WO2003054178A2 - Metalloprotease proteins - Google Patents

Metalloprotease proteins Download PDF

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Publication number
WO2003054178A2
WO2003054178A2 PCT/GB2002/005866 GB0205866W WO03054178A2 WO 2003054178 A2 WO2003054178 A2 WO 2003054178A2 GB 0205866 W GB0205866 W GB 0205866W WO 03054178 A2 WO03054178 A2 WO 03054178A2
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seq
polypeptide
nucleic acid
acid molecule
sequence
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PCT/GB2002/005866
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French (fr)
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WO2003054178A3 (en
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Richard James Mitter
Richard Joseph Fagan
Christopher Benjamin Phelps
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Inpharmatica Limited
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Priority to AU2002353208A priority Critical patent/AU2002353208A1/en
Publication of WO2003054178A2 publication Critical patent/WO2003054178A2/en
Publication of WO2003054178A3 publication Critical patent/WO2003054178A3/en

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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14Hydrolases (3)
    • C12N9/48Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • C12N9/6489Metalloendopeptidases (3.4.24)

Definitions

  • This invention relates to novel proteins (INSP003, I SP004, INSP006, INSP007, INSP007a, INSP007b and I SP008), herein identified as secreted proteins (in particular as members of the metalloprotease family) and to the use of these proteins and nucleic acid sequences from the encoding genes in the diagnosis, prevention and treatment of disease.
  • novel proteins INSP003, I SP004, INSP006, INSP007, INSP007a, INSP007b and I SP008
  • bioinformatics tools increase in potency and in accuracy, these tools are rapidly replacing the conventional techniques of biochemical characterisation. Indeed, the advanced bioinformatics tools used in identifying the present invention are now capable of outputting results in which a high degree of confidence can be placed.
  • Various institutions and commercial organisations are examining sequence data as they become available and significant discoveries are being made on an on-going basis. However, there remains a continuing need to identify and characterise further genes and the polypeptides that they encode, as targets for research and for drug discovery.
  • Secreted protein background The ability for cells to make and secrete extracellular proteins is central to many biological processes. Enzymes, growth factors, extracellular matrix proteins and signalling molecules are all secreted by cells. This is through fusion of a secretory vesicle with the plasma membrane. In most cases, but not all, proteins are directed to the endoplasmic reticulum and into secretory vesicles by a signal peptide. Signal peptides are cis-acting sequences that affect the transport of polypeptide chains from the cytoplasm to a membrane bound compartment such as a secretory vesicle. Polypeptides that are targeted to the secretory vesicles are either secreted into the extracellular matrix or are retained in the plasma membrane.
  • polypeptides that are retained in the plasma membrane will have one or more transmembrane domains.
  • secreted proteins that play a central role in the functioning of a cell are cytokines, hormones, extracellular matrix proteins (adhesion molecules), proteases, and growth and differentiation factors. Description of some of the properties of these proteins follows.
  • Proteases are enzymes that irreversibly hydrolyse amide bonds in peptides and proteins. Proteases are widely distributed and are involved in many different biological processes, from activation of proteins and peptides to degradation of proteins. Despite the fact that proteases have been shown to be involved in many different diseases, drugs targeted to proteases are still rare in pharmacy, although inhibitors of angiotensin converting enzyme (ACE) have been among the most successful antihypertensive drugs for several years. Proteases have recently received substantial publicity as valuable therapeutic targets following the approval of HIV protease inhibitors.
  • ACE angiotensin converting enzyme
  • Proteases can be divided in large Families.
  • the term "Family” is used to describe a group of proteases in which each member shows an evolutionary relationship to at least one other member, either throughout the whole sequence or at least in the part of the sequence responsible for catalytic activity.
  • the name of each Family reflects the catalytic activity type of the proteases in the Family.
  • serine proteases belong to the S family
  • threonine proteases belong to the T family
  • aspartyl proteases belong to the A family
  • cysteine proteases belong to the C family
  • metalloproteinases belong to the M family.
  • Metalloproteases and Serine proteases are commonly found in the extracellular matrix.
  • Metalloproteases can be divided in 2 major groups depending on the presence or absence of a the Zinc binding motif (HEXXH). l.l Presence of HEXXH motif (22 families ⁇ ): Prosite number: PDOC00129
  • M2 Peptidyl-dipeptidase A (Angiotensin I Coverting Enzyme: ACE)
  • Enzyme TACE/Desintegrin (other ADAM proteases).
  • the ADAMs are a large, widely expressed and developmentally regulated family of proteins with multiple potential functions in cell-cell and cell-matrix interactions. Among them TACE represents a new emerging target for arthritis disease.
  • M41 This family contains ATP-dependent metalloproteases: FtsH, proteasome proteins.
  • Matrix Metalloproteinases are a family of Zinc containing enzymes that are responsible for the remodeling of extracellular matrix throughout the body. They have been shown to be involved in cancer (increase invasiveness, effects on new blood vessels), and in arthritis (involvement in cartilage degradation (Dahlberg, L., et al, Arthritis Rheum. 2000 43(3):673-82) and also TNF- alpha conversion (Hanemaaijer, R., et al, J Biol Chem. 1997 272(50):31504-9, Shlopov, B.V., et al.,.
  • MMPs Matrix Metalloproteinases family
  • MMPs have been divided in 4 families based on amino-acid sequence homologies of their domain structure, other than the catalytic region.
  • Minimal domain family matrilysin (PUMP-1, MMP-7) cleaves proteoglycan, laminin and fibronectin
  • Hemopexin domain family Collagenases: unique ability to cleave fibrillar collagen. The role of collagenases in cartilage degradation , make them attractive targets for the treatment of rheumatoid and osteo-arthritis.
  • MME Metalloelastase
  • MMP-3 Stromelysin-1
  • MMP-10 2 (MMP-10) and 3 (MMP-11).
  • MMP-11 is excreted as an active form and it's function could be to activate other MMPs.
  • Fibronectin domain family degrades a large number of matrix substrates (gelatin, elastin, type IV collagen)
  • MMP-2 Gelatinase A
  • M24A Methionyl aminopeptidase, type 1 (including procaryotic and eucaryotic MAP-1) / Prosite number: PDOC00575
  • M24C Methionyl aminopeptidase, type 2 (including eucaryotic MAP-2) / Prosite number: PDOC00575
  • Metalloproteases are implicated across a wide variety of therapeutic areas. These include respiratory diseases (Segura-Valdez, L., et al, Chest. 2000 117(3):684-94, Tanaka, H., et al, J Allergy Clin Immunol. 2000 105(5):900-5, Hoshino, M., et al, J Allergy Clin 5 Immunol. 1999 104(2 Pt l):356-63, Mautino, G., et al, Am J Respir Crit Care Med. 1999 160(l):324-30, Dalai, S., et al, Chest.
  • Metalloproteinases are also implicated in therapies associated with modulating chorion 25 status, the zona reaction, the formation of fertilisation membranes, contraception and infertility, (Shibata et al (2000) J.Biol.Chem vol.275, No.12 p8349).
  • the invention is based on the discovery that proteins referred to herein as the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 proteins function as secreted protease molecules and moreover as secreted protease molecules of the metalloprotease class of molecule.
  • INSP007b is a splice variant of INSP007 and is not predicted to be catalytically active as a metalloprotease.
  • INSP007b may be a dominant negative form of INSP007 and/or INSP007a and may function to bind the same substrate as INSP007 and/or INSP007a, therefore acting as a natural antagonist.
  • polypeptide which polypeptide:
  • (i) comprises the amino acid sequence as recited in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and/or SEQ ID NO:14;
  • (ii) is a fragment thereof having function as a secreted protein of the metalloprotease class or having an antigenic determinant in common with the polypeptides of (i); or
  • a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 128 and more preferably, consists of the sequence recited in SEQ ID NO: 128.
  • the polypeptide having the sequence recited in SEQ ID NO: 128 is referred to hereafter as "the INSP003 polypeptide".
  • Polypeptides containing any combination of the seven INSP003 exons listed above are included in the first aspect of the invention.
  • the polypeptide having the sequence recited in SEQ ID NO:2 is referred to hereafter as "the INSP003 exon 1 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:4 is referred to hereafter as "the INSP003 exon 2 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:6 is referred to hereafter as "the INSP003 exon 3 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:8 is referred to hereafter as "the INSP003 exon 4 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 10 is referred to hereafter as "the INSP003 exon 5 polypeptide”.
  • polypeptide having the sequence recited in SEQ ID NO: 12 is referred to hereafter as "the INSP003 exon 6 polypeptide".
  • polypeptide having the sequence recited in SEQ ID NO: 14 is referred to hereafter as "the INSP003 exon 7 polypeptide”.
  • polypeptide which polypeptide:
  • (i) comprises an amino acid sequence as recited in SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:
  • (ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
  • a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 130 and more preferably, consists of the sequence recited in SEQ ID NO: 130.
  • the polypeptide having the sequence recited in SEQ ID NO: 130 is referred to hereafter as "the INSP004 polypeptide".
  • Polypeptides containing any combination of the fourteen INSP004 exons listed above are included in the first aspect of the invention.
  • the polypeptide having the sequence recited in SEQ ID NO: 16 is referred to hereafter as "the INSP004 exon 1 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 18 is referred to hereafter as "the INSP004 exon 2 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:20 is referred to hereafter as "the INSP004 exon 3 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:22 is referred to hereafter as "the INSP004 exon 4 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:24 is referred to hereafter as "the INSP004 exon 5 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:26 is referred to hereafter as "the INSP004 exon 6 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:28 is referred to hereafter as "the INSP004 exon 7 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:30 is referred to hereafter as "the INSP004 exon 8 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:32 is referred to hereafter as "the INSP004 exon 9 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:34 is referred to hereafter as "the INSP004 exon 10 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:36 is referred to hereafter as "the INSP004 exon 11 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:38 is referred to hereafter as "the INSP004 exon 12 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:40 is referred to hereafter as "the INSP004 exon 13 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:42 is referred to hereafter as "the INSP004 exon 14 polypeptide".
  • the invention provides a polypeptide, which polypeptide: (i) comprises an amino acid sequence as recited in SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and/or SEQ ID NO: 104;
  • (ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or
  • a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 134 and more preferably, consists of the sequence recited in SEQ ID NO: 134.
  • the polypeptide having the sequence recited in SEQ ID NO: 134 is referred to hereafter as "the INSP006 polypeptide".
  • Polypeptides containing any combination of the twenty-six INSP006 exons listed above are included in the first aspect of the invention.
  • the polypeptide having the sequence recited in SEQ ID NO: 54 is referred to hereafter as "the INSP006 exon 1 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:56 is referred to hereafter as "the INSP006 exon 2 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:58 is referred to hereafter as "the INSP006 exon 3 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:60 is referred to hereafter as "the INSP006 exon 4 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:62 is referred to hereafter as "the INSP006 exon 5 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:64 is referred to hereafter as "the INSP006 exon 6 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:66 is referred to hereafter as "the INSP006 exon 7 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:68 is referred to hereafter as "the INSP006 exon 8 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO: 70 is referred to hereafter as "the INSP006 exon 9 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:72 is referred to hereafter as "the INSP006 exon 10 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:74 is referred to hereafter as "the INSP006 exon 11 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:76 is referred to hereafter as "the INSP006 exon 12 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:78 is referred to hereafter as "the INSP006 exon 13 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:80 is referred to hereafter as "the INSP006 exon 14 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 82 is referred to hereafter as "the INSP006 exon 15 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:84 is referred to hereafter as "the INSP006 exon 16 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:86 is referred to hereafter as "the INSP006 exon 17 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:88 is referred to hereafter as "the INSP006 exon 18 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:90 is referred to hereafter as "the INSP006 exon 19 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:92 is referred to hereafter as "the INSP006 exon 20 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:94 is referred to hereafter as "the INSP006 exon 21 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:96 is referred to hereafter as "the INSP006 exon 22 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:98 is referred to hereafter as "the INSP006 exon 23 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO: 100 is referred to hereafter as "the INSP006 exon 24 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 102 is referred to hereafter as "the INSP006 exon 25 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO: 104 is referred to hereafter as "the INSP006 exon 26 polypeptide”.
  • the invention provides a polypeptide, which polypeptide:
  • (i) comprises an amino acid sequence as recited in SEQ ID NO: 106, SEQ ID NO: 108 and/or SEQ ID NO: 110;
  • (ii) is a fragment thereof which functions as a metalloprotease protein, preferably, of the stromelysin class or has an antigenic determinant in common with the polypeptides of (i); or
  • a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 136 and more preferably, consists of the sequence recited in SEQ ID NO: 136.
  • the polypeptide having the sequence recited in SEQ ID NO: 136 is referred to hereafter as "the INSP007 polypeptide". This is a partial sequence that forms part of the full length INSP007 sequence as this is set out below.
  • Polypeptides containing any combination of the three INSP007 exons listed above are also included in the first aspect of the invention.
  • the polypeptide having the sequence recited in SEQ ID NO: 106 is referred to hereafter as "the INSP007 exon 1 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 108 is referred to hereafter as "the INSP007 exon 2 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO: 110 is referred to hereafter as "the INSP007 exon 3 polypeptide".
  • the full length INSP007 sequence has now been obtained and this will be referred to herein as the INSP007a polypeptide.
  • the sequence of this polypeptide is recited in SEQ ID NO: 152. More preferably therefore, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 152 and more preferably, consists of the sequence recited in SEQ ID NO: 152.
  • This aspect of the invention thus provides a polypeptide, which polypeptide is a secreted polypeptide and which:
  • (i) comprises the amino acid sequence as recited in SEQ ID NO: 152;
  • (ii) is a fragment thereof which functions as a metalloprotease, preferably of the stromelysin class or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
  • polypeptides according to this aspect of the invention function as metalloproteases, preferably of the stromelysin class.
  • metalloprotease is well understood in the art and the skilled worker will readily be able to ascertain metalloprotease activity using one of a variety of assays known in the art.
  • a commonly- applied assay is quantitative [3H]gelatin assay (Martin et al., (1989) Kidney Int. 36, 790- 801).
  • Another assay gelatin zymography (Herron GS et al., J Biol Chem 1986;261 :2814- 2818).
  • BI260666 comes from a cervical carcinoma cell line.
  • An image clone (GenBank Ace: BE336821) from a renal cell adenocarcinoma library may represent an alternative splice variant of INSP007a that splices directly from exon 1 to 3, missing exon2.
  • the image clone contains an extra base at the boundary of the deleted exon. In the absence of the exon, this single nucleotide insertion leads to a frame shift and creates a downstream premature stop codon. This creates an alternative protein product that does not contain the active site residues and is predicted to be inactive. This protein is referred to herein as INSP007b.
  • polypeptide which polypeptide is a member of the metalloprotease family and which: i. comprises the amino acid sequence as recited in SEQ ID NO: 164; ii. is a fragment thereof or has an antigenic determinant in common with the polypeptides of (i); or iii. is a functional equivalent of (i) or (ii).
  • This polypeptide is catalytically inactive as a metalloprotease, but nevertheless may have some physiological role, such as a role in binding to polypeptides or other ligands to which the active INSP007a polypeptide binds and thus affecting the function of the catalytically active polypeptide.
  • the invention provides a polypeptide, which polypeptide: (i) comprises an amino acid sequence as recited in SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124 and/or SEQ ID NO: 126;
  • (ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
  • a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 138 and more preferably, consists of the sequence recited in SEQ ID NO:138.
  • the polypeptide having the sequence recited in SEQ ID NO:138 is referred to hereafter as "the INSP008 polypeptide".
  • Polypeptides containing any combination of the eight I SP008 exons listed above are included in the first aspect of the invention.
  • the polypeptide having the sequence recited in SEQ ID NO: 112 is referred to hereafter as "the INSP008 exon 1 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 114 is referred to hereafter as "the INSP008 exon 2 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO:116 is referred to hereafter as "the INSP008 exon 3 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO:l 18 is referred to hereafter as "the INSP008 exon 4 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 120 is referred to hereafter as "the INSP008 exon 5 polypeptide”.
  • polypeptide having the sequence recited in SEQ ID NO: 122 is referred to hereafter as "the INSP008 exon 6 polypeptide".
  • the polypeptide having the sequence recited in SEQ ID NO: 124 is referred to hereafter as "the INSP008 exon 7 polypeptide”.
  • the polypeptide having the sequence recited in SEQ ID NO: 126 is referred to hereafter as "the INSP008 exon 8 polypeptide”.
  • polypeptides according to the above-described aspects of the invention function as metalloproteases.
  • the term "metalloprotease” is well understood in the art and the skilled worker will readily be able to ascertain metalloprotease activity using one of a variety of assays known in the art.
  • the invention provides a purified nucleic acid molecule which encodes a polypeptide of the first aspect of the invention.
  • the purified nucleic acid molecule has the nucleic acid sequence as recited in SEQ ID NO:l (encoding the INSP003 exon 1 polypeptide), SEQ ID NO:3 (encoding the INSP003 exon 2 polypeptide), SEQ ID NO:5 (encoding the INSP003 exon 3 polypeptide), SEQ ID NO:7 (encoding the INSP003 exon 4 polypeptide), SEQ ID NO:9 (encoding the INSP003 exon 5 polypeptide), SEQ ID NO: 11 (encoding the INSP003 exon 6 polypeptide), SEQ ID NO: 13 (encoding the INSP003 exon 7 polypeptide), SEQ ID NO: 15 (encoding the INSP004 exon 1 polypeptide), SEQ ID NO: 17 (encoding the INSP004 exon 2 polypeptide), SEQ ID NO: 19
  • the invention provides a vector, such as an expression vector, that contains a nucleic acid molecule of the second or third aspect of the invention.
  • the invention provides a host cell transformed with a vector of the fourth aspect of the invention.
  • the invention provides a ligand which binds specifically to, and which preferably inhibits the metalloprotease activity of a polypeptide of the first aspect of the invention.
  • Ligands to a polypeptide according to the invention may come in various forms, including natural or modified substrates, enzymes, receptors, small organic molecules such as small natural or synthetic organic molecules of up to 2000Da, preferably 800Da or less, peptidomimetics, inorganic molecules, peptides, polypeptides, antibodies, structural or functional mimetics of the aforementioned.
  • the invention provides a compound that is effective to alter the expression of a natural gene which encodes a polypeptide of the first aspect of the invention or to regulate the activity of a polypeptide of the first aspect of the invention.
  • a compound of the seventh aspect of the invention may either increase (agonise) or decrease (antagonise) the level of expression of the gene or the activity of the polypeptide.
