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WO2003066887A1 - Proteines proteases humaines isolees, molecules d'acides nucleiques codant des proteines proteases et utilisations de ces dernieres - Google Patents

Proteines proteases humaines isolees, molecules d'acides nucleiques codant des proteines proteases et utilisations de ces dernieres Download PDF

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Publication number
WO2003066887A1
WO2003066887A1 PCT/US2003/003966 US0303966W WO03066887A1 WO 2003066887 A1 WO2003066887 A1 WO 2003066887A1 US 0303966 W US0303966 W US 0303966W WO 03066887 A1 WO03066887 A1 WO 03066887A1
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nucleic acid
ofthe
seq
amino acid
protease
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PCT/US2003/003966
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Karen Ketchum
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Applera Corporation
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Publication of WO2003066887A1 publication Critical patent/WO2003066887A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/566—Immunoassay; Biospecific binding assay; Materials therefor using specific carrier or receptor proteins as ligand binding reagents where possible specific carrier or receptor proteins are classified with their target compounds
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value
    • G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)

Definitions

  • the present invention is in the field of protease proteins that are related to the sentrin-specific protease subfamily, recombinant DNA molecules, and protein production.
  • the present invention specifically provides novel peptides and proteins that effect protein cleavage/processing/turnover and nucleic acid molecules encoding such peptide and protein molecules, all of which are useful in the development of human therapeutics and diagnostic compositions and methods.
  • the proteases may be categorized into families by the different amino acid sequences (generally between 2 and 10 residues) located on either side of the cleavage site of the protease.
  • the proper functioning of the cell requires careful control of the levels of important structural proteins, enzymes, and regulatory proteins.
  • One of the ways that cells can reduce the steady state level of a particular protein is by proteolytic degradation.
  • one of the ways cells produce functioning proteins is to produce pre or pro-protein precursors that are processed by proteolytic degradation to produce an active moiety.
  • complex and highly-regulated mechanisms have been evolved to accomplish this degradation.
  • protease activity regulate many different cell proliferation, differentiation, and signaling processes by regulating protein turnover and processing. Uncontrolled protease activity (either increased or decreased) has been implicated in a variety of disease conditions including inflammation, cancer, arteriosclerosis, and degenerative disorders.
  • proteolysis An additional role of intracellular proteolysis is in the stress-response.
  • Cells that are subject to stress such as starvation, heat-shock, chemical insult or mutation respond by increasing the rates of proteolysis.
  • One function of this enhanced proteolysis is to salvage amino acids from non-essential proteins. These amino acids can then be re-utilized in the synthesis of essential proteins or metabolized directly to provide energy.
  • Another function is in the repair of damage caused by the stress. For example, oxidative stress has been shown to damage a variety of proteins and cause them to be rapidly degraded.
  • the International Union of Biochemistry and Molecular Biology (IUBMB) has recommended to use the term peptidase for the subset of peptide bond hydrolases ( Subclass E.C 3.4.).
  • protease is synonymous wit peptidase.
  • Peptidases comprise two groups of enzymes: the endopeptidases and the exopeptidases, which cleave peptide bonds at points within the protein and remove amino acids sequentially from either N or C-terminus respectively.
  • proteinase is also used as a synonym word for endopeptidase and four mechanistic classes of proteinases are recognized by the IUBMB: two of these are described below (also see: Handbook of Proteolytic Enzymes by Barrett, Rawlings, and Woessner AP Press, NY 1998).
  • SP serine proteases
  • the serine proteases are a large family of proteolytic enzymes that include the digestive enzymes, trypsin and chymotrypsin, components of the complement cascade and of the blood-clotting cascade, and enzymes that control the degradation and turnover of macromolecules of the extracellular matrix. SP are so named because of the presence of a serine residue in the active catalytic site for protein cleavage. SP have a wide range of substrate specificities and can be subdivided into subfamilies on the basis of these specificities.
  • the main sub-families are trypases (cleavage after arginine or lysine), aspases (cleavage after aspartate), chymases (cleavage after phenylalanine or leucine), metases (cleavage after methionine), and serases (cleavage after serine).
  • a series of six SP have been identified in murine cytotoxic T-lymphocytes (CTL) and natural killer (NK) cells. These SP are involved with CTL and NK cells in the destruction of virally transformed cells and tumor cells and in organ and tissue transplant rejection (Zunino, S. J. et al. (1990) J. Immunol. 144:2001-9; Sayers, T. J. et al. (1994) J. Immunol. 152:2289-97). Human homologs of most of these enzymes have been identified (Trapani, J. A. et al. (1988) Proc. Natl. Acad. Sci. 85:6924-28; Caputo, A. et al. (1990) J. Immunol.
  • the CTL-SP share three distinguishing features: 1) the presence of a catalytic triad of histidine, serine, and aspartate residues which comprise the active site; 2) the sequence GDSGGP which contains the active site serine; and 3) an N-terminal IIGG sequence which characterizes the mature SP.
  • the SP are secretory proteins which contain N-terminal signal peptides that serve to export the immature protein across the endoplasmic reticulum and are then cleaved (von Heijne (1986) Nuc. Acid. Res. 14:5683-90). Differences in these signal sequences provide one means of distinguishing individual SP.
  • SP particularly the digestive enzymes
  • Some SP exist as inactive precursors or preproenzym.es, and contain a leader or activation peptide sequence 3' of the signal peptide.
  • This activation peptide may be 2-12 amino acids in length, and it extends from the cleavage site of the signal peptide to the N-terminal IIGG sequence of the active, mature protein. Cleavage of this sequence activates the enzyme.
  • This sequence varies in different SP according to the biochemical pathway and/or its substrate (Zunino et al, supra; Sayers et al, supra).
  • S 1 substrate binding region is defined by residues extending from approximately +17 to +29 relative to the N-terminal I (+1). Differences in this region of the molecule are believed to determine SP substrate specificities (Zunino et al, supra).
  • Trypsinogens are serine proteases secreted by exocrine cells of the pancreas (Travis J and Roberts R. Biochemistry 1969; 8: 2884-9; Mallory P and Travis J, Biochemistry 1973; 12: 2847-51).
  • Two major types of trypsinogen isoenzymes have been characterized, trypsinogen- 1, also called cationic trypsinogen, and trypsinogen-2 or anionic trypsinogen.
  • trypsinogen proenzymes are activated to trypsins in the intestine by enterokinase, which removes an activation peptide from the N-terminus of the trypsinogens.
  • trypsinogens show a high degree of sequence homology, but they can be separated on the basis of charge differences by using electrophoresis or ion exchange chromatography.
  • the major form of trypsinogen in the pancreas and pancreatic juice is trypsinogen-1 (Guy CO et al., Biochem Biophys Res Commun 1984; 125: 516-23).
  • trypsinogen-1 In serum of healthy subjects, trypsinogen-1 is also the major form, whereas in patients with pancreatitis, trypsinogen-2 is more strongly elevated (Itkonen et al., J Lab Clin Med 1990; 115:712-8).
  • Trypsinogens also occur in certain ovarian tumors, in which trypsinogen-2 is the major form (Koivunen et al., Cancer Res 1990; 50: 2375-8). Trypsin-1 in complex with alpha- 1-antitrypsin, also called alpha- 1-antiprotease, has been found to occur in serum of patients with pancreatitis (Borgstrom A and Ohlsson K, Scand J Clin Lab Invest 1984; 44: 381-6) but determination of this complex has not been found useful for differentiation between pancreatic and other gastrointestinal diseases (Borgstrom et al., Scand J Clin Lab Invest 1989; 49:757-62). Trypsinogen-1 and -2 are closely related immunologically (Kimland et al.,
  • AAT is a 58 kilodalton serine protease inhibitor synthesized in the liver and is one of the main protease inhibitors in blood.
  • Inflammation of the pancreas or pancreatitis may be classified as either acute or chronic by clinical criteria. With treatment, acute pancreatitis can often be cured and normal function restored. Chronic pancreatitis often results in permanent damage. The precise mechanisms which trigger acute inflammation are not understood. However, some causes in the order of their importance are alcohol ingestion, biliary tract disease, post-operative trauma, and hereditary pancreatitis.
  • autodigestion the premature activation of proteolytic enzymes in the pancreas rather than in the duodenum, causes acute pancreatitis. Any number of other factors including endotoxins, exotoxins, viral infections, ischemia, anoxia, and direct trauma may activate the proenzymes.
  • any internal or external blockage of pancreatic ducts can also cause an accumulation of pancreatic juices in the pancreas resulting cellular damage.
  • the metalloproteases may be one of the older classes of proteinases and are found in bacteria, fungi as well as in higher organisms. They differ widely in their sequences and their structures but the great majority of enzymes contain a zinc atom which is catalytically active. In some cases, zinc may be replaced by another metal such as cobalt or nickel without loss of the activity.
  • Bacterial thermolysin has been well characterized and its crystallographic structure indicates that zinc is bound by two histidines and one glutamic acid.
  • HEXXH histidine ligands for the zinc whereas the third ligand is either a glutamic acid (thermolysin, neprilysin, alanyl aminopeptidase) or a histidine (astacin).
  • Other families exhibit a distinct mode of binding of the Zn atom.
  • the catalytic mechanism leads to the formation of a non covalent tetrahedral intermediate after the attack of a zinc-bound water molecule on the carbonyl group of the scissile bond. This intermediate is further decomposed by transfer of the glutamic acid proton to the leaving group.
  • Metalloproteases contain a catalytic zinc metal center which participates in the hydrolysis of the peptide backbone (reviewed in Power and Harper, in Protease Inhibitors, A. J. Barrett and G. Salversen (eds.) Elsevier, Amsterdam, 1986, p. 219).
  • the active zinc center differentiates some of these proteases from calpains and trypsins whose activities are dependent upon the presence of calcium.
  • metalloproteases include carboxypeptidase A, carboxypeptidase B, and thermolysin.
  • Metalloproteases have been isolated from a number of procaryotic and eucaryotic sources, e.g. Bacillus subtilis (McConn et al., 1964, J.
  • Neutral metalloproteases specifically those having optimal activity at neutral pH have, for example, been isolated from Aspergillus sojae (Sekine, 1973, Agric. Biol. Chem. 37:1945-1952). Neutral metalloproteases obtained from Aspergillus have been classified into two groups, npl and npll (Sekine, 1972, Agric. Biol. Chem. 36:207-216). So far, success in obtaining amino acid sequence information from these fungal neutral metalloproteases has been limited.
  • npll metalloprotease isolated from Aspergillus oryzae has been cloned based on amino acid sequence presented in the literature (Tatsumi et al., 1991, Mol. Gen. Genet. 228:97-103). However, to date, no npl fungal metalloprotease has been cloned or sequenced. Alkaline metalloproteases, for example, have been isolated from Pseudomonas aeruginosa (Baumann et al., 1993, EMBO J 12:3357-3364) and the insect pathogen Xenorhabdus luminescens (Schmidt et al., 1998, Appl. Environ. Microbiol. 54:2793-2797).
  • Metalloproteases have been devided into several distinct families based primarily on activity and sturcture: 1) water nucleophile; water bound by single zinc ion ligated to two His (within the motif HEXXH) and Glu, His or Asp; 2) water nucleophile; water bound by single zinc ion ligated to His, Glu (within the motif HXXE) and His; 3) water nucleophile; water bound by single zinc ion ligated to His, Asp and His; 4) Water nucleophile; water bound by single zinc ion ligated to two His (within the motif HXXEH) and Glu and 5) water nucleophile; water bound by two zinc ions ligated by Lys, Asp, Asp, Asp, Glu.
