of any of the above-mentioned types of material, such as polylactic acid and hydroxyapatite or collagen and tricalcium phosphate. The bioceramics may be altered in composition, such as in calcium-aluminate-phosphate and processing to alter pore size, particle size, particle shape, and biodegradability.

One specific embodiment is a 50:50 (mole wei ght) copolymer of lactic acid and glycolic acid in the form of porous particles having diameters ranging from 150 to 800 microns. In some applications, it will be useful to utilize a sequestering agent, such as carboxymethyl cellulose or autologous blood clot, to prevent the polypeptide compositions from disassociating from the matrix.

One suitable family of sequestering agents is cellulosic materials such as alkylcelluloses (including hydroxyalkylcelluloses), including methylcellulose, ethylcellulose, hydoxyethylcellulose, hydroxypropylcellulose, hydroxypropyimethylcellulose, and carboxymethylcellulose, one preferred being cationic salts of carboxymethylcellulose (CMC). Other preferred sequestering agents include hyaluronic acid, sodium alginate, : poly(ethylene glycol), polyoxyethylene oxide, carboxyvinyl polymer, and poly(viny} alcohol). The amount of sequestering agent useful herein is 0.5-20 wt, preferably 1-10 wt%, based on total formulation weight, which represents the amount necessary to prevent desorption of the polypeptide (or its antagonist) from the polymer matrix and to provide appropriate handling of the composition, yet not so much that the progenitor cells are prevented from infiltrating the matrix, thereby providing the polypeptide (or its antagonist) the opportunity to assist the osteogenic activity of the progenitor cells. xii. Combination Therapies

The effectiveness of the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO203, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROS8S or PRO8S7 polypeptide or an agonist or antagonist thereof in preventing or treating the disorder in question may be improved by administering the active agent serially or in combination with another agent that is effective for those purposes, either in the same composition or as separate compositions.

For example, for treatment of cardiac hypertrophy. PRO polypeptide therapy can be combined with the administration of inhibitors of known cardiac myocyte hypertrophy factors, e.g., inhibitors of a-adrenergic agonists such as phenylephrine; endothelin- inhibitors such as BOSENTAN™ and MOXONODIN™: inhibitors to CT-1 (US Pat. No. 5,679,545); inhibitors to LIF; ACE inhibitors: des-aspartate-angiotensin I inhibitors (U.S. Pat. No.

5,773,415), and angiotensin II inhibitors. } For treatment of cardiac hypertrophy associated with hypertension, the PRO polypeptide can be administered in combination with B-adrenergic receptor blocking agents, e.g., propranolol, timolol, tertalolol, carteolol, nadolol, betaxolol, penbutolol, acetobutolol, atenolol, metoprolol, or carvedilol; ACE inhibitors, e.g., quinapril, captopril, enalapril, ramipril, benazepril, fosinopril, or lisinopril; diuretics, e.g., chlorothiazide, hydrochlorothiazide, hydroflumethazide, methylchlothiazide, benzthiazide, dichlorphenamide, acetazolamide, or indapamide; and/or calcium channel blockers, e.g., diltiazem, nifedipine, verapamil, or nicardipine. Pharmaceutical compositions comprising the therapeutic agents identified herein by their generic names are commercially available, and are to be administered following the manufacturers’ instructions for dosage, administration, adverse effects, contraindications, etc. See, e. §-, Physicians’ Desk Reference (Medical Economics Data Production Co.: Montvale,

N.J., 1997), 51th Edition.

Preferred candidates for combination therapy in the treatment of hypertrophic cardiomyopathy are [- adrenergic-blocking drugs (e.g., propranolol, timolol, tertalolol, carteolol, nadolol, betaxolol, penbutolo}, acetobutolol, atenolol. metoprolol, or carvedilol), verapamil, difedipine, or diltiazem. Treatment of hypertrophy associated with high blood pressure may require the use of antihypertensive drug therapy, using calcium channel blockers, e.g., diltiazem, nifedipine, verapamil, or nicardipine; [-adrenergic blocking agents; diuretics, e.g., chlorothiazide, hydrochlorothiazide, hydroflumethazide, methylchlothiazide, benzthiazide, dichlorphenamide, acetazolamide, or indapamide; and/or ACE-inhibitors, e.g., quinapril, captopril, enalapril, ramipril, benazepril, fosinopril, or lisinopril.

For other indications, PRO polypeptides or their antagonists may be combined with other agents beneficial to the treatment of the bone and/or cartilage defect, wound, or tissue in question. These agents include various . growth factors such as EGF, PDGF, TGF-a or TGF-8, IGF, FGF, and CTGF.

In addition, PRO polypeptides or their antagonists used to treat cancer may be combined with cytotoxic, chemotherapeutic, or growth-inhibitory agents as identified above. Also, for cancer treatment, the PRO polypeptide or antagonist thereof is suitably administered serially or in combination with radiological treatments, whether involving irradiation or administration of radioactive substances.

The effective amounts of the therapeutic agents administered in combination with the PRO polypeptide or antagonist thereof will be at the physician's or veterinarians discretion. Dosage administration and adjustment is done to achieve maximal management of the conditions to be treated. For example. for treating hypertension, these amounts ideally take into account use of diuretics or digitalis, and conditions such as hyper- or hypotension, renal impairment, etc. The dose will additionally depend on such factors as the type of the therapeutic agent to be used and the specific patient being treated. Typically, the amount employed will be the same dose as that used, if the given therapeutic agent is administered without the PRO polypeptide. xiii. Articles of Manufacture

An article of manufacture such as akit containing PRO179, PRO238, PRO364. PRO844, PRO846, PRO1760),

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882. PRO8SS5 or PRO887 polypeptide or agonists or antagonists thereof useful for the diagnosis or treatment of the disorders described above comprises at least a container and a label. Suitable containers include, for example, bottles, vials, syringes, and test tubes.

The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition that is effective for diagnosing or treating the condition and may have a sterile access port (for ] example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). The active agent in the composition is the PRO179, PRO238, PRO364, PRO844, PRO846,

PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO8S7 polypeptide or an agonist or antagonist thereto, The label on, or associated with, the container indicates that the composition is used for diagnosing or treating the condition of choice. The article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline,

Ringer's solution, and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use. The article of manufacture may also comprise a second or third container with another active agent as described above.

E. Antibodies

Some of the most promising drug candidates according 10 the present invention are antibodies and antibody fragments that may inhibit the production or the gene product of the genes identified herein and/or reduce the activity of the gene products. i. Polycional Antibodies

Methods of preparing polyclonal antibodies are known to the skilled artisan. Polyclonal antibodies can be raised in a mammal, for example, by one or more injections of an immunizing agent and, if desired, an adjuvant.

Typically, the immunizing agent and/or adjuvant will be injected in the mammal by multiple subcutaneous or intraperitoneal injections. The immunizing agent may include the PRO179, PRO238, PRO3G4, PRO844, PRO846,

PRO1760, PRO205, PRO321, PRO333, PRO840. PRO877, PRO878, PRO879, PRO882, PROSSS or PRO8S7 polypeptide or a fusion protein thereof. It may be useful to conjugate the immunizing agent to a protein known to be immunogenic in the mammal being immunized. Examples of such immunogenic proteins include, but are not limited to, keyhole limpet hemocyanin, serum albumin, bovine thyroglobulin, and soybean trypsin inhibitor.

Examples of adjuvants that may be employed include Freund's complete adjuvant and MPL-TDM adjuvant (manophosphoryl Lipid A or synthetic trehalose dicorynomycolate). The immunization protocol may be selected by one skilled in the art without undue experimentation. ii. Monoclonal Antibodies

The anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844. anti-PROS46. anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333. anti-PRO840, anti-PRO877, anti-PROS7S, anti-PROS79, anti-PRO8S2, anti-PROSSS or anti-PRO887 antibodies may, alternatively, be monoclonal antibodies. Monoclonal antibodies may be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). Ina hybridoma method, a mouse, hamster, or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in virro.

The immunizing agent will typically include the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, . PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide or a fusion protein thereof. Generally, either peripheral blood lymphocytes ("PBLs") are used if cells of human origin are desired, or spleen cells or lymph node cells are used if non-human mammalian sources are desired. The lymphocytes are then fused with an immortalized cell line using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell. Goding, Monoclonal Antibodies: Principles and Practice (New York: Academic Press, 1986), pp. 59-103. immortalized cell lines are usually transformed mammalian cells, particularly myeloma cells of rodent, bovine, and human origin. Usually, rat or mouse myeloma cell lines are employed. The hybridoma cells may be cultured in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, immortalized cells. For example, if the parental cells lack the enzyme hypoxanthine guanine phosphoribosy! transferase (HGPRT or HPRT), the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine ("HAT medium”), which substances prevent the growth of

HGPRT-deficient cells.

Preferred immortalized cell lines are those that fuse efficiently, support stable high-level expression of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium. More preferred immortalized cell lines are murine myeloma lines, which can be obtained, for instance, from the Salk

Institute Cell Distribution Center, San Diego, California and the American Type Culture Collection, Manassas,

Virginia. Human myeloma and mouse-human heteromyeloma cel lincs also have been described for the production of human monoclonal antibodies. Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al., Monoclonal Antibody

Production Techniques and Applications (Marcel Dekker, Inc.: New York, 1987) pp. 51-63.

The culture medium in which the hybridoma cells are cultured can then be assayed for the presence of monoclonal antibodies directed against the PRO 179, PR0238, PRO364, PRO844, PRO846, PRO 1760, PRO205,

PRO321,PR0O333,PRO840, PRO877,PRO878, PRO879, PRORS2, PROS or PROSR7 polypeptide. Preferably, ] the binding specificity of monoclonal antibodies produced by the hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay. such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA). Such techniques and assays are known in the art. The binding affinity of the monoclonal antibody can, for example, be determined by the Scatchard analysis of Munson and Pollard, Anal.

Biochem, 107:220 (1980).

After the desired hybridoma cells are identified, the clones may be subcloned by limiting dilution procedures and grown by standard methods. Goding, supra. Suitable culture media for this purpose include, for example,

Dulbecco's Modified Eagle's Medium and RPMI-1640 medium. Alternatively, the hybridoma cells may be grown in vivo as ascites in a mammal.

The monoclonal antibodies secreted by the subclones may be isolated or purified from the culture medium or ascites fluid by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis. or affinity chromatography.

The monoclonal antibodies may also be made by recombinant DNA methods, such as those described in U.S.

Patent No. 4,816,567. DNA encoding the monoclonal antibodies of the invention can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). The hybridoma cells of the invention serve as a preferred source of such DNA. Once isolated, the DNA may be placed into expression vectors, which are then transfected into host cells such as simian COS cells, Chinese hamster ovary (CHO) cells, or . myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. The DNA also may be modified, for example, by substituting the coding sequence for human heavy- and light-chain constant domains in place of the homologous murine sequences (U.S.

Patent No. 4,816,567; Morrison et al., supra) or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide. Such a non-immunoglobulin polypeptide can be substituted for the constant domains of an antibody of the invention, or can be substituted for the variable domains of one antigen-combining site of an antibody of the invention to create a chimeric bivalent antibody.

The antibodies may be monovalent antibodies. Methods for preparing monovalent antibodies are well known in the art. For example, one method involves recombinant expression of immunoglobulin light chain and modified heavy chain. The heavy chain is truncated generally at any point in the Fc region so as to prevent heavy-chain crosslinking. Alternatively, the relevant cysteine residues are substituted with another amino acid residue or are deleted so as to prevent crosslinking.

In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly Fab fragments, can be accomplished using routine techniques known in the art. iii. Human and Humanized Antibodies

The anti-PRO179, anti-PRO238, anti-PR0O364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PROR4(), anti-PRO877, anti-PROSTS, anti-PRO879, anti-PROSR’?, anti-PROBSS or anti-PRO887 antibodies may further comprise humanized antibodies or human antibodies. Humanized forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains. or fragments thereof (such as Fv, Fab, Fab’, F(ab"), or other antigen-binding subsequences of antibodies) that contain minimal sequence derived from non-human immunoglobulin. Humanized antibodies include human immunoglobulins } (recipient antibody) in which residues from a CDR of the recipient are replaced by residues from a CDR of a non- human species (donor antibody) such as mouse, rat, or rabbit having the desired specificity. affinity. and capacity.

In some instances, Fv framework residues of the human immunoglobulin are replaced by corresponding non-human residues. Humanized antibodies may also comprise residues that are found neither in the recipient antibody nor in the imported CDR or framework sequences. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin, and all or substantially all of the FR regions are those of a human immunoglobulin consensus sequence. The humanized antibody preferably also will comprise at least a portion of an immunoglobulin constant region (Fc). typically that of a human immunoglobulin. Jones ef al.. Nature, 321: 522- 525 (1986); Riechmann er al., Nature, 332: 323-329 (1988); Presta, Curr. Op. Struct. Biol.. 2:593-596 (1992).

Methods for humanizing non-human antibodies are well known in the art. Generally. a humanized antibody has one or more amino acid residues introduced into it from a source that is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken froman "import" variable domain.

Humanization can be essentially performed following the method of Winter and co-workers (Jones er al., Nature, 321: 522-525 (1986); Riechmann ef al, Nature, 332: 323-327 (1988); Verhoeyen er al., Science. 239: 1534-1536

(1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody.

Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Patent No. 4,816,567), wherein substantially less than an intact human variable domain has been substituted by the corresponding scquence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

Human antibodies can also be produced using various techniques known in the art, including phage display libraries. Hoogenboom and Winter, J. Mol, Biol., 227: 381 (1991); Marks et al., J. Mol. Biol, 222: 581 (1991).

The techniques of Cole et al. and Boerner et al. are also available for the preparation of human monoclonal antibodies. Cole er al., Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985) and Boerner et al., )._Immunol., 147(1): 86-95 (1991). Similarly, human antibodies can be made by introducing human immunoglobulin loci into transgenic animals, e.g., mice in which the endogenous immunoglobulin gencs have been partially or completely inactivated. Upon challenge, human antibody production is observed that closely resembles that seen in humans in all respects, including gene rearrangement, assembly, and antibody repertoire. This approach is described, for example, in U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5.625,126; 5,633,425; and 5,661,016,andinthe following scientific publications: Marks eral., Bio/Technology, 10: 779-783 (1992); Lonberg etal, Nature, 368: 856-859 (1994); Morrison, Nature, 368: 812-813 (1994); Fishwild et al., Nature Biotechnology, 14: 845-851 (1996); Neuberger, Nature Biotechnology, 14: 826 (1996); Lonberg and Huszar, Intern. Rev. Immunol., 13: 65-93 (1995). iv. Bispecific Antibodies

Bispecific antibodies are monaclonal, preferably human or humanized, antibodics that have binding : specificities for at least two different antigens. In the present case, one of the binding specificities is for the

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide, the other one is for any other antigen, and preferably for a cell-surface protein or receptor or receptor subunit.

Methods for making bispecific antibodies are known in the art. Traditionally. the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities. Milstein and Cuello, Nature, 305: 537-539 (1983). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of ten different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunccker eral., EMBO 1., 10: 3655-3659 (1991).

Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant-domain sequences. The fusion preferably is with an immunoglobulin heavy- chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CH1) containing the site necessary for light-chain binding present in at lcast one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired. the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. For further details of generating bispecific antibodies, see, for example, Suresh er al., Methods in Enzymology, 121: 210 v. Heteroconjugate Antibodies

Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune-system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HIV infection. WO 91/00360; WO 92/200373; EP 03089. Itis contemplated that the antibodies may be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins may be constructed using a disulfide-exchange reaction or by forming a thioether bond. Examples of suitable reagents for this purpose include iminothiolate and methyl-4- mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980. vi. Effector Function Engineering

It may be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) may be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated may have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See, Caron et al., J. Exp. Med., 176: 1191-1195 (1992) and

Shopes, J. Immunol., 148: 2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross-linkers as described in Wolff ef al., Cancer Research, 53: 2560-2565 (1993). Alternatively. an antibody can be engineered that has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See, Stevenson et al., Anti-Cancer Drug Design, 3: 219-230 (1989). vii. Iminunoconjugates

The invention also pertains to immunoconjugates comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, toxin (e.g., an enzymatically active toxin of bacterial. fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e¢., a radioconjugate).

Chemotherapeutic agents useful in the generation of such immunoconjugates have been described above.

Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurires fordii proteins, dianthin proteins, Phyviolaca americana proteins (PAPI,

PAPI], and PAP-S), momordica charantia inhibitor. curcin, crotin. sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. A variety of radionuclides arc available tor the production of radioconjugated antibodies. Examples include **Bi, "I, "In, *Y, and "Re.

Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP). iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HC), active esters (such as disuccinimidyl suberate), aldehydes (such as glutareldehyde), bis-azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoy!)-ethylenediamine), diisocyanates (such as tolyene 2,6-diisocyanate), and bis- active fluorine compounds (such as 1.5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be i WoO 00/53757 } PCT/US00/05004 prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon-14-labeled 1-isothiocyanatobenzyl-3- - methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See, W094/11026.

In another embodiment, the antibody may be conjugated to a “receptor” (such as streptavidin) for utilization in tumor pretargeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a “ligand” (e.g., avidin) that is conjugated to a cytotoxic agent (e.g., a radionucleotide). viii. Immunoliposomes

The antibodies disclosed herein may also be formulated as immunoliposomes. Liposomes containing the antibody are prepared by methods known in the art, such as described in Epstein et al., Proc. Natl. Acad. Sci. USA, 82: 3688 (1985); Hwang et al, Proc. Natl. Acad. Sci. USA, 77: 4030 (1980); and U.S. Pat. Nos. 4,485,045 and 4,544,545. Liposomes with enhanced circulation time are disclosed in U.S. Patent No. 5,013,556.

Particularly useful liposomes can be generated by the reverse-phase evaporation method with a lipid composition comprising phosphatidylcholine, cholesterol, and PEG-dcrivatized phosphatidylethanolamine (PEG-

PE). Liposomes are extruded through filters of defined pore size to yield liposomes with the desired diameter. Fab’ fragments of the antibody of the present invention can be conjugated to the liposomes as described in Martin et al., 1. Biol. Chem, 257: 286-288 (1982) via a disulfide-interchange reaction. A chemotherapeutic agent (such as

Doxorubicin) is optionally contained within the liposome. See, Gabizon ef al, J. National Cancer Inst., 81(19): 1484 (1989). ’ 20 ix. Pharmaceutical Compositions of Antibodies

Antibodies specifically binding a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205,

PRO321, PRO333. PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRORRT polypeptide identified herein, as well as other molecules identified by the screening assays disclosed hereinbefore, can be administered for the treatment of various disorders as noted above and below in the form of pharmaceutical compositions.