  • the identification of the function of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides allows for the design of screening methods capable of identifying compounds that are effective in the treatment and/or diagnosis of disease.
  • the invention provides a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, for use in therapy or diagnosis.
  • These molecules may also be used in the manufacture of a medicament for the treatment of cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
  • the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide of the first aspect of the invention or the activity of a polypeptide of the first aspect of the invention in tissue from said patient and comparing said level of expression or activity to a control level, wherein a level that is different to said control level is indicative of disease.
  • a method will preferably be carried out in vitro.
  • Similar methods may be used for monitoring the therapeutic treatment of disease in a patient, wherein altering the level of expression or activity of a polypeptide or nucleic acid molecule over the period of time towards a control level is indicative of regression of disease.
  • a preferred method for detecting polypeptides of the first aspect of the invention comprises the steps of: (a) contacting a ligand, such as an antibody, of the sixth aspect of the invention with a biological sample under conditions suitable for the formation of a ligand-polypeptide complex; and (b) detecting said complex.
  • a number of different such methods according to the ninth aspect of the invention exist, as the skilled reader will be aware, such as methods of nucleic acid hybridization with short probes, point mutation analysis, polymerase chain reaction (PCR) amplification and methods using antibodies to detect aberrant protein levels. Similar methods may be used on a short or long term basis to allow therapeutic treatment of a disease to be monitored in a patient.
  • the invention also provides kits that are useful in these methods for diagnosing disease.
  • the invention provides for the use of a polypeptide of the first aspect of the invention as a secreted protein, preferably as a metalloprotease.
  • a use according to this aspect of the invention may be as a metalloprotease, preferably of the stromelysin class.
  • this polypeptide may be used as an inactive form of the INSP007a polypeptide and may thus have properties in antagonising the function of the INSP007a polypeptide.
  • the invention provides a pharmaceutical composition comprising a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, in conjunction with a pharmaceutically-acceptable carrier.
  • the present invention provides a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, for use in the manufacture of a medicament for the diagnosis or treatment of a disease, such as cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
  • a disease such as cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
  • the invention provides a method of treating a disease in a patient comprising administering to the patient a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention.
  • the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an agonist.
  • the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an antagonist.
  • antagonists include antisense nucleic acid molecules, ribozymes and ligands, such as antibodies.
  • the invention provides transgenic or knockout non-human animals that have been transformed to express higher, lower or absent levels of a polypeptide of the first aspect of the invention.
  • Such transgenic animals are very useful models for the study of disease and may also be used in screening regimes for the identification of compounds that are effective in the treatment or diagnosis of such a disease.
  • polypeptide includes any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e. peptide isosteres. This term refers both to short chains (peptides and oligopeptides) and to longer chains (proteins).
  • the polypeptide of the present invention may be in the form of a mature protein or may be a pre-, pro- or prepro- protein that can be activated by cleavage of the pre-, pro- or prepro- portion to produce an active mature polypeptide.
  • the pre-, pro- or prepro- sequence may be a leader or secretory sequence or may be a sequence that is employed for purification of the mature polypeptide sequence.
  • polypeptide of the first aspect of the invention may form part of a fusion protein.
  • additional amino acid sequences which may contain secretory or leader sequences, pro-sequences, sequences which aid in purification, or sequences that confer higher protein stability, for example during recombinant production.
  • the mature polypeptide may be fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol).
  • Polypeptides may contain amino acids other than the 20 gene-encoded amino acids, modified either by natural processes, such as by post-translational processing or by chemical modification techniques which are well known in the art.
  • glycosylation lipid attachment, sulphation, gamma-carboxylation, for instance of glutamic acid residues, hydroxylation and ADP-ribosylation.
  • Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini.
  • blockage of the amino or carboxyl terminus in a polypeptide, or both, by a covalent modification is common in naturally-occurring and synthetic polypeptides and such modifications may be present in polypeptides of the present invention.
  • the modifications that occur in a polypeptide often will be a function of how the polypeptide is made.
  • the nature and extent of the modifications in large part will be determined by the post-translational modification capacity of the particular host cell and the modification signals that are present in the amino acid sequence of the polypeptide in question. For instance, glycosylation patterns vary between different types of host cell.
  • polypeptides of the present invention can be prepared in any suitable manner.
  • Such polypeptides include isolated naturally-occurring polypeptides (for example purified from cell culture), recombinantly-produced polypeptides (including fusion proteins), synthetically-produced polypeptides or polypeptides that are produced by a combination of these methods.
  • the functionally-equivalent polypeptides of the first aspect of the invention may be polypeptides that are homologous to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides.
  • Two polypeptides are said to be "homologous", as the term is used herein, if the sequence of one of the polypeptides has a high enough degree of identity or similarity to the sequence of the other polypeptide.
  • Homologous polypeptides therefore include natural biological variants (for example, allelic variants or geographical variations within the species from which the polypeptides are derived) and mutants (such as mutants containing amino acid substitutions, insertions or deletions) of the INSP003, INSP004, INSP006, INSP007 or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides.
  • natural biological variants for example, allelic variants or geographical variations within the species from which the polypeptides are derived
  • mutants such as mutants containing amino acid substitutions, insertions or deletions
  • Such mutants may include polypeptides in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code.
  • Typical such substitutions are among Ala, Val, Leu and He; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gin; among the basic residues Lys and Arg; or among the aromatic residues Phe and Tyr.
  • Particularly preferred are variants in which several, i.e. between 5 and 10, 1 and 5, 1 and 3, 1 and 2 or just 1 amino acids are substituted, deleted or added in any combination.
  • silent substitutions, additions and deletions which do not alter the properties and activities of the protein. Also especially preferred in this regard are conservative substitutions.
  • Such mutants also include polypeptides in which one or more of the amino acid residues includes a substituent group;
  • polypeptides of the first aspect of the invention have a degree of sequence identity with the INSP003, INSP004, INSP006, INSP007 or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides, or with active fragments thereof, of greater than 30%. More preferred polypeptides have degrees of identity of greater than 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or more, respectively.
  • the functionally-equivalent polypeptides of the first aspect of the invention may also be polypeptides which have been identified using one or more techniques of structural alignment.
  • the Inpharmatica Genome Threader technology that forms one aspect of the search tools used to generate the Biopendium search database may be used (see co-pending PCT patent application PCT/GBO 1/01105) to identify polypeptides of presently-unknown function which, while having low sequence identity as compared to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides, are predicted to have secreted molecule activity, by virtue of sharing significant structural homology with the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptide sequences.
  • polypeptides of the first aspect of the invention also include fragments of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides and fragments of the functional equivalents of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides, provided that those fragments retain metalloprotease activity or have an antigenic determinant in common with the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides.
  • fragment refers to a polypeptide having an amino acid sequence that is the same as part, but not all, of the amino acid sequence of the INSP003 polypeptides or one of its functional equivalents.
  • the fragments should comprise at least n consecutive amino acids from the sequence and, depending on the particular sequence, n preferably is 7 or more (for example, 8, 10, 12, 14, 16, 18, 20 or more). Small fragments may form an antigenic determinant.
  • INSP007b or INSP008 polypeptides may consist of combinations of 2, 3, 4, 5 etc. of neighbouring exon sequences in the polypeptide sequences.
  • the component exons of the INSP007a and INSP007b polypeptides are presented in SEQ ID Nos: 140, 142, 144, 146, 148 and 150 (INSP007a) and 154, 156, 158, 160 and 162 (INSP007b) respectively.
  • fragments may be "free-standing", i.e. not part of or fused to other amino acids or polypeptides, or they may be comprised within a larger polypeptide of which they form a part or region.
  • the fragment of the invention When comprised within a larger polypeptide, the fragment of the invention most preferably forms a single continuous region.
  • certain preferred embodiments relate to a fragment having a pre - and/or pro- polypeptide region fused to the amino terminus of the fragment and/or an additional region fused to the carboxyl terminus of the fragment.
  • several fragments may be comprised within a single larger polypeptide.
  • polypeptides of the present invention or their immunogenic fragments can be used to generate ligands, such as polyclonal or monoclonal antibodies, that are immunospecific for the polypeptides.
  • ligands such as polyclonal or monoclonal antibodies
  • Such antibodies may be employed to isolate or to identify clones expressing the polypeptides of the invention or to purify the polypeptides by affinity chromatography.
  • the antibodies may also be employed as diagnostic or therapeutic aids, amongst other applications, as will be apparent to the skilled reader.
  • immunospecific means that the antibodies have substantially greater affinity for the polypeptides of the invention than their affinity for other related polypeptides in the prior art.
  • antibody refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')2 and Fv, which are capable of binding to the antigenic determinant in question. Such antibodies thus bind to the polypeptides of the first aspect of the invention.
  • substantially greater affinity we mean that there is a measurable increase in the affinity for a polypeptide of the invention as compared with the affinity for known secreted proteins.
  • the affinity is at least 1.5-fold, 2-fold, 5-fold 10-fold, 100-fold, 10 3 -fold, 10 4 - fold, 10 5 -fold or 10 6 -fold greater for a polypeptide of the invention than for known secreted proteins such as metalloproteases.
  • a selected mammal such as a mouse, rabbit, goat or horse
  • a polypeptide of the first aspect of the invention may be immunised with a polypeptide of the first aspect of the invention.
  • the polypeptide used to immunise the animal can be derived by recombinant DNA technology or can be synthesized chemically.
  • the polypeptide can be conjugated to a carrier protein.
  • Commonly used carriers to which the polypeptides may be chemically coupled include bovine serum albumin, thyroglobulin and keyhole limpet haemocyanin.
  • the coupled polypeptide is then used to immunise the animal. Serum from the immunised animal is collected and treated according to known procedures, for example by immunoaffinity chromatography.
  • Monoclonal antibodies to the polypeptides of the first aspect of the invention can also be readily produced by one skilled in the art.
  • the general methodology for making monoclonal antibodies using hybridoma technology is well known (see, for example, Kohler, G. and Milstein, C, Nature 256: 495-497 (1975); Kozbor et al, Immunology Today 4: 72 (1983); Cole et al, 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985).
  • Panels of monoclonal antibodies produced against the polypeptides of the first aspect of the invention can be screened for various properties, i.e., for isotype, epitope, affinity, etc.
  • Monoclonal antibodies are particularly useful in purification of the individual polypeptides against which they are directed.
  • genes encoding the monoclonal antibodies of interest may be isolated from hybridomas, for instance by PCR techniques known in the art, and cloned and expressed in appropriate vectors.
  • Chimeric antibodies in which non-human variable regions are joined or fused to human constant regions (see, for example, Liu et al, Proc. Natl. Acad. Sci. USA, 84, 3439 (1987)), may also be of use.
  • the antibody may be modified to make it less immunogenic in an individual, for example by humanisation (see Jones et al, Nature, 321, 522 (1986); Verhoeyen et al, Science, 239, 1534 (1988); Kabat et al, J. Immunol., 147, 1709 (1991); Queen et al, Proc. Natl Acad. Sci. USA, 86, 10029 (1989); Gorman et al, Proc. Natl Acad. Sci. USA, 88, 34181 (1991); and Hodgson et al, Bio/Technology, 9, 421 (1991)).
  • humanisation see Jones et al, Nature, 321, 522 (1986); Verhoeyen et al, Science, 239, 1534 (1988); Kabat et al, J. Immunol., 147, 1709 (1991); Queen et al, Proc. Natl Acad. Sci. USA, 86, 10029 (1989); Gorman et
  • humanised antibody refers to antibody molecules in which the CDR amino acids and selected other amino acids in the variable domains of the heavy and/or light chains of a non-human donor antibody have been substituted in place of the equivalent amino acids in a human antibody.
  • the humanised antibody thus closely resembles a human antibody but has the binding ability of the donor antibody.
  • the antibody may be a "bispecific" antibody, that is an antibody having two different antigen binding domains, each domain being directed against a different epitope.
  • Phage display technology may be utilised to select genes which encode antibodies with binding activities towards the polypeptides of the invention either from repertoires of PCR amplified V-genes of lymphocytes from humans screened for possessing the relevant antibodies, or from naive libraries (McCafferty, J. et al, (1990), Nature 348, 552-554; Marks, J. et al, (1992) Biotechnology 10, 779-783).
  • the affinity of these antibodies can also be improved by chain shuffling (Clackson, T. et al, (1991) Nature 352, 624-628).
  • Antibodies generated by the above techniques have additional utility in that they may be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA).
  • the antibodies can be labelled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme.
  • Preferred nucleic acid molecules of the second and third aspects of the invention are those which encode the polypeptide sequences recited in SEQ ID NO:2, SEQ ID NO:4,
  • nucleic acid molecules may be used in the methods and applications described herein.
  • the nucleic acid molecules of the invention preferably comprise at least n consecutive nucleotides from the sequences disclosed herein where, depending on the particular sequence, n is 10 or more (for example, 12, 14, 15, 18, 20, 25, 30, 35, 40 or more).
  • nucleic acid molecules of the invention also include sequences that are complementary to nucleic acid molecules described above (for example, for antisense or probing purposes).
  • Nucleic acid molecules of the present invention may be in the form of RNA, such as mRNA, or in the form of DNA, including, for instance cDNA, synthetic DNA or genomic DNA. Such nucleic acid molecules may be obtained by cloning, by chemical synthetic techniques or by a combination thereof. The nucleic acid molecules can be prepared, for example, by chemical synthesis using techniques such as solid phase phosphoramidite chemical synthesis, from genomic or cDNA libraries or by separation from an organism. RNA molecules may generally be generated by the in vitro or in vivo transcription of DNA sequences.
  • the nucleic acid molecules may be double-stranded or single-stranded.
  • Single-stranded DNA may be the coding strand, also known as the sense strand, or it may be the non- coding strand, also referred to as the anti-sense strand.
  • the term "nucleic acid molecule” also includes analogues of DNA and RNA, such as those containing modified backbones, and peptide nucleic acids (PNA).
  • PNA peptide nucleic acids
  • PNA refers to an antisense molecule or an anti-gene agent which comprises an oligonucleotide of at least five nucleotides in length linked to a peptide backbone of amino acid residues, which preferably ends in lysine.
  • PNAs may be pegylated to extend their lifespan in a cell, where they preferentially bind complementary single stranded DNA and RNA and stop transcript elongation (Nielsen, P.E. et al. (1993) Anticancer Drug Des. 8:53-63).
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:2 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:4 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:3.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:6 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:5.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 8 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:7.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 10 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:9.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 12 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 1.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 14 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 13.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 16 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 15.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 18 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 17.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:20 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 19.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:22 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:21.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:24 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:23.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:26 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:25.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:28 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:27.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:30 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:29.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:32 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:31.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:34 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:33.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:36 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:35.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:38 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:37.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:40 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:39.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:42 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:41
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 54 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:53.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:56 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:55.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:58 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:57.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:60 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:59.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:62 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:61.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:64 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:63.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:66 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:65.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:68 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:67.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:70 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:69.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:72 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:71.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 74 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:73.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:76 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 75.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:78 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:77.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 80 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:79.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 82 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:81.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 84 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:83.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 86 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:85.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 88 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:87.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:90 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:89.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:92 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:91.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 94 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:93.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:96 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:95.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:98 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:97.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 100 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:99.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 102 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 101.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 104 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 103.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 106 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 105.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 108 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 107.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 110 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 109.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:112 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 11
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 114 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 13.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:116 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 15.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO:118 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 17.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 120 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 19.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 122 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:121.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 124 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 123.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 126 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 125.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 128 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 127.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 130 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 129.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 134 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 133.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 136 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 135.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 138 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 137.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 152 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:151.
  • a nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 164 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 163.
  • SEQ ID NO:2 SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68,
  • nucleic acid molecules may include, but are not limited to, the coding sequence for the mature polypeptide by itself; the coding sequence for the mature polypeptide and additional coding sequences, such as those encoding a leader or secretory sequence, such as a pro-, pre- or prepro- polypeptide sequence; the coding sequence of the mature polypeptide, with or without the aforementioned additional coding sequences, together with further additional, non-coding sequences, including non-coding 5' and 3' sequences, such as the transcribed, non-translated sequences that play a role in transcription (including termination signals), ribosome binding and mRNA stability.
  • the nucleic acid molecules may also include additional sequences which encode additional amino acids, such as those which provide additional functionalities.
  • nucleic acid molecules of the second and third aspects of the invention may also encode the fragments or the functional equivalents of the polypeptides and fragments of the first aspect of the invention.
  • a nucleic acid molecule may be a naturally- occurring variant such as a naturally-occurring allelic variant, or the molecule may be a variant that is not known to occur naturally.
  • non-naturally occurring variants of the nucleic acid molecule may be made by mutagenesis techniques, including those applied to nucleic acid molecules, cells or organisms.
  • variants in this regard are variants that differ from the aforementioned nucleic acid molecules by nucleotide substitutions, deletions or insertions. The substitutions, deletions or insertions may involve one or more nucleotides.
  • the variants may be altered in coding or non-coding regions or both. Alterations in the coding regions may produce conservative or non-conservative amino acid substitutions, deletions or insertions.
  • the nucleic acid molecules of the invention can also be engineered, using methods generally known in the art, for a variety of reasons, including modifying the cloning, processing, and/or expression of the gene product (the polypeptide). DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides are included as techniques which may be used to engineer the nucleotide sequences. Site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations and so forth.
  • Nucleic acid molecules which encode a polypeptide of the first aspect of the invention may be ligated to a heterologous sequence so that the combined nucleic acid molecule encodes a fusion protein.
  • Such combined nucleic acid molecules are included within the second or third aspects of the invention.
  • a fusion protein that can be recognised by a commercially-available antibody.
  • a fusion protein may also be engineered to contain a cleavage site located between the sequence of the polypeptide of the invention and the sequence of a heterologous protein so that the polypeptide may be cleaved and purified away from the heterologous protein.
  • the nucleic acid molecules of the invention also include antisense molecules that are partially complementary to nucleic acid molecules encoding polypeptides of the present invention and that therefore hybridize to the encoding nucleic acid molecules (hybridization).
  • antisense molecules such as oligonucleotides, can be designed to recognise, specifically bind to and prevent transcription of a target nucleic acid encoding a polypeptide of the invention, as will be known by those of ordinary skill in the art (see, for example, Cohen, J.S., Trends in Pharm. Sci., 10, 435 (1989), Okano, J. Neurochem. 56, 560 (1991); O'Connor, J. Neurochem 56, 560 (1991); Lee et al, Nucleic Acids Res 6, 3073 (1979); Cooney et al, Science 241, 456 (1988); Dervan et al, Science 251, 1360 (1991).