  • Examples of members of the metalloproteinase family include, but are not limited to, membrane alanyl aminopeptidase (Homo sapiens), germinal peptidyl- dipeptidase A (Homo sapiens), thimet oligopeptidase (Rattus norvegicus), oligopeptidase F (Lactococcus lactis), mycolysin (Streptomyces cacaoi), immune inhibitor A (Bacillus thuringiensis), snapalysin (Streptomyces lividans), leishmanolysin (Leishmania major), microbial collagenase (Vibrio alginolyticus), microbial collagenase, class I (Clostridium perfringens), collagenase 1 (Homo sapiens), serralysin (Serratia marcescens), fragilysin (Bacteroides fragilis), gametolysin (Chlamydomonas reinhardtii
  • Metalloproteases have been found to have a number of uses. For example, there is strong evidence that a metalloprotease is involved in the in vivo proteolytic processing of the vasoconstrictor, endothelin-1. Rat metalloprotease has been found to be involved in peptide hormone processing. One important subfamily of the metalloproteases are the matrix metalloproteases.
  • a number of diseases are thought to be mediated by excess or undesired metalloprotease activity or by an imbalance in the ratio of the various members of the protease family of proteins. These include: a) osteoarthritis (Woessner, et al., J. Biol.Chem. 259(6), 3633, 1984; Phadke, et al., J. Rheumatol. 10, 852, 1983), b) rheumatoid arthritis (Mullins, et al., Biochim. Biophys. Acta 695, 117, 1983;
  • Aspartic proteases have been divided into several distinct families based primarily on activity and structure. These include 1) water nucleophile; water bound by two Asp from monomer or dimer; all endopeptidases, from eukaryote organisms, viruses or virus-like organisms and 2) endopeptidases that are water nucleophile and are water bound by Asp and Asn.
  • aspartic proteases belong to the pepsin family.
  • the pepsin family includes digestive enzymes such as pepsin and chymosin as well as lysosomal cathepsins D and processing enzymes such as renin, and certain fungal proteases (penicillopepsin, rhizopuspepsin, endothiapepsin).
  • a second family comprises viral proteases such as the protease from the AIDS virus (HIV) also called retropepsin. Crystallographic studies have shown that these enzymes are bilobed molecules with the active site located between two homologous lobes. Each lobe contributes one aspartate residue of the catalytically active diad of aspartates.
  • Retropepsins are monomeric, i.e carry only one catalytic aspartate and then dimerization is required to form an active enzyme.
  • aspartic protease family of proteins include, but are not limited to, pepsin A (Homo sapiens), HIV1 retropepsin (human immunodeficiency virus type 1), endopeptidase (cauliflower mosaic virus), bacilhform virus putative protease (rice tungro bacilliform virus), aspergillopepsin II (Aspergillus niger), thermopsin (Sulfolobus acidocaldarius), nodavirus endopeptidase (flock house virus), pseudomonapepsin (Pseudomonas sp.
  • pepsin A Homo sapiens
  • HIV1 retropepsin human immunodeficiency virus type 1
  • endopeptidase cauliflower mosaic virus
  • bacilhform virus putative protease rice tungro bacilliform virus
  • aspergillopepsin II Aspergillus niger
  • thermopsin Sulfo
  • signal peptidase II Eryichia coli
  • polyprotein peptidase human spumaretrovirus
  • copia transposon Drosophila melanogaster
  • SIRE-1 peptidase Glycine max
  • retrotransposon bsl endopeptidase Zea mays
  • retrotransposon peptidase Drosophila buzzatii
  • Tas retrotransposon peptidase Ascaris lumbricoides
  • Pao retrotransposon peptidase Boo retrotransposon peptidase (Bombyx mori)
  • putative proteinase of Skippy retrotransposon Fusarium oxysporum
  • tetravirus endopeptidase Nudaurelia capensis omega virus
  • presenilin 1 Homo sapiens
  • Proteases are critical elements at several stages in the progression of metastatic cancer.
  • the proteolytic degradation of structural protein in the basal membrane allows for expansion of a tumor in the primary site, evasion from this site as well as homing and invasion in distant, secondary sites.
  • tumor induced angiogenesis is required for tumor growth and is dependent on proteolytic tissue remodeling.
  • Transfection experiments with various types of proteases have shown that the matrix metalloproteases play a dominant role in these processes in particular gelatinases A and B (MMP-2 and MMP-9, respectively).
  • gelatinases A and B MMP-2 and MMP-9, respectively.
  • TIMP-2 a protein
  • TJMP-2 tumor-induced angiogenesis in experimental systems
  • the novel human protein, and encoding gene, provided by the present invention shows the highest degree of similarity to sentrin-specific proteases (SENP), particularly SENP5.
  • SENP sentrin-specific proteases
  • SENP5 sentrin-specific proteases
  • Sentrin which is also referred to as SUMO, is distantly related to ubiquitin, as well as to a recently discovered ubiquitin-like protein known as NEDD8.
  • Yeh et al (Gene 2000 May 2;248(1-2):1-14) provide a review of the biology and biochemistry of the Sentrin/SUMO and NEDD8 modification pathways.
  • protease proteins particularly members of the sentrin-specific protease subfamily, are a major target for drug action and development. Accordingly, it is valuable to the field of pharmaceutical development to identify and characterize previously unknown members of this subfamily of protease proteins.
  • the present invention advances the state of the art by providing a previously unidentified human protease proteins that have homology to members of the sentrin-specific protease subfamily.
  • the present invention is based in part on the identification of amino acid sequences of human protease peptides and proteins that are related to the sentrin- specific protease subfamily, as well as allelic variants and other mammalian orthologs thereof.
  • These unique peptide sequences, and nucleic acid sequences that encode these peptides can be used as models for the development of human therapeutic targets, aid in the identification of therapeutic proteins, and serve as targets for the development of human therapeutic agents that modulate protease activity in cells and tissues that express the protease.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • FIGURE 1 provides the nucleotide sequence of a transcript sequence that encodes the protease protein ofthe present invention. (SEQ ID NO: 1)
  • structure and functional information is provided, such as ATG start, stop and tissue distribution, where available, that allows one to readily determine specific uses of inventions based on this molecular sequence.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • FIGURE 2 provides the predicted amino acid sequence ofthe protease ofthe present invention.
  • SEQ ID NO:2 structure and functional information such as protein family, function, and modification sites is provided where available, allowing one to readily determine specific uses of inventions based on this molecular sequence.
  • FIGURE 3 provides genomic sequences that span the gene encoding the protease protein ofthe present invention.
  • SEQ ID NO: 3 structure and functional information, such as intron/exon structure, promoter location, etc., is provided where available, allowing one to readily determine specific uses of inventions based on this molecular sequence.
  • SNPs have been identified at 69 different nucleotide positions in the gene encoding the protease protein of the present invention.
  • the present invention is based on the sequencing ofthe human genome.
  • analysis ofthe sequence information revealed previously unidentified fragments ofthe human genome that encode peptides that share structural and/or sequence homology to protein/peptide/domains identified and characterized within the art as being a protease protein or part of a protease protein and are related to the sentrin-specific protease subfamily. Utilizing these sequences, additional genomic sequences were assembled and transcript and/or cDNA sequences were isolated and characterized.
  • the present invention provides amino acid sequences of human protease peptides and proteins that are related to the sentrin-specific protease subfamily, nucleic acid sequences in the form of transcript sequences, cDNA sequences and/or genomic sequences that encode these protease peptides and proteins, nucleic acid variation (allelic information), tissue distribution of expression, and information about the closest art known protein/peptide/domain that has structural or sequence homology to the protease ofthe present invention.
  • the peptides that are provided in the present invention are selected based on their ability to be used for the development of commercially important products and services. Specifically, the present peptides are selected based on homology and/or structural relatedness to known protease proteins ofthe sentrin-specific protease subfamily and the expression pattern observed. Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow. The art has clearly established the commercial importance of members of this family of proteins and proteins that have expression patterns similar to that ofthe present gene.
  • the present invention provides nucleic acid sequences that encode protein molecules that have been identified as being members ofthe protease family of proteins and are related to the sentrin-specific protease subfamily (protein sequences are provided in Figure 2, transcript/cDNA sequences are provided in Figure 1 and genomic sequences are provided in Figure 3).
  • the peptide sequences provided in Figure 2, as well as the obvious variants described herein, particularly allelic variants as identified herein and using the information in Figure 3, will be referred herein as the protease peptides ofthe present invention, protease peptides, or peptides/proteins of the present invention.
  • the present invention provides isolated peptide and protein molecules that consist of, consist essentially of romanceor comprise the amino acid sequences ofthe protease peptides disclosed in the Figure 2, (encoded by the nucleic acid molecule shown in Figure 1, transcript/cDNA or Figure 3, genomic sequence), as well as all obvious variants of these peptides that are within the art to make and use. Some of these variants are described in detail below.
  • a peptide is said to be "isolated” or “purified” when it is substantially free of cellular material or free of chemical precursors or other chemicals.
  • the peptides ofthe present invention can be purified to homogeneity or other degrees of purity. The level of purification will be based on the intended use. The critical feature is that the preparation allows for the desired function ofthe peptide, even if in the presence of considerable amounts of other components (the features of an isolated nucleic acid molecule is discussed below).
  • substantially free of cellular material includes preparations ofthe peptide having less than about 30% (by dry weight) other proteins (i.e., contaminating protein), less than about 20% other proteins, less than about 10% other proteins, or less than about 5% other proteins.
  • the peptide when it is recombinantly produced, it can also be substantially free of culture medium, i.e., culture medium represents less than about 20% ofthe volume ofthe protein preparation.
  • the language "substantially free of chemical precursors or other chemicals” includes preparations ofthe peptide in which it is separated from chemical precursors or other chemicals that are involved in its synthesis.
  • the language "substantially free of chemical precursors or other chemicals” includes preparations of the protease peptide having less than about 30% (by dry weight) chemical precursors or other chemicals, less than about 20% chemical precursors or other chemicals, less than about 10% chemical precursors or other chemicals, or less than about 5% chemical precursors or other chemicals.
  • the isolated protease peptide can be purified from cells that naturally express it, purified from cells that have been altered to express it (recombinant), or synthesized using known protein synthesis methods.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • a nucleic acid molecule encoding the protease peptide is cloned into an expression vector, the expression vector introduced into a host cell and the protein expressed in the host cell.
  • the protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Many of these techniques are described in detail below.
  • the present invention provides proteins that consist ofthe amino acid sequences provided in Figure 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in Figure 1 (SEQ ID NO:l) and the genomic sequences provided in Figure 3 (SEQ JD NO:3).
  • the amino acid sequence of such a protein is provided in Figure 2.
  • a protein consists of an amino acid sequence when the amino acid sequence is the final amino acid sequence ofthe protein.
  • the present invention further provides proteins that consist essentially ofthe amino acid sequences provided in Figure 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in Figure 1 (SEQ JD NO: 1) and the genomic sequences provided in Figure 3 (SEQ ID NO:3).
  • a protein consists essentially of an amino acid sequence when such an amino acid sequence is present with only a few additional amino acid residues, for example from about 1 to about 100 or so additional residues, typically from 1 to about 20 additional residues in the final protein.
  • the present invention further provides proteins that comprise the amino acid sequences provided in Figure 2 (SEQ ID NO:2), for example, proteins encoded by the transcript/cDNA nucleic acid sequences shown in Figure 1 (SEQ ID NO: 1) and the genomic sequences provided in Figure 3 (SEQ ID NO:3).
  • a protein comprises an amino acid sequence when the amino acid sequence is at least part ofthe final amino acid sequence ofthe protein. In such a fashion, the protein can be only the peptide or have additional amino acid molecules, such as amino acid residues (contiguous encoded sequence) that are naturally associated with it or heterologous amino acid residues/peptide sequences. Such a protein can have a few additional amino acid residues or can comprise several hundred or more additional amino acids.
  • the preferred classes of proteins that are comprised ofthe protease peptides ofthe present invention are the naturally occurring mature proteins. A brief description of how various types of these proteins can be made/isolated is provided below.