If the PRO179, PRO238, PRO364, PRO344, PRO846, PRO1760, PRO20S, PRO321, PRO333. PROB40,

PRO877. PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide is intracellular and whole antibodies are used as inhibitors, internalizing antibodies arc preferred. However, lipofections or liposomes can also be used to deliver the antibody, or an antibody fragment, into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is preferred. For example, based upon the variable-region sequences of an antibody, peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad. Sci. USA. 90: 7889-7893 (1993).

The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.

Alternatively, or in addition, the composition may comprise an agent that enhances its function, such as, for example, a cytotoxic agent, cytokine, chemotherapeutic agent, or growth-inhibitory agent. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.

The active ingredients may also be entrapped in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcelulose or gelatin-microcapsules and poly- : (methylmethacylate) microcapsules, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles, and nanocapsules) or in macroemulsions. Such techniques aredisclosed in Remington's Pharmaceutical Sciences, supra.

The formulations to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes.

Sustained-release preparations may be prepared. Suitable examples of sustained-relcase preparations include semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shapedarticies, e.g., films, or microcapsules. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and y ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOT ™ (injectable microspheres composed of lactic acid- glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3-hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated antibodies remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37 °C, resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing fromacidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions. ’

X. Methods of Treatment using the Antibody

It is contemplated that the antibodies to a PRO179, PRO238, PRO364, PRO844. PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 or PRO8S7 polypeptide may be used to treat various cardiovascular, endothelial, and angiogenic conditions as noted above.

The antibodies are administered 10 a mammal, preferably a human, in accord with known methods, such as intravenous administration as a bolus or by continuous infusion over a period of time, by intramuscular, intraperitoneal, intracerobrospinal, subcutaneous, intra-articular, intrasynovial, intrathecal, oral, topical, or inhalation routes. Intravenous administration of the antibody is preferred.

Other therapeutic regimens may be combined with the administration of the antibodies of the instant invention as noted above. For example, if the antibodies are to treat cancer, the patient to be treated with such antibodies may also receive radiation therapy. Alternatively, or in addition, a chemotherapeutic agent may be administered to the patient. Preparation and dosing schedules for such chemotherapeutic agents may be used according to manufacturers’ instructions or as determined empirically by the skilled practitioner. Preparation and dosing schedules for such chemotherapy are also described in Chemotherapy Service, Ed., M.C. Perry (Williams &

Wilkins: Baltimore, MD, 1992). The chemotherapeutic agent may precede, or follow administration of the antibody. or may be given simultaneously therewith. The antibody may be combined with an anti-estrogen compound such as tamoxifen or EVISTA™ or an anti-progesterone such as onapristone (see, EP 616812) in dosages known for such molecules.

If the antibodies are used for treating cancer, it may be desirable also to administer antibodics against other tumor-associated antigens, such as antibodies that bind to one or more of the ErbB2, EGFR, ErbB3, ErbB4, or

S VEGF receptor(s). These also include the agents set forth above. Also, the antibody is suitably administered serially or in combination with radiological treatments, whether involving irradiation or administration of radioactive substances. Alternatively, or in addition, two or more antibodies binding the same or two or more different antigens disclosed herein may be co-administered to the patient. Sometimes, it may be beneficial also to administer one or more cytokines to the patient. In a preferred embodiment, the antibodies herein are co- administered with a growth-inhibitory agent. For example, the growth-inhibitory agent may be administered first, followed by an antibody of the present invention, However, simultaneous administration or administration of the antibody of the present invention first is also contemplated. Suitable dosages for the growth-inhibitory agent are those presently used and may be lowered due to the combined action (synergy) of the growth-inhibitory agent and the antibody herein.

In one embodiment, vascularization of tumors is attacked in combination therapy. The anti-PRO polypeptide antibody and another antibody (e.g., anti-VEGF) are administered to tumor-bearing patients at therapeutically effective doses as determined, for example, by observing necrosis of the tumor or its metastatic foci, if any. This therapy is continued until such time as no further beneficial effect is observed or clinical examination shows no trace of the tumor or any metastatic foci. Then TNF is administered, alone or in combination with an auxiliary agent such as alpha-, beta-, or gamma-interferon, anti-HER? antibody, heregulin, anti-heregulin antibody, D-factor, interleukin-1 (IL-1), interleukin-2 (IL-2), granulocyte-macrophage colony stimulating tactor (GM-CSF), or agents that promote microvascular coagulation in tumors, such as anti-protein C antibody, anti-protein § antibody, or C4b binding protein (see, WO 91/01753, published 21 February 1991), or heat or radiation.

Since the auxiliary agents will vary in their effectiveness, it is desirable to compare their impact on the tumor by matrix screening in conventional fashion. The administration of anti-PRO polypeptide antibody and TNF is repeated until the desired clinical effect is achieved. Alternatively, the anti-PRO polypeptide antibody is administered together with TNF and, optionally, auxiliary agent(s). In instances where solid tumors are found in the limbs or in other locations susceptible to isolation from the general circulation, the therapeutic agents described herein are administered to the isolated tumor or organ. In other embodiments, a FGF or PDGF antagonist, such as ananti-FGF or an anti-PDGF neutralizing antibody, is administered to the patient in conjunction with the anti-PRO polypeptide antibody. Treatment with anti-PRO polypeptide antibodies preferably may be suspended during periods of wound healing or desirable neovascularization.

For the prevention or treatment of cardiovascular, endothelial, and angiogenic disorder. the appropriate dosage of an antibody herein will depend on the type of disorder to be treated, as defined above. the severity and course of the disease, whether the antibody is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response 10 the antibody, and the discretion of the attending physician. Thc antibody is suitably administered to the patient at one time or over a series of treatments.

For example, depending on the type and severity of the disorder, about 1 ug/kg 10 50 mg/kg (e.g., 0.1-20 mg/kg) of antibody is an initial candidate dosage for administration to the patient, whether. for example, by one or 103

E more separate administrations, or by continuous infusion. A typical daily or weekly dosage might range from about 1 ug/g to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment is repeated or sustained until a desired suppression of disorder symptoms occurs. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays, including, for example, radiographic tumor imaging. xi. Articles of Manufacture with Antibodies

An article of manufacture containing a container with the antibody and a label is also provided. Such articles are described above, wherein the active agent is an anti-PRO179, anti-PR0O238, anti-PRO364, anti-PRO844, anti- PROY46, anti-PRO1760, anti-PRO20S, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PROR7S, anti-PRO879, anti-PRO882, anti-PRO885 or anti-PROSS7 antibody. xii. Diagnosis and Prognosis of Tumors using Antibodies

If the indication for which the antibodies are used is cancer, while cell-surface proteins, such as growth receptors over expressed in certain tumors, are excellent targets for drug candidates or tumor (e. £., cancer) treatment, the same proteins along with PRO polypeptides find additional use in the diagnosis and prognosis of tumors. For example, antibodies directed against the PRO polypeptides may be used as tumor diagnostics or prognostics.

For example, antibodies, including antibody fragments, can be used qualitatively or quantitatively to detect the expression of genes including the gene encoding the PRO polypeptide. The antibody preferably is equipped with a detectable, c.g., fluorescent label, and binding can be monitored by light microscopy, flow cytometry, fluorimetry, or other techniques known in the art. Such binding assays are performed essentially as described above.

In situ detection of antibody binding to the marker gene products can be performed. for exampie, by immunofluorescence or immunoelectron microscopy. For this purpose, a histological specimen is removed from the patient, and a labeled antibody is applied to it, preferably by overlaying the antibody on a biological sample.

This procedure also allows for determining the distribution of the marker gene product in the tissue examined. Tt will be apparent to those skilled in the art that a widc variety of histological methods are readily available for in situ detection.

The following Examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.

The disclosures of all patent and literature references cited in the present specification arc hereby incorporated by reference in their entirety.

EXAMPLES

Commercially available reagents referred to in the Examples were used according to manufacturer's instructions unless otherwise indicated. The source of those cells identified in the following Examples, and throughout the specification, by ATCC accession numbers is the American Type Culture Collection, Manassas, VA.

Uniess otherwise noted, the present invention uses standard procedures of recombinant DNA technology, such as those described hereinabove and in the following textbooks: Sambrook et al., supra; Ausubel er al., Current . Protocols in Molecular Biology (Green Publishing Associates and Wiley Interscience, N.Y, 1989); Innis er al., PCR

Protocols: A Guide to Methods and Applications (Academic Press, Inc.: N.Y., 1990); Harlow et al., Antibodies:

A Laboratory Manual (Cold Spring Harbor Press: Cold Spring Harbor, 1988): Gait. Oligonucleotide Synthesis (IRL

Press: Oxford, 1984); Freshney, Animal Cell Culture, 1987; Coligan et al., Current Protocols in Immunology, 1991.

EXAMPLE 1

Extracellular Domain Homology Screening to Identify Novel Polypeptides and cDNA Encoding Therefor

The extracellular domain (ECD) sequences (including the secretion signal sequence, if any) from about 950 known secreted proteins from the Swiss-Prot public database were used to search EST databases. The EST databases included public databases (e. g.. GenBank), and proprietary databases (e.g., LIFESEQ®. Incyte

Pharmaceuticals, Palo Alto, CA). The search was performed using the computer program BLAST or BLAST-2 {Altschul et al, Methods in Enzymology, 266:460-480 (1996)] as a comparison of the ECD protein sequences to a 6 frame translation of the EST sequences. Those comparisons with a BLAST score of 70 (or in some cases, 90) or greater that did not encode known proteins were clustered and assembled into consensus DNA sequences with the program "phrap" (Phil Green, University of Washington, Seattle, Washington).

Using this extracellular domain homology screen, consensus DNA sequences were assembled relative to other identified EST sequences using phrap. In addition, the consensus DNA sequences obtained were often (but not always) extended using repeated cycles of BLAST and phrap to extend the consensus sequence as far as possible using the sources of EST sequences discussed above.

Based upon the conscnsus sequences obtained as described above, oligonucleotides were then synthesized and : used to identify by PCR a cDNA library that contained the sequence of interest and for use as probes to isolate a clone of the full-length coding sequence for a PRO polypeptide. Forward and reverse PCR primers generally range from 20 to 30 nucleotides and are often designed to give a PCR product of about 100-1000 bp in length. The probe sequences are typically 40-55 bp in length. In some cases. additional oligonucicotides are synthesized when the consensus sequence is greater than about 1-1.5 kbp. In order to screen several libraries for a full-length clone. DNA from the libraries was screened by PCR amplification, as per Ausubel er al., Current Protocols in Molecular

Biology, supra. with the PCR primer pair. A positive library was then used to isolate clones encoding the gene of interest using the probe oligonucleotide and one of the primer pairs.

The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen. San Diego, CA. The cDNA was primed with oligo dT containing a Notl site, linked with blunt to Sall hemikinased adaptors, cleaved with Noll, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRKSB is a precursor of pRKSD that does not contain the Sfil site; see, Holmes er al., Science, 253:1278-1280 (1991) in the unique Xhol and NotI sites.

EXAMPLE 2

Isolation of cDNA clones by Amylase Screening 1. Preparation of oligo dT primed cDNA library mRNA was isolated from a human tissue of interest using reagents and protocols from Invitrogen, San Diego,

CA (Fast Track 2). This RNA was used to generate an oligo dT primed cDNA library in the vector pRKSD using reagents and protocols from Life Technologies, Gaithersburg, MD (Super Script Plasmid System). In this procedure, the double stranded cDNA was sized to greater than 1000 bp and the Sall/Notl linkered cDNA was cloned into Xhol/Notl cleaved vector. pRKSD is a cloning vector that has an sp6 transcription initiation site followed by an Sfil restriction enzyme site preceding the Xhol/Notl cDNA cloning sites. 2. Preparation of random primed cDNA library

A secondary cDNA library was generated in order to preferentially represent the 5’ ends of the primary cDNA clones. Sp6 RNA was generated from the primary library (described above), and this RNA was used to generate a random primed cDNA library in the vector pSST-AMY.0 using reagents and protocols from Life Technologies (Super Script Plasmid System, referenced above). In this procedure the double stranded ¢DNA was sized to 500- 1000 bp, linkered with blunt to Notl adaptors, cleaved with Sfil, and cloned into Sfil/Notl cleaved vector. pSST-

AMY .0 is a cloning vector that has a yeast alcohol dehydrogenase promoter preceding the cDNA cloning sites and the mouse amylase sequence {the mature sequence without the secretion signal) followed by the yeast alcohol dehydrogenase terminator, after the cloning sites. Thus, cDNAs cloned into this vector that are fused in frame with amylase sequence will lead to the secretion of amylase from appropriately transfected yeast colonies. 3. Transformation and Detection :

DNA from the library described in paragraph 2 above was chilled on ice to which was added electrocompetent

DHIOB bacteria (Life Technologies, 20 ml). The bacteria and vector mixture was then electroporated as recommended by the manufacturer. Subsequently, SOC media (Life Technologies, | ml) was added and the mixture was incubated at 37°C for 30 minutes. The transformants were then plated onto 20 standard 150 mm LB plates containing ampicillin and incubated for 16 hours (37°C). Positive colonies were scraped off the plates and the

DNA was isolated from the bacterial pellet using standard protocols, e.g., CsCl-gradient. The purified DNA was then carried on to the yeast protocols below.

The yeast methods were divided into three categories: (1) Transformation of yeast with the plasmid/cDNA combined vector; (2) Detection and isolation of yeast clones secreting amylase; and (3) PCR amplification of the insert directly from the yeast colony and purification of the DNA for sequencing and further analysis.

The yeast strain used was HD56-5A (ATCC-90785). This strain has the following genotype: MAT alpha, ura3-52, leu2-3, leu2-112, his3-11, his3-15, MAL, SUC", GAL". Preferably, yeast mutants can be employed that have deficient post-translational pathways. Such mutants may have translocation deficient alleles in sec71, sec72, sec62. with truncated sec | being most preferred. Alternatively, antagonists (including antisense nucleotides and/or ligands) which interfere with the normal operation of these genes, other proteins implicated in this post translation pathway (e.g., SEC61p, SEC72p, SEC62p, SEC63p, TDI1p or SSAIp-4p) or the complex formation of these proteins may also be preferably employed in combination with the amylase-expressing yeast.

Transformation was performed based on the protocol outlined by Gietz et al., Nucl. Acid. Res., 20:1425 } (1992). Transformed cells were then inoculated from agar into YEPD complex media broth (100 ml} and grown overnight at 30°C. The YEPD broth was prepared as described in Kaiser er al., Methods in Yeast Genetics, Cold

Spring Harbor Press, Cold Spring Harbor, NY, p. 207 (1994). The overnight culture was then diluted to about 2

Sx 10° celis/ml (approx. OD¢y=0.1) into fresh YEPD broth (S00 ml) and regrown to 1 x 107 cells/ml (approx.

OD,=0.4-0.5).

The cells were then harvested and prepared for transformation by transfer into GS3 rotor bottles in a Sorval

GS3 rotor at 5,000 rpm for 5 minutes, the supernatant discarded, and then resuspended into sterile water, and centrifuged again in 50 ml falcon tubes at 3,500 rpm in a Beckman GS-6KR centrifuge. The supernatant was discarded and the cells were subsequently washed with LiAc/TE (10 ml, 10 mM Tris-HCl, | mM EDTA pH 7.5, 100 mM Li,O0CCH,), and resuspended into LiAc/TE (2.5 ml).

Transformation took place by mixing the prepared cells (100 x1) with freshly denatured single stranded salmon testes DNA (Lofstrand Labs, Gaithersburg, MD) and transforming DNA (1 ug, vol. < 10 #1) in microfuge tubes.

The mixture was mixed briefly by vortexing, then 40% PEG/TE (600 ul, 40% polyethylene glycol-4000, 10 mM

Tris-HCI, | mM EDTA, 100 mM Li,OOCCH,, pH 7.5) was added. This mixture was gently mixed and incubated at 30°C while agitating for 30 minutes. The cells were then heat shocked at 42°C for 15 minutes, and the reaction vessel centrifuged in a microfuge at 12,000 rpm for 5-10 seconds, decanted and resuspended into TE (500 ul, 10 mM Tris-HCI, 1 mM EDTA pH 7.5) followed by recentrifugation. The cells were then diluted into TE (1 ml) and aliquots (200 ul) were spread onto the selective media previously prepared in 150 mm growth plates (VWR).

Alternatively, instead of multiple small reactions, the transformation was performed using a single, large scale reaction, wherein reagent amounts were scaled up accordingly. . The selective media used was a synthetic complete dextrose agar lacking uracil (SCD-Ura) prepared as described in Kaiser ef al., Mcthods in Yeast Genetics, Cold Spring Harbor Press, Cold Spring Harbor, NY, p. 208- 210 (1994). Transformants were grown at 30°C for 2-3 days.

The detection of colonies secreting amylase was performed by including red starch in the selective growth media. Starch was coupled to the red dye (Reactive Red-120, Sigma) as per the procedure described by Biely er al, Anal. Biochem., 172:176-179 (1988). The coupled starch was incorporated into the SCD-Ura agar plates ata final concentration of 0.15% (w/v), and was buffered with potassium phosphate to a pH of 7.0 (50-100 mM final concentration).

The positive colonies were picked and streaked across fresh selective media (onto 150 mm plates) in order to obtain well isolated and identifiable single colonies. Well isolated single colonies positive for amylase secretion were detected by direct incorporation of red starch into buffered SCD-Ura agar. Positive colonies were determined by their ability to break down starch resulting in a clear halo around the positive colony visualized directly. 4. Isolation of DNA by PCR Amplification

When a positive colony was isolated, a portion of it was picked by a toothpick and diluted into sterile water (30 11) in a 96 well plate. At this time, the positive colonies were either frozen and stored for subsequent analysis or immediately amplified. An aliquot of cells (5 ul) was used as a template for the PCR reaction in a 25 ul volume containing: 0.5 ul Klentag (Clontech. Palo Alto, CA); 4.0 «1 10 mM dNTPs (Perkin Elmer-Cetus); 2.5 ul Klentag 107 buffer (Clontech); 0.25 ul forward oligo 1; 0.25 ul reverse oligo 2; 12.5 ul distilled water.

The sequence of the forward oligonucleotide 1 was: }

S-TGTAAAACGACGGCCAGTTAAATAGACCTGCAATTATTAATCT-3' (SEQ ID NO:33)

The sequence of the reverse oligonucleotide 2 was: 5'-CAGGAAACAGCTATGACCACCTGCACACCTGCAAATCCATT-3 (SEQ ID NO:34)

PCR was then performed as follows: a. Denature 92°C, 5 minutes b. 3 cycles of: Denature 92°C, 30 seconds

Anneal 59°C, 30 seconds

Extend 72°C, 60 seconds ¢. 3 cycles of: Denature 92°C, 30 seconds

Anneal 57°C, 30 seconds

Extend 72°C, 60 seconds d. 25 cycles of: Denature 92°C. 30 seconds

Anneal 55°C, 30 seconds

Extend 72°C, 60 seconds e. Hold 4°C

The underlined regions of the oligonucleotides annealed to the ADH promoter region and the amylase region, respectively, and amplified a 307 bp region from vector pSST-AMY.0 when no insert was present. Typically, the first 18 nucleotides of the S' end of these oligonucleotides contained annealing sites for the sequencing primers.