  • hybridization refers to the association of two nucleic acid molecules with one another by hydrogen bonding. Typically, one molecule will be fixed to a solid support and the other will be free in solution. Then, the two molecules may be placed in contact with one another under conditions that favour hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase molecule to the solid support (Denhardt's reagent or BLOTTO); the concentration of the molecules; use of compounds to increase the rate of association of molecules (dextran sulphate or polyethylene glycol); and the stringency of the washing conditions following hybridization (see Sambrook et al. [supra]).
  • the inhibition of hybridization of a completely complementary molecule to a target molecule may be examined using a hybridization assay, as known in the art (see, for example, Sambrook et al [supra]).
  • a substantially homologous molecule will then compete for and inhibit the binding of a completely homologous molecule to the target molecule under various conditions of stringency, as taught in Wahl, G.M. and S.L. Berger (1987; Methods Enzymol. 152:399-407) and Kimmel, A.R. (1987; Methods Enzymol. 152:507-511).
  • Stringency refers to conditions in a hybridization reaction that favour the association of very similar molecules over association of molecules that differ.
  • High stringency hybridisation conditions are defined as overnight incubation at 42(C in a solution comprising 50% formamide, 5XSSC (150mM NaCl, 15mM trisodium citrate), 50mM sodium phosphate (pH7.6), 5x Denhardts solution, 10% dextran sulphate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1X SSC at approximately 65(C.
  • Low stringency conditions involve the hybridisation reaction being carried out at 35(C (see Sambrook et al. [supra]).
  • the conditions used for hybridization are those of high stringency.
  • Preferred embodiments of this aspect of the invention are nucleic acid molecules that are at least 70% identical over their entire length to a nucleic acid molecule encoding the INSP003 polypeptide (SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 128), the INSP004 polypeptide (SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 and SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO: 130), the INSP006 polypeptide (SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, S
  • a nucleic acid molecule according to this aspect of the invention comprises a region that is at least 80% identical over its entire length to the nucleic acid molecule having the sequence given in SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO: 1 1 , SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO
  • nucleic acid molecules at least 90%, preferably at least 95%, more preferably at least 98% or 99% identical over their entire length to the same are particularly preferred.
  • Preferred embodiments in this respect are nucleic acid molecules that encode polypeptides which retain substantially the same biological function or activity as the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides.
  • the invention also provides a process for detecting a nucleic acid molecule of the invention, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridizing conditions to form duplexes; and (b) detecting any such duplexes that are formed.
  • a nucleic acid molecule as described above may be used as a hybridization probe for RNA, cDNA or genomic DNA, in order to isolate full-length cDNAs and genomic clones encoding the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides and to isolate cDNA and genomic clones of homologous or orthologous genes that have a high sequence similarity to the gene encoding this polypeptide.
  • the sequencing process may be automated using machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno, NV), the Peltier Thermal Cycler (PTC200; MJ Research, Watertown, MA) and the ABI Catalyst and 373 and 377 DNA Sequencers (Perkin Elmer).
  • machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno, NV), the Peltier Thermal Cycler (PTC200; MJ Research, Watertown, MA) and the ABI Catalyst and 373 and 377 DNA Sequencers (Perkin Elmer).
  • One method for isolating a nucleic acid molecule encoding a polypeptide with an equivalent function to that of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides is to probe a genomic or cDNA library with a natural or artificially-designed probe using standard procedures that are recognised in the art (see, for example, "Current Protocols in Molecular Biology", Ausubel et al. (eds). Greene Publishing Association and John Wiley Interscience, New York, 1989,1992).
  • Probes comprising at least 15, preferably at least 30, and more preferably at least 50, contiguous bases that correspond to, or are complementary to, nucleic acid sequences from the appropriate encoding gene (SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:l l, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69
  • Such probes may be labelled with an analytically-detectable reagent to facilitate their identification.
  • Useful reagents include, but are not limited to, radioisotopes, fluorescent dyes and enzymes that are capable of catalysing the formation of a detectable product.
  • the ordinarily skilled artisan will be capable of isolating complementary copies of genomic DNA, cDNA or RNA polynucleotides encoding proteins of interest from human, mammalian or other animal sources and screening such sources for related sequences, for example, for additional members of the family, type and/or subtype.
  • isolated cDNA sequences will be incomplete, in that the region encoding the polypeptide will be cut short, normally at the 5' end.
  • Several methods are available to obtain full length cDNAs, or to extend short cDNAs. Such sequences may be extended utilising a partial nucleotide sequence and employing various methods known in the art to detect upstream sequences such as promoters and regulatory elements. For example, one method which may be employed is based on the method of Rapid Amplification of cDNA Ends (RACE; see, for example, Frohman et al, PNAS USA 85, 8998-9002, 1988).
  • RACE Rapid Amplification of cDNA Ends
  • Another method which may be used is capture PCR which involves PCR amplification of DNA fragments adjacent a known sequence in human and yeast artificial chromosome DNA (Lagerstrom, M. et al (1991) PCR Methods Applic, 1, 111-119). Another method which may be used to retrieve unknown sequences is that of Parker, J.D. et al. (1991); Nucleic Acids Res. 19:3055- 3060). Additionally, one may use PCR, nested primers, and PromoterFinderTM libraries to walk genomic DNA (Clontech, Palo Alto, CA). This process avoids the need to screen libraries and is useful in finding intron/exon junctions.
  • libraries that have been size-selected to include larger cDNAs.
  • random-primed libraries are preferable, in that they will contain more sequences that contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA.
  • Genomic libraries may be useful for extension of sequence into 5' non-transcribed regulatory regions.
  • the nucleic acid molecules of the present invention may be used for chromosome localisation.
  • a nucleic acid molecule is specifically targeted to, and can hybridize with, a particular location on an individual human chromosome.
  • the mapping of relevant sequences to chromosomes according to the present invention is an important step in the confirmatory correlation of those sequences with the gene-associated disease. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found in, for example, V. McKusick, Mendelian Inheritance in Man (available on-line through Johns Hopkins University Welch Medical Library).
  • the relationships between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the disease or syndrome has been crudely localised by genetic linkage to a particular genomic region, any sequences mapping to that area may represent associated or regulatory genes for further investigation.
  • the nucleic acid molecule may also be used to detect differences in the chromosomal location due to translocation, inversion, etc. among normal, carrier, or affected individuals.
  • the nucleic acid molecules of the present invention are also valuable for tissue localisation.
  • Such techniques allow the determination of expression patterns of the polypeptide in tissues by detection of the mRNAs that encode them.
  • These techniques include in situ hybridization techniques and nucleotide amplification techniques, such as PCR. Results from these studies provide an indication of the normal functions of the polypeptide in the organism.
  • comparative studies of the normal expression pattern of mRNAs with that of mRNAs encoded by a mutant gene provide valuable insights into the role of mutant polypeptides in disease. Such inappropriate expression may be of a temporal, spatial or quantitative nature.
  • Gene silencing approaches may also be undertaken to down-regulate endogenous expression of a gene encoding a polypeptide of the invention.
  • RNA interference (Elbashir, SM et al, Nature 2001, 411, 494-498) is one method of sequence specific post- transcriptional gene silencing that may be employed. Short dsRNA oligonucleotides are synthesised in vitro and introduced into a cell. The sequence specific binding of these dsRNA oligonucleotides triggers the degradation of target mRNA, reducing or ablating target protein expression.
  • Efficacy of the gene silencing approaches assessed above may be assessed through the measurement of polypeptide expression (for example, by Western blotting), and at the RNA level using TaqMan-based methodologies.
  • the vectors of the present invention comprise nucleic acid molecules of the invention and may be cloning or expression vectors.
  • the host cells of the invention which may be transformed, transfected or transduced with the vectors of the invention may be prokaryotic or eukaryotic.
  • the polypeptides of the invention may be prepared in recombinant form by expression of their encoding nucleic acid molecules in vectors contained within a host cell. Such expression methods are well known to those of skill in the art and many are described in detail by Sambrook et al (supra) and Fernandez & Hoeffler (1998, eds. "Gene expression systems. Using nature for the art of expression”. Academic Press, San Diego, London, Boston, New York, Sydney, Tokyo, Toronto).
  • any system or vector that is suitable to maintain, propagate or express nucleic acid molecules to produce a polypeptide in the required host may be used.
  • the appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those described in Sambrook et al. , (supra).
  • the encoding gene can be placed under the control of a control element such as a promoter, ribosome binding site (for bacterial expression) and, optionally, an operator, so that the DNA sequence encoding the desired polypeptide is transcribed into RNA in the transformed host cell.
  • suitable expression systems include, for example, chromosomal, episomal and virus-derived systems, including, for example, vectors derived from: bacterial plasmids, bacteriophage, transposons, yeast epi somes, insertion elements, yeast chromosomal elements, viruses such as baculoviruses, papova viruses such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, or combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, including cosmids and phagemids.
  • Human artificial chromosomes may also be employed to deliver larger fragments of DNA than can be contained and expressed in a plasmid.
  • Particularly suitable expression systems include microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (for example, baculovirus); plant cell systems transformed with virus expression vectors (for example, cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (for example, Ti or pBR322 plasmids); or animal cell systems.
  • Cell-free translation systems can also be employed to produce the polypeptides of the invention.
  • nucleic acid molecules encoding a polypeptide of the present invention into host cells can be effected by methods described in many standard laboratory manuals, such as Davis et al, Basic Methods in Molecular Biology (1986) and Sambrook et al, [supra]. Particularly suitable methods include calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid- mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection (see Sambrook et al, 1989 [supra]; Ausubel et al, 1991 [supra]; Spector, Goldman & Leinwald, 1998). In eukaryotic cells, expression systems may either be transient (for example, episomal) or permanent (chromosomal integration) according to the needs of the system.
  • the encoding nucleic acid molecule may or may not include a sequence encoding a control sequence, such as a signal peptide or leader sequence, as desired, for example, for secretion of the translated polypeptide into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment.
  • a control sequence such as a signal peptide or leader sequence
  • These signals may be endogenous to the polypeptide or they may be heterologous signals.
  • Leader sequences can be removed by the bacterial host in post-translational processing.
  • regulatory sequences that allow for regulation of the expression of the polypeptide relative to the growth of the host cell.
  • regulatory sequences are those which cause the expression of a gene to be increased or decreased in response to a chemical or physical stimulus, including the presence of a regulatory compound or to various temperature or metabolic conditions.
  • Regulatory sequences are those non-translated regions of the vector, such as enhancers, promoters and 5' and 3' untranslated regions. These interact with host cellular proteins to carry out transcription and translation. Such regulatory sequences may vary in their strength and specificity. Depending on the vector system and host utilised, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used.
  • inducible promoters such as the hybrid lacZ promoter of the Bluescript phagemid (Stratagene, LaJolla, CA) or pSportlTM plasmid (Gibco BRL) and the like may be used.
  • the baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (for example, heat shock, RUBISCO and storage protein genes) or from plant viruses (for example, viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of the sequence, vectors based on SV40 or EBV may be used with an appropriate selectable marker.
  • An expression vector is constructed so that the particular nucleic acid coding sequence is located in the vector with the appropriate regulatory sequences, the positioning and orientation of the coding sequence with respect to the regulatory sequences being such that the coding sequence is transcribed under the "control" of the regulatory sequences, i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence. In some cases it may be necessary to modify the sequence so that it may be attached to the control sequences with the appropriate orientation; i.e., to maintain the reading frame.
  • the control sequences and other regulatory sequences may be ligated to the nucleic acid coding sequence prior to insertion into a vector. Alternatively, the coding sequence can be cloned directly into an expression vector that already contains the control sequences and an appropriate restriction site.
  • cell lines which stably express the polypeptide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media.
  • the purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells that successfully express the introduced sequences.
  • Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
  • Mammalian cell lines available as hosts for expression are known in the art and include many immortalised cell lines available from the American Type Culture Collection (ATCC) including, but not limited to, Chinese hamster ovary (CHO), HeLa, baby hamster kidney (BHK), monkey kidney (COS), C127, 3T3, BHK, HEK 293, Bowes melanoma and human hepatocellular carcinoma (for example Hep G2) cells and a number of other cell lines.
  • ATCC American Type Culture Collection
  • CHO Chinese hamster ovary
  • BHK baby hamster kidney
  • COS monkey kidney
  • C127, 3T3, BHK, HEK 293, Bowes melanoma and human hepatocellular carcinoma (for example Hep G2) cells and a number of other cell lines.
  • the materials for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA (the "MaxBac" kit).
  • host cells include insect cells such as Drosophila S2 and Spodoptera Sf9 cells.
  • Examples of particularly preferred bacterial host cells include streptococci, staphylococci, E. coli, Streptomyces and Bacillus subtilis cells.
  • yeast cells for example, S. cerevisiae
  • Aspergillus cells Any number of selection systems are known in the art that may be used to recover transformed cell lines. Examples include the herpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11 :223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1980) Cell 22:817-23) genes that can be employed in tk- or aprt ⁇ cells, respectively.
  • antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dihydrofolate reductase (DHFR) that confers resistance to methotrexate (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14) and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. Additional selectable genes have been described, examples of which will be clear to those of skill in the art.
  • marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed.
  • transformed cells containing the appropriate sequences can be identified by the absence of marker gene function.
  • a marker gene can be placed in tandem with a sequence encoding a polypeptide of the invention under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
  • host cells that contain a nucleic acid sequence encoding a polypeptide of the invention and which express said polypeptide may be identified by a variety of procedures known to those of skill in the art.
  • DNA-DNA or DNA-RNA hybridizations include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassays, for example, fluorescence activated cell sorting (FACS) or immunoassay techniques (such as the enzyme-linked immunosorbent assay [ELISA] and radioimmunoassay [RIA]), that include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein (see Hampton, R. et al (1990) Serological Methods, a Laboratory Manual, APS Press, St Paul, MN) and Maddox, D.E. et al. (1983) J. Exp. Med, 158, 1211-1216).
  • FACS fluorescence activated cell sorting
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmunoassay
  • Means for producing labelled hybridization or PCR probes for detecting sequences related to nucleic acid molecules encoding polypeptides of the present invention include oligolabelling, nick translation, end-labelling or PCR amplification using a labelled polynucleotide.
  • sequences encoding the polypeptide of the invention may be cloned into a vector for the production of an mRNA probe.
  • RNA polymerase such as T7, T3 or SP6 and labelled nucleotides. These procedures may be conducted using a variety of commercially available kits (Pharmacia & Upjohn, (Kalamazoo, MI); Promega (Madison WI); and U.S. Biochemical Corp., Cleveland, OH)).
  • Suitable reporter molecules or labels include radionuclides, enzymes and fluorescent, chemiluminescent or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • Nucleic acid molecules according to the present invention may also be used to create transgenic animals, particularly rodent animals. Such transgenic animals form a further aspect of the present invention. This may be done locally by modification of somatic cells, or by germ line therapy to incorporate heritable modifications. Such transgenic animals may be particularly useful in the generation of animal models for drug molecules effective as modulators of the polypeptides of the present invention.
  • the polypeptide can be recovered and purified from recombinant cell cultures by well- known methods including ammonium sulphate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. High performance liquid chromatography is particularly useful for purification. Well known techniques for refolding proteins may be employed to regenerate an active conformation when the polypeptide is denatured during isolation and or purification.
  • Specialised vector constructions may also be used to facilitate purification of proteins, as desired, by joining sequences encoding the polypeptides of the invention to a nucleotide sequence encoding a polypeptide domain that will facilitate purification of soluble proteins.
  • purification-facilitating domains include metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilised metals, protein A domains that allow purification on immobilised immunoglobulin, and the domain utilised in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, WA).
  • cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the polypeptide of the invention may be used to facilitate purification.
  • One such expression vector provides for expression of a fusion protein containing the polypeptide of the invention fused to several histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification by IMAC (immobilised metal ion affinity chromatography as described in Porath, J. et al. (1992), Prof Exp.
  • the polypeptide is to be expressed for use in screening assays, generally it is preferred that it be produced at the surface of the host cell in which it is expressed. In this event, the host cells may be harvested prior to use in the screening assay, for example using techniques such as fluorescence activated cell sorting (FACS) or immunoaffinity techniques. If the polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the expressed polypeptide. If polypeptide is produced intracellularly, the cells must first be lysed before the polypeptide is recovered.
  • the polypeptide of the invention can be used to screen libraries of compounds in any of a variety of drug screening techniques.
  • Such compounds may activate (agonise) or inhibit (antagonise) the level of expression of the gene or the activity of the polypeptide of the invention and form a further aspect of the present invention.
  • Preferred compounds are effective to alter the expression of a natural gene which encodes a polypeptide of the first aspect of the invention or to regulate the activity of a polypeptide of the first aspect of the invention.
  • Agonist or antagonist compounds may be isolated from, for example, cells, cell-free preparations, chemical libraries or natural product mixtures. These agonists or antagonists may be natural or modified substrates, ligands, enzymes, receptors or structural or functional mimetics. For a suitable review of such screening techniques, see Coligan et al, Current Protocols in Immunology l(2):Chapter 5 (1991).
  • Compounds that are most likely to be good antagonists are molecules that bind to the polypeptide of the invention without inducing the biological effects of the polypeptide upon binding to it.
  • Potential antagonists include small organic molecules, peptides, polypeptides and antibodies that bind to the polypeptide of the invention and thereby inhibit or extinguish its activity. In this fashion, binding of the polypeptide to normal cellular binding molecules may be inhibited, such that the normal biological activity of the polypeptide is prevented.
  • the polypeptide of the invention that is employed in such a screening technique may be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly.
  • screening procedures may involve using appropriate cells or cell membranes that express the polypeptide that are contacted with a test compound to observe binding, or stimulation or inhibition of a functional response.
  • the functional response of the cells contacted with the test compound is then compared with control cells that were not contacted with the test compound.
  • Such an assay may assess whether the test compound results in a signal generated by activation of the polypeptide, using an appropriate detection system.
  • Inhibitors of activation are generally assayed in the presence of a known agonist and the effect on activation by the agonist in the presence of the test compound is observed.
  • a preferred method for identifying an agonist or antagonist compound of a polypeptide of the present invention comprises:
  • a further preferred method for identifying an agonist or antagonist of a polypeptide of the invention comprises:
  • the general methods that are described above may further comprise conducting the identification of agonist or antagonist in the presence of labelled or unlabelled ligand for the polypeptide.