  • the protease peptides ofthe present invention can be attached to heterologous sequences to form chimeric or fusion proteins.
  • Such chimeric and fusion proteins comprise a protease peptide operatively linked to a heterologous protein having an amino acid sequence not substantially homologous to the protease peptide. "Operatively linked" indicates that the protease peptide and the heterologous protein are fused in- frame.
  • the heterologous protein can be fused to the N-terminus or C-terminus ofthe protease peptide. In some uses, the fusion protein does not affect the activity ofthe protease peptide per se.
  • the fusion protein can include, but is not limited to, enzymatic fusion proteins, for example beta-galactosidase fusions, yeast two-hybrid GAL fusions, poly-His fusions, MYC-tagged, Hi-tagged and Ig fusions.
  • enzymatic fusion proteins for example beta-galactosidase fusions, yeast two-hybrid GAL fusions, poly-His fusions, MYC-tagged, Hi-tagged and Ig fusions.
  • Such fusion proteins, particularly poly-His fusions can facilitate the purification of recombinant protease peptide.
  • expression and/or secretion of a protein can be increased by using a heterologous signal sequence.
  • a chimeric or fusion protein can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different protein sequences are ligated together in-frame in accordance with conventional techniques.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and re- amplified to generate a chimeric gene sequence (see Ausubel et al, Current Protocols in Molecular Biology, 1992).
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST protein).
  • a protease peptide- encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the protease peptide.
  • the present invention also provides and enables obvious variants ofthe amino acid sequence ofthe proteins ofthe present invention, such as naturally occurring mature forms ofthe peptide, allelic/sequence variants ofthe peptides, non-naturally occurring recombinantly derived variants ofthe peptides, and orthologs and paralogs ofthe peptides.
  • variants can readily be generated using art-known techniques in the fields of recombinant nucleic acid technology and protein biochemistry. It is understood, however, that variants exclude any a ino acid sequences disclosed prior to the invention.
  • variants can readily be identified/made using molecular techniques and the sequence information disclosed herein. Further, such variants can readily be distinguished from other peptides based on sequence and/or structural homology to the protease peptides ofthe present invention. The degree of homology/identity present will be based primarily on whether the peptide is a functional variant or non-functional variant, the amount of divergence present in the paralog family and the evolutionary distance between the orthologs.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • at least 30%, 40%, 50%, 60%, 70%, 80%, or 90% or more ofthe length of a reference sequence is aligned for comparison purposes.
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid "homology”
  • the percent identity between the two sequences is a function ofthe number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment ofthe two sequences.
  • the comparison of sequences and determination of percent identity and similarity between two sequences can be accomplished using a mathematical algorithm.
  • Biol. (48):444- 453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com), using either a Blossom 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (Devereux, J., etal, Nucleic Acids Res.
  • the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Myers and W. Miller (CABIOS, 4:11-17 (1989)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • the nucleic acid and protein sequences ofthe present invention can further be used as a "query sequence" to perform a search against sequence databases to, for example, identify other family members or related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (J. Mol. Biol. 215:403-10 (1990)).
  • Gapped BLAST can be utilized as described in Altschul et al (Nucleic Acids Res. 25(17):3389-3402 (1997)).
  • the default parameters ofthe respective programs e.g., XBLAST and NBLAST
  • Full-length pre-processed forms, as well as mature processed forms, of proteins that comprise one ofthe peptides ofthe present invention can readily be identified as having complete sequence identity to one ofthe protease peptides ofthe present invention as well as being encoded by the same genetic locus as the protease peptide provided herein.
  • the chromosome map position was determined to be on human chromosome 3.
  • allelic variants of a protease peptide can readily be identified as being a human protein having a high degree (significant) of sequence homology/identity to at least a portion ofthe protease peptide as well as being encoded by the same genetic locus as the protease peptide provided herein. Genetic locus can readily be determined based on the genomic information provided in Figure 3, such as the genomic sequence mapped to the reference human.As indicated by the data presented in Figure 3, the chromosome map position was deterrnined to be on human chromosome 3.
  • two proteins have significant homology when the amino acid sequences are typically at least about 70-80%, 80-90%, and more typically at least about 90-95% or more homologous.
  • a significantly homologous amino acid sequence will be encoded by a nucleic acid sequence that will hybridize to a protease peptide encoding nucleic acid molecule under stringent conditions as more fully described below.
  • Figure 3 provides information on SNPs that have been identified in the gene encoding the protease protein ofthe present invention. SNPs were found at 69 different nucleotide positions, including 2 SNPs that change the encoded amino acid sequence (i.e., nonsynonymous SNPs). The changes in the amino acid sequence caused by these SNPs is indicated in Figure 3 and can readily be determined using the universal genetic code and the protein sequence provided in Figure 2 as a reference.
  • Paralogs of a protease peptide can readily be identified as having some degree of significant sequence homology/identity to at least a portion ofthe protease peptide, as being encoded by a gene from humans, and as having similar activity or function.
  • Two proteins will typically be considered paralogs when the amino acid sequences are typically at least about 60% or greater, and more typically at least about 70% or greater homology through a given region or domain.
  • Such paralogs will be encoded by a nucleic acid sequence that will hybridize to a protease peptide encoding nucleic acid molecule under moderate to stringent conditions as more fully described below.
  • Orthologs of a protease peptide can readily be identified as having some degree of significant sequence homology/identity to at least a portion ofthe protease peptide as well as being encoded by a gene from another organism.
  • Preferred orthologs will be isolated from mammals, preferably primates, for the development of human therapeutic targets and agents. Such orthologs will be encoded by a nucleic acid sequence that will hybridize to a protease peptide encoding nucleic acid molecule under moderate to stringent conditions, as more fully described below, depending on the degree of relatedness ofthe two organisms yielding the proteins.
  • the chromosome map position was determined to be on human chromosome 3.
  • Figure 3 provides information on SNPs that have been identified in the gene encoding the protease protein ofthe present invention. SNPs were found at 69 different nucleotide positions, including 2 SNPs that change the encoded amino acid sequence (i.e., nonsynonymous SNPs). The changes in the amino acid sequence caused by these SNPs is indicated in Figure 3 and can readily be determined using the universal genetic code and the protein sequence provided in Figure 2 as a reference.
  • Non-naturally occurring variants ofthe protease peptides ofthe present invention can readily be generated using recombinant techniques.
  • Such variants include, but are not limited to deletions, additions and substitutions in the amino acid sequence ofthe protease peptide.
  • one class of substitutions are conserved amino acid substitution.
  • Such substitutions are those that substitute a given amino acid in a protease peptide by another amino acid of like characteristics.
  • conservative substitutions are the replacements, one for another, among the aliphatic amino acids Ala, Val, Leu, and lie; interchange ofthe hydroxyl residues Ser and Thr; exchange ofthe acidic residues Asp and Glu; substitution between the amide residues Asn and Gin; exchange ofthe basic residues Lys and Arg; and replacements among the aromatic residues Phe and Tyr.
  • Guidance concerning which amino acid changes are likely to be phenotypically silent are found in Bowie et al, Science 247:1306-1310 (1990).
  • Variant protease peptides can be fully functional or can lack function in one or more activities, e.g. ability to bind substrate, ability to cleave substrate, ability to participate in a signaling pathway, etc.
  • Fully functional variants typically contain only conservative variation or variation in non-critical residues or in non-critical regions.
  • Figure 2 provides the result of protein analysis and can be used to identify critical domains/regions.
  • Functional variants can also contain substitution of similar amino acids that result in no change or an insignificant change in function. Alternatively, such substitutions may positively or negatively affect function to some degree.
  • Non-functional variants typically contain one or more non-conservative amino acid substitutions, deletions, insertions, inversions, or truncation or a substitution, insertion, inversion, or deletion in a critical residue or critical region.
  • Amino acids that are essential for function can be identified by methods known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham et al. , Science 244: 1081 - 1085 (1989)), particularly using the results provided in Figure 2. The latter procedure introduces single alanine mutations at every residue in the molecule. The resulting mutant molecules are then tested for biological activity such as protease activity or in assays such as an in vitro proliferative activity.
  • Sites that are critical for binding partner/substrate binding can also be determined by structural analysis such as crystallization, nuclear magnetic resonance orphotoaffinity labeling (Smith et al, J. Mol. Biol. 224:899-904 (1992); de Vos et al. Science 255:306- 312 (1992)).
  • the present invention further provides fragments ofthe protease peptides, in addition to proteins and peptides that comprise and consist of such fragments, particularly those comprising the residues identified in Figure 2.
  • the fragments to which the invention pertains are not to be construed as encompassing fragments that may be disclosed publicly prior to the present invention.
  • a fragment comprises at least 8, 10, 12, 14, 16, or more contiguous amino acid residues from a protease peptide.
  • Such fragments can be chosen based on the ability to retain one or more ofthe biological activities ofthe protease peptide or could be chosen for the ability to perform a function, e.g. bind a substrate or act as an immunogen.
  • Particularly important fragments are biologically active fragments, peptides that are, for example, about 8 or more amino acids in length.
  • Such fragments will typically comprise a domain or motif of the protease peptide, e.g., active site, a transmembrane domain or a substrate-binding domain.
  • fragments include, but are not limited to, domain or motif containing fragments, soluble peptide fragments, and fragments containing immunogenic structures.
  • Predicted domains and functional sites are readily identifiable by computer programs well known and readily available to those of skill in the art (e.g., PROSITE analysis). The results of one such analysis are provided in Figure 2.
  • Polypeptides often contain amino acids other than the 20 amino acids commonly referred to as the 20 naturally occurring amino acids. Further, many amino acids, including the terminal amino acids, may be modified by natural processes, such as processing and other post-translational modifications, or by chemical modification techniques well known in the art. Common modifications that occur naturally in protease peptides are described in basic texts, detailed monographs, and the research literature, and they are well known to those of skill in the art (some of these features are identified in Figure 2) .
  • Known modifications include, but are not limited to, acetylation, acylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, fonnation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.
  • the protease peptides ofthe present invention also encompass derivatives or analogs in which a substituted amino acid residue is not one encoded by the genetic code, in which a substituent group is included, in which the mature protease peptide is fused with another compound, such as a compound to increase the half-life of the protease peptide (for example, polyethylene glycol), or in which the additional amino acids are fused to the mature protease peptide, such as a leader or secretory sequence or a sequence for purification ofthe mature protease peptide or a pro-protein sequence.
  • a substituted amino acid residue is not one encoded by the genetic code, in which a substituent group is included, in which the mature protease peptide is fused with another compound, such as a compound to increase the half-life of the protease peptide (for example, polyethylene glycol), or in which the additional amino acids are fused to the mature protease peptide, such as a leader
  • the proteins ofthe present invention can be used in substantial and specific assays related to the functional information provided in the Figures; to raise antibodies or to elicit another immune response; as a reagent (including the labeled reagent) in assays designed to quantitatively determine levels ofthe protein (or its binding partner or ligand) in biological fluids; and as markers for tissues in which the corresponding protein is preferentially expressed (either constitutively or at a particular stage of tissue differentiation or development or in a disease state).
  • the protein binds or potentially binds to another protein or ligand (such as, for example, in a protease-effector protein interaction or protease-ligand interaction)
  • the protein can be used to identify the binding partner/ligand so as to develop a system to identify inhibitors ofthe binding interaction. Any or all of these uses are capable of being developed into reagent grade or kit format for commercialization as commercial products.
  • proteases isolated from humans and their human/mammalian orthologs serve as targets for identifying agents for use in mammalian therapeutic applications, e.g. a human drug, particularly in modulating a biological or pathological response in a cell or tissue that expresses the protease.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis.
  • the proteins ofthe present invention are useful for biological assays related to proteases that are related to members ofthe sentrin-specific protease subfamily.