Thus, the total product of the PCR reaction from an empty vector was 343 bp. However, signal sequence-fused cDNA resulted in considerably longer nucleotide sequences. :

Following the PCR, an aliquot of the reaction (5 ul) was examined by agarose gel electrophoresis in a 1% agarose gel using a Tris-Borate-EDTA (TBE) buffering system as described by Sambrook et al., supra. Clones resulting in a single strong PCR product larger than 400 bp were further analyzed by DNA sequencing after purification with a 96 Qiaquick PCR clean-up column (Qiagen Inc.. Chatsworth. CA).

EXAMPLE 3

Isolation of cDNA Clones Using Signal Aleorithin Analysis

Various polypeptide-encoding nucleic acid sequences were identified by applying a proprietary signal sequence finding algorithm developed by Genentech, Inc., (South San Francisco, CA) upon ESTs as well as clustered and assembled EST fragments from public (e.g., GenBank) and/or private (LIFESEQ®, Incyte

Pharmaceuticals, Inc., Palo Alto, CA) databases. The signal sequence algorithm computes a secretion signal score based on the character of the DNA nucleotides surrounding the first and optionally the second methionine codon(s) (ATG) at the 5'-end of the sequence or sequence fragment under consideration. The nucleotides following the first

ATG must code for at least 35 unambiguous amino acids without any stop codons. If the first ATG has the required amino acids, the second is not examined. If neither meets the requirement, the candidate sequence is not scored.

In order to determine whether the EST sequence contains an authentic signal sequence, the DNA and corresponding amino acid sequences surrounding the ATG codon are scored using a set of seven sensors (evaluation parameters)

known to be associated with secretion signals. Use of this algorithm resulted in the identification of numerous polypeptide-encoding nucleic acid sequences.

EXAMPLE 4

Isolation of cDNA Clones Encoding Human PRO179

A cDNA sequence was isolated in a screen as described in Example 2 above. The cDNAsequence isolated in the above screen was found, by BLAST and FastA sequence alignment, to have sequence homology to a nucleotide sequence encoding various angiopoietin proteins. This cDNA sequence is herein designated DNA 10028 and/or DNA 25250.

Based on the sequence homology, oligonucleotide probes were then generated from the sequence of the

DNAI10028 molecule and used to screen a human fetal liver (LIB6) library prepared as described in paragraph 1 of Example 2 above. The cloning vector was pRKSB (pRKS5B is a precursor of pRKSD that does not contain the

Sfil site; see, Holmes et al., Science, 253:1278-1280 (1991)) in the unique Xhol and Notl sites, and the cDNA size cut was less than 2800 bp.

DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO179 and the derived protein sequence for PRO179. The entire nuclcotide sequence of DNA 16451-1388 is shown in

Figure | (SEQ ID NO:1). Clone DNA16451-1388 contains a single open reading frame with an apparent transiational initiation site at nucleotide positions 37-39 and ending at the stop codon at nucleotide positions 1417- 1419 (Figure 1). The predicted polypeptide precursor is 460 amino acids long (Figure 2, SEQ ID NO:2). The full- length PRO179 protein shown in Figure 2 has an estimated molecular weight of about 53,637 daitons and a pl of about 6.61. . Analysis of the full-length PRO179 sequence shown in Figure 2 (SEQ ID NO:2) evidences the presence of a variety of important polypeptide domains as shown in Figure 2. wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO179 sequence (Figure 2; SEQID NO:2), evidences the presence of the following: a signal peptide froin about amino acid J to about amino acid 16; leucine zipper patterns from about amino acid 120 to about amino acid 142 and from about amino acid 127 to about amino acid 149; N-glycosylation sites from about amino acid 23 to about amino acid 27, from about amino acid 115 to about amino acid 119, from about amino acid 296 to about amino acid 300. and from about amino acid 357 to about amino acid 361; and fibrinogen beta and gamma chains C-terminal domains from about amino acid 271 to about amino acid 310, from about amino acid 312 to about amino acid 322, from about amino acid 331 to about amino acid 369, and from about amino acid 393 to about amino acid 424.

Clone DNA16451-1388 has been deposited with the ATCC on April 14, 1998 and is assigned ATCC deposit no. 209776. Regarding the sequence, it is understood that the deposited clone contains the correct sequence. and the sequences provided herein are based on known sequencing techniques.

Analysis of the amino acid sequence of the full-length PRO179 polypeptide suggests that it possesses significant similarity to the angiopoietin family of proteins, thereby indicating that PRO179 may be a novel angiopoietin family member. More specifically, an analysis of the Dayhoff database (version 35.45 SwissProt 35), evidenced significant homology between the PRO179 amino acid sequence and the following Dayhoft sequences:

AF004326_1, P_R94605, HSU83508_1,P_R94603, P_R94317. AF025818_t, HSY16132_1, P_R65760.13739]

EE and HUMRSC192_1.

EXAMPLE 5

Isolation of cDNA Clones Encoding Human PRQ238

A consensus DNA sequence was assembled relative to other EST scquences using phrap as described in

Example | above. This consensus sequence is herein designated DNA30908. Based on the DNA30908 consensus sequence, oligonucleotides were synthesized: 1) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PRO238. PCR primers (forward and reverse) were synthesized based upon the DNA30Y08 sequence. Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA30908 sequence.

In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al., Current Protocols in Molecular Biology, supra, with the PCR primer pair. A positive library was then used to isolate clones encoding the PRO238 gene using the probe oligonucleotide and one of the PCR primers.

The oligonucleotide sequences used in the above procedure were the following: forward PCR primer {: 5-GGTGCTAAACTGGTGCTCTGTGGC-3' (SEQ ID NO:35) forward PCR primer 2; 5-CAGGGCAAGATGAGCATTCC-3' (SEQ ID NO:36) reverse PCR primer: 5-TCATACTGTTCCATCTCGGCACGC-3' (SEQ ID NO:37) hybridization probe: 5-AATGGTGGGGCCCTAGAAGAGCTCATCAGAGAACTCACCGCTTCTCATGC-3' (SEQ ID NO:38)

RNA for construction of the cDNA libraries was isolated from human fetal liver tissue. The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA was primed with Notl site, linked with blunt to Sall hemikinased adaptors, cleaved with Notl, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRK5B is a precursor of pRKSD that does not contain the Sfil site; see, Holmes er al., Science, 253:1278-1280 (1991)) in the unique Xhol and NotI sites.

DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO238 [herein designated as DNA35600-1162] (Figure 3, SEQ ID NO:3) and the derived protein sequence for PRO238.

The entire nucleotide sequence of DNA35600-1162 is shown in Figure 3 (SEQID NO:3). Clone DNA35600- 1162 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 134- 136 and ending at the stop codon at nucleotide positions 1064-1066 (Fi gure 3). The predicted polypeptide precursor is 310 amino acids long (Figure 4; SEQ ID NO:4). and has an estimated molecular weight of about 33.524 daltons and apl of about 9.55.

Analysis of the full-length PRO238 sequence shown in Figure 4 (SEQ ID NO:4) evidenced the presence of a variety of important polypeptide domains as shown in Figure 4. wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO238 sequence (Figure . 4, SEQ ID NO:4) evidences the presence of the following: a signal peptide from about amino acid 1 to about amino acid 21; transmembrane domains from about amino acid 102 to about amino acid 119 and from about amino acid 278 to about amino acid 292; an N-glycosylation site from about amino acid 228 to about amino acid 232; a glycosaminoglycan attachment site from about amino acid 47 to about amino acid 51; a tyrosine kinase phosphorylation site from about amino acid 145 to about amino acid 153; N-myristoylation sites from about amino acid 44 to about amino acid 50, from about amino acid 105 to about amino acid 111, from about amino acid 238 to about amino acid 244, from about amino acid 242 to about amino acid 248, and from about amino acid 291 to about amino acid 297; an amidation sitc from about amino acid 265 to about amino acid 269; and a prokaryotic membrane lipoprotein lipid attachment site from about amino acid 6 to about amino acid 17. Clone DNA35600- 1162 has been deposited with ATCC on October 16, 1997 and is assigned ATCC deposit no. 209370.

Analysis of the amino acid sequence of the full-length PRO238 polypeptide suggests that portions of it possess significant homology to reductase, particularly oxidoreductase, thereby indicating that PRO238 may be a novel reductase.

EXAMPLE 6

Isolation of cDNA Clones Encoding Human PRO364

An expressed sequence tag (EST) DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, CA) was scarched and an Incyte EST sequence (Incyte EST No. 3003460) was identified that showed homology to members of the tumor necrosis factor receptor (TNFR) family of polypeptides.

A consensus DNA sequence was then assembled relative to the Incyte 3003460 EST and other EST sequences using repeated cycles of BLAST (Altshul et al., Methods in Enzymology, 266:460-480 (1996)) and “phrap” (Phil

Green, University of Washington, Seattle Washington). The consensus sequence is herein designated “<consen01>" and is also herein designated as DNA44825,

Oligonucleotide probes based upon the DNA44825 and “<consen01>" consensus sequences were then synthesized: 1) to identify by PCR a cDNA library that contained the sequence of intcrest, and 2) for use as probes toisolate a clone of the full-length coding sequence for PRO364. Forward and reverse PCR primers generally range from 20-30 nucleotides and are often designed to give a PCR product of about 100-1000 bp in length. The probe sequences are typically 40-55 bp in length. In order to screen several libraries for a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel ez al., Current Protocols in Molecular Biology, supra, with the PCR primer pair. A positive library was then used to isolate clones encoding the gene of interest using the probe oligonucleotide and one of the primer pairs.

Pairs of PCR primers (forward and reverse) were synthesized: forward PCR primer (44825 f1): 5-CACAGCACGGGGCGATGGG-3 (SEQ ID NO:39) forward PCR primer (44825 2): 5-GCTCTGCGTTCTGCTCTG-3' (SEQ ID NO:40) forward PCR primer (44825 GITR.f): 5-GGCACAGCACGGGGCGATGGGCGCGTTT-3' (SEQ ID NO:41)

reverse PCR primer (44825.r1): 5-CTGGTCACTGCCACCTTCCTGCAC-3' (SEQ ID NQ:42) } reverse PCR primer (44825.r2): 5'-CGCTGACCCAGGCTGAG-3' (SEQ ID NO:43) reverse PCR primer (44825.GITR.r):

S-“GAAGGTCCCCGAGGCACAGTCGATACA-3' (SEQ ID NO:44)

Additonally, synthetic oligonucleotide hybridization probes were constructed from the consensus DNA44825 sequence which had the following nucleotide sequences: hybridization probe (44825.p1): 5-GAGGAGTGCTGTTCCGAGTGGGACTGCATGTGTGTCCAGC-3' (SEQ ID NO:45) hybridization probe (44825.GITR.p): 5-AGCCTGGGTCAGCGCCCCACCGGGGGTCCCGGGTGCGGCC-3 (SEQ ID NO:46)

In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification with the PCR primer pairs identified above. A positive library was then used to isolate clones encoding the PRO364 gene using the probe oligonucleotides and one of the PCR primers.

RNA for construction of the cDNA libraries was isolated from human bone marrow tissue. The cDNA libraries used to isolate the cDNA clones were constructed by standard methods vsing commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA was primed with oligo dT containing a Notl site, sized appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; PRKSB is a precursor of pRKSD that does not contain the Sfil site; see, Holmes er al.

Science, 253:1278-1280 (1991)) in the unique Xhol and Not! sites.

A cDNA clone was identified and sequenced in entirety. The entire nucleotide sequence of DNA47365-1206 is shown in Figure 5 (SEQ ID NO:S). Clone DNA47365-1206 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 121-123, and a stop codon at nucleotide positions 844- 846 (Figure 5; SEQ ID NO:S). The predicted polypeptide precursor is 241 amino acids long and has a predicted molecular weight of approximately 26,000 daltons and an estimated pl of about 6.34. The full-length PRO364 protein is shown in Figure 6 (SEQ ID NO:6).

Analysis of the full-length PRO364 sequence shown in Figure 6 (SEQ IT) NQ:6) evidences the presence of important polypeptide domains as shown in Figure 6, wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO364 sequence (Figure 6; SEQ ID

NO:6) evidences the presence of the following: a signal peptide from about amino acid } to about amino acid 25; apotential transmembrane domain from about amino acid 162 to about amino acid 180; an N-glycosylation site from about amino acid 146 to about amino acid 150; N-myristoylation sites from about amino acid 5 to about amino acid 11, from about amino acid 8 to about amino acid 14, from about amino acid 25 to about amino acid 31, from about amino acid 30 to about amino acid 36, from about amino acid 33 to about amino acid 39. from about amino acid 118 to about amino acid 124, from about amino acid 122 to about amino acid 128, and from about amino acid 156 to about amino acid 162; a prokaryotic membrane lipoprotein lipid attachment site from about amino acid 166 to about amino acid 177; and a leucine zipper pattern from about amino acid 171 to about amino acid 193.

Clone DNA47365-1206 has been deposited with ATCC on November 7, 1997 and is assigned ATCC deposit no. 209436. It is understood that the deposited clone has the actual correct sequence rather than the representations provided herein.

Analysis of the amino acid sequence of the full-length PRO364 polypeptide suggests that portions of it possess homology to members of the tumor necrosis factor receptor family, thereby indicating that PRO364 may be a novel member of the tumor necrosis factor receptor family. The intracellular domain of PRO364 contains a motif (in the region of amino acids 207-214) similar to the minimal domain within CD30 receptor shown to be required for

TRAT?2 binding and which is also present within TNFR2. There are three apparent extracellular cysteine-rich domains characteristic of the TNFR family (see, Naismith and Sprang, Trends Biochem. Sci., 23:74-79 (1998)). of which the third CRD has 3 rather than the more typical 4 or 6 cysteines of the TNFR family. As compared to the mouse GITR (described below) the PRO364 amino acid sequence has 8 cysteines in the CRD] relative to 5 cysteines in CRD] of mouse GITR, and the presence of one potential N-linked glycosylation site in the ECD as compared to 4 potential N-linked glycosylation sites in mouse GITR.

A detailed review of the putative amino acid sequence of the full-length native PRO364 polypeptide and the

IS nucleotide sequence that encodes it evidences sequence homology with the mouse GITR (inGITR) protein reported by Nocentini ef al., Proc. Natl, Acad. Sci. USA, 94:6216-6221 (1997). lt is possible, therefore, that PRO364 represents the human counterpart or ortholog to the mouse GITR protein reported by Nocentini et al.

EXAMPLE 7

Isolation of cDNA Clones Encoding Human PROg44

An expressed sequence tag (EST) DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, CA) was . searched and an EST was identified that showed sequence identity with a I.P. Based on the information and discoveries provided herein, the clone for this EST, Incyte clone 2657496 from a cancerous lung library (309-

LUNGTUT09) was further examined.

A cDNA clone was identified and sequenced in entirety. The entire nucleotide sequence of DNAS9838-1462 is shown in Figure 7 (SEQ ID NQO:7). Clone DNA59838-1462 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 5-7, and a stop codon at nucleotide positions 338-340 (Figure 7; SEQ ID NO:7). The predicted polypeptide precursor is 111 amino acids long and has a predicted molecular weight of approximately 12,050 daltons and an estimated pl of about 5.45. The full-length PROB44 protein is shown in Figurc 8 (SEQ ID NO:8).

Analysis of the full-length PRO844 sequence shown in Figure 8 (SEQ 1D NO:8) evidences the presence of important polypeptide domains as shown in Figure 8, wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO844 sequence (Figure 8; SEQ ID

NO:8) evidences the presence of the following: a signal peptide from about amino acid 1 to about amino acid 19;

N-myristoylation sites from about amino acid 23 to about amino acid 29, from about amino acid 27 to about amino acid 33. from about amino acid 32 to about amino acid 38, and from about amino acid 102 10 about amino acid 108; and a WAP-type ‘four-disulfide core’ domain signature from about amino acid 49 to about amino acid 63.

Clone DNA59838- 1462 has been deposited with ATCC on June 16, 1998 and is assigned ATCC deposit no. 209976. It is understood that the deposited clone has the actual correct sequence rather than the representations 113 provided herein,

Analysis of the amino acid sequence of the full-length PRO844 polypeptide suggests that it possesses significant similarity to serine protease inhibitors, thereby indicating that PRO844 may be a novel proteinase inhibitor. More specifically, an analysis of the Dayhoff database (version 35.45 SwissProt 35) evidenced significant homology hetween the PRO844 amino acid sequence and at least the following Dayhoff sequences:

ALK HUMAN, P_P82403, P_P82402, ELAF_HUMAN and P_P60950.

EXAMPLE 8

Isolation of cDNA Clones Encoding Human PRQ846

A consensus DNA sequence was assembled relative to other EST sequences using phrap as described in

Example 1 above. This consensus sequence is herein designated DNA39949 and “<consen1322>". Based on the

DNA39949 consensus sequence and the “<consen]322>" sequnece, oligonucleotides were synthesized: J) to identify by PCR a cDNA library that contained the sequence of interest, and 2) for use as probes to isolate a clone of the full-length coding sequence for PRO846. PCR primers (forward and reverse) were synthesized based upon the DNA39949 and “<consen1322>" consensus sequences. Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA3(908 sequence.

In order to screen several libraries for a source of a full-length clone, DNA from the libraries was screened by PCR amplification, as per Ausubel et al., Current Protocols in Molecular Biology, supra, with the PCR primer pair. A positive library was then used to isolate clones encoding the PRO846 gene using the probe oligonucleotide and onc of the PCR primers.

The oligonucleotide sequences used in the above procedure were the following: forward PCR primer (39949.f1): 5'-CCCTGCAGTGCACCTACAGGGAAG-3' (SEQ ID NO:47) reverse PCR primer (39949.r1): 5-CTGTCTTCCCCTGCTTGGCTGTGG-3' (SEQ ID NO:48)

Additionally, a synthetic oligonucleotide hybridization probe was constructed from the consensus DNA39949 sequence which had the following nucleotide sequence: hybridization probe (39949.p1): 5-GGTGCAGGAAGGGTGGGATCCTCTTCTCTCGCTGCTCTGGCCACATC-3' (SEQ ID NO:49)

RNA for construction of the cDNA libraries was isolated from human fetal kidney tissue (LIB227). The cDNA libraries used to isolate the cDNA clones were constructed by standard methods using commercially available reagents such as those from Invitrogen, San Diego, CA. The cDNA was primed with Notl site, linked with blunt to Sall hemikinased adaptors, cleaved with Not, sizcd appropriately by gel electrophoresis, and cloned in a defined orientation into a suitable cloning vector (such as pRKB or pRKD; pRKS5B is a precursor of pRK5D thatdoes not contain the Sfil site; see, Holmes er al., Science, 253:1278-1280 (1991)) in the unique Xhol and Notl sites.