  • the method for identifying agonist or antagonist of a polypeptide of the present invention comprises: determining the inhibition of binding of a ligand to cells which have a polypeptide of the invention on the surface thereof, or to cell membranes containing such a polypeptide, in the presence of a candidate compound under conditions to permit binding to the polypeptide, and determining the amount of ligand bound to the polypeptide.
  • a compound capable of causing reduction of binding of a ligand is considered to be an agonist or antagonist.
  • the ligand is labelled.
  • a method of screening for a polypeptide antagonist or agonist compound comprises the steps of: (a) incubating a labelled ligand with a whole cell expressing a polypeptide according to the invention on the cell surface, or a cell membrane containing a polypeptide of the invention,
  • step (b) measuring the amount of labelled ligand bound to the whole cell or the cell membrane; (c) adding a candidate compound to a mixture of labelled ligand and the whole cell or the cell membrane of step (a) and allowing the mixture to attain equilibrium;
  • step (d) measuring the amount of labelled ligand bound to the whole cell or the cell membrane after step (c);
  • step (e) comparing the difference in the labelled ligand bound in step (b) and (d), such that the compound which causes the reduction in binding in step (d) is considered to be an agonist or antagonist.
  • polypeptides may be found to modulate a variety of physiological and pathological processes in a dose-dependent manner in the above-described assays.
  • the "functional equivalents" of the polypeptides of the invention include polypeptides that exhibit any of the same modulatory activities in the above-described assays in a dose- dependent manner.
  • the degree of dose-dependent activity need not be identical to that of the polypeptides of the invention, preferably the "functional equivalents" will exhibit substantially similar dose-dependence in a given activity assay compared to the polypeptides of the invention.
  • simple binding assays may be used, in which the adherence of a test compound to a surface bearing the polypeptide is detected by means of a label directly or indirectly associated with the test compound or in an assay involving competition with a labelled competitor.
  • competitive drug screening assays may be used, in which neutralising antibodies that are capable of binding the polypeptide specifically compete with a test compound for binding. In this manner, the antibodies can be used to detect the presence of any test compound that possesses specific binding affinity for the polypeptide.
  • Assays may also be designed to detect the effect of added test compounds on the production of mRNA encoding the polypeptide in cells.
  • an ELISA may be constructed that measures secreted or cell-associated levels of polypeptide using monoclonal or polyclonal antibodies by standard methods known in the art, and this can be used to search for compounds that may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues. The formation of binding complexes between the polypeptide and the compound being tested may then be measured.
  • Assay methods that are also included within the terms of the present invention are those that involve the use of the genes and polypeptides of the invention in overexpression or ablation assays. Such assays involve the manipulation of levels of these genes/polypeptides in cells and assessment of the impact of this manipulation event on the physiology of the manipulated cells. For example, such experiments reveal details of signaling and metabolic pathways in which the particular genes/polypeptides are implicated, generate information regarding the identities of polypeptides with which the studied polypeptides interact and provide clues as to methods by which related genes and proteins are regulated.
  • Another technique for drug screening which may be used provides for high throughput screening of compounds having suitable binding affinity to the polypeptide of interest (see International patent application WO84/03564).
  • This method large numbers of different small test compounds are synthesised on a solid substrate, which may then be reacted with the polypeptide of the invention and washed.
  • One way of immobilising the polypeptide is to use non-neutralising antibodies. Bound polypeptide may then be detected using methods that are well known in the art. Purified polypeptide can also be coated directly onto plates for use in the aforementioned drug screening techniques.
  • the polypeptide of the invention may be used to identify membrane-bound or soluble receptors, through standard receptor binding techniques that are known in the art, such as ligand binding and crosslinking assays in which the polypeptide is labelled with a radioactive isotope, is chemically modified, or is fused to a peptide sequence that facilitates its detection or purification, and incubated with a source of the putative receptor (for example, a composition of cells, cell membranes, cell supernatants, tissue extracts, or bodily fluids).
  • a source of the putative receptor for example, a composition of cells, cell membranes, cell supernatants, tissue extracts, or bodily fluids.
  • the efficacy of binding may be measured using biophysical techniques such as surface plasmon resonance and spectroscopy.
  • Binding assays may be used for the purification and cloning of the receptor, but may also identify agonists and antagonists of the polypeptide, that compete with the binding of the polypeptide to its receptor. Standard methods for conducting screening assays are well understood in the art.
  • the invention also includes a screening kit useful in the methods for identifying agonists, antagonists, ligands, receptors, substrates, enzymes, that are described above.
  • the invention includes the agonists, antagonists, ligands, receptors, substrates and enzymes, and other compounds which modulate the activity or antigenicity of the polypeptide of the invention discovered by the methods that are described above.
  • compositions comprising a polypeptide, nucleic acid, ligand or compound of the invention in combination with a suitable pharmaceutical carrier.
  • These compositions may be suitable as therapeutic or diagnostic reagents, as vaccines, or as other immunogenic compositions, as outlined in detail below.
  • a composition containing a polypeptide, nucleic acid, ligand or compound [X] is "substantially free of impurities [herein, Y] when at least 85% by weight of the total X+Y in the composition is X.
  • X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95%, 98% or even 99% by weight.
  • compositions should preferably comprise a therapeutically effective amount of the polypeptide, nucleic acid molecule, ligand, or compound of the invention.
  • therapeutically effective amount refers to an amount of a therapeutic agent needed to treat, ameliorate, or prevent a targeted disease or condition, or to exhibit a detectable therapeutic or preventative effect.
  • the therapeutically effective dose can be estimated initially either in cell culture assays, for example, of neoplastic cells, or in animal models, usually mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • an effective amount for a human subject will depend upon the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. This amount can be determined by routine experimentation and is within the judgement of the clinician. Generally, an effective dose will be from 0.01 mg/kg to 50 mg/kg, preferably 0.05 mg/kg to 10 mg/kg. Compositions may be administered individually to a patient or may be administered in combination with other agents, drugs or hormones.
  • a pharmaceutical composition may also contain a pharmaceutically acceptable carrier, for administration of a therapeutic agent.
  • a pharmaceutically acceptable carrier for administration of a therapeutic agent.
  • Such carriers include antibodies and other polypeptides, genes and other therapeutic agents such as liposomes, provided that the carrier does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity.
  • Suitable carriers may be large, slowly metabolised macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
  • Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulphates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like.
  • mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulphates, and the like
  • organic acids such as acetates, propionates, malonates, benzoates, and the like.
  • Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
  • compositions of the invention can be administered directly to the subject.
  • the subjects to be treated can be animals; in particular, human subjects can be treated.
  • compositions utilised in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra- arterial, intramedullary, intrathecal, intraventricular, transdermal or transcutaneous applications (for example, see WO98/20734), subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, intravaginal or rectal means.
  • Gene guns or hyposprays may also be used to administer the pharmaceutical compositions of the invention.
  • the therapeutic compositions may be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared.
  • Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue.
  • the compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule.
  • One approach comprises administering to a subject an inhibitor compound (antagonist) as described above, along with a pharmaceutically acceptable carrier in an amount effective to inhibit the function of the polypeptide, such as by blocking the binding of ligands, substrates, enzymes, receptors, or by inhibiting a second signal, and thereby alleviating the abnormal condition.
  • an inhibitor compound as described above
  • a pharmaceutically acceptable carrier in an amount effective to inhibit the function of the polypeptide, such as by blocking the binding of ligands, substrates, enzymes, receptors, or by inhibiting a second signal, and thereby alleviating the abnormal condition.
  • antagonists are antibodies.
  • such antibodies are chimeric and/or humanised to minimise their immunogenicity, as described previously.
  • polypeptide that retain binding affinity for the ligand, substrate, enzyme, receptor, in question, may be administered.
  • polypeptide may be administered in the form of fragments that retain the relevant portions.
  • expression of the gene encoding the polypeptide can be inhibited using expression blocking techniques, such as the use of antisense nucleic acid molecules (as described above), either internally generated or separately administered.
  • Modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA, or PNA) to the control, 5' or regulatory regions (signal sequence, promoters, enhancers and introns) of the gene encoding the polypeptide.
  • inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules.
  • the complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
  • Such oligonucleotides may be administered or may be generated in situ from expression in vivo.
  • Ribozymes are catalytically active RNAs that can be natural or synthetic (see for example Usman, N, et al, Curr. Opin. Struct. Biol (1996) 6(4), 527-33). Synthetic ribozymes can be designed to specifically cleave mRNAs at selected positions thereby preventing translation of the mRNAs into functional polypeptide. Ribozymes may be synthesised with a natural ribose phosphate backbone and natural bases, as normally found in RNA molecules.
  • ribozymes may be synthesised with non-natural backbones, for example, 2'-O-methyl RNA, to provide protection from ribonuclease degradation and may contain modified bases.
  • RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule.
  • One approach comprises administering to a subject a therapeutically effective amount of a compound that activates the polypeptide, i.e., an agonist as described above, to alleviate the abnormal condition.
  • a therapeutic amount of the polypeptide in combination with a suitable pharmaceutical carrier may be administered to restore the relevant physiological balance of polypeptide.
  • Gene therapy may be employed to effect the endogenous production of the polypeptide by the relevant cells in the subject. Gene therapy is used to treat permanently the inappropriate production of the polypeptide by replacing a defective gene with a corrected therapeutic gene. Gene therapy of the present invention can occur in vivo or ex vivo. Ex vivo gene therapy requires the isolation and purification of patient cells, the introduction of a therapeutic gene and introduction of the genetically altered cells back into the patient. In contrast, in vivo gene therapy does not require isolation and purification of a patient's cells.
  • the therapeutic gene is typically "packaged" for administration to a patient.
  • Gene delivery vehicles may be non-viral, such as liposomes, or replication-deficient viruses, such as adenovirus as described by Berkner, K.L., in Curr. Top. Microbiol. Immunol., 158, 39-66 (1992) or adeno-associated virus (AAV) vectors as described by Muzyczka, N., in Curr. Top. Microbiol. Immunol., 158, 97-129 (1992) and U.S. Patent No. 5,252,479.
  • a nucleic acid molecule encoding a polypeptide of the invention may be engineered for expression in a replication-defective retroviral vector.
  • This expression construct may then be isolated and introduced into a packaging cell transduced with a retroviral plasmid vector containing RNA encoding the polypeptide, such that the packaging cell now produces infectious viral particles containing the gene of interest.
  • These producer cells may be administered to a subject for engineering cells in vivo and expression of the polypeptide in vivo (see Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches, (and references cited therein) in Human Molecular Genetics (1996), T Strachan and A P Read, BIOS Scientific Publishers Ltd).
  • Another approach is the administration of "naked DNA" in which the therapeutic gene is directly injected into the bloodstream or muscle tissue.
  • Assay methods that are also included within the terms of the present invention are those that involve the use of the genes and polypeptides of the invention in overexpression or ablation assays. Such assays involve the manipulation of levels of these genes/polypeptides in cells and assessment of the impact of this manipulation event on the physiology of the manipulated cells. For example, such experiments reveal details of signaling and metabolic pathways in which the particular genes/polypeptides are implicated, generate information regarding the identities of polypeptides with which the studied polypeptides interact and provide clues as to methods by which related genes and proteins are regulated. In situations in which the polypeptides or nucleic acid molecules of the invention are disease-causing agents, the invention provides that they can be used in vaccines to raise antibodies against the disease causing agent.
  • vaccine development can involve the raising of antibodies or T cells against such agents (as described in WO00/29428).
  • Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection).
  • Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with pharmaceutically-acceptable carriers as described above, which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Additionally, these carriers may function as immunostimulating agents ("adjuvants").
  • the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, and other pathogens.
  • vaccines comprising polypeptides are preferably administered parenterally (for instance, subcutaneous, intramuscular, intravenous, or intradermal injection).
  • parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the recipient, and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents.
  • the vaccine formulations of the invention may be presented in unit-dose or multi-dose containers.
  • sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use.
  • the dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.
  • jet injection see, for example, www.powderject.com
  • jet injection may also be useful in the formulation of vaccine compositions.
  • This invention also relates to the use of nucleic acid molecules according to the present invention as diagnostic reagents. Detection of a mutated form of the gene characterised by the nucleic acid molecules of the invention which is associated with a dysfunction will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, or susceptibility to a disease, which results from under-expression, over-expression or altered spatial or temporal expression of the gene. Individuals carrying mutations in the gene may be detected at the DNA level by a variety of techniques. Nucleic acid molecules for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material.
  • the genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR, ligase chain reaction (LCR), strand displacement amplification (SDA), or other amplification techniques (see Saiki et al, Nature, 324, 163-166 (1986); Bej, et al, Crit. Rev. Biochem. Molec. Biol., 26, 301-334 (1991); Birkenmeyer et al, J. Virol. Meth., 35, 117-126 (1991); Van Brunt, J., Bio/Technology, 8, 291-294 (1990)) prior to analysis.
  • LCR ligase chain reaction
  • SDA strand displacement amplification
  • this aspect of the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide according to the invention and comparing said level of expression to a control level, wherein a level that is different to said control level is indicative of disease.
  • the method may comprise the steps of: a)contacting a sample of tissue from the patient with a nucleic acid probe under stringent conditions that allow the formation of a hybrid complex between a nucleic acid molecule of the invention and the probe; b)contacting a control sample with said probe under the same conditions used in step a); c)and detecting the presence of hybrid complexes in said samples; wherein detection of levels of the hybrid complex in the patient sample that differ from levels of the hybrid complex in the control sample is indicative of disease.
  • a further aspect of the invention comprises a diagnostic method comprising the steps of: a)obtaining a tissue sample from a patient being tested for disease; b)isolating a nucleic acid molecule according to the invention from said tissue sample; and c)diagnosing the patient for disease by detecting the presence of a mutation in the nucleic acid molecule which is associated with disease.
  • an amplification step for example using PCR, may be included.
  • Deletions and insertions can be detected by a change in the size of the amplified product in comparison to the normal genotype.
  • Point mutations can be identified by hybridizing amplified DNA to labelled RNA of the invention or alternatively, labelled antisense DNA sequences of the invention. Perfectly-matched sequences can be distinguished from mismatched duplexes by RNase digestion or by assessing differences in melting temperatures.
  • the presence or absence of the mutation in the patient may be detected by contacting DNA with a nucleic acid probe that hybridises to the DNA under stringent conditions to form a hybrid double-stranded molecule, the hybrid double-stranded molecule having an unhybridised portion of the nucleic acid probe strand at any portion corresponding to a mutation associated with disease; and detecting the presence or absence of an unhybridised portion of the probe strand as an indication of the presence or absence of a disease-associated mutation in the corresponding portion of the DNA strand.
  • Such diagnostics are particularly useful for prenatal and even neonatal testing.
  • Point mutations and other sequence differences between the reference gene and "mutant" genes can be identified by other well-known techniques, such as direct DNA sequencing or single-strand conformational polymorphism, (see Orita et al, Genomics, 5, 874-879 (1989)).
  • a sequencing primer may be used with double-stranded PCR product or a single-stranded template molecule generated by a modified PCR.
  • the sequence determination is performed by conventional procedures with radiolabelled nucleotides or by automatic sequencing procedures with fluorescent-tags.
  • Cloned DNA segments may also be used as probes to detect specific DNA segments. The sensitivity of this method is greatly enhanced when combined with PCR.
  • point mutations and other sequence variations can be detected as described above, for example, through the use of allele-specific oligonucleotides for PCR amplification of sequences that differ by single nucleotides.
  • DNA sequence differences may also be detected by alterations in the electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing (for example, Myers et al, Science (1985) 230:1242). Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and SI protection or the chemical cleavage method (see Cotton et al, Proc. Natl. Acad. Sci. USA (1985) 85: 4397-4401).
  • mutations such as microdeletions, aneuploidies, translocations, inversions, can also be detected by in situ analysis (see, for example, Keller et al, DNA Probes, 2nd Ed., Stockton Press, New York, N.Y., USA (1993)), that is, DNA or RNA sequences in cells can be analysed for mutations without need for their isolation and/or immobilisation onto a membrane.
  • Fluorescence in situ hybridization is presently the most commonly applied method and numerous reviews of FISH have appeared (see, for example, Trachuck et al, Science, 250, 559-562 (1990), and Trask et al, Trends, Genet., 7, 149-154 (1991)).
  • an array of oligonucleotide probes comprising a nucleic acid molecule according to the invention can be constructed to conduct efficient screening of genetic variants, mutations and polymorphisms.
  • Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability (see for example: M.Chee et al, Science (1996), Vol 274, pp 610-613).
  • the array is prepared and used according to the methods described in PCT application WO95/11995 (Chee et al); Lockhart, D. J. et al. (1996) Nat. Biotech. 14: 1675-1680); and Schena, M.
  • Oligonucleotide pairs may range from two to over 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 of the substrate by using a chemical coupling procedure and an ink jet application apparatus, as described in PCT application W095/25116 (Baldeschweiler et al).
  • 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 or 6144 oligonucleotides, or any other number between two and over one million which lends itself to the efficient use of commercially-available instrumentation.
  • diseases may be diagnosed by methods comprising determining, from a sample derived from a subject, an abnormally decreased or increased level of polypeptide or mRNA. Decreased or increased expression can be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides, such as, for example, nucleic acid amplification, for instance PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.
  • nucleic acid amplification for instance PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.
  • Assay techniques that can be used to determine levels of a polypeptide of the present invention in a sample derived from a host are well-known to those of skill in the art and are discussed in some detail above (including radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays).
  • This aspect of the invention provides a diagnostic method which comprises the steps of: (a) contacting a ligand as described above with a biological sample under conditions suitable for the formation of a ligand- polypeptide complex; and (b) detecting said complex. Protocols such as ELISA, RIA, and FACS for measuring polypeptide levels may additionally provide a basis for diagnosing altered or abnormal levels of polypeptide expression.
  • Normal or standard values for polypeptide expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably humans, with antibody to the polypeptide under conditions suitable for complex formation
  • the amount of standard complex formation may be quantified by various methods, such as by photometric means.
  • Antibodies which specifically bind to a polypeptide of the invention may be used for the diagnosis of conditions or diseases characterised by expression of the polypeptide, or in assays to monitor patients being treated with the polypeptides, nucleic acid molecules, ligands and other compounds of the invention.
  • Antibodies useful for diagnostic purposes may be prepared in the same manner as those described above for therapeutics. Diagnostic assays for the polypeptide include methods that utilise the antibody and a label to detect the polypeptide in human body fluids or extracts of cells or tissues.