  • Such assays involve any ofthe known protease functions or activities or properties useful for diagnosis and treatment of protease-related conditions that are specific for the subfamily of proteases that the one ofthe present invention belongs to, particularly in cells and tissues that express the protease.
  • Proteinase proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis.
  • the proteins ofthe present invention are also useful in drug screening assays, in cell-based or cell-free systems.
  • Cell-based systems can be native, i.e., cells that normally express the protease, as a biopsy or expanded in cell culture.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • cell-based assays involve recombinant host cells expressing the protease protein.
  • the polypeptides can be used to identify compounds that modulate protease activity ofthe protein in its natural state or an altered form that causes a specific disease or pathology associated with the protease.
  • Both the proteases ofthe present invention and appropriate variants and fragments can be used in high-throughput screens to assay candidate compounds for the ability to bind to the protease. These compounds can be further screened against a functional protease to determine the effect ofthe compound on the protease activity. Further, these compounds can be tested in animal or invertebrate systems to determine activity/effectiveness.
  • Compounds can be identified that activate (agonist) or inactivate (antagonist) the protease to a desired degree.
  • proteins ofthe present invention can be used to screen a compound for the ability to stimulate or inhibit interaction between the protease protein and a molecule that normally interacts with the protease protein, e.g. a substrate or a component ofthe signal pathway that the protease protein normally interacts (for example, a protease).
  • a molecule that normally interacts with the protease protein e.g. a substrate or a component ofthe signal pathway that the protease protein normally interacts (for example, a protease).
  • Such assays typically include the steps of combining the protease protein with a candidate compound under conditions that allow the protease protein, or fragment, to interact with the target molecule, and to detect the formation of a complex between the protein and the target or to detect the biochemical consequence ofthe interaction with the protease protein and the target, such as any ofthe associated effects of signal transduction such as protein cleavage, cAMP turnover, and adenylate cyclase activation, etc.
  • Candidate compounds include, for example, 1) peptides such as soluble peptides, including Ig-tailed fusion peptides and members of random peptide libraries (see, e.g., Lam et al, Nature 354:82-84 (1991); Houghten et al, Nature 354:84-86 (1991)) and combinatorial chemistry-derived molecular libraries made of D- and/or L- configuration amino acids; 2) phosphopeptides (e.g., members of random and partially degenerate, directed phosphopeptide libraries, see, e.g., Songyang et al, Cell 72:161-118 (1993)); 3) antibodies (e.g., polyclonal, monoclonal, humanized, anti-idiotypic, chimeric, and single chain antibodies as well as Fab, F(ab') 2 , Fab expression library fragments, and epitope- binding fragments of antibodies); and 4) small organic and inorganic molecules (e.g., molecules
  • One candidate compound is a soluble fragment ofthe receptor that competes for substrate binding.
  • Other candidate compounds include mutant proteases or appropriate fragments containing mutations that affect protease function and thus compete for substrate. Accordingly, a fragment that competes for substrate, for example with a higher affinity, or a fragment that binds substrate but does not allow release, is encompassed by the invention.
  • the invention fiirther includes other end point assays to identify compounds that modulate (stimulate or inhibit) protease activity.
  • the assays typically involve an assay of events in the signal transduction pathway that indicate protease activity.
  • the cleavage of a substrate, inactivation activation of a protein, a change in the expression of genes that are up- or down-regulated in response to the protease protein dependent signal cascade can be assayed.
  • Any of the biological or biochemical functions mediated by the protease can be used as an endpoint assay.
  • Binding and/or activating compounds can also be screened by using chimeric protease proteins in which the amino terminal extracellular domain, or parts thereof, the entire transmembrane domain or subregions, such as any ofthe seven transmembrane segments or any ofthe intracellular or extracellular loops and the carboxy te ⁇ ninal intracellular domain, or parts thereof, can be replaced by heterologous domains or subregions.
  • a substrate-binding region can be used that interacts with a different substrate then that which is recognized by the native protease. Accordingly, a different set of signal transduction components is available as an end-point assay for activation. This allows for assays to be performed in other than the specific host cell from which the protease is derived.
  • the proteins ofthe present invention are also useful in competition binding assays in methods designed to discover compounds that interact with the protease (e.g. binding partners and/or ligands).
  • a compound is exposed to a protease polypeptide under conditions that allow the compound to bind or to otherwise interact with the polypeptide.
  • Soluble protease polypeptide is also added to the mixture. If the test compound interacts with the soluble protease polypeptide, it decreases the amount of complex formed or activity from the protease target. This type of assay is particularly useful in cases in which compounds are sought that interact, with specific regions ofthe protease.
  • the soluble polypeptide that competes with the target protease region is designed to contain peptide sequences corresponding to the region of interest.
  • immobilize either the protease protein, or fragment, or its target molecule to facilitate separation of complexes from uncomplexed forms of one or both ofthe proteins, as well as to accommodate automation ofthe assay.
  • Techniques for immobilizing proteins on matrices can be used in the drug screening assays.
  • a fusion protein can be provided which adds a domain that allows the protein to be bound to a matrix.
  • glutathione-S- transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtitre plates, which are then combined with the cell lysates (e.g., 35 S-labeled) and the candidate compound, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads are washed to remove any unbound label, and the matrix immobilized and radiolabel determined directly, or in the supernatant after the complexes are dissociated.
  • glutathione sepharose beads Sigma Chemical, St. Louis, MO
  • glutathione derivatized microtitre plates which are then combined with the cell lysates (e.g., 35 S-labeled) and the candidate compound, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads
  • the complexes can be dissociated from the matrix, separated by SDS-PAGE, and the level of protease-binding protein found in the bead fraction quantitated from the gel using standard electrophoretic techniques.
  • the polypeptide or its target ' molecule can be immobilized utilizing conjugation of biotin and streptavidin using techniques well known in the art.
  • antibodies reactive with the protein but which do not interfere with binding ofthe protein to its target molecule can be derivatized to the wells ofthe plate, and the protein trapped in the wells by antibody conjugation.
  • Preparations of a protease-binding protem and a candidate compound are incubated in the protease protein-presenting wells and the amount of complex trapped in the well can be quantitated.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the protease protein target molecule, or which are reactive with protease protein and compete with the target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the target molecule.
  • Agents that modulate one ofthe proteases ofthe present invention can be identified using one or more ofthe above assays, alone or in combination. It is generally preferable to use a cell-based or cell free system first and then confirm activity in an animal or other model system. Such model systems are well known in the art and can readily be employed in this context.
  • Modulators of protease protein activity identified according to these drug screening assays can be used to treat a subject with a disorder mediated by the protease pathway, by treating cells or tissues that express the protease.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • These methods of treatment include the steps of administering a modulator of protease activity in a pharmaceutical composition to a subject in need of such treatment, the modulator being identified as described herein.
  • the protease proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent No. 5,283,317; Zervos et al (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO94/10300), to identify other proteins, which bind to or interact with the protease and are involved in protease activity.
  • a two-hybrid assay see, e.g., U.S. Patent No. 5,283,317; Zervos et al (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:120
  • protease-binding proteins are also likely to be involved in the propagation of signals by the protease proteins or protease targets as, for example, downstream elements of a protease-mediated signaling pathway. Alternatively, such protease-binding proteins are likely to be protease inhibitors.
  • the two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for a protease protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4).
  • a known transcription factor e.g., GAL-4
  • a DNA sequence from a library of DNA sequences, that encodes an unidentified protein ("prey" or “sample") is fused to a gene that codes for the activation domain ofthe known transcription factor. If the "bait” and the “prey” proteins are able to interact, in vivo, forming a protease-dependent complex, the DNA-binding and activation domains ofthe transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor.
  • a reporter gene e.g., LacZ
  • an agent identified as described herein e.g., a protease-modulating agent, an antisense protease nucleic acid molecule, a protease-specific antibody, or a protease-binding partner
  • an agent identified as described herein can be used in an animal or other model to determine the efficacy, toxicity, or side effects of treatment with such an agent.
  • an agent identified as described herein can be used in an animal or other model to determine the mechanism of action of such an agent.
  • this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.
  • the protease proteins ofthe present invention are also useful to provide a target for diagnosing a disease or predisposition to disease mediated by the peptide. Accordingly, the invention provides methods for detecting the presence, or levels of, the protein (or encoding mRNA) in a cell, tissue, or organism. Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow. The method involves contacting a biological sample with a compound capable of interacting with the protease protein such that the interaction can be detected. Such an assay can be provided in a single detection format or a multi-detection format such as an antibody chip array.
  • a biological sample includes tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject.
  • the peptides ofthe present invention also provide targets for diagnosing active protein activity, disease, or predisposition to disease, in a patient having a variant peptide, particularly activities and conditions that are known for other members ofthe family of proteins to which the present one belongs.
  • the peptide can be isolated from a biological sample and assayed for the presence of a genetic mutation that results in aberrant peptide. This includes amino acid substitution, deletion, insertion, rearrangement, (as the result of aberrant splicing events), and inappropriate post- translational modification.
  • Analytic methods include altered electrophoretic mobility, altered tryptic peptide digest, altered protease activity in cell-based or cell-free assay, alteration in substrate or antibody-binding pattern, altered isoelectric point, direct amino acid sequencing, and any other ofthe known assay techniques useful for detecting mutations in a protein.
  • Such an assay can be provided in a single detection format or a multi-detection format such as an antibody chip array.
  • peptide detection techniques include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence using a detection reagent, such as an antibody or protein binding agent.
  • a detection reagent such as an antibody or protein binding agent.
  • the peptide can be detected in vivo in a subject by introducing into the subject a labeled anti-peptide antibody or other types of detection agent.
  • the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques. Particularly useful are methods that detect the allelic variant of a peptide expressed in a subj ect and methods which detect fragments of a peptide in a sample.
  • the peptides are also useful in pharmacogenomic analysis.
  • Pharmacogenomics deal with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, e.g., Eichelbaum, M. (Clin. Exp. Pharmacol. Physiol. 23(10-11):983-985 (1996)), andLinder, M.W. (Clin. Chem. 43(2):254-266 (1997)).
  • the clinical outcomes of Ihese variations result in severe toxicity of therapeutic drugs in certain individuals or therapeutic failure of drugs in certain individuals as a result of individual variation in metabolism.
  • the genotype of the individual can determine the way a therapeutic compound acts on the body or the way the body metabolizes the compound.
  • the activity of drug metabolizing enzymes effects both the intensity and duration of drug action.
  • the pharmacogenomics ofthe individual permit the selection of effective compounds and effective dosages of such compounds for prophylactic or therapeutic treatment based on the individual's genotype.
  • the discovery of genetic polymorphisms in some drug metabolizing enzymes has explained why some patients do not obtain the expected drug effects, show an exaggerated drug effect, or experience serious toxicity from standard drug dosages. Polymorphisms can be expressed in the phenotype ofthe extensive metabolizer and the phenotype ofthe poor metabolizer. Accordingly, genetic polymorphism may lead to allelic protein variants ofthe protease protein in which one or more ofthe protease functions in one population is different from those in another population.
  • polymorphism may give rise to amino terminal extracellular domains and/or other substrate-binding regions that are more or less active in substrate binding, and protease activation. Accordingly, substrate dosage would necessarily be modified to maximize the therapeutic effect within a given population containing a polymorphism.
  • genotyping specific polymorphic peptides could be identified.
  • the peptides are also useful for treating a disorder characterized by an absence of, inappropriate, or unwanted expression ofthe protein.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow. Accordingly, methods for treatment include the use ofthe protease protein or fragments.
  • the invention also provides antibodies that selectively bind to one ofthe peptides ofthe present invention, a protein comprising such a peptide, as well as variants and fragments thereof.
  • an antibody selectively binds a target peptide when it binds the target peptide and does not significantly bind to unrelated proteins.