DNA sequencing of the clones isolated as described above gave the full-length DNA sequence for PRO846

[herein designated as DNA44196-1353) (Figure 9, SEQ ID NO:9) and the derived protein sequence for PRO846.

The entire nucleotide sequence of DNA44196-1353 is shown in Figure 9 (SEQ ID NO:9). Clone DNA44196- 1353 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 25-27 and ending at the stop codon at nucleotide positions 1021-1023 (Figure 9). The predicted polypeptide precursor is 332 amino acids long and has an estimated molecular weight of approximately 36,143 daltons and pl of about 5.89 (Figure 10; SEQ ID NO:10).

Analysis of the full-length PRO846 sequence shown in Figure 10 (SEQ ID NO: 10) evidenced the presence of a variety of important polypeptide domains as shown in Figure 10, wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO846 sequence (Figure 10; SEQ ID NO:10) evidences the presence of the following: a signal peptide from about amino acid 1 to about amino acid 17; a transmembrane domain from about amino acid 248 to about amino acid 269; an N- glycosylation site from about amino acid 96 to about amino acid 100; a fibrinogen beta and gamma chains C- terminal domain from about amino acid 104 to about amino acid 114; and a Ig like V-type domain from about amino acid 13 10 about amino acid 128. Clone DNA44196-1353 has been deposited with ATCC on May 6, 1998 and is assigned ATCC deposit no. 209847.

EXAMPLES

Isolation of cDNA Clones Encoding Human PRO[760

Usc of the signal sequence algorithm described in Example 3 above allowed identification of an EST cluster sequence from the Incyte database. This EST cluster sequence was then compared to a variety of expressed sequence tag (EST) databases which included public EST databases (e.g., GenBank) and a proprietary EST DNA database (LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, CA) to identify existing homologies. One or more of the

ESTs was derived from a prostate tumor library. The homology search was performed using the computer program

BLAST or BLAST2 (Altshul et al., Methods in Enzymology, 266:460-480 (1996). Thosc comparisons resulting in a BLAST score of 70 (or in some cases, 90) or greater that did not encode known proteins were clustered and assembled into a consensus DNA sequence with the program *phrap™ (Phil Green, University of Washington,

Seattle, Washington). The consensus sequence obtained therefrom is herein designated DNAS8798.

In light of an observed sequence homology between the DNAS58798 consensus sequence and the Incyte EST 3358745, the clone including this EST was purchased and the cDNA insert was obtained and sequenced. It was found herein that that insert encoded a full-length protein. The sequence of this cDNA insert is shown in Figure 11 (SEQID NO:11)and is herein designated DNA76532-1702.

Clone DNA76532-1702 contains a single open reading frame with an apparent translational initiation site at nucleotide positions 60-62 and ending at the stop codon at nucleotide positions 624-626 (Figure 11). The predicted polypeptide precursor is 188 amino acids long (Figure 12; SEQ ID NO:12). The full-length PRO1760 protein shown in Figure 12 has an estimated molecular weight of about 21.042 daltons and a pl of about 5.36.

Analysis of the full-length PRO1760 sequence shown in Figure 12 (SEQ ID NO: 12) evidences the presence of a variety of important polypeptide domains as shown in Figure 12, wherein the locations given for those important polypeptide domains are approximate as described above. Analysis of the full-length PRO 1760 sequence evidences the presence of the following features: a signal peptide from about amino acid | to about amino acid 20;

N-glycosylation sites from about amino acid 121 to about amino acid 125 and from about amino acid 171 to about amino acid 175; a tyrosine kinase phosphorylation site from about amino acid 25 to about amino acid 32; and N- myristoylation sites from about amino acid 54 to about amino acid 60 and from about amino acid 160 to about amino acid 166. Clone DNA76532-1702 has been deposited with ATCC on November 17, 1998 and is assigned

ATCC deposit no. 203473.

An analysis of the Dayhoff database (version 35.45 SwissProt 35), using a WU-BLAST2 sequence alignment analysis of the full-length sequence shown in Figure 12 (SEQ ID NO: 12), evidenced sequence identity between the

PRO1760 amino acid sequence and the following Dayhoff sequences: CELTO7F12_2, T22J1 8_16, ATF1C12_3,

APE3_YECAST,P_W22471,SAU56908_1, SCPA_STRPY, ATAC00423817, SAPURCLUS_2 and AF04] 468_9.

EXAMPLE 10

Stimulation of Heart Neonatal Hypertrophy (Assay 1)

This assay is designed to measure the ability of PRO polypeptides to stimulate hypertrophy of neonatal heart.

PRO polypeptides testing positive in this assay are expected to be useful for the therapeutic trcatment of various cardiac insufficiency disorders.

Cardiac myocytes from 1-day old Harlan Sprague Dawley rats were obtained. Cells (180 ;.1 at 7.5 x 10*/ml, . serum <0.1%, freshly isolatcd) are added on day 1 to 96-well plates previously coated with DMEM/F12 + 4% FCS. . Test samples containing the test PRO polypeptide or growth medium only (negative control) (20 ul/well) are added . directly to the wells on day 1. PGF (20 ul/well) is then added on day 2 at a final concentration of 10* M. The cells . are then stained on day 4 and visually scored on day 5, wherein cells showing no increase in size (as compared to . 20 negative controls) are scored 0.0, cells showing a small to moderate increase in size (as compared to negative controls) are scored 1.0 and cells showing a large increase in size (as compared to negative controls) are scored 2.0.

A positive result in the assay is a score of 1.0 or greater.

PROB88?2 tested positive in this assay as shown in TABLE 4 below:

TABLE 4

ERO# Concentration/Dilution Relative Increase in Size {Compared to Negative Control)

PRO882 0.01% 3

PROS882 0.01% 3

PRO8S2 0.10% 4

PROSS2 0.10% 4

PRO882 1.00% 6

PROS8RK2 1.00% 6

PRO882 0.01% 3

PRO882 0.10% 4.5

PROSS8? 1.00% 6

PRO8S2 1.00% 5.5

PRO8S2 2.6 nM 5.75

EXAMPLE 11

Inhibition of Vascular Endothelial Growth Factor (VEGF) Stimulated Proliferation of Endothelial Cell Growth (Assay 9)

The ability of various PRO polypeptides to inhibit VEGF stimulated proliferation of endothelial cells was

S tested. Polypeptides testing positive in this assay are useful for inhibiting endothelial cell growth in mammals where such an effect would be beneficial, e.g., for inhibiting tumor growth.

Specifically, bovine adrenal cortical capillary endothelial cells (ACE) (from primary culture, maximum of 12- 14 passages) were plated in 96-well plates at 500 cells/well per 100 microliter. Assay media included low glucose

DMEM, 10% calf serum, 2 mM glutamine, and 1X penicillin/streptomycin/fungizone. Control wells included the 10 following: (1) no ACE cells added; (2) ACE cells alone; (3) ACE cells plus 5 ng/ml FGF; (4) ACE cells plus 3 ng/ml VEGF, (5) ACE cells plus 3 ng/ml VEGF plus 1 ng/ml TGF-beta; and (6) ACE cells plus 3 ng/ml VEGF plus ng/ml LIF. The test samples, poly-his tagged PRO polypeptides (in 100 microliter volumes), were then added to the wells (at dilutions of 1%, 0.1% and 0.01%, respectively). The cell cultures were incubated for 6-7 days at 37°C/5% CO,. After the incubation, the media in the wells was aspirated, and the cells were washed 1X with PBS.

Anacid phosphatase reaction mixture (100 microliter: 0.1M sodium acetate, pH 5.5, 0.1% Triton X-100, 10 mM p-nitrophenyl phosphate) was then added to each well. After a 2 hour incubation at 37°C, the reaction was stopped by addition of 10 microliters IN NaOH. Optical density (OD) was measured on a microplate reader at 405 nm. : The activity of PRO polypeptides was calculated as the percent inhibition of VEGF (3 ng/ml) stimulated proliferation (as determined by measuring acid phosphatase activity at OD 405 nm) relative to the cells without stimulation. TGF-beta was employed as an activity reference at I ng/ml, since TGF-beta blocks 70-90% of VEGF- stimulated ACE cell proliferation. The results, as shown in TABLE 5 below, are indicative of the utility of the PRO polypeptides in cancer therapy and specifically in inhibiting tumor angiogenesis. The numerical values (relative inhibition) shown in TABLE 5 are determined by calculating the percent inhibition of VEGF stimulated proliferation by the PRO polypeptides relative to cells without stimulation and then dividing that percentage into the percent inhibition obtained by TGF-B at 1 ng/ml which is known to block 70-90% of VEGF stimulated cell proliferation. The results are considered positive if the PRO ploypeptide exhibits 30% or greater inhibition of

VEGF stimulation of endothelial cell growth (relative inhibition 30% or greater).

TABLES

Inhibition of VEGF Stimilated Endothelial Cell Growth

PRO Name PRO Concentration Relative % Inhibition

PRO333 0.01% 97.0

PRO333 0.10% 90.0

PRO333 1.00% 63.0

PROR77 0.01% 101.0

PRO877 0.01% 108.0

PRO877 0.10% 86.0

PROS877 0.10% 99.0

PROS877 1.00% 46.0

PRO877 1.00% 46.0

PRO879 0.01% 100.0

PRO879 0.01% 105.0

PROS879 0.10% 97.0

PRO879 0.10% 101.0

PRO879 1.00% 55.0

PRO879 1.00% 66.0

PROS882 0.01% 96.0

PROSS2 0.10% 86.0

PROS882 1.00% 70.0

PRO88S 0.01% 100.0

PROS8S8S 0.10% 93.0

PROS8S8S 1.00% 64.0

EXAMPLE 12

Induction of c-fos in Endothelial Cells (Assay 34)

This assay is designed to determine whether PRO polypeptides show the ability to induce c-fos in endothelial cells. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of conditions or disorders where angiogenesis would be beneficial including, for example, wound healing, and the like (as would agonists of these PRO polypeptides). Antagonists of the PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of cancerous tumors.

Human venous umbilical vein endothelial cells (HUVEC, Cell Systems) in growth media (50% Ham's F12 w/o GHT: low glucose, and 50% DMEM without glycine: with NaHCO3, 1% glutamine, 10 mM HEPES, 10%

FBS, 10 ng/ml bFGF) were plated on 96-well microtiter plates at a cell density of 1x10" cells/well. The day after plating, the cells were starved by removing the growth media and treating the cells with 100 ul/well test samples and controls (positive control: growth media; negative control: 10 mM HEPES, 140 mM NaCl, 4% (w/v) mannitol, pH 6.8). The cells were incubated for 30 minutes at 37°C, in 5% CO,. The samples were removed, and the first part of the bDNA kit protocol (Chiron Diagnostics, cat. #6005-037) was followed, where each capitalized reagent/buffer listed below was available from the kit. 40 Briefly, the amounts of the TM Lysis Buffer and Probes needed for the tests were caiculated based on information provided by the manufacturer. The appropriate ainounts of thawed Probes were added to the TM Lysis

Buffer. The Capture Hybridization Buffer was warmed to room temperature. The bDNA strips were set up in the metal strip holders, and 100 ul of Capture Hybridization Buffer was added to each b-DNA well needed, followed by incubation for at least 30 minutes. The test plates with the cells were removed from the incubator, and the media was gently removed using the vacuum manifold. 100 ul of Lysis Hybridization Buffer with Probes were quickly pipetted into each well of the microtiter plates. The plates were then incubated at 55°C for 15 minutes. Upon removal from the incubator, the plates were placed on the vortex mixer with the microtiter adapter head and vortexed on the #2 setting for one minute. 80 ul of the lysate was removed and added to the hDNA wells containing the Capture Hybridization Buffer, and pipetted up and down to mix. The plates were incubated at 53°C for at least 16 hours.

On the next day, the second part of the bDNA kit protocol was followed. Specifically, the plates were removed from the incubator and placed on the bench to cool for 10 minutes. The volumes of additions needed were calculated based upon information provided by the manufacturer. An Amplifier Working Solution was prepared by making a 1:100 dilution of the Amplifier Concentrate (20 fm/ul) in AL Hybridization Buffer. The hybridization mixture was removed from the plates and washed twice with Wash A. 50 ul of Amplifier Working Solution was added to each well and the wells were incubated at 53°C for 30 minutes. The plates were then removed from the incubator and allowed to cool for 10 minutes. The Label Probe Working Solution was prepared by making a 1:100 dilution of Label Concentrate (40 pmoles/ul) in AL Hybridization Buffer. After the 10-minute cool-down period, the amplifier hybridization mixture was removed and the plates were washed twice with Wash A. 50 wu! of Label

Probe Working Solution was added to each well and the wells were incubated at 53°C for 15 minutes. After cooling for 10 minutes, the Substrate was warmed to room temperature. Upon addition of 3 ul of Substrate

Enhancer to each ml of Substrate needed for the assay, the plates were allowed to cool for 10 minutes, the label : hybridization mixture was removed, and the plates were washed twice with Wash A and three times with Wash D. 50 11 of the Substrate Solution with Enhancer was added to each well. The plates were incubated for 30 minutes } at 37°C and RLU was read in an appropriate luminometer.

The replicates were averaged and the cocfficicnt of variation was determined. The measure of activity of the fold increase over the negative control (HEPES buffer described above) value was indicated by chemiluminescence units (RLU). The results are shown in TABLE 6 below, and are considered positive if the PRO polypeptide exhibits at least a two-fold value over the negative control. Negative control = 1.00 RLU at 1.00% dilution. Positive control = 8.39 RLU at 1.00% dilution.

TABLE 6

Induction of c-fos in Endothelial Cells

PRO Name PRO Concentration RLU values

PRO321 0011 nM 1.51 : 5 PRO32I 0.11 nM 1.07

PRO321 1.1 nM 2.11

PRO321 0.0Il nM 2.13

PRO321 0.11 nM 2.27

PRO321 1.10 nM 2.65

PRO840 244 iM 1.85

PRO840 244 nM 2.21 - PRO840 244 nM 3.04

PROS840 2.44 nM 2.82

PRO840 24.4 nM 2.90

PROS840 244 nM 1.01

PROB78 0.01% 243

PROS78 0.10% 2.71

PRO878 1.00% 1.39

PRO878 0.01% 2.48 PROB78 0.10% 245

PRO878 1.00% 1.89

PRO879 0.01% 1.23

PROS879 0.10% 1.33

PRO879 1.00% 2.54

PROS879 0.01% 2.06

PROS879 0.10% 1.65

PRO879 1.00% 2.25

EXAMPLE 13

Enhancement of Heart Neonatal Hypertrophy Induced by F2a (Assay 37)

This assay is designed to measure the ability of PRO polypeptides to stimulate hypertrophy of neonatal heart.

PRO polypeptides testing positive in this assay are expected to be useful for the therapeutic treatment of various cardiac insufficiency disorders.

Cardiac myocytes from {-day old Harlan Sprague Dawley rats were obtained. Cells (180 wi at 7.5 x 10°/mi, serum <0.1%, freshly isolated) are added on day 1 to 96-well plates previously coated with DMEM/F12 + 4% FCS.

Test samples containing the test PRO polypeptide (20 wi/well) are added directly to the wells on day 1. PGF (20 ul/well) is then added on day 2 at a final concentration of 10° M. The cells are then stained on day 4 and visually scored on day 5. Visual scores are based on cell size, wherein cells showing no increase in size as compared to negative controls are scored 0.0, cells showing a small to moderate increase in size as compared to negative controls are scored 1.0 and cells showing a large increase in size as compared to negative controls are scored 2.0. A score 40 of 1.0 or greater is considered positive.

No PBS is included, since calcium concentration is critical for assay response. Plates are coated with : DMEM/F12 plus 4% FCS (200 ul/well). Assay media included: DMEM/F12 (with 2.44 gm bicarbonate), 10 ug/ml transferrin, 1 ug/ml insulin, 1 ug/ml aprotinin, 2 mmol/L glutamine, 100 U/ml penicillin G, 100 xg/ml streptomycin. Protein buffer containing mannitol (4%) gave a positive signal (score 3.5) at 1/10 (0.4%) and 1/100 (0.04%), but not at 1/1000 (0.004%). Therefore the test sample buffer containing mannitol is not run.

PRO205, PRO882 and PRO887 polypeptides tested positive in this assay:

EXAMPLE 14

Inhibition of Heart Adult Hypertrophy (Assay 42)

This assay is designed to measure the inhibition of heart adult hypertrophy. PRO polypeptides testing positive in this assay may find use in the therapeutic treatment of cardiac disorders associated with cardiac hypertrophy.

Ventricular myocytes are freshly isolated from adult (250g) Harlan Sprague Dawley rats and the cells are plated at 200(/well in 180 wl volume. On day two, test samples (20 w1) containing the test PRO polypeptide are added. On day five, the cells are fixed and then stained. An increase in ANP message can also be measured by

PCR from cells after a few hours. Results are based on a visual score of cell size: 0 = no inhibition, -1 =small inhibition, -2 = large inhibition. A score of less than 0 is considered positive. Activity reference corresponds to phenylephrin (PE) at 0.1 mM, as a positive control. Assay media included: M199 (modified)-glutamine free,

NaHCO,, phenol red, supplemented with 100 nM insulin, 0.2% BSA, 5 mM creatine, 2 mM L-carnitine, 5S mM taurine, 100 U/ml penicillin G, 100 pg/ml streptomycin (CCT medium). Only inner 60 wells are used in 96 well plates. Of these, 6 wells are reserved for negative and positive (PE) controls.

PROB878 polypeptide provided a score of less than 0 in the above assay:

EXAMPLE 15

Induction of Endothelial Cell Apoptosis (Assay 73)

The ability of PRO polypeptides to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial celis (HUVEC, Cell Systems). A positive test in the assay is indicative of the usefulness of the polypeptide in therapeutically treating tumors as well as vascular disorders where inducing apoptosis of endothelial cells would be beneficial.

The ability of PRO polypeptides to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial cells (HUVEC, Cell Systems), using a 96-well format, in 0% serum media supplemented with 100 ng/ml VEGF. (As HUVEC cells are easily dislodged from the plating surface, all pipetting in the wells must be done as gently as practicable.)

The medium was aspirated and the cells washed once with PBS. 5 ml of | x trypsin was added to the cells in a T-175 flask, and the cells were allowed to stand until they were released from the plate (about 5-10 minutes).