  • the antibodies may be used with or without modification, and may be labelled by joining them, either covalently or non-covalently, with a reporter molecule.
  • a wide variety of reporter molecules known in the art may be used, several of which are described above.
  • Diagnostic assays may be used to distinguish between absence, presence, and excess expression of polypeptide and to monitor regulation of polypeptide levels during therapeutic intervention. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials or in monitoring the treatment of an individual patient.
  • a diagnostic kit of the present invention may comprise: (a) a nucleic acid molecule of the present invention
  • a diagnostic kit may comprise a first container containing a nucleic acid probe that hybridises under stringent conditions with a nucleic acid molecule according to the invention; a second container containing primers useful for amplifying the nucleic acid molecule; and instructions for using the probe and primers for facilitating the diagnosis of disease.
  • the kit may further comprise a third container holding an agent for digesting unhybridised RNA.
  • a diagnostic kit may comprise an array of nucleic acid molecules, at least one of which may be a nucleic acid molecule according to the invention.
  • a diagnostic kit may comprise one or more antibodies that bind to a polypeptide according to the invention; and a reagent useful for the detection of a binding reaction between the antibody and the polypeptide.
  • kits will be of use in diagnosing a disease or susceptibility to disease, particularly cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
  • a disease or susceptibility to disease particularly cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
  • Figure 1 The polypeptide sequence of INSP003 (SEQ ID NO: 128 or SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined).
  • Figure 2 Results from BLASTp of INSP003 (SEQ ID NO:128 or SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined) polypeptide sequence against the NCBI nr database.
  • Figure 3 Alignment generated by results of BLASTp of NCBI nr database between INSP003 (SEQ ID NO: 128 or SEQ ID:2, SEQID:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined) polypeptide sequence and closest related sequence.
  • Figure 4 The polypeptide sequence of INSP004 (SEQ ID NO: 130 or SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined).
  • Figure 5 Results from BLASTp of INSP004 (SEQ ID NO:130 or SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined) polypeptide sequence against the. NCBI nr database.
  • Figure 6 Alignment generated by results of BLASTp of NCBI nr database between INSP004 (SEQ ID NO: 130 or SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined) polypeptide sequence and closest related sequence.
  • Figure 7 The polypeptide sequence of INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined).
  • Figure 8 Results from BLASTp of INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined) polypeptide sequence against the NCBI nr database.
  • Figure 9 Alignment generated by results of BLASTp of NCBI nr database between INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined) polypeptide sequence and closest related sequence.
  • Figure 10 The polypeptide sequence of INSP007 (SEQ ID NO: 136 or SEQ ID NO
  • Figure 11 Results from BLASTp of INSP007 (SEQ ID NO: 136 or SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:1 10 combined) polypeptide sequence against the NCBI nr database.
  • Figure 12 Alignment generated by results of BLASTp of NCBI nr database between INSP007 (SEQ ID NO: 136 or SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:110 combined) polypeptide sequence and closest related sequence.
  • Figure 13 Predicted nucleotide sequence and translation of the full length, INSP007a polypeptide.
  • Figure 14 Alignment of INSP007a with Image 2957838 translation.
  • Figure 15 Alignment of INSP007, INSP007a, and INSP007b with KIAA1950 .
  • Figure 16 The polypeptide sequence of INSP008 (SEQ ID NO:138 or SEQ ID NO: 112, SEQ ID NO:l 14, SEQ ID NO: 116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 combined)
  • Figure 17 Results from BLASTp of INSP008 (SEQ ID NO:138 or SEQ ID NO:l 12, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124 and SEQ ID NO: 126 combined) polypeptide sequence against the NCBI nr database.
  • Figure 18 Alignment generated by results of BLASTp of NCBI nr database between INSP008 (SEQ ID NO:138 or SEQ ID NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 combined) polypeptide sequence and closest related sequence.
  • polypeptide sequence derived from combining SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14 is SEQ ID NO: 128 which represents the translation of consecutive exons from INSP003 and is given in Figure 1.
  • the polypeptide sequence derived from combining SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14 was used as a query for a BLASTp of the NCBI non-redundant database.
  • top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity ( Figure 2).
  • Figure 3 shows the alignment of the INSP003 query sequence to the sequence of Matrix Metalloproteinase-21 (Cynops pyrrhogaster) a member of the matrix metalloproteinase family.
  • Matrix Metalloproteinase-21 (Cynops pyrrhogaster) a member of the matrix metalloproteinase family.
  • Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
  • Example 2 INSP004 The polypeptide sequence derived from combining SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 is SEQ ID NO: 130 which represents the translation of consecutive exons from INSP004 and is given in Figure 4.
  • polypeptide sequence derived from combining SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 was used as a query for a BLASTp of the NCBI non-redundant database.
  • the top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 5).
  • Figure 6 shows the alignment of the INSP04 query sequence to the sequence of ADAMTS-12 (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
  • ADAMTS-12 Homo sapiens
  • polypeptide sequence derived from combining SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 is SEQ ID NO: 134 which represents the translation of consecutive exons from INSP006 and is given in Figure 7.
  • polypeptide sequence derived from combining SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 was used as a query for a BLASTp of the NCBI non-redundant database.
  • Figure 9 shows the alignment of the INSP006 query sequence to the sequence of ADAMTS-9 Precursor (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
  • polypeptide sequence derived from combining SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:l 10 is SEQ ID NO: 136 which represents the translation of consecutive exons from INSP007 and is given in Figure 10.
  • the polypeptide sequence derived from combining SEQ ID NO:106, SEQ ID NO:108 and SEQ ID NO:110 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity ( Figure 11).
  • Figure 12 shows the alignment of the INSP007 query sequence to the sequence of Matrix Metalloproteinase 11 Preproprotein (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
  • Matrix Metalloproteinase 11 Preproprotein Homo sapiens
  • Example 4b Summary of INSP007 cloning
  • the full length INSP007a polypeptide is a full length prediction for a novel metalloprotease related to stromelysin 1 (see Figure 13).
  • KIAA1950 (GenBank Ace: AB075830 - 26/02/2002) that subsumes all 3 exons of INSP007.
  • KIAA1950 also lacks a predicted start methionine and signal peptide.
  • KIAA1950 appears to be a true representative of the INSP007 metalloproteinase. All efforts to repredict KIAA1950, so as to identify both a start methionine and a signal peptide, have failed. However, a candidate start methionine has been identified that does not result in a signal peptide. The candidate methionine resides in exonl of KIAA1950 and is the first available in the largest ORF. The resultant protein is herein referred to as INSP007a.
  • BI260666 predicts an alternative first non-coding exon to KIAA1950 that splices to exon2.
  • BI260666 comes from a cervical carcinoma cell line.
  • An image clone (GenBank Ace: BE336821) from a renal cell adenocarcinoma library may represent an alternative splice variant of INSP007 that splices directly from exon 1 to 3, missing exon2. This corresponds to exons 4-6 of KIAA1950.
  • the image clone contains an extra base at the boundary of the deleted exon. In the absence of the exon, this single nucleotide insertion leads to a frame shift and creates a downstream premature stop codon. This creates an alternative protein product that does not contain the active site residues and is predicted to be inactive. This protein is referred to herein as INSP007b.
  • INSP007b is backed up by an additional cDNA clone (GenBack Ace: AK092107.1 - deposited 15/7/2002) from differentiated NT2 neuronal precursor cells.
  • AK092107.1 does not have a corresponding protein entry in GenBank and is not annotated. However, a translation of AK092107.1 matches INSP007b.
  • polypeptide sequence derived from combining SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO:116, SEQ ID NO:l 18, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO: 126 is SEQ ID NO: 138 which represents the translation of consecutive exons from INSP008 and is given in Figure 16.
  • the polypeptide sequence derived from combining SEQ ID NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 was used as a query for a BLASTp of the NCBI non-redundant database.
  • Figure 18 shows the alignment of the INSP008 query sequence to the sequence of ADAMTS-7 Preproprotein (Homo Sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
  • SEQ ID NO 20 (INSP004 Protein sequence exon 3)
  • SEQ ID NO 26 (INSP004 Protein sequence exon 6)
  • SEQ ID NO 58 (INSP006 Protein sequence exon 3)
  • EDICSSKEKC NMLG SEQ ID NO 6 5 (INSP006 Nucleotide sequence exon 7) 1 GTTTATCATA TTTAGGTACC ATATGTGATC CTTTACAAAG CTGCTTTATT
  • SEQ ID NO: 140 (INSP007A protein sequence exon 1) 1 MLQCRPAQEF SFGPRALKDA LVSTDAALQQ LYVSAFSPAE RLFLAEAYNP 51 QRTLFCTLLI RTGFDWLLSR PEAPEDFQTF HASLQHRKPR LARKHIYLQP 101 ID
  • SEQ ID NO: 141 (INSP007A nucleotide sequence exon 2) 1 ACCTGAGCGA GGAGCCGGTG GGAAGCTCCC TGCTGCACCA GCTGTGCAGC 51 TGCACAGAGG CCTTCTTCCT GGGCCTGCGC GTCAAGTGCC TGCCGTCGGT 101 GGCAGCCGCG TCCATCCGCT GCTCCTCGCG GCCCAGCCGG GACTCTGACA 151 GGCTCCAGCT CCACACAG SEQ ID NO: 142 (INSP007A protein sequence exon 2)
  • SEQ ID NO: 143 (INSP007A nucleotide sequence exon 3) 1 ACGGCATCCT GTCCTTCTTG AAGAACAACA AGCCAGGGGA CGCGCTGTGT 51 GTGCTGGGCC TCACACTGTC TGACCTGTAC CCCCATGAGG CCTGGAGCTT 101 CACCTTCAGC AAGTTCCTTC CAGGGCACG
  • SEQ ID NO: 144 (INSP007A protein sequence exon 3) 1 GILSFLKNNK PGDALCVLGL TLSDLYPHEA WSFTFSKFLP GHE
  • SEQ ID NO: 145 (INSP007A nucleotide sequence exon 4)
  • SEQ ID NO: 146 (INSP007A protein sequence exon 4)
  • SEQ ID NO: 147 (INSP007A nucleotide sequence exon 5)
  • SEQ ID NO: 148 (INSP007A protein sequence exon 5)
  • SEQ ID NO: 149 (INSP007A nucleotide sequence exon 6)
  • SEQ ID NO: 150 (INSP007A protein sequence exon 6)
  • SEQ ID NO: 152 (INSP007A full protein sequence)
  • SEQ ID NO: 154 (INSP007B protein sequence exon 1)
  • SEQ ID NO: 156 (INSP007B protein sequence exon 2)
  • SEQ ID NO: 158 (INSP007B protein sequence exon 3) 1 GILSFLKNNK PGDALCVLGL TLSDLYPHEA WSFTFSKFLP GHG
  • SEQ ID NO: 159 (INSP007B nucleotide sequence exon 4) 1 GTCACGTGCC ACGAGCTCTG CCACCTTCTG GGCCTGGGGA ACTGCCGCTG 51 GCTCCGCTGC CTCATGCAGG GTGCGCTCAG CCTGGACGAG GCCCTGCGGC 101 GGCCCCTGGA CCTCTGTCCC ATCTGCCTGA GGAAGCTGCA GCATGTCCTG 151 GGTTTCAGGC TCATCGAGAG GTACCAG SEQ ID NO: 160 (INSP007B protein sequence exon 4)
  • SEQ ID NO: 161 (INSP007B nucleotide sequence exon 5) 1 AGACTCTACA CCTGGACTCA GGCGGTGGTG GGGACGTGGC CCAGCCAGGA 51 GGCGGGGGAG CCGTCAGTGT GGGAGGACAC CCCGCCTGCC AGCGCCGACT 101 CGGGCATGTG CTG
  • SEQ ID NO: 162 (INSP007B protein sequence exon 5) 1 TLHLDSGGGG DVAQPGGGGA VSVGGHPACQ RRLGHVL
  • SEQ ID NO: 163 (INSP007B full nucleotide sequence)

Abstract

This invention relates to novel proteins identified herein as secreted proteins (in particular as members of the metalloprotease family) and to the use of these proteins and nucleic acid sequences from the encoding genes in the diagnosis, prevention and treatment of disease.

Description

Metalloprotease proteins
This invention relates to novel proteins (INSP003, I SP004, INSP006, INSP007, INSP007a, INSP007b and I SP008), herein identified as secreted proteins (in particular as members of the metalloprotease family) and to the use of these proteins and nucleic acid sequences from the encoding genes in the diagnosis, prevention and treatment of disease.
All publications, patents and patent applications cited herein are incorporated in full by reference.
BACKGROUND The process of drug discovery is presently undergoing a fundamental revolution as the era of functional genomics comes of age. The term "functional genomics" applies to an approach utilising bioinformatics tools to ascribe function to protein sequences of interest. Such tools are becoming increasingly necessary as the speed of generation of sequence data is rapidly outpacing the ability of research laboratories to assign functions to these protein sequences.
As bioinformatics tools increase in potency and in accuracy, these tools are rapidly replacing the conventional techniques of biochemical characterisation. Indeed, the advanced bioinformatics tools used in identifying the present invention are now capable of outputting results in which a high degree of confidence can be placed. Various institutions and commercial organisations are examining sequence data as they become available and significant discoveries are being made on an on-going basis. However, there remains a continuing need to identify and characterise further genes and the polypeptides that they encode, as targets for research and for drug discovery.
Secreted protein background The ability for cells to make and secrete extracellular proteins is central to many biological processes. Enzymes, growth factors, extracellular matrix proteins and signalling molecules are all secreted by cells. This is through fusion of a secretory vesicle with the plasma membrane. In most cases, but not all, proteins are directed to the endoplasmic reticulum and into secretory vesicles by a signal peptide. Signal peptides are cis-acting sequences that affect the transport of polypeptide chains from the cytoplasm to a membrane bound compartment such as a secretory vesicle. Polypeptides that are targeted to the secretory vesicles are either secreted into the extracellular matrix or are retained in the plasma membrane. The polypeptides that are retained in the plasma membrane will have one or more transmembrane domains. Examples of secreted proteins that play a central role in the functioning of a cell are cytokines, hormones, extracellular matrix proteins (adhesion molecules), proteases, and growth and differentiation factors. Description of some of the properties of these proteins follows.
Proteases are enzymes that irreversibly hydrolyse amide bonds in peptides and proteins. Proteases are widely distributed and are involved in many different biological processes, from activation of proteins and peptides to degradation of proteins. Despite the fact that proteases have been shown to be involved in many different diseases, drugs targeted to proteases are still rare in pharmacy, although inhibitors of angiotensin converting enzyme (ACE) have been among the most successful antihypertensive drugs for several years. Proteases have recently received substantial publicity as valuable therapeutic targets following the approval of HIV protease inhibitors.
Proteases can be divided in large Families. The term "Family" is used to describe a group of proteases in which each member shows an evolutionary relationship to at least one other member, either throughout the whole sequence or at least in the part of the sequence responsible for catalytic activity. The name of each Family reflects the catalytic activity type of the proteases in the Family. Thus, serine proteases belong to the S family, threonine proteases belong to the T family, aspartyl proteases belong to the A family, cysteine proteases belong to the C family and metalloproteinases belong to the M family. Metalloproteases and Serine proteases are commonly found in the extracellular matrix. Metalloproteases (M family):
Metalloproteases can be divided in 2 major groups depending on the presence or absence of a the Zinc binding motif (HEXXH). l.l Presence of HEXXH motif (22 families^): Prosite number: PDOC00129
Families with interesting members: M2: Peptidyl-dipeptidase A (Angiotensin I Coverting Enzyme: ACE)
M13: Neprilysin (Enkephalinase A=neutal endopeptidase=NEP), Endothelial Converting Enzyme (ECE)
M10B: Matrixin (Matrix Metalloproteases=MMPs) M12B:Reprolysin (ADAM- 10; ADAM- 17= TNF-alpha Converting
Enzyme=TACE)/Desintegrin (other ADAM proteases). The ADAMs are a large, widely expressed and developmentally regulated family of proteins with multiple potential functions in cell-cell and cell-matrix interactions. Among them TACE represents a new emerging target for arthritis disease. M41: This family contains ATP-dependent metalloproteases: FtsH, proteasome proteins.
One of the largest therapeutically interesting group of metalloproteinases is the Matrix Metalloproteinases family (MMPs). Matrix metalloproteinases are a family of Zinc containing enzymes that are responsible for the remodeling of extracellular matrix throughout the body. They have been shown to be involved in cancer (increase invasiveness, effects on new blood vessels), and in arthritis (involvement in cartilage degradation (Dahlberg, L., et al, Arthritis Rheum. 2000 43(3):673-82) and also TNF- alpha conversion (Hanemaaijer, R., et al, J Biol Chem. 1997 272(50):31504-9, Shlopov, B.V., et al.,. Arthritis Rheum. 1997 40(11):2065-74)). Indeed, different MMPs have been shown to be overexpressed in diseases such as arthritis (Seitz, M., et al, Rheumatology (Oxford). 2000 39(6):637-645, Yoshihara, Y., et al, Ann Rheum Dis. 2000 59(6):455-61, Yamanaka, H., et al, Lab Invest. 2000 80(5):677-87, Jovanovic, D.V., et al, Arthritis Rheum. 2000 May;43(5): 1134-44, Ribbens, C, et al, J Rheumatol. 2000 27(4):888-93) and cancer (Sakamoto, Y., et al, Int J Oncol. 2000 17(2):237-43, Kerkela, E., et al, J Invest Dermatol. 2000 114(6):1 1 13-9, Fang, J., et al, Proc Natl Acad Sci U S A. 2000 97(8):3884-9, Sun, Y., et al, J Biol Chem. 2000 275(15):1 1327-32, McCawley, L.J., et al, Mol Med Today. 2000 6(4): 149-56, Ara,T., et al, J Pediatr Surg. 2000 35(3):432-7, Shigemasa, K., et al, Med Oncol. 2000 17(l):52-8, Nakanishi, K., et al, Hum Pathol. 2000 31(2): 193-200, Dalberg, K., et al, World J Surg. 2000 24(3):334-40). Inhibitors of these enzymes have been suggested as potential therapeutic agents for the use in the treatment of both cancer and arthritis. More recently it has been shown that MMPs may also have a role in the release of soluble cytokine receptors, growth factors and other cell mediators, suggesting that selective MMPs inhibitors may have wider therapeutic applications than previously proposed. MMPs have been divided in 4 families based on amino-acid sequence homologies of their domain structure, other than the catalytic region.