  • An antibody is still considered to selectively bind a peptide even if it also binds to other proteins that are not substantially homologous with the target peptide so long as such proteins share homology with a fragment or domain ofthe peptide target ofthe antibody. In this case, it would be understood that antibody binding to the peptide is still selective despite some degree of cross-reactivity.
  • an antibody is defined in terms consistent with that recognized within the art: they are multi-subunit proteins produced by a mammalian organism in response to an antigen challenge.
  • the antibodies ofthe present invention include polyclonal antibodies and monoclonal antibodies, as well as fragments of such antibodies, including, but not limited to, Fab or F(ab') 2 , and Fv fragments.
  • an isolated peptide is used as an immunogen and is administered to a mammaUan organism, such as a rat, rabbit or mouse.
  • a mammaUan organism such as a rat, rabbit or mouse.
  • the full- length protein, an antigenic peptide fragment or a fusion protein can be used.
  • Particularly important fragments are those covering functional domains, such as the domains identified in Figure 2, and domain of sequence homology or divergence amongst the family, such as those that can readily be identified using protein alignment methods and as presented in the Figures.
  • Antibodies are preferably prepared from regions or discrete fragments ofthe protease proteins. Antibodies can be prepared from any region ofthe peptide as described herein. However, preferred regions will include those involved in function/activity and/or protease/binding partner interaction. Figure 2 can be used to identify particularly important regions while sequence alignment can be used to identify conserved and unique sequence fragments.
  • An antigenic fragment will typically comprise at least 8 contiguous amino acid residues.
  • the antigenic peptide can comprise, however, at least 10, 12, 14, 16 or more amino acid residues.
  • Such fragments can be selected on a physical property, such as fragments correspond to regions that are located on the surface ofthe protein, e.g., hydrophilic regions or can be selected based on sequence uniqueness (see Figure 2).
  • Detection on an antibody ofthe present invention can be faciUtated by coupling (i.e., physically linking) the antibody to a detectable substance.
  • detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, ⁇ -galactosidase, or acetylcholmesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125 I, 131 I, 35 S or 3 H.
  • the antibodies can be used to isolate one ofthe proteins ofthe present invention by standard techniques, such as affinity chromatography or immunoprecipitation.
  • the antibodies can faciUtate the purification ofthe natural protein from cells and recombinantly produced protein expressed in host cells.
  • such antibodies are useful to detect the presence of one ofthe proteins ofthe present invention in cells or tissues to determine the pattern of expression ofthe protein among various tissues in an organism and over the course of normal development.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis.
  • antibodies can be used to detect protein in situ, in vitro, or in a cell lysate or supernatant in order to evaluate the abundance and pattern of expression. Also, such antibodies can be used to assess abnormal tissue distribution or abnormal expression during development or progression of a biological condition. Antibody detection of circulating fragments of he full length protein can be used to identify turnover.
  • the antibodies can be used to assess expression in disease states such as in active stages ofthe disease or in an individual with a predisposition toward disease related to the protein's function.
  • a disorder is caused by an inappropriate tissue distribution, developmental expression, level of expression of he protein, or expressed/processed form
  • the antibody can be prepared against the normal protein.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow. If a disorder is characterized by a specific mutation in the protein, antibodies specific for this mutant protein can be used to assay for the presence ofthe specific mutant protein.
  • the antibodies can also be used to assess normal and aberrant subceUular localization of cells in the various tissues in an organism.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • the diagnostic uses can be applied, not only in genetic testing, but also in monitoring a treatment modality. Accordingly, where treatment is ultimately aimed at correcting expression level or the presence of aberrant sequence and aberrant tissue distribution or developmental expression, antibodies directed against the protein or relevant fragments can be used to monitor therapeutic efficacy.
  • antibodies are useful in pharmacogenomic analysis.
  • antibodies prepared against polymorphic proteins can be used to identify individuals that require modified treatment modalities.
  • the antibodies are also useful as diagnostic tools as an immunological marker for aberrant protein analyzed by electrophoretic mobility, isoelectric point, tryptic peptide digest, and other physical assays known to those in the art.
  • the antibodies are also useful for tissue typing. Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow. Thus, where a specific protein has been correlated with expression in a specific tissue, antibodies that are specific for this protein can be used to identify a tissue type.
  • the antibodies are also useful for inhibiting protein function, for example, blocking the binding ofthe protease peptide to a binding partner such as a substrate. These uses can also be applied in a therapeutic context in which treatment involves inhibiting the protein's function.
  • An antibody can be used, for example, to block binding, thus modulating (agonizing or antagonizing) the peptides activity.
  • Antibodies can be prepared against specific fragments containing sites required for function or against intact protein that is associated with a cell or cell membrane. See Figure 2 for structural information relating to the proteins ofthe present invention.
  • kits for using antibodies to detect the presence of a protein in a biological sample can comprise antibodies such as a labeled or labelable antibody and a compound or agent for detecting protein in a biological sample; means for determining the amount of protein in the sample; means for comparing the amount of protein in the sample with a standard; and instructions for use.
  • Such a kit can be supphed to detect a single protein or epitope or can be configured to detect one of a multitude of epitopes, such as in an antibody detection array. Arrays are described in detail below for nucleic acid arrays and similar methods have been developed for antibody arrays.
  • nucleic Acid Molecules The present invention further provides isolated nucleic acid molecules that encode a protease peptide or protein ofthe present invention (cDNA, transcript and genomic sequence). Such nucleic acid molecules will consist of, consist essentially of, or comprise a nucleotide sequence that encodes one ofthe protease peptides ofthe present invention, an allelic variant thereof, or an ortholog or paralog thereof. As used herein, an "isolated" nucleic acid molecule is one that is separated from other nucleic acid present in the natural source ofthe nucleic acid.
  • an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends ofthe nucleic acid) in the genomic DNA ofthe organism from which the nucleic acid is derived.
  • flanking nucleotide sequences for example up to about 5KB, 4KB, 3KB, 2KB, or 1KB or less, particularly contiguous peptide encoding sequences and peptide encoding sequences within the same gene but separated by introns in the genomic sequence.
  • nucleic acid is isolated from remote and unimportant flanking sequences such that it can be subjected to the specific manipulations described herein such as recombinant expression, preparation of probes and primers, and other uses specific to the nucleic acid sequences.
  • an "isolated" nucleic acid molecule such as a transcript/cDNA molecule
  • the nucleic acid molecule can be fused to other coding or regulatory sequences and still be considered isolated.
  • recombinant DNA molecules contained in a vector are considered isolated.
  • Further examples of isolated DNA molecules include recombinant DNA molecules maintained in heterologous host cells or purified (partially or substantially) DNA molecules in solution.
  • Isolated RNA molecules include in vivo or in vitro RNA transcripts ofthe isolated DNA molecules ofthe present invention. Isolated nucleic acid molecules according to the present invention further include such molecules produced synthetically.
  • nucleic acid molecules that consist ofthe nucleotide sequence shown in Figure 1 or 3 (SEQ ID NO:l, transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in Figure 2, SEQ ID NO:2.
  • a nucleic acid molecule consists of a nucleotide sequence when the nucleotide sequence is the complete nucleotide sequence ofthe nucleic acid molecule.
  • the present invention further provides nucleic acid molecules that consist essentially of the nucleotide sequence shown in Figure 1 or 3 (SEQ ID NO : 1 , transcript sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in Figure 2, SEQ ID NO:2.
  • a nucleic acid molecule consists essentiaUy of a nucleotide sequence when such a nucleotide sequence is present with only a few additional nucleic acid residues in the final nucleic acid molecule.
  • the present invention further provides nucleic acid molecules that comprise the nucleotide sequences shown in Figure 1 or 3 (SEQ ID NO:l, fransc ⁇ pt sequence and SEQ ID NO:3, genomic sequence), or any nucleic acid molecule that encodes the protein provided in Figure 2, SEQ ID NO:2.
  • a nucleic acid molecule comprises a nucleotide sequence when the nucleotide sequence is at least part ofthe final nucleotide sequence of the nucleic acid molecule. In such a fashion, the nucleic acid molecule can be only the nucleotide sequence or have additional nucleic acid residues, such as nucleic acid residues that are naturally associated with it or heterologous nucleotide sequences. Such a nucleic acid molecule can have a few additional nucleotides or can comprises several hundred or more additional nucleotides. A brief description of how various types of these nucleic acid molecules can be readily made/isolated is provided below.
  • both coding and non-coding sequences are provided. Because ofthe source ofthe present invention, humans genomic sequence ( Figure 3) and cDNA/transcript sequences ( Figure 1), the nucleic acid molecules in the Figures will contain genomic intronic sequences, 5' and 3' non-coding sequences, gene regulatory regions and non-coding intergenic sequences. In general such sequence features are either noted in Figures 1 and 3 or can readily be identified using computational tools known in the art. As discussed below, some ofthe non-coding regions, particularly gene regulatory elements such as promoters, are useful for a variety of purposes, e.g. control of heterologous gene expression, target for identifying gene activity modulating compounds, and are particularly claimed as fragments ofthe genomic sequence provided herein.
  • the isolated nucleic acid molecules can encode the mature protein plus additional amino or carboxyl-terminal amino acids, or amino acids interior to the mature peptide (when the mature form has more than one peptide chain, for instance).
  • Such sequences may play a role in processing of a protein from precursor to a mature form, facilitate protein trafficking, prolong or shorten protein half-life or facilitate manipulation of a protein for assay or production, among other things.
  • the additional amino acids may be processed away from the mature protein by cellular enzymes.
  • the isolated nucleic acid molecules include, but are not limited to, the sequence encoding the protease peptide alone, the sequence encoding the mature peptide and additional coding sequences, such as a leader or secretory sequence (e.g., a pre-pro or pro-protein sequence), the sequence encoding the mature peptide, with or without the additional coding sequences, plus additional non-coding sequences, for example introns and non-coding 5' and 3' sequences such as transcribed but non- translated sequences that play a role in transcription, mRNA processing (including splicing and polyadenylation signals), ribosome binding and stability of mRNA.
  • the nucleic acid molecule maybe fused to a marker sequence encoding, for example, a peptide that facilitates purification.
  • Isolated nucleic acid molecules can be in the form of RNA, such as mRNA, or in the form DNA, including cDNA and genomic DNA obtained by cloning or produced by chemical synthetic techniques or by a combination thereof.
  • the nucleic acid, especially DNA can be double-stranded or single-stranded.
  • Single-stranded nucleic acid can be the coding strand (sense strand) or the non-coding strand (anti-sense strand).
  • the invention further provides nucleic acid molecules that encode fragments of the peptides ofthe present invention as well as nucleic acid molecules that encode obvious variants ofthe protease proteins ofthe present invention that are described above.
  • nucleic acid molecules may be naturally occurring, such as allelic variants (same locus), paralogs (different locus), and orthologs (different organism), or may be constructed by recombinant DNA methods or by chemical synthesis.
  • Such non-naturally occurring variants may be made by mutagenesis techniques, including those applied to nucleic acid molecules, cells, or organisms. Accordingly, as discussed above, the variants can contain nucleotide substitutions, deletions, inversions and insertions.
  • Variation can occur in either or both the coding and non-coding regions.
  • the variations can produce both conservative and non-conservative amino acid substitutions.
  • the present invention further provides non-coding fragments ofthe nucleic acid molecules provided in Figures 1 and 3.
  • Preferred non-coding fragments include, but are not limited to, promoter sequences, enhancer sequences, gene modulating sequences and gene termination sequences. Such fragments are useful in controlling heterologous gene expression and in developing screens to identify gene-modulating agents.
  • a promoter can readily be identified as being 5' to the ATG start site in the genomic sequence provided in Figure 3.
  • a fragment comprises a contiguous nucleotide sequence greater than 12 or more nucleotides. Further, a fragment could at least 30, 40, 50, 100, 250 or 500 nucleotides in length. The length ofthe fragment will be based on its intended use.