Trypsinization was stopped by adding 5 ml of growth media. The cells were spun at 1000 rpm for 53 minutes at4°C.

The media was aspirated and the cells were resuspended in 10 ml of 10% serum complemented medium (Celi

Systems), 1 x penicillin/streptomycin.

The cells were plated on 96-well microtiter plates (Amersham Life Science, cytostar-T scintillating microplate,

RPNQIGO, sterile, tissue-culture treated, individually wrapped). in 10% serum (CSG-medium, Cell Systems), at a density of 2 x 10° cells per well in a total volume of 100 #1. Test PRO polypeptide samples were added in triplicate at dilutions of 1%, 0.33% and 0.11%. Wells without cells were used as a blank and wells with cells only . were used as a negative control. As a positive control 1:3 serial dilutions of 50 ul of a 3x stock of staurosporine were used. The ability of the test PRO polypeptide to induce apoptosis was determined using Annexin-V, a member

S of the calcium and phospholipid binding proteins, to detect apoptosis. 0.2 mi Annexin V - Biotin stock solution (100 pg/ml) were diluted in 4.6 mm] 2 x Ca binding buffer and 2.5% ) BSA (1:25 dilution). 50 pls of the diluted Annexin V - Biotin solution were added to each well (except controls) to a final concentration of 1.0 ug/ml. The samples were incubated for 10-15 minutes with Annexin-Biotin prior i to direct addition of *S-Streptavidin. ¥*S-Streptavidin was diluted in 2x Ca?" Binding buffer, 2.5% BSA and was added to all wells at a final concentration of 3 x 10° cpm/well. The plates were then sealed, centrifuged at 1000 rpm for 15 minutes and placed on orbital shaker for 2 hours. The analysis was performed on 1450 Microbeta Trilux (Wallac). The results are shown in TABLE 7 below where percent above background represents the percentage amount of counts per minute above the negative controls. Percents greater than or equal to 30% above background are considered positive. i 15 PRO333, PRO364 and PRO879 scored positive results in the above described assay. - TABLE?

Induction of Endothelial Cell Apoptosis

PRO Name PRO Concentration Percent Above Background

PRO333 0.11% 61.7%

PRO333 0.33% 37.6 %

PRO364 2.99 nM 193 %

PRO364 8.99 nM 69 %

PRO364 27.23 nM 315%

PROS879 1.00% 64.2 %

PRO879 0.11% 65.5%

PROS87Y 0.33% 14.7%

EXAMPLE 16

Inhibition of Heart Neonatal Hypertrophy Induced by LIF plus Endothelin-1 (ET-1) (Assay 74)

This assay is designed to determine whether PRO polypeptides of the present invention show the ability to inhibit neonatal heart hypertrophy induced by LIF and endothelin-1 (ET-1). A test compound that provides a positiveresponse in the present assay would be useful for the therapeutic treatment of cardiac insufficiency diseases or disorders characterized or associated with an undesired hypertrophy of the cardiac muscle.

Cardiac myocytes from 1-day old Harlan Sprague Dawley rats (180 wl at 7.5 x 10"/ml. serum <0.1. freshly isolated) are introduced on day 1 to 96-well plates previously coated with DMEM/FI2 + 4%FCS. Test PRO polypeptide samples or growth medium alone (negative control) are then added direct] y tothe wells on day 2 in 20 ul volume. LIF + ET-1 are then added to the wells on day 3. The cells are stained after an additional 2 days in culture and are then scored visuall y the nextday. A positive in the assay occurs when the PRO polypeptide treated myocytes are visually smaller on the average or less numerous than the untreated myocytes. . PRO238 and PRO1760 polypeptides tested positive in this assay.

EXAMPLE 17

Stimulation of Endothelial Tube Formation - Sprout formation (Assay 86)

S This assay is designed to detcrmine whether PRO polypeptides show the ability to promote endothelial vacuole and lumen formation in the absence of exogenous growth factors. PRO polypeptides testing positive in this assay would be expected to be useful for the therapeutic treatment of disorders where endothelial vacuole and/or lumen formation would be beneficial including, for example, where the stimulation of pinocytosis, ion pumping, vascular permeability and/or junctional formation would be beneficial.

HUVEC cells (passage <8 from primary) are mixed with type I rat tail collagen (final concentration 2.6 mg/ml) at a density of 6x10° cells per ml and plated at 50 1 per well of M199 culture media supplemented with 1% FBS and 1 uM 6-FAM-FITC dye to stain the vacuoles while they are forming and in the presence of the PRO polypeptide. The cells are then incubated at 37°C/5% CO, for 48 hours, fixed with 3.7% formalin at room temperature for 10 minutes, washed 5 times with M199 medium and then stained with Rh-Phalloidin at 4°C overnight followed by nuclear staining with 4 uM DAPI. A positive result in the assay is equal to or less than 2 [1 = cells are all round, 2 = cells are elongated, 3 cells are forming tubes with some connections, 4 = cells are forming complex tubular networks).

PRO179 polypeptide tested positive in this assay.

EXAMPLE 18 : 20 Induction of Endothelial Cell Apoptosis (ELISA) (Assay 109)

The ability of PRO polypeptides to induce apoptosis in endothelial cells was tested in human venous umbilical vein endothelial cells (HUVEC, Cell Systems) using a 96-well format, in 0% serum media supplemented with 100 ng/ml VEGF, 0.1% BSA, 1X penn/strep. A positive result in this assay indicates the usefulness of the polypeptide for therapeutically treating any of a variety of conditions associated with undesired endothelial cell growth including, for example, the inhibition of tumor growth. The 96-well plates used were manufactured by Falcon (No. 3072). Coating of 96 well plates were prepared by allowing gelatinization to occur for >30 minutes with 100 ul of 0.2% gelatin in PBS solution. The gelatin mix was aspirated thoroughly before plating HUVEC cells at a final concentration of 2 x 10“ cells/ml in 10% serum containing medium - 100 ul volume per well. The cells were grown for 24 hours before adding test samples containing the PRO polypeptide of interest.

To all wells, 100 uI of 0% serum media (Cell Systems) complemented with 100 ng/ml VEGF, 0.1% BSA, 1X penn/strep was added. Test samples containing PRO polypeptides were added in triplicate at dilutions of 1%, 0.33% and 0.11%. Wells without cells were used as a blank and wells with cells only were used as a negative control. As a positive control, 1:3 serial dilutions of 50 w! of a 3x stack of staurosporine were used. The cells were incubated for 24 to 35 hours prior to ELISA.

ELISA was used to determine levels of apoptosis preparing solutions according to the Boehringer Manual (Bochringer, Cell Death Detection ELISA plus, Cat No. 1 920 685]. Sample preparations: 96 well plates were spun down at 1 kepm for 10 minutes (200g); the supernatant was removed by fast inversion, placing the plate upside down on a paper towel to remove residual liquid. To each well, 200 ul of 1X Lysis buffer was added and : incubation allowed at room temperature for 30 minutes without shaking. The plates were spun down for 10 minutes . at 1 krpm, and 20 ul of the lysate (cytoplasmic fraction) was transferred into streptavidin coated MTP. 80 ul of immunoreagent mix was added to the 20 ul lystate in each well. The MTP was covered with adhesive foil and incubated at room tempearature for 2 hours by placing it on an orbital shaker (200 rpm). After two hours, the supernatant was removed by suction and the wells rinsed three times with 250 ul of 1X incubation buffer per well (removed by suction). Substrate solution was added (100 1) into each well and incubated on an orbital shaker at room temperature at 250 rpm until color development was sufficient for a photometric analysis (approx. after 10-20 minutes). A 96 well reader was used to read the plates at 405 nm, reference wavelength, 492 nm. The levels obtained for PIN 32 (control buffer) was set to 100%. Samples with levels >130% were considered positive for induction of apoptosis.

PRO846, and PRO844 polypeptides tested positive in this assay.

EXAMPLE {9

In situ hybridization is a powerful and versatile technique for the detection and localization of nucleic acid sequences within cell or tissue preparations. It may be useful, for example, to identify sites of gene expression, analyze the tissue distribution of transcription, identify and localize viral infection, follow changes in specific mRNA synthesis, and aid in chromosome mapping.

In situ hybridization was performed following an optimized version of the protocol by Lu and Gillett, Cell

Vision, 1: 169-176 (1994), using PCR-generated **P-labeled riboprobes. Bricfly, formalin-fixed, paraffin-cmbedded human tissues were sectioned, deparaffinized, deproteinated in proteinase K (20 g/ml) for 15 minutes at 37°C, and - further processed for in situ hybridization as described by Lu and Gillett. supra. A (¥-P)UTP-labeled antisense riboprobe was generated from a PCR product and hybridized at 55°C overnight. The slides were dipped in Kodak

NTB2™ nuclear track emulsion and exposed for 4 weeks. 2p_Riboprobe synthesis 6.0 w1 (125 mCi) of ®P-UTP (Amersham BF 1002, SA<2000 Ci/mmol) were speed-vacuum dried. To each tube containing dried *P-UTP, the following ingredients were added: 2.0 wl 5x transcription buffer 1.0 ul DTT (100 mM) 2.0 wl NTP mix (2.5 mM: 10 ui each of 10 mM GTP, CTP & ATP + 10 ul H,0) 1.0 ul UTP (50 uM) 1.0 1 RNAsin 1.0 ul DNA template (1 1g) 1.0 «1 H.O 1.0 ul RNA polymerase (for PCR products T3 = AS, T7 = S. usually)

The tubes were incubated at 37°C for one hour. A total of 1.0 41 RQI DNase was added, followed by incubation at 37°C for 15 minutes. A total of 90 ul TE (10 mM Tris pH 7.6/1 mM EDTA pH 8.0) was added, and the mixture was pipetted onto DES] paper. The remaining solution was loaded in a MICROCON-50"

ultrafiltration unit, and spun using program 10 (6 minutes). The filtration unit was inverted over a second tube and . spun using program 2 (3 minutes). After the final recovery spin, a total of 100 11 TE was added, then 1 ul of the final product was pipetted on DE81 paper and counted in 6 ml of BIOFLUOR [I™.

The probe was run on a TBE/urea gel. A total of 1-3 pl of the probe or 5 ul of RNA Mik III was added to 3uof loading buffer. After heating on a 95°C heat block for three minutes, the gel was immediately placed on ice. The wells of gel were flushed, and the sample was loaded and run at 180-250 volts for 45 minutes. The gel was wrapped in plastic wrap (SARAN™ brand) and exposed to XAR film with an intensifying screen in a -70°C freezer one hour to overnight. 2P.Hybridization

A. Pretreatment of frozen sections

The slides were removed from the freezer, placed on aluminum trays, and thawed at room temperature tor 5 minutes. The trays were placed in a 55°C incubator for five minutes to reduce condensation. The slides were fixed for 10 minutes in 4% paraformaldehyde on ice in the fume hood, and washed in 0.5 x SSC for 5 minutes, at room temperature (25 ml 20 x SSC +975 ml SQ H.0). After deproteination in 0.5 ug/ml proteinase K for 10 minutes at37°C (12.5 ut of 10 mg/ml stock in 250 mi prewarmed RNAse-free RNAse buffer), the sections were washed in 0.5 x SSC for 10 minutes at room temperature. The sections were dehydrated in 70%, 95%, and 100% ethanol, 2 minutes each.

B. Pretreatment of paraffin-embedded sections

The slides were deparaffinized, placed in SQ H,0, and rinsed twice in 2 x SSC at room temperature, for 5 minutes each time. The sections were deproteinated in 20 ug/ml proteinase K (500 ui of 10 mg/mi in 250 ml . RNase-free RNase buffer; 37°C, 15 minutes) for human embryo tissue, or 8 x proteinase K (100 xl in 250 ml Rnase buffer. 37°C, 30 minutes) for formalin tissues. Subsequent rinsing in 0.5 x SSC and dehydration were performed as described above.

C. Prehybridization

The slides were laid out in a plastic box lined with Box buffer (4 x SSC, 50% formamide) - saturated filter paper. The tissue was covered with 50 ul of hybridization buffer (3.75 g dextran sulfate + 6 ml SQ H,O). vortexed, and heated in the microwave for 2 minutes with the cap loosened. After cooling on ice, 18.75 ml formamide, 3.75 ml 20 x SSC, and 9 m! SQ H,0 were added, and the tissue was vortexed well and incubated at 42°C for 1-4 hours.

D. Hybridization 1.0 x 10° cpm probe and 1.0 x1 tRNA (50 mg/m! stock) per slide were heated at 95°C for 3 minutes. The slides were cooled on ice, and 48 1 hybridization buffer was added per slide. After vortexing, 50 «:} “P mix was added to 50 1 prehybridization on the slide. The slides were incubated overnight at 55°C.

E. Washes

Washing was done for 2x 10 minutes with 2xSSC, EDTA at room temperature (400 ml 20 x SSC + 16 m1 0.25

MEDTA, V=4L), followed by RNAseA treatment at 37°C for 30 minutes (500 x1 of 10 mg/ml in 250 ml Rnase buffer = 20 ug/ml), The slides were washed 2 x10 minutes with 2 x SSC, EDTA at room temperature. The stringency wash conditions were as follows: 2 hours at 55°C, 0.1 x SSC, EDTA (20 mt 20 x SSC + 16 ml EDTA,

V4.

I. Oligonucleotides

In situ analysis was performed on three of the DNA sequences disclosed herein. The oligonucleotides employed for these analyses are as follows: (1) DNA47365-1206 (PRO364) (TNF receptor homolog) , 5 pl: i 5'-GGA TTC TAA TACGAC TCA CTA TAG GGC AAC CCG AGC ATG GCA CAG CAC-3' (SEQ TD NO:50) p2: 3 5-CTA TGA AAT TAA CCC TCA CTA AAG GGA TCT CCC AGC CGC CCC TTC TC-3' (SEQ ID NO:51) (2) DNA30868 (PRO20S) (follistatin homolog) pi: 5-GGA TTC TAA TAC GAC TCA CTA TAG GGC AGA GAC AGG GCA AGC AGA ATG-3' (SEQIDNO:52) p2: 5-CTATGA AATTAA CCC TCA CTA AAG GGA GAA GGG GAT GAC TGG AGG AAC-3' (SEQID NO:53) (3) DNA41374 (PRO333) (CD33 homolog) pt: 5'-GGA TTC TAA TAC GAC TCA CTA TAG GGC CTC CAC AGA ACC TCG CCA TCA-3' (SEQ ID NO:54) p2: 5-CTA TGA AATTAA CCC TCA CTA AAG GGA TGG GGC AAG ACT CAC AAG CAG -3' (SEQID NO:55)

G. Results ’

In situ analysis was performed on the above three DNA sequences disclosed herein. The results from these analyses are as follows: . (1) DNA47365-1206 (PRO364) (TNF receptor homolog)

In the fetus, there was expression in the fascia lining the anterior surface of the vertebral body. There was also expression over the fetal retina. However, there was low level expression over the fetal neurones. All other tissues were negative. (2) DNA3(868 (PRQ20S5) (follistatin homolog)

In fetal tissuc, there was expression in the spinal cord, autonomic ganglia. enteric nerves, sacral plexus, peripheral and cranial nerves. All other fetal and adult tissues were negative.

Fetal tissues (12-16 weeks) examined included: placenta, umbilical cord, liver. kidney. adrenals, thyroid, lungs, heart, great vessels, oesophagus, stomach, small intestine, spleen, thymus, pancreas, brain, eye, spinal cord, body wall, pelvis and lower limb.

Adult tissues included: liver, kidney. adrenal, myocardium, aorta, spleen, lymph node, pancreas, lung and skin.

(3) DNA41374 (PRQ333) (CD33 homolog) . This molecule has been shown to be immunostimulatory (enhances T lymphocyte proliferation in the one-way mixed lymphocyte reaction in T lymphocyte co-stimulation assays). The distribution pattern of this molecule was evaluated with a limited tissue screen comprising tissues available at the initiation of this study.

In numerous tissucs evaluated, a weak diffuse expression was detected in thymic T lymphocytes (spleen and lymph node were not evaluated). This result was confirmed in the subscquent in situ hybridization study. The results of that study showed similar low level expression in non-human primate thymus and in human tonsil in T lymphocyte specific regions. The limited distribution pattern suggests expression by T lymphocytes or cells closely associated with T lymphocytes such as antigen presenting cells (dendritic cell populations, etc). In inflamed human tdssue withsi gnificant lymphocytic inflammation and presence of reactive follicle formation (in inflammatory bowel disease and chronic lymphocytic interstitial pneumonia/bronchitis) there was no detectable expression in areas which contained significant numbers of T lymphocytes.

The distribution discrepancy (i.e. expression in thymic and tonsillar T lymphocyte areas but not in areas with

T lymphocytic inflammation) suggests the following possibilities: 1. That there is selective/restricted expression in a T lymphocyte subset population present in thymus and tonsillar lymph node but not inflamed tissue. Immature, non-committed T lymphocytes are present in both tonsil and thymus but likely would not be a major population in chronically inflamed tissues. 2. That expression in T lymphocytes is weak and differences in detection in tissues with T lymphocytes is a reflection of RNA quality in those tissues sections rather than a reflection of different T lymphocyte cell population types. 3. That expression in thymus and tonsil is not in lymphocytes but rather in a specific cell population closely . associated with T lymphocytes, that is not present in the inflamed jung and bowel evaluated. One such possibility is a dendritic cell subpopulation.

In a non-human primate there was weak diffuse expression in thymic lymphocytes.

In a subsequent study, the following results were reported:

Inflammed lung: (chronic lymphocytic and granulomatous pneumonitis): a weak to negative signal was observed in the interstitium compared to the control sense probe; therc was weak expression in the normal chimp thymus (human thymus not available) and in the human tonsil. In the later, the expression was predominantly in T lymphocyte areas of this structure including the perifollicular marginal zone and in the paracortex.

There was no detectable expression in the following human tissues: inflammatory bowel disease (8 patient specimens), chronically inflamed and normal lung (6 patient specimens), chronic sclerosing nephritis (] patient specimen), chronically and acutely inflammed and cirrhotic liver (10 specimen multiblock), normal and psoriatic skin, and peripheral lymph node (non-reactive).

EXAMPLE 20

Use of PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S. PRO321. PRO333, PRO840,

PRO877, PRO878 PRO879, PRO882, PRO88S or PRO887 as a Hybridization Probe

The following method describes use of a nucleotide sequence encoding PRO 179, PRO238, PRO364, PROS44,

PRO846, PRO 1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878. PRO879, PRO882, PROSSS or

PROB887 as a hybridization probe.

DNA comprising the coding sequence of full-length or mature PRO179, PRO238, PRO364, PRO844, .

PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROSSS or

PRO887 (as shown in Figures 1, 3,5, 7,9, 11, 13,15, 17, 19, 21, 23, 25, 27, 29, and 31, respectively, SEQ ID NOS: 1,3,57,911,13,15,17,19, 21,23, 25,27, 29, and 31, respectively) or a fragment thereof is employed as a probe to screen for homologous DNAs (such as those encoding naturally-occurring variants of PRO179, PR0238,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PR0O333, PRO840, PRO877, PRO878, PRO879,

PROB882, PRO885 or PRO887) in human tissue cDNA libraries or human tissue genomic libraries.

Hybridization and washing of filters containing either library DNAs is performed under the following high- suingency conditions. Hybridization of radiolabeled probe derived from the gene encoding PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO%79,

PROB882, PRO88S or PRO887 polypeptide to the filters is performed in a solution of 50% formamide, 5x SSC, 0.1% SDS, 0.1% sodium pyrophosphate, 50 mM sodium phosphate, pH 6.8, 2x Denhardt's solution. and 10% dextran sulfate at 42°C for 20 hours. Washing of the filters is performed in an aqueous solution of 0.1x $SC and 0.1% SDS at 42°C.

DNAs having a desired sequence identity with the DNA encoding full-length native sequence can then he identified using standard techniques known in the art.

EXAMPLE 21

Expression of Nucleic Acid Encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRQ205,

PRO32!, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8BSS5 or PRO887 in E. coli

This Example illustrates preparation of an unglycosylated form of PRO179, PRO238, PRO364, PRO844, .

PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or

PRO887 by recombinant expression in E. coli. )

The DNA sequence encoding PRO179, PRO238, PRO364, PRO844, PRO846. PRO1760,PRO205. PRO321,

PRO333, PRO840. PRO877, PRO878, PRO879, PRO882, PRO8RS or PRO887 (SEQ ID NOS: 1,3,5,7,9. 11, 13,15.17,19,21,23,25,27,29, or 31, respectively) is initially amplified using selected PCR primers. The primers should contain restriction enzyme sites that correspond to the restriction enzyme sites on the selected expression vector. A variety of expression vectors may be employed. An example of a suitable vector is pBR322 (derived from E. coli; see Bolivar etal., Gene, 2: 95 (1977)), which contains genes for ampicillin and tetracycline resistance.

The vector is digested with restriction enzyme and dephosphorylated. The PCR-amplified sequences arc then ligated into the vector. The vector will preferably include sequences that encode an antibiotic-resistance gene. a trp promoter, a poly-His leader (including the first six STII codons, poly-His sequence. and enterokinase cleavage site), theregion encoding PRO179, PRO238, PRO364, PR0O844. PROR46, PRO 1760. PRO205, PRO321, PRO333,

PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO$Y7, lambda transcriptional terminator, and an argU gene.

The ligation mixture is then used to transform a selected E. coli strain using the methods described in

Sambrook ef al.. supra. Transformants are identified by their ability to grow on LB plates and antibiotic-resistant colonies are then selected. Plasmid DNA can be isolated and confirmed by restriction analysis and DNA sequencing. . Selected clones can be grown overnight in liquid culture medium such as LB broth supplemented with antibiotics. The overnight culture may subsequently be used to inoculate a larger-scale culture. The cells are then grown to a desired optical density, during which the expression promoter is turned on.

After culturing the cells for several more hours, the cells can be harvested by centrifugation. The cell pellet obtained by the centrifugation can be solubilized using various agents known in the art, and the solubilized PRO 179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PROS87S,

PRO87Y, PRO882, PRO885 or PRO887 polypeptide can then be purified using a metal-chelating column under conditions that allow tight binding of the polypeptide.

PR0O238, PRO364 and PRO1760 were successfully expressed in E. coli in a poly-His tagged form by the above procedure.

EXAMPLE 22

Expression of Nucleic Acid Encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S,

PRO321, PRO333, PRO840, PRO877, PRORTR, PRO’79, PRO882, PROSSS or PRO887 in Mammalian Cells

This Example illustrates preparation of a potentially glycosylated form of PRO179, PRO238, PRO364,

PRO844, PROB46, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PROB885 or PRO887 by recombinant expression in mammalian cells.

The vector, pRKS (see, EP 307,247, published March 15, 1989), is employed as the expression vector.

Optionally, the PRO179,PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PR0O321, PRO333, PRO840, PRO877, PRORT8, PRO879, PRO882, PRO88S5 or PRO887 DNA is ligated into pRKS with selected restriction . enzymes to allow inscrtion of the DNA encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, . PRO205,PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 or PROBST using ligation : methods such as described in Sambrook er al., supra. The resulting vector is called pRKS-(DNA encoding

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S5, PR0O321, PRO333, PRO840, PROR77,

PROS78, PRO879, PRO882, PRO88S5 or PRO88S7).

In one embodiment, the selected host cells are 293 cells. Human 293 cells (ATCC CCL 1573) are grown to . confluence in tissue culture plates in medium such as DMEM supplemented with fetal calf serum and optionally, nutrient components and/or antibiotics. About 10 4g DNA of pRK5-(DNA encoding PRO179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882,

PROS$85 or PRO887) is mixed with about } ug DNA encoding the VA RNA gene (Thimmappaya er al., Cell, 31: 543 (1982)) and dissolved in 500 a of } mM Tris-HCI, 0.1 mM EDTA, 0.227 M CaCl,. To this mixture is added, dropwise, 500 ul of S50 mM HEPES (pH 7.35), 280 mM NaCl. t.5 mM NaPO,. and a precipitate is allowed to form for 10 minutes at 25°C. The precipitate is suspended and added to the 293 cells and allowed to settle for about four hours at 37°C. The culture medium is aspirated off and 2 mi of 20% glycerol in PBS is added for 30 seconds. The 293 cells are then washed with serum-free medium, fresh medium is added, and the cells are incubated for about 5 days.

Approximately 24 hours after the transfections, the culture medium is removed and replaced with culture medium (alone) or culture medium containing 200 ./Ci/m! **S-cysteine and 200 4Ci/ml **S-methionine. Aftera 12-

hour incubation, the conditioned medium is collected, concentrated on a spin filter, and loaded onto a 15% SDS gel. The processed gel may be dried and exposed to film for a selected period of time to reveal the presence of the .

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877,

PRO878, PRO879, PRO882, PRO88S or PRO&87 polypeptide. The cultures containing transfected cells may undergo further incubation (in serum-free medium) and the medium is tested in selected bioassays.

In an alternative technique, the gene encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 may be introduced into 293 cells transiently using the dextran sulfate method described by Somparyruc ef al., Proc. Natl,

Acad. Sci., 12: 7575 (1981). 293 cells are grown to maximal density in a spinner flask and 700 ug pRK5-(DNA encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PROS40,

PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887) is added. The cells are first concentrated from the spinner flask by centrifugation and washed with PBS. The DNA-dextran precipitate is incubated on the cell pellet for four hours. The cells are treated with 20% glycerol for 90 seconds, washed with tissuc culture medium, and re- introduced into the spinner flask containing tissue culture medium, 5 g/ml bovine insulin, and 0.1 ug/ml bovine transferrin. After about four days, the conditioned media is centrifuged and filtered to remove cells and debris.

The sample containing the expressed gene encoding the PRO179, PRO238, PRO364, PRO844, PRO846, PRO 1760,

PRQO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide can then be concentrated and purified by any selected method, such as dialysis and/or column chromatography.

In another embodiment, the gene encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PROS887 can be expressed in CHO cells. The pRKS-(DNA encoding PRO179, PRO238, PRO364, PRO844. PRO846, PRO1760,

PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRORSS or PRO887) nucleic acid . can be transfected into CHO cells using known reagents such as CaPO, or DEAE-dextran. As described above, the cell cultures can be incubated, and the medium replaced with culture medium (alone) or medium containing a radiolabel such as **S-methionine. After determining the presence of PRO179. PRO238. PRO364, PRO844,

PROg46, PRO1760, PRO20S, PRO321, PR0O333, PRO840, PRO877, PRO878, PRO879. PRO882, PROSSS or

PRO887 polypeptide, the culture medium may be replaced with serum-free medium. Preferably. the cultures are incubated for about 6 days, and then the conditioned medium is harvested. The medium containing the expressed

PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO&40, PRO877,

PROS878.PRO879, PRO882, PRO88S or PRO887 can then be concentrated and purified by any sclected method.

Epitope-tagged gene encoding the PRO179, PRO238, PRO364, PRO844, PRO846. PROI760, PRO205,

PRO321, PRO333, PRO840, PROR77, PRO878, PRO879, PRO882, PRO88BS or PRO887 polypeptide may also be expressed in host CHO cells. The gene encoding PRO179, PRO238, PRO364, PRO844. PROR46, PRO1760,

PRO205. PR0O321, PRO333, PRO840, PRO877. PRO878, PRO%79, PRO882, PRO88S or PRO887 may be subcloned out of the pRKS vector. The subclone insert can undergo PCR amplification 10 fuse in frame with a selected epitope tag such as a poly-His tag into a baculovirus expression vector. The gene insert encoding the poly-

His-tagged-|PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321. PRO333, PRO840,

PRO877, PRO878, PRO879, PRO882, PRO8SS or PRO8S7] can then be subcloned into a SV40- driven vector containing a selection marker such as DHFR for selection of stable clones. Finally. the CHO cells can be transfected (as described above) with the SV40-driven vector. Labeling may be performed, as described above, to } verify expression. The culture medium containing the expressed gene encoding the poly-His-tagged-[PRO179,

PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO87S,

PRO879, PRO882, PRO885 or PRO887] can then be concentrated and purified by any selected method, such as by Ni*chelate affinity chromatography.

PRO179, PRO364, PRO840, PRO844, PROB46 and PRO205 were stably expressed in CHO cells by the above described method. In addition, PRO364 and PRO846 were expressed in CHO cells by a transient procedure.

EXAMPLE 23

Expression of Nucleic Acid Encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S5,

PRO321, PRO333, PRO840. PRO877, PRO878, PRO879, PRO882, PRO8ES or PROBST in Yeast

The following method describes recombinant expression of the gene encoding PRO179, PRO238, PRO364,

PROB44, PRO846, PRO1760, PRO205, PRO321, PR0O333, PRO840, PRO877, PRO878, PRO879, PR0O8S2,

PRO885 or PRO887 in yeast.

First, yeast expression vectors are constructed for intracellular production or secretion of PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879,

PRO882, PRO88S or PRO887 from the ADH2/GAPDH promoter. DNA encoding PRO179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO20S, PRO321, PR0O333, PRO840, PRO877, PRO878, PRO879, PROSS2,

PRO88S5 or PRO887 and the promoter is inserted into suitable restriction enzyme sites in the selected plasmid to direct intracellular expression of the gene encoding PRO179, PRO238, PRO3G4, PRO844, PROR4G, PRO1760,

PRO205,PRO321,PRO333, PRO840, PRO877, PRO878, PRO87Y, PRO882, PRO88S or PRO887. For secretion, - DNA encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840,

PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 can be cloned intw the selected plasmid, together with

DNA encoding the ADH2/GAPDH promoter, a native PRO 179, PRO238, PRO364, PRO844, PRO846, PRO1760,

PRO205,PRO321,PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROS8S or PRO887 signal peptide or other mammalian signal peptide, or, for example, a yeast alpha-factor or invertase secretory signal/leader sequence, and linker sequences (if needed) for expression of the gene encoding PRO179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PROSS2,

PRO88S or PROS887.

Yeast cells, such as yeast strain AB1 10, can then be transformed with the expression plasmids described above and cultured in selected fermentation media. The transformed yeast supernatants can be analyzed by precipitation with 10% trichloroacetic acid and separation by SDS-PAGE, followed by staining of the gels with Coomassie Blue stain.

Recombinant PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PR0O333,

PRO840, PRO877, PRO878, PRO879, PRO&82, PRO885 or PROSR7 can subsequently be isolated and purified by removing the yeast cells from the fermentation medium by centrifugation and then concentrating the medium using selected cartridge filters. The concentrate containing PRO179, PRO238, PRO364, PRO844, PROS46,

PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 may further be purified using selected column-chromatography resins.

EXAMPLE 24

Expression of Nucleic Acid Encoding PRO179, PRO238, PRO364, PRO844, PROR46, PRO1760, PRO205, .

PRO32}, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PROBS or PROYS7 in Baculovirus-

Infected Insect Cells

The following method describes recombinant expression in Baculovirus-infected insect cells.

The sequence coding for PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321,

PRO333, PRO840, PRO&77, PRO878, PRO879, PRO882, PRO885 or PRO887 is fused upstream of an epitope tag contained within a baculovirus expression vector. Such epitope tags include poly-His tags and immunoglobulin tags (like Fc regions of IgG). A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pVL1393 (Novagen). Briefly, the sequence encoding PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO87Y,

PRO882, PROSRS or PRO887 or the desired portion of the coding sequence of PRO179, PR0O238, PRO364,

PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PRO885 or PRO887 [such as the sequence encoding the extracellular domain of a transmembrane protein or the

A 15 sequence encoding the mature protein if the protein is extracellular] is amplified by PCR with primers complementary to the 5' and 3' regions. The §' primer may incorporate flanking (selected) restriction enzyme sites. } The product is then digested with those sclccted restriction enzymes and subcloned into the expression vector.

Recombinant baculovirus is generated by co-transfecting the above plasmid and BaculoGoldTM virus DNA (Pharmingen) into Spodoptera frugiperda ("S£9") cells (ATCC CRL 1711) using lipofectin (commercially available from GIBCO-BRL). After4-5 days of incubation at 28 °C, the released viruses are harvested and used for further amplifications. Viral infection and protein expression are performed as described by OReilley et al., Baculovirus

Expression Vectors: A Laboratory Manual (Oxford: Oxford University Press (1994)). :

Expressed poly-His tagged-[PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321,

PRO333,PR0O840,PRO877,PRO878,PRO879, PROBE2, PRO8]S or PRO887] can then be purified, forexample, } by Ni chelate affinity chromatography as foliows. Extracts are prepared from recombinant virus-infected Sf9 cells as described by Rupert et al., Nature, 362:175-179 (1993). Briefly, Sf9 cells are washed, resuspended in sonication buffer (25 ml Hepes, pH 7.9; 12.5 mM MgCl,; 0.1] mM EDTA; 10% glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 seconds on ice. The sonicates are cleared by centrifugation, and the supernatant is diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10% glycerol, pH 7.8) and filtered through a 0.45 umfilter. A Ni-NTA agarose column (commercially available from Qiagen) is prepared with a bed volume of 5 ml, washed with 25 ml of water and equilibrated with 25 mi of loading buffer. The filtered cell extract is loaded onto the column at 0.5 ml per minute. The column is washed to baseline A, with loading buffer. at which point fraction collection is started. Next, the column is washed with a secondary wash buffer (50 mM phosphate: 300 mM NaCl. 10% glycerol, pH 6 0), which elutes non-specifically- bound protein. After reaching Ay, baseline again, the column is devcloped with a 0 to 500 mM imidazole gradient in the secondary wash buffer. One ml fractions are collected and analyzed by SDS-PAGE and silver staining or Western blot with Ni *"-NTA-conjugated to alkaline phosphatase (Qiagen). Fractions containing the eluted His, -tagged-[PRO179, PRO238, PRO364,

PRO844, PROR46, PRO1760, PRO205, PRO321, PR0O333. PR0O840, PRO877, PRO878, PRO879, PRO882,

PROB88S5 or PROBST), respectively, are pooled and dialyzed against loading buffer.

Alternatively, purification of the 1gG-tagged (or Fc tagged)-[PRO179, PRO238, PRO364, PRO844, PRO846, . PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887] can be performed using known chromatography techniques, including for instance, Protein A or protein G column chromatography.

While expression was actually performed in a 0.5-2 L scale, it can be readily scaled up for larger (e.g., 8 L) preparations. The proteins were expressed as an IgG construct (immunoadhesin), in which the protein extracellular region was fused to an IgG1 constant region sequence containing the hinge, CH2 and CH3 domains and/or in poly-His tagged forms.

Following PCR amplification, the respective coding sequences were subcloned into a baculovirus expression vector (pb.PH.IgG for IgG fusions and pb.PH.His.c for poly-His tagged proteins), and the vector and Baculogold® baculovirus DNA (Pharmingen) were co-transfected into 105 Spodoptera frugiperda ("Sf9") cells (ATCC CRL 1711), using Lipofectin (Gibco BRL). pb.PH.IgG and pb.PH.His are modifications of the commercially available baculovirus expression vector pYL1393 (Pharmingen), with modified polylinker regions to include the His or Fc tag sequences. The cells were grown in Hink's TNM-FH medium supplemented with 10% FBS (Hyclone). Cells were incubated for 5 days at 28°C. The supernatant was harvested and subsequently used for the first viral amplification by infecting Sf9 cells in Hink's TNM-FH medium supplemented with 10% FBS at an approximate multiplicity of infection (MOI) of 10. Cells were incubated for 3 days at 28°C. The supernatant was harvested and the expression of the constructs in the baculovirus expression vector was determined by batch binding of | mi of supernatant to 25 ml of Ni 2*-NTA beads (QIAGEN) for histidine tagged proteins or Protein-A Sepharose CL-4B beads (Pharmacia) for IgG tagged proteins followed by SDS-PAGE analysis comparing to a known concentration of protein standard by Coomassie blue staining. . The first viral amplification supernatant was used to infect a spinner culture (500 ml) of Sf9 cells grown in

ESF-921 medium (Expression Systems LLC) at an approximate MOI of 0.1. Cells were incubated for 3 days at 28°C. The supernatant was harvested and filtered. Batch binding and SDS-PAGE analysis were repeated, as necessary. until expression of the spinner culture was confirmed.

The conditioned medium from the transfected cells (0.5 to 3 L) was harvested by centrifugation to remove the cells and filtered through 0.22 micron filters. For the poly-His tagged constructs, the protein construct was purified using a Ni *-NTA column (Qiagen). Before purification, imidazole was added to the conditioned media to a concentration of 5 mM. The conditioned media was pumped onto a 6 ml Ni 2*-NTA column equilibrated in 20 mM

Hepes. pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 ml/min. at 4°C. After loading. the column was washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein was subsequently desalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -80°C.

Immunoadhesin (Fc containing) constructs of proteins were purified from the conditioned media as follows.

The conditioned media was pumped onto a 5 ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading, the column was washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5. The eluted protein was immediately neutralized by collecting | ml fractions into tubes containing 275 ml of 1 M Tris buffer, pH 9. The highly purified protein was subsequently desalted into storage buffer as described above for the poly-His tagged proteins. The homogeneity of the proteins was verified by SDS polyacrylamide gel (PEG) electrophoresis and N-terminal amino acid sequencing by Edman . degradation.

PRO205, PRO321, PRO840, PRO846, PRO88S and PRO887 were successfully expressed in Baculovirus- infected insect Sf9 cells by the above procedure.