Minimal domain family: matrilysin (PUMP-1, MMP-7) cleaves proteoglycan, laminin and fibronectin
Hemopexin domain family: Collagenases: unique ability to cleave fibrillar collagen. The role of collagenases in cartilage degradation , make them attractive targets for the treatment of rheumatoid and osteo-arthritis.
■ collagenases fibroblast collagenase (interstitial collagenase, MMP-1)
■ neutrophil collagenase (MMP-8) ■ collagenase-3 (MMP-13)
Metalloelastase: MME (MMP-12)
Stromelysin-1 (MMP-3), 2 (MMP-10) and 3 (MMP-11). MMP-11 is excreted as an active form and it's function could be to activate other MMPs.
Fibronectin domain family: degrades a large number of matrix substrates (gelatin, elastin, type IV collagen)
Gelatinase A (MMP-2); beside it's involvement in cancer (tumor invasivness), it is proposed as a potential target for the discovery of antiplatelet agent as it may play an important role in platelet activation.
Gelatinase B (MMP-9) Transmembrane domain family:
MT-l-MMP, MT-4-MMP, MMP-14, MMP-17 A lot of studies concerning the different specificities of MMPs and their relative involvement in some diseases are on going.
1 2 Absence of HEXXH motifs (18 families^):
Families with interesting members:
M24A: Methionyl aminopeptidase, type 1 (including procaryotic and eucaryotic MAP-1) / Prosite number: PDOC00575
M24C: Methionyl aminopeptidase, type 2 (including eucaryotic MAP-2) / Prosite number: PDOC00575
Table 1. Summary of metalloproteases and their function
Figure imgf000006_0001
Figure imgf000007_0001
Metalloproteases are implicated across a wide variety of therapeutic areas. These include respiratory diseases (Segura-Valdez, L., et al, Chest. 2000 117(3):684-94, Tanaka, H., et al, J Allergy Clin Immunol. 2000 105(5):900-5, Hoshino, M., et al, J Allergy Clin 5 Immunol. 1999 104(2 Pt l):356-63, Mautino, G., et al, Am J Respir Crit Care Med. 1999 160(l):324-30, Dalai, S., et al, Chest. 2000 117(5 Suppl 1):227S-8S, Ohnishi, K., et al, Lab Invest. 1998 78(9): 1077-87), cardiovascular disease (Taniyama, Y., et al, Circulation. 2000 102(2):246-52, Hong, B.K., et al, Yonsei Med J. 2000 41(l):82-8, Galis, Z.S., et al, Proc Natl Acad Sci U S A. 1995 92(2):402-6), bacterial infections
10 (Scozzafava, A., et al, J Med Chem. 2000 43(9): 1858-65, Vencill, C.F., et al, Biochemistry. 1985 24(13):3149-57, Steinbrink, D.R, et al, J Biol Chem. 1985 260(5):2771-6, Lopez-Boado, Y.S., et al, J Cell Biol. 2000 148(6):1305-15, Chang, J.C., et al, Thorax. 1996 51(3):306-11, Dammann, T., et al, Mol. Microbiol. 6:2267- 2278(1992), Wassif, C, et al, J. Bacteriol. 177 (20), 5790-5798 (1995), oncology
15 (Sakamoto, Y., et al, Int J Oncol. 2000 17(2):237-43, Kerkela, E., et al, J Invest Dermatol. 2000 114(6):1113-9, Fang, J., et al, Proc Natl Acad Sci U S A. 2000 97(8):3884-9, Sun, Y., et al, J Biol Chem. 2000 275(15):11327-32, McCawley, L.J., et al, Mol Med Today. 2000 6(4): 149-56, Ara,T., et al, J Pediatr Surg. 2000 35(3):432-7, Shigemasa, K., et al, Med Oncol. 2000 17(l):52-8, Nakanishi, K., et al, Hum Paihol.
20 2000 31(2): 193-200, Dalberg, K., et al, World J Surg. 2000 24(3):334-40), and Inflammation (rheumatoid and osteo-arthritis (Ribbens, C, et al, J Rheumatol. 2000 27(4):888-93, Kageyama, Y., et al, Clin Rheumatol. 2000 19(l):14-20, Shlopov, B.V., et al, Arthritis Rheum. 2000 Jan;43(l):195-205)).
Metalloproteinases are also implicated in therapies associated with modulating chorion 25 status, the zona reaction, the formation of fertilisation membranes, contraception and infertility, (Shibata et al (2000) J.Biol.Chem vol.275, No.12 p8349).
Accordingly, identification of novel metalloproteases is of extreme importance in increasing understanding of the underlying pathways that lead to certain disease states in which these proteins are implicated, and in developing more effective gene or drug therapies to treat these disorders.
THE INVENTION
The invention is based on the discovery that proteins referred to herein as the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 proteins function as secreted protease molecules and moreover as secreted protease molecules of the metalloprotease class of molecule. INSP007b is a splice variant of INSP007 and is not predicted to be catalytically active as a metalloprotease. INSP007b may be a dominant negative form of INSP007 and/or INSP007a and may function to bind the same substrate as INSP007 and/or INSP007a, therefore acting as a natural antagonist.
In one embodiment of the first aspect of the invention, there is provided a polypeptide, which polypeptide:
(i) comprises the amino acid sequence as recited in SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and/or SEQ ID NO:14;
(ii) is a fragment thereof having function as a secreted protein of the metalloprotease class or having an antigenic determinant in common with the polypeptides of (i); or
(iii) is a functional equivalent of (i) or (ii). Preferably, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 128 and more preferably, consists of the sequence recited in SEQ ID NO: 128. The polypeptide having the sequence recited in SEQ ID NO: 128 is referred to hereafter as "the INSP003 polypeptide".
Polypeptides containing any combination of the seven INSP003 exons listed above are included in the first aspect of the invention.
The polypeptide having the sequence recited in SEQ ID NO:2 is referred to hereafter as "the INSP003 exon 1 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:4 is referred to hereafter as "the INSP003 exon 2 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:6 is referred to hereafter as "the INSP003 exon 3 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:8 is referred to hereafter as "the INSP003 exon 4 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 10 is referred to hereafter as "the INSP003 exon 5 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 12 is referred to hereafter as "the INSP003 exon 6 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 14 is referred to hereafter as "the INSP003 exon 7 polypeptide".
In a second embodiment of the first aspect of the invention, the invention provides a polypeptide, which polypeptide:
(i) comprises an amino acid sequence as recited in SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID
NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and/or SEQ ID NO:42;
(ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
Preferably, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 130 and more preferably, consists of the sequence recited in SEQ ID NO: 130. The polypeptide having the sequence recited in SEQ ID NO: 130 is referred to hereafter as "the INSP004 polypeptide". Polypeptides containing any combination of the fourteen INSP004 exons listed above are included in the first aspect of the invention.
The polypeptide having the sequence recited in SEQ ID NO: 16 is referred to hereafter as "the INSP004 exon 1 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 18 is referred to hereafter as "the INSP004 exon 2 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:20 is referred to hereafter as "the INSP004 exon 3 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:22 is referred to hereafter as "the INSP004 exon 4 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:24 is referred to hereafter as "the INSP004 exon 5 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:26 is referred to hereafter as "the INSP004 exon 6 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:28 is referred to hereafter as "the INSP004 exon 7 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:30 is referred to hereafter as "the INSP004 exon 8 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:32 is referred to hereafter as "the INSP004 exon 9 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:34 is referred to hereafter as "the INSP004 exon 10 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:36 is referred to hereafter as "the INSP004 exon 11 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:38 is referred to hereafter as "the INSP004 exon 12 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:40 is referred to hereafter as "the INSP004 exon 13 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:42 is referred to hereafter as "the INSP004 exon 14 polypeptide".
In a third embodiment of the first aspect of the invention, the invention provides a polypeptide, which polypeptide: (i) comprises an amino acid sequence as recited in SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and/or SEQ ID NO: 104;
(ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or
(iii) is a functional equivalent of (i) or (ii). Preferably, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 134 and more preferably, consists of the sequence recited in SEQ ID NO: 134. The polypeptide having the sequence recited in SEQ ID NO: 134 is referred to hereafter as "the INSP006 polypeptide".
Polypeptides containing any combination of the twenty-six INSP006 exons listed above are included in the first aspect of the invention.
The polypeptide having the sequence recited in SEQ ID NO: 54 is referred to hereafter as "the INSP006 exon 1 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:56 is referred to hereafter as "the INSP006 exon 2 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:58 is referred to hereafter as "the INSP006 exon 3 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:60 is referred to hereafter as "the INSP006 exon 4 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:62 is referred to hereafter as "the INSP006 exon 5 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:64 is referred to hereafter as "the INSP006 exon 6 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:66 is referred to hereafter as "the INSP006 exon 7 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:68 is referred to hereafter as "the INSP006 exon 8 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 70 is referred to hereafter as "the INSP006 exon 9 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:72 is referred to hereafter as "the INSP006 exon 10 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:74 is referred to hereafter as "the INSP006 exon 11 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:76 is referred to hereafter as "the INSP006 exon 12 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:78 is referred to hereafter as "the INSP006 exon 13 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:80 is referred to hereafter as "the INSP006 exon 14 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 82 is referred to hereafter as "the INSP006 exon 15 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:84 is referred to hereafter as "the INSP006 exon 16 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:86 is referred to hereafter as "the INSP006 exon 17 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:88 is referred to hereafter as "the INSP006 exon 18 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:90 is referred to hereafter as "the INSP006 exon 19 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:92 is referred to hereafter as "the INSP006 exon 20 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:94 is referred to hereafter as "the INSP006 exon 21 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:96 is referred to hereafter as "the INSP006 exon 22 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:98 is referred to hereafter as "the INSP006 exon 23 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 100 is referred to hereafter as "the INSP006 exon 24 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 102 is referred to hereafter as "the INSP006 exon 25 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 104 is referred to hereafter as "the INSP006 exon 26 polypeptide".
In a fourth embodiment of the first aspect of the invention, the invention provides a polypeptide, which polypeptide:
(i) comprises an amino acid sequence as recited in SEQ ID NO: 106, SEQ ID NO: 108 and/or SEQ ID NO: 110;
(ii) is a fragment thereof which functions as a metalloprotease protein, preferably, of the stromelysin class or has an antigenic determinant in common with the polypeptides of (i); or
(iii) is a functional equivalent of (i) or (ii).
Preferably, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 136 and more preferably, consists of the sequence recited in SEQ ID NO: 136. The polypeptide having the sequence recited in SEQ ID NO: 136 is referred to hereafter as "the INSP007 polypeptide". This is a partial sequence that forms part of the full length INSP007 sequence as this is set out below.
Polypeptides containing any combination of the three INSP007 exons listed above are also included in the first aspect of the invention.
The polypeptide having the sequence recited in SEQ ID NO: 106 is referred to hereafter as "the INSP007 exon 1 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 108 is referred to hereafter as "the INSP007 exon 2 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 110 is referred to hereafter as "the INSP007 exon 3 polypeptide".
The full length INSP007 sequence has now been obtained and this will be referred to herein as the INSP007a polypeptide. The sequence of this polypeptide is recited in SEQ ID NO: 152. More preferably therefore, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 152 and more preferably, consists of the sequence recited in SEQ ID NO: 152. This aspect of the invention thus provides a polypeptide, which polypeptide is a secreted polypeptide and which:
(i) comprises the amino acid sequence as recited in SEQ ID NO: 152;
(ii) is a fragment thereof which functions as a metalloprotease, preferably of the stromelysin class or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
Preferably, polypeptides according to this aspect of the invention function as metalloproteases, preferably of the stromelysin class. The term "metalloprotease" is well understood in the art and the skilled worker will readily be able to ascertain metalloprotease activity using one of a variety of assays known in the art. A commonly- applied assay is quantitative [3H]gelatin assay (Martin et al., (1989) Kidney Int. 36, 790- 801). Another assay gelatin zymography (Herron GS et al., J Biol Chem 1986;261 :2814- 2818).
A 5'EST, BI260666, predicts an alternative first non-coding exon of INSP007a that splices to exon2. BI260666 comes from a cervical carcinoma cell line. An image clone (GenBank Ace: BE336821) from a renal cell adenocarcinoma library may represent an alternative splice variant of INSP007a that splices directly from exon 1 to 3, missing exon2. The image clone contains an extra base at the boundary of the deleted exon. In the absence of the exon, this single nucleotide insertion leads to a frame shift and creates a downstream premature stop codon. This creates an alternative protein product that does not contain the active site residues and is predicted to be inactive. This protein is referred to herein as INSP007b.
This aspect of the invention thus provides a polypeptide, which polypeptide is a member of the metalloprotease family and which: i. comprises the amino acid sequence as recited in SEQ ID NO: 164; ii. is a fragment thereof or has an antigenic determinant in common with the polypeptides of (i); or iii. is a functional equivalent of (i) or (ii).
This polypeptide is catalytically inactive as a metalloprotease, but nevertheless may have some physiological role, such as a role in binding to polypeptides or other ligands to which the active INSP007a polypeptide binds and thus affecting the function of the catalytically active polypeptide.
In a fifth embodiment of the first aspect of the invention, the invention provides a polypeptide, which polypeptide: (i) comprises an amino acid sequence as recited in SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124 and/or SEQ ID NO: 126;
(ii) is a fragment thereof which functions as a secreted protein or has an antigenic determinant in common with the polypeptides of (i); or (iii) is a functional equivalent of (i) or (ii).
Preferably, a polypeptide according to part i) above comprises the sequence recited in SEQ ID NO: 138 and more preferably, consists of the sequence recited in SEQ ID NO:138. The polypeptide having the sequence recited in SEQ ID NO:138 is referred to hereafter as "the INSP008 polypeptide". Polypeptides containing any combination of the eight I SP008 exons listed above are included in the first aspect of the invention.
The polypeptide having the sequence recited in SEQ ID NO: 112 is referred to hereafter as "the INSP008 exon 1 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 114 is referred to hereafter as "the INSP008 exon 2 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:116 is referred to hereafter as "the INSP008 exon 3 polypeptide". The polypeptide having the sequence recited in SEQ ID NO:l 18 is referred to hereafter as "the INSP008 exon 4 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 120 is referred to hereafter as "the INSP008 exon 5 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 122 is referred to hereafter as "the INSP008 exon 6 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 124 is referred to hereafter as "the INSP008 exon 7 polypeptide". The polypeptide having the sequence recited in SEQ ID NO: 126 is referred to hereafter as "the INSP008 exon 8 polypeptide". Preferably, with the exception of the INSP007b polypeptide, polypeptides according to the above-described aspects of the invention function as metalloproteases. The term "metalloprotease" is well understood in the art and the skilled worker will readily be able to ascertain metalloprotease activity using one of a variety of assays known in the art.
In a second aspect, the invention provides a purified nucleic acid molecule which encodes a polypeptide of the first aspect of the invention. Preferably, the purified nucleic acid molecule has the nucleic acid sequence as recited in SEQ ID NO:l (encoding the INSP003 exon 1 polypeptide), SEQ ID NO:3 (encoding the INSP003 exon 2 polypeptide), SEQ ID NO:5 (encoding the INSP003 exon 3 polypeptide), SEQ ID NO:7 (encoding the INSP003 exon 4 polypeptide), SEQ ID NO:9 (encoding the INSP003 exon 5 polypeptide), SEQ ID NO: 11 (encoding the INSP003 exon 6 polypeptide), SEQ ID NO: 13 (encoding the INSP003 exon 7 polypeptide), SEQ ID NO: 15 (encoding the INSP004 exon 1 polypeptide), SEQ ID NO: 17 (encoding the INSP004 exon 2 polypeptide), SEQ ID NO: 19 (encoding the INSP004 exon 3 polypeptide), SEQ ID NO:21 (encoding the INSP004 exon 4 polypeptide), SEQ ID NO:23 (encoding the INSP004 exon 5 polypeptide), SEQ ID NO:25 (encoding the INSP004 exon 6 polypeptide), SEQ ID NO:27 (encoding the INSP004 exon 7 polypeptide), SEQ ID NO:29 (encoding the TNSP004 exon 8 polypeptide), SEQ ID NO:31 (encoding the INSP004 exon 9 polypeptide), SEQ ID NO:33 (encoding the INSP004 exon 10 polypeptide), SEQ ID NO:35 (encoding the INSP004 exon 11 polypeptide), SEQ ID NO:37 (encoding the INSP004 exon 12 polypeptide), SEQ ID NO:39 (encoding the INSP004 exon 13 polypeptide), SEQ ID NO:41 (encoding the INSP004 exon 14 polypeptide), SEQ ID NO:53 (encoding the INSP006 exon 1 polypeptide) SEQ ID NO:55 (encoding the INSP006 exon 2 polypeptide), SEQ ID NO:57 (encoding the INSP006 exon 3 polypeptide), SEQ ID NO:59 (encoding the INSP006 exon 4 polypeptide), SEQ ID NO:61 (encoding the INSP006 exon 5 polypeptide), SEQ ID NO:63 (encoding the INSP006 exon 6 polypeptide), SEQ ID NO:65 (encoding the INSP006 exon 7 polypeptide), SEQ ID NO:67 (encoding the INSP006 exon 8 polypeptide), SEQ ID NO:69 (encoding the INSP006 exon 9 polypeptide), SEQ ID NO:71 (encoding the I SP006 exon 10 polypeptide), SEQ ID NO:73 (encoding the INSP006 exon 11 polypeptide), SEQ ID NO:75 (encoding the INSP006 exon 12 polypeptide), SEQ ID NO:77 (encoding the INSP006 exon 13 polypeptide), SEQ ID NO:79 (encoding the INSP006 exon 14 polypeptide), SEQ ID NO:81 (encoding the INSP006 exon 15 polypeptide) SEQ ID NO:83 (encoding the INSP006 exon 16 polypeptide), SEQ ID NO:85 (encoding the INSP006 exon 17 polypeptide), SEQ ID NO: 87 (encoding the INSP006 exon 18 polypeptide), SEQ ID NO: 89 (encoding the INSP006 exon 19 polypeptide), SEQ ID NO:91 (encoding the INSP006 exon 20 polypeptide), SEQ ID NO:93 (encoding the INSP006 exon 21 polypeptide), SEQ ID NO: 95 (encoding the INSP006 exon 22 polypeptide), SEQ ID NO: 97 (encoding the INSP006 exon 23 polypeptide), SEQ ID NO:99 (encoding the INSP006 exon 24 polypeptide), SEQ ID NO: 101 (encoding the INSP006 exon 25 polypeptide), SEQ ID NO: 103 (encoding the INSP006 exon 26 polypeptide), SEQ ID NO: 105 (encoding the INSP007 exon 1 polypeptide), SEQ ID NO: 107 (encoding the INSP007 exon 2 polypeptide), SEQ ID NO: 109 (encoding the INSP007 exon 3 polypeptide), SEQ ID NO:l l l (encoding the INSP008 exon 1 polypeptide), SEQ ID NO:113 (encoding the INSP008 exon 2 polypeptide), SEQ ID NO: 115 (encoding the INSP008 exon 3 polypeptide), SEQ ID NO:117 (encoding the INSP008 exon 4 polypeptide), SEQ ID NO:119 (encoding the INSP008 exon 5 polypeptide), SEQ ID NO:121 (encoding the INSP008 exon 6 polypeptide), SEQ ID NO: 123 (encoding the INSP008 exon 7 polypeptide), SEQ ID NO: 125 (encoding the INSP008 exon 8 polypeptide), SEQ ID NO: 127 (encoding the INSP003 polypeptide), SEQ ID NO: 129 (encoding the INSP004 polypeptide), SEQ ID NO: 133 (encoding the INSP006 polypeptide), SEQ ID NO: 135 (encoding the INSP007 polypeptide), SEQ ID NO: 137 (encoding the INSP008 polypeptide), SEQ ID NO:151 (encoding the INSP007a polypeptide), SEQ ID NO: 163 (encoding the INSP007b polypeptide), or is a redundant equivalent or fragment of either of these sequences. In a third aspect, the invention provides a purified nucleic acid molecule which hydridizes under high stringency conditions with a nucleic acid molecule of the second aspect of the invention.