  • the fragment can encode epitope bearing regions ofthe peptide, or can be useful as DNA probes and primers.
  • Such fragments can be isolated using the known nucleotide sequence to synthesize an oligonucleotide probe.
  • a labeled probe can then be used to screen a cDNA library, genomic DNA Ubrary, or mRNA to isolate nucleic acid corresponding to the coding region.
  • primers can be used in PCR reactions to clone specific regions of gene.
  • a probe/primer typically comprises substantially a purified oUgonucleotide or oligonucleotide pair.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, 20, 25, 40, 50 or more consecutive nucleotides.
  • Orthologs, homologs, and alleUc variants can be identified using methods well known in the art. As described in the Peptide Section, these variants comprise a nucleotide sequence encoding a peptide that is typically 60-70%, 70-80%, 80-90%, and more typically at least about 90-95% or more homologous to the nucleotide sequence shown in the Figure sheets or a fragment of this sequence. Such nucleic acid molecules can readily be identified as being able to hybridize under moderate to stringent conditions, to the nucleotide sequence shown in the Figure sheets or a fragment ofthe sequence. AlleUc variants can readily be determined by genetic locus ofthe encoding gene.
  • the conditions can be such that sequences at least about 60%, at least about 70%, or at least about 80% or more homologous to each other typically remain hybridized to each other.
  • stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65C. Examples of moderate to low stringency hybridization conditions are well known in the art.
  • the nucleic acid molecules ofthe present invention are useful for probes, primers, chemical intermediates, and in biological assays.
  • the nucleic acid molecules are useful as a hybridization probe for messenger RNA, transcript/cDNA and genomic DNA to isolate full-length cDNA and genomic clones encoding the peptide described in Figure 2 and to isolate cDNA and genomic clones that correspond to variants (alleles, orthologs, etc.) producing the same or related peptides shown in Figure 2.
  • SNPs have been identified at 69 different nucleotide positions in the gene encoding the protease protein ofthe present invention.
  • the probe can co ⁇ espond to any sequence along the entire length ofthe nucleic acid molecules provided in the Figures.
  • nucleic acid molecules are also useful as primers for PCR to amplify any given region of a nucleic acid molecule and are useful to synthesize antisense molecules of desired length and sequence.
  • the nucleic acid molecules are also useful for constructing recombinant vectors. Such vectors include expression vectors that express a portion of, or aU of, the peptide sequences.
  • Vectors also include insertion vectors, used to integrate into another nucleic acid molecule sequence, such as into the cellular genome, to alter in situ expression of a gene and/or gene product.
  • an endogenous coding sequence can be replaced via homologous recombination with all or part ofthe coding region containing one or more specifically introduced mutations.
  • the nucleic acid molecules are also useful for expressing antigenic portions of the proteins.
  • the nucleic acid molecules are also useful as probes for determining the chromosomal positions ofthe nucleic acid molecules by means of in situ hybridization methods. As indicated by the data presented in Figure 3, the chromosome map position was determined to be on human chromosome 3.
  • nucleic acid molecules are also useful in making vectors containing the gene regulatory regions of the nucleic acid molecules of the present invention.
  • the nucleic acid molecules are also useful for designing ribozymes conesponding to all, or a part, ofthe mRNA produced from the nucleic acid molecules described herein.
  • nucleic acid molecules are also useful for making vectors that express part, or all, ofthe peptides.
  • the nucleic acid molecules are also useful for constructing host cells expressing a part, or all, ofthe nucleic acid molecules and peptides.
  • the nucleic acid molecules are also useful for constructing transgenic animals expressing all, or a part, ofthe nucleic acid molecules and peptides.
  • the nucleic acid molecules are also useful as hybridization probes for determining the presence, level, form and distribution of nucleic acid expression.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis. Accordingly, the probes can be used to detect the presence of, or to determine levels of, a specific nucleic acid molecule in cells, tissues, and in organisms.
  • the nucleic acid whose level is determined can be DNA or RNA. Accordingly, probes corresponding to the peptides described herein can be used to assess expression and/or gene copy number in a given cell, tissue, or organism. These uses are relevant for diagnosis of disorders involving an increase or decrease in protease protein expression relative to normal results.
  • In vitro techniques for detection of mRNA include Northern hybridizations and in situ hybridizations.
  • In vitro techniques for detecting DNA includes Southern hybridizations and in situ hybridization.
  • Probes can be used as a part of a diagnostic test kit for identifying cells or tissues that express a protease protein, such as by measuring a level of aprotease-encoding nucleic acid in a sample of cells from a subject e.g., mRNA or genomic DNA, or deterrnining if a protease gene has been mutated.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis.
  • Nucleic acid expression assays are useful for drug screening to identify compounds that modulate protease nucleic acid expression.
  • the invention thus provides a method for identifying a compound that can be used to treat a disorder associated with nucleic acid expression ofthe protease gene, particularly biological and pathological processes that are mediated by the protease in cells and tissues that express it.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • the method typically includes assaying the ability ofthe compound to modulate the expression ofthe protease nucleic acid and thus identifying a compound that can be used to treat a disorder characterized by undesired protease nucleic acid expression.
  • the assays can be performed in cell- based and cell-free systems.
  • Cell-based assays include cells naturally expressing the protease nucleic acid or recombinant cells genetically engineered to express specific nucleic acid sequences.
  • the assay for protease nucleic acid expression can involve direct assay of nucleic acid levels, such as mRNA levels, or on collateral compounds involved in the signal pathway. Further, the expression of genes that are up- or down-regulated in response to the protease protein signal pathway can also be assayed. In this embodiment the regulatory regions of these genes can be operably linked to a reporter gene such as luciferase.
  • modulators of protease gene expression can be identified in a method wherein a cell is contacted with a candidate compound and the expression of mRNA determined.
  • the level of expression of protease mRNA in the presence ofthe candidate compound is compared to the level of expression of protease mRNA in the absence of the candidate compound.
  • the candidate compound can then be identified as a modulator of nucleic acid expression based on this comparison and be used, for example to treat a disorder characterized by aberrant nucleic acid expression.
  • expression of mRNA is statistically significantly greater in the presence ofthe candidate compound than in its absence, the candidate compound is identified as a stimulator of nucleic acid expression.
  • nucleic acid expression is statistically significantly less in the presence ofthe candidate compound than in its absence, the candidate compound is identified as an inhibitor of nucleic acid expression.
  • the invention further provides methods of treatment, with the nucleic acid as a target, using a compound identified through drug screening as a gene modulator to modulate protease nucleic acid expression in cells and tissues that express the protease.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis. Modulation includes both up-regulation (i.e. activation or agonization) or down-regulation (suppression or antagonization) or nucleic acid expression.
  • a modulator for protease nucleic acid expression can be a small molecule or drug identified using the screening assays described herein as long as the drug or small molecule inhibits the protease nucleic acid expression in the cells and tissues that express the protein.
  • Experimental data as provided in Figure 1 indicates expression in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow.
  • the nucleic acid molecules are also useful for monitoring the effectiveness of modulating compounds on the expression or activity ofthe protease gene in clinical trials or in a treatment regimen.
  • the gene expression pattern can serve as a barometer for the continuing effectiveness of treatment with the compound, particularly with compounds to which a patient can develop resistance.
  • the gene expression pattern can also serve as a marker indicative of a physiological response ofthe affected cells to the compound. Accordingly, such monitoring would allow either increased administration ofthe compound or the administration of alternative compounds to which the patient has not become resistant. Similarly, if the level of nucleic acid expression falls below a desirable level, administration ofthe compound could be commensurately decreased.
  • the nucleic acid molecules are also useful in diagnostic assays for qualitative changes in protease nucleic acid expression, and particularly in qualitative changes that lead to pathology.
  • the nucleic acid molecules can be used to detect mutations in protease genes and gene expression products such as mRNA.
  • the nucleic acid molecules can be used as hybridization probes to detect naturally occurring genetic mutations in the protease gene and thereby to determine whether a subject with the mutation is at risk for a disorder caused by the mutation. Mutations include deletion, addition, or substitution of one or more nucleotides in the gene, chromosomal rearrangement, such as inversion or transposition, modification of genomic DNA, such as aberrant methylation patterns or changes in gene copy number, such as amplification. Detection of a mutated form ofthe protease gene associated with a dysfunction provides a diagnostic tool for an active disease or susceptibility to disease when the disease results from overexpression, underexpression, or altered expression of a protease protein.
  • Figure 3 provides information on SNPs that have been identified in the gene encoding the protease protein ofthe present invention. SNPs were found at 69 different nucleotide positions, including 2 SNPs that change the encoded amino acid sequence (i.e., nonsynonymous SNPs). The changes in the amino acid sequence caused by these SNPs is indicated in Figure 3 and can readily be determined using the universal genetic code and the protein sequence provided in Figure 2 as a reference. As indicated by the data presented in Figure 3, the chromosome map position was determined to be on human chromosome 3.
  • Genomic DNA can be analyzed directly or can be ampUfied by using PCR prior to analysis.
  • RNA or cDNA can be used in the same way.
  • detection ofthe mutation involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g. U.S. Patent Nos.
  • PCR polymerase chain reaction
  • This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells ofthe sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a gene under conditions such that hybridization and amplification ofthe gene (if present) occurs, and detecting the presence or absence of an ampUfication product, or detecting the size ofthe ampUfication product and comparing the length to a control sample. Deletions and insertions can be detected by a change in size ofthe ampUfied product compared to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to normal RNA or antisense DNA sequences.
  • nucleic acid e.g., genomic, mRNA or both
  • mutations in a protease gene can be directly identified, for example, by alterations in restriction enzyme digestion patterns determined by gel electrophoresis.
  • sequence-specific ribozymes U.S. Patent No. 5,498,531
  • Perfectly matched sequences can be distinguished from mismatched sequences by nuclease cleavage digestion assays or by differences in melting temperature. Sequence changes at specific locations can also be assessed by nuclease protection assays such as RNase and SI protection or the chemical cleavage method.
  • sequence differences between a mutant protease gene and a wild-type gene can be detennined by direct DNA sequencing.
  • a variety of automated sequencing procedures can be utiUzed when performing the diagnostic assays (Naeve, C.W., (1995) Biotechniques .79:448), including sequencing by mass spectrometry (see, e.g., PCT
  • RNA/RNA or RNA/DNA duplexes Other methods for detecting mutations in the gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA duplexes (Myers et al, Science 230:1242 (1985)); Cotton et al, PNAS 85:4391 (1988); Saleeba et al, Meth. Enzymol. 217:286-295 (1992)), electrophoretic mobility of mutant and wild type nucleic acid is compared (Orita et al, PNAS 86:2166 (1989); Cotton et al, Mutat. Res. 255:125-144 (1993); and Hayashi et al, Genet. Anal. Tech. Appl.
  • nucleic acid molecules are also useful for testing an individual for a genotype that while not necessarily causing the disease, nevertheless affects the treatment modatity.
  • the nucleic acid molecules can be used to study the relationship between an individual's genotype and the individual's response to a compound used for treatment (pharmacogenomic relationship). Accordingly, the nucleic acid molecules described herein can be used to assess the mutation content ofthe protease gene in an individual in order to select an appropriate compound or dosage regimen for treatment.
  • nucleic acid molecules displaying genetic variations that affect treatment provide a diagnostic target that can be used to tailor treatment in an individual. Accordingly, the production of recombinant cells and animals containing these polymorphisms allow effective clinical design of treatment compounds and dosage regimens.
  • the nucleic acid molecules are thus useful as antisense constructs to control protease gene expression in cells, tissues, and organisms.
  • a DNA antisense nucleic acid molecule is designed to be complementary to a region ofthe gene involved in transcription, preventing transcription and hence production of protease protein.
  • An antisense RNA or DNA nucleic acid molecule would hybridize to the mRNA and thus block translation of mRNA into protease protein.