Alternatively, a modified baculovirus procedure may be used incorporating high-5 cells. In this procedure, the DNA encoding the desired sequence was amplified with suitable systems, such as Pfu (Stratagene), or fused upstream (5'-of) of an epitope tag contained with a baculovirus expression vector. Such epitope tags include poly-His tags and immunoglobulin tags (like Fc regions of IgG). A variety of plasmids may be employed, including plasmids derived from commercially available plasmids such as pIEl-1 (Novagen). The pIE1-1 and pIE1-2 vectors are designed for constitutive expression of recombinant proteins from the baculovirus iel promoter in stably-transformed insect cells. The plasmids differ only in the orientation of the multiple cloning sites and contain all promoter sequences known to be important for iel-mediated gene expression in uninfected insect cells as well as the hr5 enhancer element. pIE1-1 and pIE1-2 include the translation initiation site and can be used to produce fusion proteins. Briefly, the desired sequence or the desired portion of the sequence (such as the sequence encoding the extracellular domain of a transmembrane protein) was amplified by PCR with primers complementary to the 5'and 3' regions. The 5’ primer may incorporate flanking (sclected) restriction enzyme sites. The product was then digested with those selected restriction enzymes and subcloned into the expression vector. For example, derivatives of pIEI-1 can include the Fc region of human IgG (pb.PH.IgG) or an 8 histidine (pb.PH.His) tag downstream (3'-of) the desired sequence. Preferably, the vector construct is sequenced for confirmation.

High-5 cells are grown to a confluency of 50% under the conditions of, 27°C, no CO,, NO pen/strep. For each 150 mm plate. 30 rg of pIE based vector containing the sequence was mixed with 1 ml Ex-Cell medium (Media: .

Ex-Cell 401 + 1/100 L-Glu JRH Biosciences #14401-78P (note: this media is light sensitive)). and in a separate tube, 100 ul of CellFectin (CelIFECTIN (GibcoBRL #10362-010) (vortexed to mix)) was mixed with 1 ml of Ex-Cell medium. The two solutions were combined and allowed to incubate at room temperature for 15 minutes. 8 ml of Ex-Cell media was added to the 2 ml of DNA/CellFECTIN mix and this is layered on high-5 cells that have been washed once with Ex-Cell media. The plate is then incubated in darkness for 1 hour at room temperature. The

DNA/CellFECTIN mix is then aspirated, and the cells are washed once with Ex-Cell to remove excess

CellFECTIN, 30 ml of fresh Ex-Cell media was added and the cells are incubated for 3 days at 28°C. The supernatant was harvested and the expression of the sequence in the baculovirus expression vector was determined by batch binding of 1 ml of supcrnatant to 25 ml of Ni »*-NTA beads (QIAGEN) for histidine tagged proteins or

Protein-A Sepharose CL-4B beads (Pharmacia) for 1gG tagged proteins followed by SDS-PAGE analysis comparing to a known concentration of protein standard by Coomassie blue staining.

The conditioned media from the transfected cells (0.5 to 3 L) was harvested by centrifugation to remove the cells and filtered through 0.22 micron filters. For the poly-His tagged constructs, the protein comprising the sequence is purified using a Ni **-NTA column (Qiagen). Before purification, imidazole is added to the conditioned media to a concentration of 5 mM. The conditioned media was pumped onto a 6 mi Ni *'-NTA column equilibrated in 20 mM Hepes, pH 7.4, buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5 mi/min. at 48°C.

After loading, the column was washed with additional equilibration buffer and the protein eluted with equilibration buffer containing 0.25 M imidazole. The highly purified protein was then subsequently desalted into a storage . butfer containing 10 mM Hepes, 0.14 M NaCl and 4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column and stored at -80°C.

Immunoadhesin (Fc containing) constructs of proteins were purified from the conditioned media as follows.

The conditioned media was pumped onto a 5 ml! Protein A column (Pharmacia) which had been equilibrated in 20 mM Na phosphate buffer, pH 6.8. After loading, the column was washed extensively with equilibration buffer before elution with 100 mM citric acid, pH 3.5. The eluted protein was immediately neutralized by collecting 1 ml fractions into tubes containing 275 ml of 1 M Tris buffer, pH 9. The highly purified protein was subscquently desalted into storage buffer as described above for the poly-His tagged proteins. The homogeneity of the sequence was assessed by SDS polyacrylamide gels and by N-terminal amino acid sequencing by Edman degradation and other analytical procedures as desired or necessary.

PRO179, PRO20S, PRO321, PRO333, PRO364, PRO844, PRO846, PRO877, PRO879, PRO882, PRO88S and PRO1760 were expressed in high 5 cells by the above described method.

EXAMPLE 25

Preparation of Antibodies that Bind PRO179, PRO238, PRO364, PRO844. PRO846, PRO1760, PRO20S5.

PRO321, PRO333, PRO840, PRO877, PRO878. PRO879, PRO882. PRORSS or PROBS?

This Example illustrates preparation of monoclonal antibodies that can specifically bind PRO179, PRO238,

PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879,

PRO882, PRO885 or PROBST.

Techniques for producing the monoclonal antibodies are known in the art and are described, for instance, in : Goding, supra. Immunogens that may be employed include purified PRO179. PRO238, PRO364, PRO844,

PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS5 or } PROB887 fusion proteins containing PRO179, PRO238, PRO364, PRO844, PRO846. PRO1760, PRO205, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887. and cells expressing the gene encoding PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO2035, PRO321, PRO333, PRO840,

PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 on the cell surface. Selection of the immunogen can be made by the skilled artisan without undue experimentation.

Mice, such as Balb/c, are immunized with the PRO179, PRO238, PRO364. PRO844, PRO%46, PRO1760,

PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PROSS7 immunogen emulsified in complete Freund's adjuvant and injected subcutaneously or intraperitoneally in an amount from 1 to 100 micrograms. Alternatively, the immunogen is emulsified in MPL-TDM adjuvant (Ribi Immunochemical

Research, Hamilton, MT) and injected into the animal's hind foot pads. ‘The immunized mice are then boosted 10 to 12 days later with additional immunogen emulsified in the selected adjuvant. Thereafter, for several weeks, the mice may also be boosted with additional immunization injections. Serum samples may be periodically obtained from the mice by retro-orbital bleeding for testing in ELISA assays to detect anti-PRO179, anti-PRO238, anti-

PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO20S, anti-PRO321. anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO882, anti-PROS8S or anti-PROS]7 antibodies.

After a suitable antibody titer has been detected, the animals “positive” for antibodies can be injected with a final intravenous injection of PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321,

PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887. Three to four days later, the mice . are sacrificed and the spleen cells are harvested. The spleen ceils are then fused (using 35% polyethylene glycol) to a selected murine myeloma cell line such as P3X63AgU.1, available from ATCC, No. CRL 1597. The fusions generate hybridoma cells that can then be plated in 96-well tissue culture plates containing HAT medium to inhibit proliferation of non-fused cells, myeloma hybrids, and spleen cell hybrids.

The hybridoma cells will be screened in an ELISA for reactivity against PRO179, PRO238, PRO364,

PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2,

PROB885 or PRO887. Determination of “positive” hybridoma cells secreting the desired monoclonal antibodies against PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840,

PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 is within the skill in the art.

The positive hybridoma cells can be injected intraperitoneally into syngeneic Balb/c mice to produce ascites containing the anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1 760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO&78, anti-PRO879, anti-PRO882, anti-PRO8SS . 15 or anti-PRO887 monoclonal antibodies. Alternatively, the hybridoma cells can be grown in tissue-culture flasks or roller bottles. Purification of the monoclonal antibodies produced in the ascites can be accomplished using ammonium-sulfate precipitation, followed by gel-exclusion chromatography. Alternatively, affinity chromatography based upon binding of antibody to protein A or protein G can be employed.

Deposit of Material

The following material(s) has/have been deposited with the American Type Culture Collection, 10801

University Blvd., Manassas, VA 20110-2209, USA (ATCC): ’

Material ATCC Dep. No. Deposit Date

DNA16451-1388 209776 April 14, 1998 .

DNA35600-1162 209370 October 16, 1997

DNA47365-1206 209436 November 7, 1997

DNAS9838-1462 209976 June 16, 1998

DNA44196-1353 209847 May 6, 1998

DNA76532-1702 203473 November 17, 1998

DNA34433 209719 March 31, 1998

DNAS3987 209858 May 12, 1998

This deposit was made under the provisions of the Budapest Treaty on the International Recognition of the

Deposit of Microorganisms for the Purpose of Patent Procedure and the Regulations thereunder (Budapest Treaty).

This assures maintenance of a viable culture of the deposit for 30 years from the date of deposit. The deposit will be made available by ATCC under the terms of the Budapest Treaty, and subject to an agreement between

Genentech, Inc., and ATCC, which assures permanent and unrestricted availability of the progeny of the culture of the deposit to the public upon issuance of the pertinent U.S. patent or upon laying open to the public of any U.S. or foreign patent application, whichever comes first, and assures availability of the progeny to one determined by the U.S. Commissioner of Patents and Trademarks to be entitled thereto according to 35 USC §122 and the . Commissioner's rules pursuant thereto (including 37 CFR §1.14 with particular reference to 886 OG 638).

The assignee of the present application has agreed that if a culture of the material(s) on deposit should die or be lost or destroyed when cultivated under suitable conditions, the material(s) will be promptly replaced on

S notification with another of the same. Availability of the deposited material(s) is not to be construed as a license to practice the invention in contravention of the rights granted under the authority of any government in accordance with its patent laws.

The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the invention. The present invention is not to be limited in scope by the construct(s) deposited, since the deposited embodiment(s) is/are intended as single illustration(s) of certain aspects of the invention and any constructs that are functionally equivalent are within the scope of this invention. The deposit of material(s) herein does not constitute an admission that the written description herein contained is inadequate to enable the practice of any aspect of the invention, including the best mode thereof, nor is it to be construed as limiting the scope of the claims to the specific illustrations that it represents. Indeed, various modifications of the invention in addition to those shown and described herein will become apparent to thosc skilled in the art from the foregoing description and fall within the scope of the appended claims.

Claims (1)

1. WHATS CLAIMED IS:

   l. A composition comprising a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, . PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8R2, PRO88S or PROS? polypeptide or agonist or antagonist thereof, in admixture with a pharmaceutically acceptable carrier.

   2. The composition of Claim | comprising a therapeutically effective amount of said polypeptide or said agonist or antagonist thereot.

   3. "The composition of Claim 1, wherein the agonist is an anti-PRO179, anti-PRO238, anti-PRO364, anti- PRO844, anti-PRO846, anti-PRO1760, anti-PR(0205, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PRO8S7 antibody.

   4. The composition of Claim 1, wherein the antagonist is an anti-PRO179, anti-PR0O238, anti-PRO364, anti- PRO844, anti-PRO846, anti-PRO1760, anti-PR0O205, anti-PRO321, anti-PRO333, anti-PRO840, anli-PRO877, anti-PRO878, anti-PRO879, anti-PRO882, anti-PROSSS or anti-PROSS? antibody.

   5. The composition of Claim 1 further comprising a cardiovascular, endothelial, angiogenic or angiostatic agent.

   6. A method of preparing the composition of Claim 1 comprising admixing a PRO179, PRO238, PRO364, ] PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PROB40, PRO877. PRO878, PRO879, PROSS2, PRO885 or PRO887 polypeptide or agonist or antagonist thereof, with a pharmaceutically acceptable carrier.

   7. An article of manufacture comprising: . (1) acomposition comprising (a) a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide, (b) an agonist of a PRO179, PR0O238, PRO364, PRO844, PRO846, PRO1760, PRO20S. PRO321, PRO333, PRO840, PRO&77, PRO878, PRO879, PRO882, PRO8SS or PRO8S7 polypeptide, or (c) an antagonist of a PROI79, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO%40, PRO877, PROSTS, PRO879, PRORS2, PRO88S or PRO8BS7 polypeptide, in admixture with a pharmaceutically acceptable carrier; (2) a container containing said composition; and 3) a label affixed to said container, or a package insert included in said container, referring to the use of said composition, in the treatment of a cardiovascular, endothelial, and angiogenic disorder.

   8. The article of manufacture of Claim 7, wherein said agonist is an anti-PRO179, anti-PRO238, anti- PRO364, anti-PRO844. anti-PRO846, anti-PRO1760, anti-PRO205, anti-PR0O321, anti-PRO333, anti-PRO8S40, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PRO8S7 antibody.

   9. The article of manufacture of Claim 7, wherein said antagonist is an anti-PRO179, anti-PRO238, anti.

   PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PR0O205, anti-PRO321, anti-PR0O333, anti-PRO840, . anti-PRO877, anti-PRO878, anti-PRO879, anti-PROSS2, anti-PRO8SS or anti-PRO887 antibody.

   10. The article of manufacture of Claim 7, wherein said composition comprises a therapeutically effective amount of said polypeptide or agonist or antagonist thereof, in admixture with said pharmaceutically acceptable carrier.

   11. A method for identifying an agonist of a PRO179, PR0O238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S5 or PRO887 polypeptide comprising: (a) contacting cells and a test compound to be screened under conditions suitable for the induction of a cellular response normally induced by a PRO179, PRO238, PR0O364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide; and (b) determining the induction of said cellular response to determine if the test compound is an effective agonist, wherein the induction of said cellular response is indicative of said test compound being an effective agonist.

   12. The method of Claim 11, wherein the cellular response normally induced by said polypeptide is stimulation of cell proliferation.

   13. A method for idemifying a compound that inhibits an activity of a PRO179, PRO238, PRO364, PRO844, : PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878. PRO879, PRO882, PROSSS or PRO887 polypeptide comprising contacting a test compound with said polypeptide under conditions and for a time sufficient to allow the test compound and polypeptide to interact and determining whether the activity of said polypeptide is inhibited.

   14. A method for identifying a compound the inhibits an activity of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878. PRO879, PRO882, PRO88S or PROB887 polypeptide comprising the steps of: (a) contacting cells and a test compound to be screened in the presence of said polypeptide under conditions suitable for the induction of a cellular response normally induced by said polypeptide; and (b) determining the induction of said cellular response to determine if the test compound is an effective antagonist.

   15. The method of Claim 14, wherein the cellular response normally induced by said polypeptide is stimulation of cell proliferation.

   16. A method for identifying a compound that inhibits the expression of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877. PRO878, PRO879, PRO8S2, 139 N = A

   REET. PRO885 or PROBST polypeptide in cells that normally expresses the polypeptide, wherein the method comprises contacting the cells with atest compound under conditions suitable for allowing expression of said polypeptide and . determining whether the expression of said polypeptide is inhibited.

   17. An agonist of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PROB40, PRO877, PRO878, PRO879, PRO8S2, PRO8SS or PRO8S7 polypeptide.

   18. An antagonist of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PROSS2, PRO8SS or PROSS7 polypeptide.

   19. A compound that inhibits the expression of a PRO179,PR0O238,PRO364, PRO844, PRO846,PRO1760), PRO20S, PRO321, PRO333, PRO840, PRO877, PROSTS, PRG879, PROB82, PRO88S or PROSST polypeptide: in a mammalian cell which expresses said polypeptide.

   20. The compound of Claim 19, wherein said compound is an antisense oligonucleotide.

   21. An isolated antibody that binds to a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO$78, PRO879, PRO8R2, PRO8SS or PROBST polypeptide.

   22. The antibody of Claim 21 which is a monoclonal antibody.

   23. The antibody of Claim 21 which is an antibody fragment. ’

   24. The antibody of Claim 21 which is a single-chain antibody.

   25. A method for diagnosing a disease or susceptibility to a disease which is related to a mutation in a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PROSS7 polypeptide-encoding nucleic acid sequence comprising determining the presence or abscnce of said mutation in said polypeptide-encoding nucleic acid sequence. wherein the presence or absence of said mutation is indicative of the presence of said disease or susceptibility to said disease.

   26. A method of diagnosing a cardiovascular, endothelial or angiogenic disorder in a mammal which comprises analyzing the level of expression of a gene encoding a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877. PROS TS. PRO879, PRO882, PRO88SS or PROB polypeptide (a) in a test sample of tissue cells obtained from said mammal. and (b) in a control sample of known normal tissue cells of the same cell type, wherein a higher or lower expression level in the test sample as compared to the control sample is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in said mammal.

   27. A method of diagnosing a cardiovascular, endothelial or angiogenic disorder in a mammal which . comprises detecting the presence or absence of a PRQ179, PRO238, PRO364, PROB44, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS5 or PROSS7 polypeptide in a test sample of tissue cells obtained from said mammal, wherein the presence or absence of said polypeptide in said test sample is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in said mammal.

   28. A method of diagnosing a cardiovascular, endothelial or angiogenic disorder in a mammal comprising (a) contacting an anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844, antj-PRO846, anti-PRO1760, anti- PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO§79, anti-PRO882, anti- PRO#S8S or anti-PRO8S7 antibody with a test sample of tissue cells obtained from the mammal, and (b) detecting the formation of a complex between said antibody and a PRO179, PR0O238, PRO364, PRO844, PRO84E, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO8TS, PRO879, PRO882, PRO88S or PRO887 polypeptide in the test sample, wherein the formation of said complex is indicative of the presence of a cardiovascular, endothelial or angiogenic disorder in the mammal.

   29. A method for determining the presence of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20s5, PRO321, PRO333, PRO840, PROR77, PRO878, PRO879, PRO8S2, PRO8SS or PROSST polypeptide in a sample comprising contacting a sample suspected of containing said polypeptide with an anti-PRO179, anti- PRO238. anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO20S5, anti-PRO321, anti-PRO333, anti-PRO840, anti-PR0O877, anti-PRO87S. anti-PRO879, anti-PRO882, anti-PRO88S or anti-PRO8§ 7antibody and determining binding of said antibody to a component of said sample.

   30. A cardiovascular, endothelial or angiogenic disorder diagnostic kit comprising an anti-PRO179, anti- PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, amti-PRO333, anti-PRO840, anti-PRO877, anti-PRO87S, anti-PRO87Y, anti-PRO8E2, anti-PRO8SS or anti-PROYS7 antibody and a carrier in suitable packaging.

   31. A PROI179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide or agonist or antagonist thereof, for use in a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal a therapeutically effective amount of the polypeptide or agonist or antagonist. :

   32. The polypeptide, agonist or antagonist according to Claim 31, wherein the mammal is human.

   33. The polypeptide, agonist or antagonist of Claim 32, wherein the human has suffered myocardial infarction.

   34. The polypeptide, agonist or antagonist of Claim 32, wherein the human has cardiac hypertrophy, trauma, a cancer, or age-related macular degeneration.

   3s. The polypeptide, agonist or antagonist of Claim 34, wherein the cardiac hypertrophy is characterized by the presence of an elevated level of PGF,,.