In a fourth aspect, the invention provides a vector, such as an expression vector, that contains a nucleic acid molecule of the second or third aspect of the invention.
In a fifth aspect, the invention provides a host cell transformed with a vector of the fourth aspect of the invention.
In a sixth aspect, the invention provides a ligand which binds specifically to, and which preferably inhibits the metalloprotease activity of a polypeptide of the first aspect of the invention. Ligands to a polypeptide according to the invention may come in various forms, including natural or modified substrates, enzymes, receptors, small organic molecules such as small natural or synthetic organic molecules of up to 2000Da, preferably 800Da or less, peptidomimetics, inorganic molecules, peptides, polypeptides, antibodies, structural or functional mimetics of the aforementioned.
In a seventh aspect, the invention provides a compound that is effective to alter the expression of a natural gene which encodes a polypeptide of the first aspect of the invention or to regulate the activity of a polypeptide of the first aspect of the invention.
A compound of the seventh aspect of the invention may either increase (agonise) or decrease (antagonise) the level of expression of the gene or the activity of the polypeptide. Importantly, the identification of the function of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides allows for the design of screening methods capable of identifying compounds that are effective in the treatment and/or diagnosis of disease.
In an eighth aspect, the invention provides a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, for use in therapy or diagnosis. These molecules may also be used in the manufacture of a medicament for the treatment of cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions. In a ninth aspect, the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide of the first aspect of the invention or the activity of a polypeptide of the first aspect of the invention in tissue from said patient and comparing said level of expression or activity to a control level, wherein a level that is different to said control level is indicative of disease. Such a method will preferably be carried out in vitro. Similar methods may be used for monitoring the therapeutic treatment of disease in a patient, wherein altering the level of expression or activity of a polypeptide or nucleic acid molecule over the period of time towards a control level is indicative of regression of disease. A preferred method for detecting polypeptides of the first aspect of the invention comprises the steps of: (a) contacting a ligand, such as an antibody, of the sixth aspect of the invention with a biological sample under conditions suitable for the formation of a ligand-polypeptide complex; and (b) detecting said complex.
A number of different such methods according to the ninth aspect of the invention exist, as the skilled reader will be aware, such as methods of nucleic acid hybridization with short probes, point mutation analysis, polymerase chain reaction (PCR) amplification and methods using antibodies to detect aberrant protein levels. Similar methods may be used on a short or long term basis to allow therapeutic treatment of a disease to be monitored in a patient. The invention also provides kits that are useful in these methods for diagnosing disease.
In a tenth aspect, the invention provides for the use of a polypeptide of the first aspect of the invention as a secreted protein, preferably as a metalloprotease. In the case of the INSP007a polypeptide, which is not thought to be secreted, a use according to this aspect of the invention may be as a metalloprotease, preferably of the stromelysin class. In the case of the INSP007b polypeptide, which is not thought to be catalytically active as a metalloprotease, this polypeptide may be used as an inactive form of the INSP007a polypeptide and may thus have properties in antagonising the function of the INSP007a polypeptide.
In an eleventh aspect, the invention provides a pharmaceutical composition comprising a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, in conjunction with a pharmaceutically-acceptable carrier. In a twelfth aspect, the present invention provides a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention, for use in the manufacture of a medicament for the diagnosis or treatment of a disease, such as cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
In a thirteenth aspect, the invention provides a method of treating a disease in a patient comprising administering to the patient a polypeptide of the first aspect of the invention, or a nucleic acid molecule of the second or third aspect of the invention, or a vector of the fourth aspect of the invention, or a host cell of the fifth aspect of the invention, or a ligand of the sixth aspect of the invention, or a compound of the seventh aspect of the invention.
For diseases in which the expression of a natural gene encoding a polypeptide of the first aspect of the invention, or in which the activity of a polypeptide of the first aspect of the invention, is lower in a diseased patient when compared to the level of expression or activity in a healthy patient, the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an agonist. Conversely, for diseases in which the expression of the natural gene or activity of the polypeptide is higher in a diseased patient when compared to the level of expression or activity in a healthy patient, the polypeptide, nucleic acid molecule, ligand or compound administered to the patient should be an antagonist. Examples of such antagonists include antisense nucleic acid molecules, ribozymes and ligands, such as antibodies.
In a fourteenth aspect, the invention provides transgenic or knockout non-human animals that have been transformed to express higher, lower or absent levels of a polypeptide of the first aspect of the invention. Such transgenic animals are very useful models for the study of disease and may also be used in screening regimes for the identification of compounds that are effective in the treatment or diagnosis of such a disease.
A summary of standard techniques and procedures which may be employed in order to utilise the invention is given below. It will be understood that this invention is not limited to the particular methodology, protocols, cell lines, vectors and reagents described. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and it is not intended that this terminology should limit the scope of the present invention. The extent of the invention is limited only by the terms of the appended claims.
Standard abbreviations for nucleotides and amino acids are used in this specification.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, recombinant DNA technology and immunology, which are within the skill of the those working in the art. Such techniques are explained fully in the literature. Examples of particularly suitable texts for consultation include the following: Sambrook Molecular Cloning; A Laboratory Manual, Second Edition (1989); DNA Cloning, Volumes I and II (D.N Glover ed. 1985); Oligonucleotide Synthesis (M.J. Gait ed. 1984); Nucleic Acid Hybridization (B.D. Hames & S.J. Higgins eds. 1984); Transcription and Translation (B.D. Hames & S.J. Higgins eds. 1984); Animal Cell Culture (R.I. Freshney ed. 1986); Immobilized Cells and Enzymes (IRL Press, 1986); B. Perbal, A Practical Guide to Molecular Cloning (1984); the Methods in Enzymology series (Academic Press, Inc.), especially volumes 154 & 155; Gene Transfer Vectors for Mammalian Cells (J.H. Miller and M.P. Calos eds. 1987, Cold Spring Harbor Laboratory); Immunochemical Methods in Cell and Molecular Biology (Mayer and Walker, eds. 1987, Academic Press, London); Scopes, (1987) Protein Purification: Principles and Practice, Second Edition (Springer Verlag, N.Y.); and Handbook of Experimental Immunology, Volumes I-IV (D.M. Weir and C. C. Blackwell eds. 1986).
As used herein, the term "polypeptide" includes any peptide or protein comprising two or more amino acids joined to each other by peptide bonds or modified peptide bonds, i.e. peptide isosteres. This term refers both to short chains (peptides and oligopeptides) and to longer chains (proteins).
The polypeptide of the present invention may be in the form of a mature protein or may be a pre-, pro- or prepro- protein that can be activated by cleavage of the pre-, pro- or prepro- portion to produce an active mature polypeptide. In such polypeptides, the pre-, pro- or prepro- sequence may be a leader or secretory sequence or may be a sequence that is employed for purification of the mature polypeptide sequence.
The polypeptide of the first aspect of the invention may form part of a fusion protein. For example, it is often advantageous to include one or more additional amino acid sequences which may contain secretory or leader sequences, pro-sequences, sequences which aid in purification, or sequences that confer higher protein stability, for example during recombinant production. Alternatively or additionally, the mature polypeptide may be fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol). Polypeptides may contain amino acids other than the 20 gene-encoded amino acids, modified either by natural processes, such as by post-translational processing or by chemical modification techniques which are well known in the art. Among the known modifications which may commonly be present in polypeptides of the present invention are glycosylation, lipid attachment, sulphation, gamma-carboxylation, for instance of glutamic acid residues, hydroxylation and ADP-ribosylation. Other potential modifications include acetylation, acylation, amidation, covalent attachment of flavin, covalent attachment of a haeme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid derivative, covalent attachment of phosphatidylinositol, cross-linking, cyclization, disulphide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, GPI anchor formation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination. Modifications can occur anywhere in a polypeptide, including the peptide backbone, the amino acid side-chains and the amino or carboxyl termini. In fact, blockage of the amino or carboxyl terminus in a polypeptide, or both, by a covalent modification is common in naturally-occurring and synthetic polypeptides and such modifications may be present in polypeptides of the present invention. The modifications that occur in a polypeptide often will be a function of how the polypeptide is made. For polypeptides that are made recombinantly, the nature and extent of the modifications in large part will be determined by the post-translational modification capacity of the particular host cell and the modification signals that are present in the amino acid sequence of the polypeptide in question. For instance, glycosylation patterns vary between different types of host cell.
The polypeptides of the present invention can be prepared in any suitable manner. Such polypeptides include isolated naturally-occurring polypeptides (for example purified from cell culture), recombinantly-produced polypeptides (including fusion proteins), synthetically-produced polypeptides or polypeptides that are produced by a combination of these methods.
The functionally-equivalent polypeptides of the first aspect of the invention may be polypeptides that are homologous to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides. Two polypeptides are said to be "homologous", as the term is used herein, if the sequence of one of the polypeptides has a high enough degree of identity or similarity to the sequence of the other polypeptide. "Identity" indicates that at any particular position in the aligned sequences, the amino acid residue is identical between the sequences. "Similarity" indicates that, at any particular position in the aligned sequences, the amino acid residue is of a similar type between the sequences. Degrees of identity and similarity can be readily calculated (Computational Molecular Biology, Lesk, A.M., ed., Oxford University Press, New York, 1988; Biocomputing. Informatics and Genome Projects, Smith, D.W., ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part 1, Griffin, A.M., and Griffin, H.G., eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991).
Homologous polypeptides therefore include natural biological variants (for example, allelic variants or geographical variations within the species from which the polypeptides are derived) and mutants (such as mutants containing amino acid substitutions, insertions or deletions) of the INSP003, INSP004, INSP006, INSP007 or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides. Such mutants may include polypeptides in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code. Typical such substitutions are among Ala, Val, Leu and He; among Ser and Thr; among the acidic residues Asp and Glu; among Asn and Gin; among the basic residues Lys and Arg; or among the aromatic residues Phe and Tyr. Particularly preferred are variants in which several, i.e. between 5 and 10, 1 and 5, 1 and 3, 1 and 2 or just 1 amino acids are substituted, deleted or added in any combination. Especially preferred are silent substitutions, additions and deletions, which do not alter the properties and activities of the protein. Also especially preferred in this regard are conservative substitutions.
Such mutants also include polypeptides in which one or more of the amino acid residues includes a substituent group;
Typically, greater than 30% identity between two polypeptides is considered to be an indication of functional equivalence. Preferably, functionally equivalent polypeptides of the first aspect of the invention have a degree of sequence identity with the INSP003, INSP004, INSP006, INSP007 or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides, or with active fragments thereof, of greater than 30%. More preferred polypeptides have degrees of identity of greater than 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% or more, respectively.
The functionally-equivalent polypeptides of the first aspect of the invention may also be polypeptides which have been identified using one or more techniques of structural alignment. For example, the Inpharmatica Genome Threader technology that forms one aspect of the search tools used to generate the Biopendium search database may be used (see co-pending PCT patent application PCT/GBO 1/01105) to identify polypeptides of presently-unknown function which, while having low sequence identity as compared to the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides, are predicted to have secreted molecule activity, by virtue of sharing significant structural homology with the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptide sequences. By "significant structural homology" is meant that the Inpharmatica Genome Threader predicts two proteins to share structural homology with a certainty of 10% and above.
The polypeptides of the first aspect of the invention also include fragments of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides and fragments of the functional equivalents of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides, provided that those fragments retain metalloprotease activity or have an antigenic determinant in common with the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 exon polypeptides or the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides.
As used herein, the term "fragment" refers to a polypeptide having an amino acid sequence that is the same as part, but not all, of the amino acid sequence of the INSP003 polypeptides or one of its functional equivalents. The fragments should comprise at least n consecutive amino acids from the sequence and, depending on the particular sequence, n preferably is 7 or more (for example, 8, 10, 12, 14, 16, 18, 20 or more). Small fragments may form an antigenic determinant.
Fragments of the full length INSP003, INSP004, INSP006, INSP007, INSP007a,
INSP007b or INSP008 polypeptides may consist of combinations of 2, 3, 4, 5 etc. of neighbouring exon sequences in the polypeptide sequences. The component exons of the INSP007a and INSP007b polypeptides are presented in SEQ ID Nos: 140, 142, 144, 146, 148 and 150 (INSP007a) and 154, 156, 158, 160 and 162 (INSP007b) respectively.
Such fragments may be "free-standing", i.e. not part of or fused to other amino acids or polypeptides, or they may be comprised within a larger polypeptide of which they form a part or region. When comprised within a larger polypeptide, the fragment of the invention most preferably forms a single continuous region. For instance, certain preferred embodiments relate to a fragment having a pre - and/or pro- polypeptide region fused to the amino terminus of the fragment and/or an additional region fused to the carboxyl terminus of the fragment. However, several fragments may be comprised within a single larger polypeptide. The polypeptides of the present invention or their immunogenic fragments (comprising at least one antigenic determinant) can be used to generate ligands, such as polyclonal or monoclonal antibodies, that are immunospecific for the polypeptides. Such antibodies may be employed to isolate or to identify clones expressing the polypeptides of the invention or to purify the polypeptides by affinity chromatography. The antibodies may also be employed as diagnostic or therapeutic aids, amongst other applications, as will be apparent to the skilled reader.
The term "immunospecific" means that the antibodies have substantially greater affinity for the polypeptides of the invention than their affinity for other related polypeptides in the prior art. As used herein, the term "antibody" refers to intact molecules as well as to fragments thereof, such as Fab, F(ab')2 and Fv, which are capable of binding to the antigenic determinant in question. Such antibodies thus bind to the polypeptides of the first aspect of the invention.
By "substantially greater affinity" we mean that there is a measurable increase in the affinity for a polypeptide of the invention as compared with the affinity for known secreted proteins.
Preferably, the affinity is at least 1.5-fold, 2-fold, 5-fold 10-fold, 100-fold, 103-fold, 104- fold, 105-fold or 106-fold greater for a polypeptide of the invention than for known secreted proteins such as metalloproteases.
If polyclonal antibodies are desired, a selected mammal, such as a mouse, rabbit, goat or horse, may be immunised with a polypeptide of the first aspect of the invention. The polypeptide used to immunise the animal can be derived by recombinant DNA technology or can be synthesized chemically. If desired, the polypeptide can be conjugated to a carrier protein. Commonly used carriers to which the polypeptides may be chemically coupled include bovine serum albumin, thyroglobulin and keyhole limpet haemocyanin. The coupled polypeptide is then used to immunise the animal. Serum from the immunised animal is collected and treated according to known procedures, for example by immunoaffinity chromatography.
Monoclonal antibodies to the polypeptides of the first aspect of the invention can also be readily produced by one skilled in the art. The general methodology for making monoclonal antibodies using hybridoma technology is well known (see, for example, Kohler, G. and Milstein, C, Nature 256: 495-497 (1975); Kozbor et al, Immunology Today 4: 72 (1983); Cole et al, 77-96 in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc. (1985). Panels of monoclonal antibodies produced against the polypeptides of the first aspect of the invention can be screened for various properties, i.e., for isotype, epitope, affinity, etc. Monoclonal antibodies are particularly useful in purification of the individual polypeptides against which they are directed. Alternatively, genes encoding the monoclonal antibodies of interest may be isolated from hybridomas, for instance by PCR techniques known in the art, and cloned and expressed in appropriate vectors.
Chimeric antibodies, in which non-human variable regions are joined or fused to human constant regions (see, for example, Liu et al, Proc. Natl. Acad. Sci. USA, 84, 3439 (1987)), may also be of use.
The antibody may be modified to make it less immunogenic in an individual, for example by humanisation (see Jones et al, Nature, 321, 522 (1986); Verhoeyen et al, Science, 239, 1534 (1988); Kabat et al, J. Immunol., 147, 1709 (1991); Queen et al, Proc. Natl Acad. Sci. USA, 86, 10029 (1989); Gorman et al, Proc. Natl Acad. Sci. USA, 88, 34181 (1991); and Hodgson et al, Bio/Technology, 9, 421 (1991)). The term "humanised antibody", as used herein, refers to antibody molecules in which the CDR amino acids and selected other amino acids in the variable domains of the heavy and/or light chains of a non-human donor antibody have been substituted in place of the equivalent amino acids in a human antibody. The humanised antibody thus closely resembles a human antibody but has the binding ability of the donor antibody.
In a further alternative, the antibody may be a "bispecific" antibody, that is an antibody having two different antigen binding domains, each domain being directed against a different epitope.
Phage display technology may be utilised to select genes which encode antibodies with binding activities towards the polypeptides of the invention either from repertoires of PCR amplified V-genes of lymphocytes from humans screened for possessing the relevant antibodies, or from naive libraries (McCafferty, J. et al, (1990), Nature 348, 552-554; Marks, J. et al, (1992) Biotechnology 10, 779-783). The affinity of these antibodies can also be improved by chain shuffling (Clackson, T. et al, (1991) Nature 352, 624-628).
Antibodies generated by the above techniques, whether polyclonal or monoclonal, have additional utility in that they may be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA). In these applications, the antibodies can be labelled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme.