  • Figure 3 provides information on SNPs that have been identified in the gene encoding the protease protein ofthe present invention. SNPs were found at 69 different nucleotide positions, including 2 SNPs that change the encoded amino acid sequence (i.e., nonsynonymous SNPs). The changes in the amino acid sequence caused by these SNPs is indicated in Figure 3 and can readily be determined using the universal genetic code and the protein sequence provided in Figure 2 as a reference.
  • a class of antisense molecules can be used to inactivate mRNA in order to decrease expression of protease nucleic acid. Accordingly, these molecules can treat a disorder characterized by abnormal or undesired protease nucleic acid expression.
  • This technique involves cleavage by means of ribozymes containing nucleotide sequences complementary to one or more regions in the mRNA that attenuate the abitity ofthe mRNA to be translated. Possible regions include coding regions and particularly coding regions corresponding to the catalytic and other functional activities ofthe protease protein, such as substrate binding.
  • the nucleic acid molecules also provide vectors for gene therapy in patients containing cells that are aberrant in protease gene expression. Thus, recombinant cells, which include the patient's cells that have been engineered ex vivo and returned to the patient, are introduced into an individual where the cells produce the desired protease protein to treat the individual.
  • the invention also encompasses kits for detecting the presence of a protease nucleic acid in a biological sample.
  • Experimental data as provided in Figure 1 indicates that protease proteins ofthe present invention are expressed in placenta, breast, testis, head/neck, cervix, melanocytes, uterus (high grade serous papillary carcinoma tumors), and marrow, as indicated by virtual northern blot analysis.
  • the kit can comprise reagents such as a labeled or labelable nucleic acid or agent capable of detecting protease nucleic acid in a biological sample; means for deterrnining the amount of protease nucleic acid in the sample; and means for comparing the amount of protease nucleic acid in the sample with a standard.
  • the compound or agent can be packaged in a suitable container.
  • the kit can further comprise instructions for using the kit to detect protease protein mRNA or DNA.
  • the present invention further provides nucleic acid detection kits, such as arrays or microarrays of nucleic acid molecules that are based on the sequence information provided in Figures 1 and 3 (SEQ ID NOS:l and 3).
  • a ⁇ ays or “Microarrays” refers to an array of distinct polynucleotides or oligonucleotides synthesized on a substrate, such as paper, nylon or other type of membrane, filter, chip, glass slide, or any other suitable solid support.
  • the microarray is prepared and used according to the methods described in US Patent 5,837,832, Chee et al, PCT application W095/11995 (Chee et al.), Lockhart, D. J. et al. (1996; Nat. Biotech. 14: 1675-1680) and Schena, M. et al. (1996; Proc. Natl. Acad. Sci. 93: 10614-10619), all of which are incorporated herein in their entirety by reference.
  • such arrays are produced by the methods described by Brown et al. , US Patent No. 5,807,522.
  • the microa ⁇ ay or detection kit is preferably composed of a large number of unique, single-stranded nucleic acid sequences, usually either synthetic antisense oligonucleotides or fragments of cDNAs, fixed to a solid support.
  • the oligonucleotides are preferably about 6-60 nucleotides in length, more preferably 15- 30 nucleotides in length, and most preferably about 20-25 nucleotides in length. For a certain type of microarray or detection kit, it may be preferable to use oligonucleotides that are only 7-20 nucleotides in length.
  • the microarray or detection kit may contain oligonucleotides that cover the known 5', or 3', sequence, sequential oligonucleotides which cover the full length sequence; or unique oligonucleotides selected from particular areas along the length ofthe sequence.
  • Polynucleotides used in the microarray or detection kit may be oligonucleotides that are specific to a gene or genes of interest.
  • the gene(s) of interest or an ORF identified from the contigs ofthe present invention
  • a computer algorithm which starts at the 5' or at the 3' end ofthe nucleotide sequence.
  • Typical algorithms will then identify oligomers of defined length that are unique to the gene, have a GC content within a range suitable for hybridization, and lack predicted secondary structure that may interfere with hybridization.
  • pairs of oligonucleotides on a microarray or detection kit.
  • the "pairs" will be identical, except for one nucleotide that preferably is located in the center ofthe sequence.
  • the second oligonucleotide in the pair serves as a control.
  • the number of oligonucleotide pairs may range from two to one million.
  • the oligomers are synthesized at designated areas on a substrate using a light-directed chemical process.
  • the substrate may be paper, nylon or other type of membrane, filter, chip, glass slide or any other suitable solid support.
  • an oligonucleotide may be synthesized on the surface ofthe substrate by using a chemical coupling procedure and an ink jet application apparatus, as described in PCT application W095/251116 (Baldeschweiler et al.) which is incorporated herein in its entirety by reference.
  • a "gridded" array analogous to a dot (or slot) blot may be used to arrange and link cDNA fragments or oligonucleotides to the surface of a substrate using a vacuum system, thermal, UV, mechanical or chemical bonding procedures.
  • An array such as those described above, may be produced by hand or by using available devices (slot blot or dot blot apparatus), materials (any suitable solid support), and machines (including robotic instruments), and may contain 8, 24, 96, 384, 1536, 6144 or more oligonucleotides, or any other number between two and one million which lends itself to the efficient use of commercially available instrumentation.
  • RNA or DNA from a biological sample is made into hybridization probes.
  • the mRNA is isolated, and cDNA is produced and used as a template to make antisense RNA (aRNA).
  • aRNA antisense RNA
  • the aRNA is amplified in the presence of fluorescent nucleotides, and labeled probes are incubated with the microarray or detection kit so that the probe sequences hybridize to complementary oligonucleotides ofthe microa ⁇ ay or detection kit. Incubation conditions are adjusted so that hybridization occurs with precise complementary matches or with various degrees of less complementarity.
  • a scanner is used to determine the levels and patterns of fluorescence.
  • the scanned images are examined to determine degree of complementarity and the relative abundance of each oligonucleotide sequence on the microarray or detection kit.
  • the biological samples may be obtained from any bodily fluids (such as blood, urine, saliva, phlegm, gastric juices, etc.), cultured cells, biopsies, or other tissue preparations.
  • a detection system may be used to measure the absence, presence, and amount of hybridization for all ofthe distinct sequences simultaneously. This data may be used for large-scale correlation studies on the sequences, expression patterns, mutations, variants, or polymo ⁇ hisms among samples.
  • the present invention provides methods to identify the expression ofthe protease proteins/peptides ofthe present invention.
  • such methods comprise incubating a test sample with one or more nucleic acid molecules and assaying for binding ofthe nucleic acid molecule with components within the test sample.
  • Such assays will typically involve anays comprising many genes, at least one of which is a gene ofthe present invention and or alleles ofthe protease gene of the present invention.
  • Figure 3 provides information on SNPs that have been identified in the gene encoding the protease protein ofthe present invention.
  • SNPs were found at 69 different nucleotide positions, including 2 SNPs that change the encoded amino acid sequence (i.e., nonsynonymous SNPs).
  • the changes in the amino acid sequence caused by these SNPs is indicated in Figure 3 and can readily be determined using the universal genetic code and the protein sequence provided in Figure 2 as a reference.
  • Conditions for incubating a nucleic acid molecule with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature ofthe nucleic acid molecule used in the assay.
  • any one ofthe commonly available hybridization, amplification or array assay formats can readily be adapted to employ the novel fragments ofthe Human genome disclosed herein.
  • test samples ofthe present invention include cells, protein or membrane extracts of cells.
  • the test sample used in the above-described method will vary based on the assay format, nature ofthe detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing nucleic acid extracts or of cells are well known in the art and can be readily be adapted in order to obtain a sample that is compatible with the system utilized.
  • kits which contain the necessary reagents to carry out the assays ofthe present invention.
  • the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one ofthe nucleic acid molecules that can bind to a fragment ofthe Human genome disclosed herein; and (b) one or more other containers comprising one or more ofthe following: wash reagents, reagents capable of detecting presence of a bound nucleic acid.
  • a compartmentalized kit includes any kit in which reagents are contained in separate containers.
  • Such containers include small glass containers, plastic containers, strips of plastic, glass or paper, or a ⁇ aying material such as silica.
  • Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another.
  • Such containers will include a container which will accept the test sample, a container which contains the nucleic acid probe, containers which contain wash reagents (such as phosphate buffered saline, Tris- buffers, etc.), and containers which contain the reagents used to detect the bound probe.
  • protease gene ofthe present invention can be routinely identified using the sequence information disclosed herein can be readily incorporated into one ofthe estabUshed kit formats which are well known in the art, particularly expression arrays.
  • the invention also provides vectors containing the nucleic acid molecules described herein.
  • the term "vector” refers to a vehicle, preferably a nucleic acid molecule, which can transport the nucleic acid molecules.
  • the vector is a nucleic acid molecule, the nucleic acid molecules are covalently linked to the vector nucleic acid.
  • the vector includes a plasmid, single or double stranded phage, a single or double stranded RNA or DNA viral vector, or artificial chromosome, such as a BAC, PAC, YAC, OR MAC.
  • a vector can be maintained in the host cell as an extrachromosomal element where it replicates and produces additional copies ofthe nucleic acid molecules.
  • the vector may integrate into the host cell genome and produce additional copies ofthe nucleic acid molecules when the host cell repUcates.
  • the invention provides vectors for the maintenance (cloning vectors) or vectors for expression (expression vectors) ofthe nucleic acid molecules.
  • the vectors can function in prokaryotic or eukaryotic cells or in both (shuttle vectors).
  • Expression vectors contain cis-acting regulatory regions that are operably linked in the vector to the nucleic acid molecules such that transcription ofthe nucleic acid molecules is allowed in a host cell.
  • the nucleic acid molecules can be introduced into the host cell with a separate nucleic acid molecule capable of affecting transcription.
  • the second nucleic acid molecule may provide a trans-acting factor interacting with the cis-regulatory control region to allow transcription ofthe nucleic acid molecules from the vector.
  • a trans-acting factor may be supplied by the host cell.
  • a trans-acting factor can be produced from the vector itself. It is understood, however, that in some embodiments, transcription and/or translation ofthe nucleic acid molecules can occur in a cell-free system.
  • the regulatory sequence to which the nucleic acid molecules described herein can be operably linked include promoters for directing mRNA transcription. These include, but are not limited to, the left promoter from bacteriophage ⁇ , the lac, TRP, and TAC promoters from E. coli, the early and late promoters from SV40, the CMV immediate early promoter, the adenovirus early and late promoters, and retiovirus long- terminal repeats.
  • expression vectors may also include regions that modulate transcription, such as repressor binding sites and enhancers.
  • regions that modulate transcription include the SV40 enhancer, the cytomegalovirus immediate early enhancer, polyoma enhancer, adenovirus enhancers, and retrovirus LTR enhancers.
  • expression vectors can also contain sequences necessary for transcription termination and, in the transcribed region a ribosome binding site for translation.
  • Other regulatory control elements for expression include initiation and termination codons as well as polyadenylation signals.
  • the person of ordinary skill in the art would be aware ofthe numerous regulatory sequences that are useful in expression vectors. Such regulatory sequences are described, for example, in Sambrook et al, Molecular Cloning: A Laboratory Manual. 2nd. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, (1989).
  • a variety of expression vectors can be used to express a nucleic acid molecule.
  • Such vectors include chromosomal, episomal, and virus-derived vectors, for example vectors derived from bacterial plasmids, from bacteriophage, from yeast episomes, from yeast chromosomal elements, including yeast artificial chromosomes, from viruses such as baculoviruses, papovaviruses such as SV40, Vaccinia viruses, adenoviruses, poxviruses, pseudorabies viruses, and retroviruses. Vectors may also be derived from combinations of these sources such as those derived from plasmid and bacteriophage genetic elements, e.g. cosmids and phagemids.