   AJ

   36. The polypeptide, agonist or antagonist of Claim 31, wherein the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PROSS2, PRO885 or PROBST polypeptide is administered together with a cardiovascular, endothelial or angiogenic agent.

   37. The polypeptide, agonist or antagonist of Claim 34, wherein the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO&78, PRO879, PRO8S2, PRO88S5 or PRO887 polypeptide is administered following primary angioplasty.

   38. The polypeptide, agonist or antagonist of Claim 31, wherein the cardiovascular, endothelial or angiogenic disorder is cancer.

   39. The polypeptide, agonist or antagonist of Claim 38, wherein the PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO8S2, PROB885 or PRO887 polypeptide is administered in combination with a chemotherapeutic agent, a growth inhibitory agent or a cytotoxic agent.

   40. The polypeptide, agonist or antagonist of Claim 31, wherein said agonist is an anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, anti- PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO882, anti-PRO88S or anti-PRO8S7 antibody.

   41. The polypeptide, agonist or antagonist of Claim 31, wherein said antagonist is an anti- PRO179, anti-PRO238, anti-PRO364, anti-PRO844, anti-PROS46, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PROSTS, anti-PRO879, anti-PRO882, anti-PRO8SS or anti- PRO887 antibody

   42. A nucleic acid molecule that encodes a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO88S or PRO887 polypeptide or agonist or antagonist thereof for use in a method for treating a cardiovascular, endothelial or angiogenic disorder in 2 mammal comprising administering to the mammal the nucleic acid molecule.

   43. The nucleic acid molecule of Claim 42, wherein said agonist is an anti-PRO179, anti- PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO879 anti-PRO8S2, anti-PROSSS or anti-PROZS7 antibody. : 44, The nucleic acid molecule of Claim 42, wherein said antagonist is an anti-PRO179, anti- PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO20S, anti-PRO321, anti-PRO333, anti-PRO840, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PRO887 antibody.

   45. The nucleic acid molecule of Claim 42, wherein the mammal is human, 142 "Amended Sheet 14/06/2002

   46. The nucleic acid molecule of Claim 42, which is administered via ex vivo gene therapy.

   47. A recombinant retroviral particle comprising a retroviral vector consisting essentially of (1) a promoter, (2) nucleic acid encoding a PRO179, PR0O238, PRO364, PRO8&44, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or PRO8S7 polypeptide or agonist or antagonist thereof, and (3) a signal sequence for cellular secretion of the polypeptide, wherein the retroviral vector is in association with retroviral structural proteins.

   48. An ex vivo producer cell comprising a nucleic acid construct that expresses retroviral structural proteins and also comprises a retroviral vector consisting essentially of a (1) promoter, (2) nucleic acid encoding a PRO179, PR0O238, PRO364, PRO844, PRO84S6, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO8S7 polypeptide or agonist or antagonist thereof, and (3) a signal sequence for cellular secretion of the polypeptide, wherein said producer cell packages the retroviral vector in association with the structural proteins to produce recombinant retroviral particles. 49, A PRO333, PRO364, PRO877, PRO879, PRO882 or PRO8SSS polypeptide or agonist thereof for use in a method for inhibiting endothelial cell growth in a mammal comprising administering to the mammal the polypeptide or agonist, wherein endothelial cell growth in said mammal is inhibited.

   50. A PROI179, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO879 polypeptide or agonist thereof for use in a method for stimulating endothelial cell growth in a mammal comprising administering to the mammal the polypeptide or agonist, wherein endothelial cell growth in said mammal is stirnulated.

   51. An antagonist of a PRO179, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO879 polypeptide for use in a method of inhibiting endothelial cell growth in a mammal comprising administering to the mammal the antagonist, wherein endothelial cell growth in said mammal is inhibited.

   52. An antagonist of a PRO333, PRO364, PRO877, PRO879, PRO882 or PROSSS polypeptide for use in a method of stimulating endothelial cell growth in a mammal comprising administering to the mammal the antagonist, wherein endothelial cell growth in said mammal is stimulated.

   53. A PRO205, PRO882 or PRO887 polypeptide or agonist thereof for use in a method for : inducing cardiac hypertrophy in 2 mammal comprising administering to the mammal the polypeptide or agonist, wherein cardiac hypertrophy in said mammal is induced.

   54. A PRO238, PRO878 or PRO1760 polypeptide or agonist thereof for use in a method of reducing cardiac hypertrophy in a mammal comprising administering to the mammal the polypeptide or agonist, wherein cardiac hypertrophy in said mammal is reduced. 143 Amended Sheet 14/06/2002

   55. An antagonist of a PRO238, PRO878 or PRO1760 polypeptide for use in a method of inducing cardiac hypertrophy in a mammal comprising administering to the mammal the antagonist, wherein cardiac hypertrophy in said mammal is induced.

   56. An antagonist of a PRO205, PRO882 or PRO887 polypeptide for use in a method of reducing cardiac hypertrophy in a mammal comprising administering to the mammal the antagonist, wherein cardiac hypertrophy in said marnmal is reduced.

   57. An anti- PRO179, anti-PRO321, anti-PRO840, anti-PRO844, anti-PRO846, anti-PRO87S or anti-PRO879 antibody for use in a method for inhibiting angiogenesis induced by PRO179, PRO321, PRO840, PROB844, PRO846, PRO878 or PRO879 polypeptide in a mammal comprising administering a therapeutically effective amount of the antibody to the mammal, wherein said angiogenesis is inhibited.

   58. A PRO179, PRO321, PROR40, PRO844, PRO846, PRO878 or PROS79 polypeptide for use in a method for stimulating angiogenesis induced by said polypeptide in a mammal comprising administering a therapeutically effective amount of said polypeptide to the mammal, wherein said angiogenesis is stimulated.

   59. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence that

   . encodes an amino acid sequence selected from the group consisting of the amino acid sequence shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ [D NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ } ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO:14), Figure 16 (SEQ ID NQO:16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NO:28), Figure 30 (SEQ ID NO:30), and Figure 32 (SEQ ID NO:32).

   60. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the nucleotide sequence shown in Figure 1 (SEQ ID NO:1), Figure 3 (SEQ ID NO:3), Figure 5 (SEQ ID NO:5), Figure 7 (SEQ ID NO:7). Figure 9 (SEQ ID NO:9), Figure 11 (SEQ ID NO:11). Figure 13 (SEQ ID NO:13), Figure 15 (SEQ ID NO:15), Figure 17 (SEQ ID NO:17), Figuce 19 (SEQ ID NO:19), Figure 21 (SEQ ID NO:21), Figure 23 (SEQ ID NO:23), Figure 25 (SEQ ID NO:25), Figure 27 (SEQ ID NO:27), Figure 29 (SEQ ID NO:29), and Figure 31 (SEQ ID NO:31).

   61. Isolated nucleic acid having at least 80% nucleic acid sequence identity to a nucleotide sequence selected from the group consisting of the full-length coding sequence of the nucleotide sequence shown in Figure 1 (SEQ ID NO:1), Figure 3 (SEQ ID NO:3), Figure 5 (SEQ ID NO:5), Figure 7 (SEQ ID NO:7), Figura 9 (SEQ ID NO:9), Figure 11 (SEQ ID NO:11), Figure 13 (SEQ ID NO:13), Figure 15 (SEQ ID NO:15), Figure 17 (SEQ ID NOQ:17), Figure 19 (SEQ ID NO:19), Figure 21 (SEQ ID NO:21), Figure 23 (SEQ ID NO:23), Figure 25 (SEQ ID NO:25), Figure 27 (SEQ ID NO:27), Figure 29 (SEQ ID NO:29), and [igure 31 (SCQ ID NO:31).

   62. Isolated nucleic acid having at least 80% nucleic acid sequence identity to the full-length coding sequence of the DNA deposited under ATCC accession number 209776, 209370, 209436, 209976, 209847. 144 Amended Sheet 14/06/2002

   203473, 209719, or 209858.

   63. A vector comprising the nucleic acid of any one of Claims 59 to 62.

   64. The vector of Claim 63 operably linked to control sequences recognized by a host cell transformed with the vector.

   65. A host cell comprising the vector of Claim 63.

   66. The host cell of Claim 65, wherein said cell is a CHO cell.

   67. The host cell of Claim 65, wherein said cell is an E. coli.

   68. The host cell of Claim 65, wherein said cell is a yeast cell.

   69. The host cell of Claim 65, wherein said cell is a Baculovirus infected insect cell.

   70. A process for producing a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO887 polypeptide comprising culturing the host cell of Claim 65 under conditions suitable for expression of said polypeptide and recovering said polypeptide from the cell culture.

   71. An isolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence selected from the group consisting of the amino acid sequence shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6). Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO: 14), Figure 16 (SEQ ID NO:16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NO:28), Figure 30 (SEQ ID NO:30), and Figure 32 (SEQ ID NQ:32).

   72. An isolated polypeptide scoring at least 80% positives when compared 10 an amino acid sequence selected from the group consisting of thc amino acid sequence shown in Figure 2 (SEQ ID NO:2). Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO:14), Figure 16 (SEQ ID NO:16), Figure 18 (SEQ ID NO: 18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24). Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NO:28). Figure 30 (SEQ ID NO:30), and Figure 32 (SEQ ID NO:32).

   73. Anisolated polypeptide having at least 80% amino acid sequence identity to an amino acid sequence encoded by the full-length coding sequence of the DNA deposited under ATCC accession number 209776, 209370, 209436, 209976, 209847, 203473, 209719, or 209858.

   74. A chimeric molecule comprising a polypeptide according to any one of Claims 71 to 73 fused to a heterologous amino acid sequence.

   75. The chimeric molecule of Claim 74, wherein said heterologous amino acid sequence is an epitope tag sequence.

   76. The chimeric molecule of Claim 74, wherein said heterologous amino acid sequence is a Fc region of an immunoglobulin.

   77. An antibody which specifically binds to a polypeptide according to any one of Claims 71 to 73.

   78. The antibody of Claim 77, wherein said antibody is a monoclonal antibody, a humanized antibody or a single-chain antibody.

   79. Isolated nucleic acid having at least 80% nucleic acid sequence identity 10: (2) a nucleotide sequence encoding the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO:14), Figure 16 (SEQ ID NO:16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NO:28). Figure 30 (SEQ ID NO:30), or Figure 32 (SEQ ID NO:32), lacking its associated signal peptide; (b} a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8). Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO: 14), Figure 16 (SEQ ID NO: 16). Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24). Figure 26 (SEQ 1D NO:26), Figure 28 (SEQ ID NO:28). Figure 30 (SEQ ID NO:30). or Figure 32 (SEQ ID NO:32). with its associated signal peptide; or (c) a nucleotide sequence encoding an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2). Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12). Figure 14 (SEQ ID NO: 14), Figure 16 (SEQ ID NO:16). Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24). Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NO:28), Figure 30 (SEQ ID NO:30), or Figure 32 (SEQ ID NO:32). lacking its associated signal peptide.

   80. An isolated polypeptide having at least 80% amino acid sequence identity to: (a) the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4). Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12). Figure 14 (SEQ ID NO: 14), Figure 16 (SEQ ID NQ:16), Figure 18 (SEQ ID NO: 18), Figure 20 (SEQ ID NO:20). Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ 1D NO:28). Figure 30 (SEQ ID NO:30), or Figure 32 (SEQ ID NO:32), lacking its associated signal peptide;

   (b) an extracellular domain of the polypeptide shown in Figure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), : Figure 6 (SEQID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQ ID NO:10), Figure 12 (SEQ ID NO:12), Figure 14 (SEQ ID NO:14), Figure 16 (SEQ ID NO: 16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20}, Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQID NO:26), Figure 28 (SEQ ID NO:28), Figure (SEQ ID NO:30), or Figure 32 (SEQ ID NO:32), with its associated signal peptide; or oo (c) an extracellular domain of the polypeptide shown in Fi gure 2 (SEQ ID NO:2), Figure 4 (SEQ ID NO:4), Figure 6 (SEQ ID NO:6), Figure 8 (SEQ ID NO:8), Figure 10 (SEQID NO:10), Figure 12 (SEQ ID NOQ:12), Figure 14 (SEQID NO: 14), Figure 16 (SEQ ID NO:16), Figure 18 (SEQ ID NO:18), Figure 20 (SEQ ID NO:20), Figure 22 (SEQ ID NO:22), Figure 24 (SEQ ID NO:24), Figure 26 (SEQ ID NO:26), Figure 28 (SEQ ID NQ:28), Figure 30 (SEQ ID NO:30), or Figure 32 (SEQ ID NO:32), lacking its associated signal peptide.

   81. The use of a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO885 or PRO8S7 polypeptide or agonist or antagonist thereof in a method of making a medicament for use in a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal a therapeutically effective amount of the polypeptide, agonist or antagonist.

   82. The use according to Claim 81, wherein the mammal is human.

   83. The use of Claim 82, wherein the human has suffered myocardial infarction.

   84. The use of Claim 82, wherein the human has cardiac hypertrophy, trauma, a cancer, or age- related macular degeneration.

   85. The use of Claim 84, wherein the cardiac hypertrophy is characterized by the presence of an elevated level of PGF,,.

   86. The use of Claim 81, wherein the PRO179, PRO238, PRO364, PROS44, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PRO879, PRO882, PRO8SS or PROB887 polypeptide is administered together with a cardiovascular, endothelial or angiogenic agent.

   87. The use of Claim 84, wherein the PRO179, PRO238, PRO364, PRO844, PROB84G, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO878, PROS79, PRO882, PROSSS or PRO887 polypeptide is administered following primary angioplasty.

   88. The use of Claim 81, wherein the cardiovascular, endothelial or angiogenic disorder is cancer. 147 : : Amended Sheet 14/06/2002

   89. The use of Claim 88, wherein the PRO179, PRO238, PRO364, PRO844, PROS46, PRO1760, PRO20S, PRO321, PRO333, PRO840, PRO877, PROS78, PRO882, PRO’79, PROSSS or PROB887 polypeptide is administered in combination with a chemotherapeutic agent, a growth inhibitory agent or a cytotoxic agent.

   90. The use of Claim 81, wherein said agonist is an anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti- PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PROSS7 antibody.

   91. The use of Claim 81, wherein said antagonist is an anti-PRO179, anti-PR0O238, anti- PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PR0O205, anti-PRO321, anti-PRO333, anti- PRO840, anti-PRO877, anti-PROB78, anti-PROB7Y, anti-PROS8S2, anti-PROSSS or anti-PROSS7 antibody.

   92. The use of a nucleic acid molecule that encodes a PRO179, PRO238, PRO364, PRO844, PRO846, PRO1760, PRO205, PRO321, PRO333, PRO840, PRO877, PRO87S, PROS§79, PRO882, PROSSS or PRO887 polypeptide or agonist or antagonist thereof for use in a method of making a medicament for use in a method for treating a cardiovascular, endothelial or angiogenic disorder in a mammal comprising administering to the mammal the nucleic acid.

   93. The use of Claim 92 wherein said agonist is an anti-PRO179, anti-PRO238, anti-PRO364, anti-PRO844, anti-PRO846, anti-PRO1760, anti-PRO205, anti-PRO321, anti-PRO333, anti-PRO840, anti- PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PRO8S7 antibody.

   94. The use of Claim 92 wherein said antagonist is an anti-PRO179, anti-PRO238, anti- PRO364, anti-PRO844, anti-PROB46, anti-PRO1760, anti-PRO20S5, anti-PRO321, anti-PRO333, anti- PRO840, anti-PRO877, anti-PRO878, anti-PRO879, anti-PRO8S2, anti-PROSSS or anti-PROSS7 antibody.

   9s. The use of Claim 92, wherein the mammal is human.

   96. The use of Claim 92, wherein the nucleic acid molecule is administered via ex vivo gene therapy.

   97. The use of a PRO333, PRO364, PRO877, PRO879, PRO882 or PRO8SS polypeptide or agonist thereof in a method of making a medicament for use in a method for inhibiting endothelial ce]l growth in a mammal comprising administering to the mammal the polypeptide or agonist, wherein endothelial cell growth in said mammal is inhibited. 148 Amended Sheet 14/06/2002

   98. The use of a PRO179, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO879 polypeptide or agonist thereof in a method of making a medicament for use in a method for stimulating endothelial cell growth in a mammal comprising administering to the mammal the polypeptide or agonist, wherein endothelial cell growth in said mammal is stimulated.

   99. The use of an antagonist of a PRO179, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO&79 polypeptide in a method of making a medicament for use in a method of inhibiting endothelial cell growth in a mammal comprising administering to the mammal the antagonist, wherein endothelial cell growth in said mammal is inhibited.

   100. The use of an antagonist of a PRO333, PRO364, PRO877, PRO879, PRO882 or PRO8S8S polypeptide in a method of making a medicament for use in a method of stimulating endothelial cell growth in a mammal comprising administering to the mammal the antagonist, wherein endothelial cell growth in said mammal is stimulated.

   101. The use of a PRO20S, PRO882 or PRO887 polypeptide or agonist thereof in a method of making a medicament for use in a method for inducing cardiac hypertrophy in a mammal comprising administering to the mammal the polypeptide or agonist, wherein cardiac hypertrophy in said mammal is induced.

   102. The use of a PRO238, PRO878 or PRO1760 polypeptide or agonist thereof in a method of making a medicament for use in a method of reducing cardiac hypertrophy in a mammal comprising administering to the mammal the polypeptide or agonist, wherein cardiac hypertrophy in said mammal is reduced.

   103. The use of an antagonist of a PRO238, PRO878 or PRO1760 polypeptide in a method of making a medicament for use in a method of inducing cardiac hypertrophy in 2 mammal comprising administering to the mammal the antagonist, wherein cardiac hypertrophy in said mammal is induced. 104, The use of an antagonist of a PRO205, PRO882 or PRO887 polypeptide in a method of making a medicament for use in a method of reducing cardiac hypertrophy in a mammal comprising administering to the mammal the antagonist, wherein cardiac hypertrophy in said mammal is reduced.

   105. The use of an anti- PRO179, anti-PRO321, anti-PR0O840, anti-PRO844, anti-PRO846, anti- PRO878 or anti-PRO879 antibody in a method of making a medicament for use in a method for inhibiting angiogenesis induced by a PRO179, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO879 polypeptide in a mammal comprising administering a therapeutically effective amount of the antibody to the mammal, wherein said angiogenesis is inhibited. 149 Amandad Sheet 14/06/2002

   106. The use of a PROL79, PRO321, PRO840, PRO844, PRO846, PRO878 or PRO879 polypeptide in 2 method of making a medicament for use in a method for stimulating angiogenesis induced by said polypeptide in a mammal comprising administering a therapeutically effective amount of said polypeptide to the mammal, wherein said angiogenesis is stimulated. 150 Amended Sheet 14/06/2002