  • the regulatory sequence may provide constitutive expression in one or more host cells (i.e. tissue specific) or may provide for inducible expression in one or more cell types such as by temperature, nutrient additive, or exogenous factor such as a hormone or other ligand.
  • host cells i.e. tissue specific
  • inducible expression in one or more cell types such as by temperature, nutrient additive, or exogenous factor such as a hormone or other ligand.
  • the nucleic acid molecules can be inserted into the vector nucleic acid by well- known methodology.
  • the DNA sequence that wiU ultimately be expressed is joined to an expression vector by cleaving the DNA sequence and the expression vector with one or more restriction enzymes and then ligating the fragments together. Procedures for restriction enzyme digestion and ligation are well known to those of ordinary skill in the art.
  • Bacterial cells include, but are not limited to, E. coli, Streptomyces, and Salmonella typhimurium.
  • Eukaryotic cells include, but are not Umited to, yeast, insect cells such as Drosophila, animal cells such as COS and CHO cells, and plant cells.
  • the invention provides fusion vectors that allow for the production ofthe peptides.
  • Fusion vectors can increase the expression of a recombinant protein, increase the solubility ofthe recombinant protein, and aid in the purification ofthe protein by acting for example as a ligand for affinity purification.
  • a proteolytic cleavage site may be introduced at the junction ofthe fusion moiety so that the desired peptide can ultimately be separated from the fusion moiety.
  • Proteolytic enzymes include, but are not limited to, factor Xa, thrombin, and enteroprotease.
  • Typical fusion expression vectors include pGEX (Smith et al, Gene 67:31-40 (1988)), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S- transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • GST glutathione S- transferase
  • suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al, Gene 69:301-315 (1988)) and pET lid (Studier et al, Gene Expression Technology: Methods in Enzymology 185:60-89 (1990)).
  • Recombinant protein expression can be maximized in host bacteria by providing a genetic background wherein the host cell has an impaired capacity to proteolytically cleave the recombinant protein.
  • the sequence ofthe nucleic acid molecule of interest can be altered to provide preferential codon usage for a specific host cell, for example E. coli. (Wada et al, Nucleic Acids Res. 20:2111-2118 (1992)).
  • the nucleic acid molecules can also be expressed by expression vectors that are operative in yeast. Examples of vectors for expression in yeast e.g., S.
  • cerevisiae include pYepSecl (Baldari, et al, EMBOJ. 6:229-234 (1987)), pMFa (Kurjan et al, Cell 30:933-943(1982)), pJRY88 (Schultz etal, Gene 54:113-123 (1987)), andpYES2 (Invitrogen Corporation, San Diego, CA).
  • the nucleic acid molecules can also be expressed in insect cells using, for example, baculovirus expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al, Mol Cell Biol. 3:2156-2165 (1983)) andthepVL series (Lucklow et al, Virology 770:31-39 (1989)).
  • the nucleic acid molecules described herein are expressed in mammalian cells using mammaUan expression vectors.
  • mammalian expression vectors include pCDM8 (Seed, B. Nature 329:840(1987)) andpMT2PC (Kaufinan et al, EMBOJ. 6:187-195 (1987)).
  • the expression vectors listed herein are provided by way of example only of the well-known vectors available to those of ordinary skill in the art that would be useful to express the nucleic acid molecules.
  • the person of ordinary skill in the art would be aware of other vectors suitable for maintenance propagation or expression ofthe nucleic acid molecules described herein. These are found for example in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
  • the invention also encompasses vectors in which the nucleic acid sequences described herein are cloned into the vector in reverse orientation, but operably linked to a regulatory sequence that permits transcription of antisense RNA.
  • an antisense transcript can be produced to all, or to a portion, ofthe nucleic acid molecule sequences described herein, including both coding and non-coding regions. Expression of this antisense RNA is subject to each ofthe parameters described above in relation to expression ofthe sense RNA (regulatory sequences, constitutive or inducible expression, tissue-specific expression).
  • the invention also relates to recombinant host cells containing the vectors described herein.
  • Host cells therefore include prokaryotic cells, lower eukaryotic cells such as yeast, other eukaryotic cells such as insect cells, and higher eukaryotic cells such as mammaUan cells.
  • the recombinant host cells are prepared by introducing the vector constructs described herein into the cells by techniques readily available to the person of ordinary skill in the art.
  • Host cells can contain more than one vector.
  • different nucleotide sequences can be introduced on different vectors ofthe same cell.
  • the nucleic acid molecules can be introduced either alone or with other nucleic acid molecules that are not related to the nucleic acid molecules such as those providing trans-acting factors for expression vectors.
  • the vectors can be introduced independently, co-introduced or joined to the nucleic acid molecule vector.
  • bacteriophage and viral vectors these can be introduced into cells as packaged or encapsulated virus by standard procedures for infection and transduction.
  • Viral vectors can be repUcation-competent or replication-defective. In the case in which viral replication is defective, replication will occur in host ceUs providing functions that complement the defects.
  • Vectors generally include selectable markers that enable the selection ofthe subpopulation of cells that contain the recombinant vector constructs.
  • the marker can be contained in the same vector that contains the nucleic acid molecules described herein or maybe on a separate vector.
  • Markers include tetracycline or ampicillin-resistance genes for prokaryotic host cells and dihydrofolate reductase or neomycin resistance for eukaryotic host cells. However, any marker that provides selection for a phenotypic trait will be effective.
  • RNA derived from the DNA constructs described herein can also be used to produce these proteins using RNA derived from the DNA constructs described herein.
  • secretion ofthe peptide is desired, which is difficult to achieve with multi-transmembrane domain containing proteins such as proteases, appropriate secretion signals are inco ⁇ orated into the vector.
  • TThe signal sequence can be endogenous to the peptides or heterologous to these peptides.
  • the protein can be isolated from the host cell by standard disruption procedures, including freeze thaw, sonication, mechanical disruption, use of lysing agents and the like.
  • the peptide can then be recovered and purified by well-known purification methods including ammomum sulfate precipitation, acid extraction, anion or cationic exchange chromatography, phosphocellulose chromatography, hydrophobic- interaction chromatography, affinity chromatography, hydroxylapatite chromatography, lectin chromatography, or high performance liquid chromatography.
  • the peptides can have various glycosylation patterns, depending upon the cell, or maybe non-glycosylated as when produced in bacteria.
  • the peptides may include an initial modified methionine in some cases as a result of a host-mediated process.
  • the recombinant host cells expressing the peptides described herein have a variety of uses.
  • the cells are useful for producing a protease protein or peptide that can be further purified to produce desired amounts of protease protein or fragments.
  • host cells containing expression vectors are useful for peptide production.
  • Host cells are also useful for conducting cell-based assays involving the protease protein or protease protein fragments, such as those described above as well as other formats known in the art.
  • a recombinant host cell expressing a native protease protein is useful for assaying compounds that stimulate or inhibit protease protein function.
  • Host cells are also useful for identifying protease protein mutants in which these functions are affected. If the mutants naturally occur and give rise to a pathology, host cells containing the mutations are useful to assay compounds that have a desired effect on the mutant protease protein (for example, stimulating or inhibiting function) which may not be indicated by their effect on the native protease protein.
  • a desired effect on the mutant protease protein for example, stimulating or inhibiting function
  • a transgenic animal is preferably a mammal, for example a rodent, such as a rat or mouse, in which one or more ofthe cells ofthe animal include a transgene.
  • a transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome ofthe mature animal in one or more cell types or tissues ofthe transgenic animal. These animals are useful for studying the function of a protease protein and identifying and evaluating modulators of protease protein activity.
  • Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, and amphibians.
  • a transgenic animal can be produced by introducing nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal.
  • Any ofthe protease protein nucleotide sequences can be introduced as a transgene into the genome of a non- human animal, such as a mouse.
  • any ofthe regulatory or other sequences useful in expression vectors can form part ofthe transgenic sequence. This includes intionic sequences and polyadenylation signals, if not already included.
  • a tissue-specific regulatory sequence(s) can be operably linked to the transgene to direct expression ofthe protease protein to particular cells.
  • transgenic founder animal can be identified based upon the presence ofthe transgene in its genome and or expression of transgenic mRNA in tissues or cells ofthe animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene.
  • transgenic animals carrying a transgene can further be bred to other transgenic animals carrying other transgenes.
  • a transgenic animal also includes animals in which the entire animal or tissues in the animal have been produced using the homologously recombinant host cells described herein.
  • transgenic non-human animals can be produced which contain selected systems that allow for regulated expression ofthe transgene.
  • a system is the cre/loxP recombinase system of bacteriophage PI.
  • cre ⁇ oxP recombinase system see, e.g., Lakso et al PNAS 89:6232- 6236 (1992).
  • FLP recombinase system of S. cerevisiae (O'Gorman et al. Science 257:1351-1355 (1991).
  • mice containing transgenes encoding both the Cre recombinase and a selected protein is required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • Clones ofthe non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al. Nature 355:810-813 (1997) and PCT International Publication Nos. WO 97/07668 and WO 97/07669.
  • a cell e.g., a somatic cell
  • the quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal ofthe same species from which the quiescent cell is isolated.
  • the reconstructed oocyte is then cultured such that it develops to morula or blastocyst and then transferred to pseudopregnant female foster animal.
  • the offspring born of this female foster animal will be a clone ofthe animal from which the cell, e.g., the somatic cell, is isolated.
  • Transgenic animals containing recombinant cells that express the peptides described herein are useful to conduct the assays described herein in an in vivo context. Accordingly, the various physiological factors that are present in vivo and that could effect substrate binding, protease protein activity/activation, and signal transduction, may not be evident from in vitro cell-free or cell-based assays.
  • non-human transgenic animals to assay in vivo protease protein function, including substrate interaction, the effect of specific mutant protease proteins on protease protein function and substrate interaction, and the effect of chimeric protease proteins. It is also possible to assess the effect of null mutations, that is mutations that substantially or completely eliminate one or more protease protein functions.

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Abstract

La présente invention concerne des séquences d'acides aminés de peptides qui sont codés par des gènes au sein du génome humain, les peptides protéases de la présente invention. Cette invention concerne plus spécifiquement des molécules isolées de peptide et d'acide nucléique, des méthodes d'identification d'orthologues et de paralogues des peptides protéases ainsi que des méthodes d'identification de modulateurs des peptides protéases.
PCT/US2003/003966 2002-02-08 2003-02-10 Proteines proteases humaines isolees, molecules d'acides nucleiques codant des proteines proteases et utilisations de ces dernieres WO2003066887A1 (fr)

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Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999055721A1 (fr) * 1998-04-24 1999-11-04 Alphagene, Inc. Proteines secretees et polynucleotides les codant
WO2001009292A2 (fr) * 1999-07-31 2001-02-08 Board Of Regents, The University Of Texas System Composition et procedes relatifs a la protease a specificite sentrine, senp1

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1999055721A1 (fr) * 1998-04-24 1999-11-04 Alphagene, Inc. Proteines secretees et polynucleotides les codant
WO2001009292A2 (fr) * 1999-07-31 2001-02-08 Board Of Regents, The University Of Texas System Composition et procedes relatifs a la protease a specificite sentrine, senp1

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DATABASE PROTEIN [online] 12 July 2001 (2001-07-12), STRAUSBERG R.: "Protein with", XP002963694, accession no. NCBI Database accession no. (AAH08589) *
DATABASE PROTEIN [online] 13 July 2001 (2001-07-13), WANG Y.-G. ET AL.: "SUMO/sentrin-specific protease", XP002963692, accession no. NCBI Database accession no. (AAK6930) *
DATABASE PROTEIN [online] 15 June 2002 (2002-06-15), HASHIMOTO K. ET AL.: "Sentrin-specific protease 5", XP002963693, accession no. NCBI Database accession no. (Q8WP32) *

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