Preferred nucleic acid molecules of the second and third aspects of the invention are those which encode the polypeptide sequences recited in SEQ ID NO:2, SEQ ID NO:4,
SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID
NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID
NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID
NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID
NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID
NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID
NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID
NO:96, SEQ ID NO:98, SEQ ID NO:100, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO:l 10, SEQ ID NO:l 12, SEQ ID NO:l 14, SEQ ID NO:l 16, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO:138, SEQ ID NO:140, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:146, SEQ ID NO: 148, SEQ ID NO: 150, SEQ ID NO: 152, SEQ ID NO: 154, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 164 and functionally equivalent polypeptides. These nucleic acid molecules may be used in the methods and applications described herein. The nucleic acid molecules of the invention preferably comprise at least n consecutive nucleotides from the sequences disclosed herein where, depending on the particular sequence, n is 10 or more (for example, 12, 14, 15, 18, 20, 25, 30, 35, 40 or more).
The nucleic acid molecules of the invention also include sequences that are complementary to nucleic acid molecules described above (for example, for antisense or probing purposes).
Nucleic acid molecules of the present invention may be in the form of RNA, such as mRNA, or in the form of DNA, including, for instance cDNA, synthetic DNA or genomic DNA. Such nucleic acid molecules may be obtained by cloning, by chemical synthetic techniques or by a combination thereof. The nucleic acid molecules can be prepared, for example, by chemical synthesis using techniques such as solid phase phosphoramidite chemical synthesis, from genomic or cDNA libraries or by separation from an organism. RNA molecules may generally be generated by the in vitro or in vivo transcription of DNA sequences.
The nucleic acid molecules may be double-stranded or single-stranded. Single-stranded DNA may be the coding strand, also known as the sense strand, or it may be the non- coding strand, also referred to as the anti-sense strand. The term "nucleic acid molecule" also includes analogues of DNA and RNA, such as those containing modified backbones, and peptide nucleic acids (PNA). The term "PNA", as used herein, refers to an antisense molecule or an anti-gene agent which comprises an oligonucleotide of at least five nucleotides in length linked to a peptide backbone of amino acid residues, which preferably ends in lysine. The terminal lysine confers solubility to the composition. PNAs may be pegylated to extend their lifespan in a cell, where they preferentially bind complementary single stranded DNA and RNA and stop transcript elongation (Nielsen, P.E. et al. (1993) Anticancer Drug Des. 8:53-63).
A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:2 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:4 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:3. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:6 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:5. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 8 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:7. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 10 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:9. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 12 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 1. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 14 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 13. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 16 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 15. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 18 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 17. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:20 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 19. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:22 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:21. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:24 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:23. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:26 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:25. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:28 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:27. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:30 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:29. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:32 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:31. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:34 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:33. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:36 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:35. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:38 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:37. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:40 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:39. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:42 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:41 A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 54 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:53. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:56 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:55. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:58 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:57. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:60 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:59. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:62 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:61. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:64 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:63. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:66 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:65. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:68 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:67. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:70 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:69.A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:72 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:71. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 74 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:73. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:76 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 75. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:78 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:77. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 80 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:79. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 82 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:81. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 84 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:83. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 86 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:85. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 88 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:87. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:90 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:89. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:92 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:91. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 94 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:93. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:96 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:95. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:98 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:97. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 100 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:99. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 102 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 101. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 104 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 103. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 106 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 105. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 108 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 107. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 110 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 109. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:112 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 11 A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 114 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 13. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:116 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 15. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO:118 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 17. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 120 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:l 19. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 122 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:121. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 124 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 123. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 126 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 125. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 128 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 127. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 130 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 129. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 134 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 133. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 136 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 135. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 138 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 137. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 152 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO:151. A nucleic acid molecule which encodes the polypeptide of SEQ ID NO: 164 may be identical to the coding sequence of the nucleic acid molecule shown in SEQ ID NO: 163.
These molecules also may have a different sequence which, as a result of the degeneracy of the genetic code, encodes a polypeptide of SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO:l 10, SEQ ID NO:l 12, SEQ ID NO:l 14, SEQ ID NO.l 16, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO: 128, SEQ ID NO: 130, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 152 and SEQ ID NO: 164. Such nucleic acid molecules may include, but are not limited to, the coding sequence for the mature polypeptide by itself; the coding sequence for the mature polypeptide and additional coding sequences, such as those encoding a leader or secretory sequence, such as a pro-, pre- or prepro- polypeptide sequence; the coding sequence of the mature polypeptide, with or without the aforementioned additional coding sequences, together with further additional, non-coding sequences, including non-coding 5' and 3' sequences, such as the transcribed, non-translated sequences that play a role in transcription (including termination signals), ribosome binding and mRNA stability. The nucleic acid molecules may also include additional sequences which encode additional amino acids, such as those which provide additional functionalities.
The nucleic acid molecules of the second and third aspects of the invention may also encode the fragments or the functional equivalents of the polypeptides and fragments of the first aspect of the invention. Such a nucleic acid molecule may be a naturally- occurring variant such as a naturally-occurring allelic variant, or the molecule may be a variant that is not known to occur naturally. Such non-naturally occurring variants of the nucleic acid molecule may be made by mutagenesis techniques, including those applied to nucleic acid molecules, cells or organisms. Among variants in this regard are variants that differ from the aforementioned nucleic acid molecules by nucleotide substitutions, deletions or insertions. The substitutions, deletions or insertions may involve one or more nucleotides. The variants may be altered in coding or non-coding regions or both. Alterations in the coding regions may produce conservative or non-conservative amino acid substitutions, deletions or insertions. The nucleic acid molecules of the invention can also be engineered, using methods generally known in the art, for a variety of reasons, including modifying the cloning, processing, and/or expression of the gene product (the polypeptide). DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides are included as techniques which may be used to engineer the nucleotide sequences. Site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations and so forth.
Nucleic acid molecules which encode a polypeptide of the first aspect of the invention may be ligated to a heterologous sequence so that the combined nucleic acid molecule encodes a fusion protein. Such combined nucleic acid molecules are included within the second or third aspects of the invention. For example, to screen peptide libraries for inhibitors of the activity of the polypeptide, it may be useful to express, using such a combined nucleic acid molecule, a fusion protein that can be recognised by a commercially-available antibody. A fusion protein may also be engineered to contain a cleavage site located between the sequence of the polypeptide of the invention and the sequence of a heterologous protein so that the polypeptide may be cleaved and purified away from the heterologous protein.
The nucleic acid molecules of the invention also include antisense molecules that are partially complementary to nucleic acid molecules encoding polypeptides of the present invention and that therefore hybridize to the encoding nucleic acid molecules (hybridization). Such antisense molecules, such as oligonucleotides, can be designed to recognise, specifically bind to and prevent transcription of a target nucleic acid encoding a polypeptide of the invention, as will be known by those of ordinary skill in the art (see, for example, Cohen, J.S., Trends in Pharm. Sci., 10, 435 (1989), Okano, J. Neurochem. 56, 560 (1991); O'Connor, J. Neurochem 56, 560 (1991); Lee et al, Nucleic Acids Res 6, 3073 (1979); Cooney et al, Science 241, 456 (1988); Dervan et al, Science 251, 1360 (1991).
The term "hybridization" as used here refers to the association of two nucleic acid molecules with one another by hydrogen bonding. Typically, one molecule will be fixed to a solid support and the other will be free in solution. Then, the two molecules may be placed in contact with one another under conditions that favour hydrogen bonding. Factors that affect this bonding include: the type and volume of solvent; reaction temperature; time of hybridization; agitation; agents to block the non-specific attachment of the liquid phase molecule to the solid support (Denhardt's reagent or BLOTTO); the concentration of the molecules; use of compounds to increase the rate of association of molecules (dextran sulphate or polyethylene glycol); and the stringency of the washing conditions following hybridization (see Sambrook et al. [supra]).
The inhibition of hybridization of a completely complementary molecule to a target molecule may be examined using a hybridization assay, as known in the art (see, for example, Sambrook et al [supra]). A substantially homologous molecule will then compete for and inhibit the binding of a completely homologous molecule to the target molecule under various conditions of stringency, as taught in Wahl, G.M. and S.L. Berger (1987; Methods Enzymol. 152:399-407) and Kimmel, A.R. (1987; Methods Enzymol. 152:507-511). "Stringency" refers to conditions in a hybridization reaction that favour the association of very similar molecules over association of molecules that differ. High stringency hybridisation conditions are defined as overnight incubation at 42(C in a solution comprising 50% formamide, 5XSSC (150mM NaCl, 15mM trisodium citrate), 50mM sodium phosphate (pH7.6), 5x Denhardts solution, 10% dextran sulphate, and 20 microgram/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1X SSC at approximately 65(C. Low stringency conditions involve the hybridisation reaction being carried out at 35(C (see Sambrook et al. [supra]). Preferably, the conditions used for hybridization are those of high stringency.
Preferred embodiments of this aspect of the invention are nucleic acid molecules that are at least 70% identical over their entire length to a nucleic acid molecule encoding the INSP003 polypeptide (SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 128), the INSP004 polypeptide (SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26 and SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO: 130), the INSP006 polypeptide (SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO 134), the INSP007 polypeptide (SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO:l 10, SEQ ID NO: 136), the INSP007a polypeptide (SEQ ID NO: 152), the INSP007b polypeptide (SEQ ID NO: 164), the INSP008 polypeptide (SEQ ID NO:l 12, SEQ ID NO:l 14, SEQ ID NO:l 16, SEQ ID NO:l 18, SEQ ID NO: 120, SEQ ID NO:122 SEQ ID NO:124, SEQ ID NO:126, SEQ ID NO:138), and nucleic acid molecules that are substantially complementary to such nucleic acid molecules. Preferably, a nucleic acid molecule according to this aspect of the invention comprises a region that is at least 80% identical over its entire length to the nucleic acid molecule having the sequence given in SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO: 1 1 , SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO:l l l, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:1 17, SEQ ID NO:119, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 125, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:151, SEQ ID NO:163 or a nucleic acid molecule that is complementary thereto. In this regard, nucleic acid molecules at least 90%, preferably at least 95%, more preferably at least 98% or 99% identical over their entire length to the same are particularly preferred. Preferred embodiments in this respect are nucleic acid molecules that encode polypeptides which retain substantially the same biological function or activity as the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b or INSP008 polypeptides.
The invention also provides a process for detecting a nucleic acid molecule of the invention, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridizing conditions to form duplexes; and (b) detecting any such duplexes that are formed.
As discussed additionally below in connection with assays that may be utilised according to the invention, a nucleic acid molecule as described above may be used as a hybridization probe for RNA, cDNA or genomic DNA, in order to isolate full-length cDNAs and genomic clones encoding the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides and to isolate cDNA and genomic clones of homologous or orthologous genes that have a high sequence similarity to the gene encoding this polypeptide.
In this regard, the following techniques, among others known in the art, may be utilised and are discussed below for purposes of illustration. Methods for DNA sequencing and analysis are well known and are generally available in the art and may, indeed, be used to practice many of the embodiments of the invention discussed herein. Such methods may employ such enzymes as the Klenow fragment of DNA polymerase I, Sequenase (US Biochemical Corp, Cleveland, OH), Taq polymerase (Perkin Elmer), thermostable T7 polymerase (Amersham, Chicago, IL), or combinations of polymerases and proof-reading exonucleases such as those found in the ELONGASE Amplification System marketed by Gibco/BRL (Gaithersburg, MD). Preferably, the sequencing process may be automated using machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno, NV), the Peltier Thermal Cycler (PTC200; MJ Research, Watertown, MA) and the ABI Catalyst and 373 and 377 DNA Sequencers (Perkin Elmer). One method for isolating a nucleic acid molecule encoding a polypeptide with an equivalent function to that of the INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides is to probe a genomic or cDNA library with a natural or artificially-designed probe using standard procedures that are recognised in the art (see, for example, "Current Protocols in Molecular Biology", Ausubel et al. (eds). Greene Publishing Association and John Wiley Interscience, New York, 1989,1992). Probes comprising at least 15, preferably at least 30, and more preferably at least 50, contiguous bases that correspond to, or are complementary to, nucleic acid sequences from the appropriate encoding gene (SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:l l, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:73, SEQ ID NO:75, SEQ ID NO:77, SEQ ID NO:79, SEQ ID NO:81, SEQ ID NO:83, SEQ ID NO:85, SEQ ID NO:87, SEQ ID NO:89, SEQ ID NO:91, SEQ ID NO:93, SEQ ID NO:95, SEQ ID NO:97, SEQ ID NO:99, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO:l l l, SEQ ID NO: 113, SEQ ID NO: 115, SEQ ID NO:l 17, SEQ ID NO:l 19, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 125, SEQ ID NO:127, SEQ ID NO:129, SEQ ID NO:133, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO: 151, SEQ ID NO: 163), are particularly useful probes. Such probes may be labelled with an analytically-detectable reagent to facilitate their identification. Useful reagents include, but are not limited to, radioisotopes, fluorescent dyes and enzymes that are capable of catalysing the formation of a detectable product. Using these probes, the ordinarily skilled artisan will be capable of isolating complementary copies of genomic DNA, cDNA or RNA polynucleotides encoding proteins of interest from human, mammalian or other animal sources and screening such sources for related sequences, for example, for additional members of the family, type and/or subtype.
In many cases, isolated cDNA sequences will be incomplete, in that the region encoding the polypeptide will be cut short, normally at the 5' end. Several methods are available to obtain full length cDNAs, or to extend short cDNAs. Such sequences may be extended utilising a partial nucleotide sequence and employing various methods known in the art to detect upstream sequences such as promoters and regulatory elements. For example, one method which may be employed is based on the method of Rapid Amplification of cDNA Ends (RACE; see, for example, Frohman et al, PNAS USA 85, 8998-9002, 1988). Recent modifications of this technique, exemplified by the Marathon™ technology (Clontech Laboratories Inc.), for example, have significantly simplified the search for longer cDNAs. A slightly different technique, termed "restriction-site" PCR, uses universal primers to retrieve unknown nucleic acid sequence adjacent a known locus (Sarkar, G. (1993) PCR Methods Applic. 2:318-322). Inverse PCR may also be used to amplify or to extend sequences using divergent primers based on a known region (Triglia, T. et al (1988) Nucleic Acids Res. 16:8186). Another method which may be used is capture PCR which involves PCR amplification of DNA fragments adjacent a known sequence in human and yeast artificial chromosome DNA (Lagerstrom, M. et al (1991) PCR Methods Applic, 1, 111-119). Another method which may be used to retrieve unknown sequences is that of Parker, J.D. et al. (1991); Nucleic Acids Res. 19:3055- 3060). Additionally, one may use PCR, nested primers, and PromoterFinderTM libraries to walk genomic DNA (Clontech, Palo Alto, CA). This process avoids the need to screen libraries and is useful in finding intron/exon junctions.
When screening for full-length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. Also, random-primed libraries are preferable, in that they will contain more sequences that contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into 5' non-transcribed regulatory regions.
In one embodiment of the invention, the nucleic acid molecules of the present invention may be used for chromosome localisation. In this technique, a nucleic acid molecule is specifically targeted to, and can hybridize with, a particular location on an individual human chromosome. The mapping of relevant sequences to chromosomes according to the present invention is an important step in the confirmatory correlation of those sequences with the gene-associated disease. Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. Such data are found in, for example, V. McKusick, Mendelian Inheritance in Man (available on-line through Johns Hopkins University Welch Medical Library). The relationships between genes and diseases that have been mapped to the same chromosomal region are then identified through linkage analysis (coinheritance of physically adjacent genes). This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the disease or syndrome has been crudely localised by genetic linkage to a particular genomic region, any sequences mapping to that area may represent associated or regulatory genes for further investigation. The nucleic acid molecule may also be used to detect differences in the chromosomal location due to translocation, inversion, etc. among normal, carrier, or affected individuals.
The nucleic acid molecules of the present invention are also valuable for tissue localisation. Such techniques allow the determination of expression patterns of the polypeptide in tissues by detection of the mRNAs that encode them. These techniques include in situ hybridization techniques and nucleotide amplification techniques, such as PCR. Results from these studies provide an indication of the normal functions of the polypeptide in the organism. In addition, comparative studies of the normal expression pattern of mRNAs with that of mRNAs encoded by a mutant gene provide valuable insights into the role of mutant polypeptides in disease. Such inappropriate expression may be of a temporal, spatial or quantitative nature. Gene silencing approaches may also be undertaken to down-regulate endogenous expression of a gene encoding a polypeptide of the invention. RNA interference (RNAi) (Elbashir, SM et al, Nature 2001, 411, 494-498) is one method of sequence specific post- transcriptional gene silencing that may be employed. Short dsRNA oligonucleotides are synthesised in vitro and introduced into a cell. The sequence specific binding of these dsRNA oligonucleotides triggers the degradation of target mRNA, reducing or ablating target protein expression.
Efficacy of the gene silencing approaches assessed above may be assessed through the measurement of polypeptide expression (for example, by Western blotting), and at the RNA level using TaqMan-based methodologies.
The vectors of the present invention comprise nucleic acid molecules of the invention and may be cloning or expression vectors. The host cells of the invention, which may be transformed, transfected or transduced with the vectors of the invention may be prokaryotic or eukaryotic. The polypeptides of the invention may be prepared in recombinant form by expression of their encoding nucleic acid molecules in vectors contained within a host cell. Such expression methods are well known to those of skill in the art and many are described in detail by Sambrook et al (supra) and Fernandez & Hoeffler (1998, eds. "Gene expression systems. Using nature for the art of expression". Academic Press, San Diego, London, Boston, New York, Sydney, Tokyo, Toronto).
Generally, any system or vector that is suitable to maintain, propagate or express nucleic acid molecules to produce a polypeptide in the required host may be used. The appropriate nucleotide sequence may be inserted into an expression system by any of a variety of well-known and routine techniques, such as, for example, those described in Sambrook et al. , (supra). Generally, the encoding gene can be placed under the control of a control element such as a promoter, ribosome binding site (for bacterial expression) and, optionally, an operator, so that the DNA sequence encoding the desired polypeptide is transcribed into RNA in the transformed host cell.
Examples of suitable expression systems include, for example, chromosomal, episomal and virus-derived systems, including, for example, vectors derived from: bacterial plasmids, bacteriophage, transposons, yeast epi somes, insertion elements, yeast chromosomal elements, viruses such as baculoviruses, papova viruses such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, or combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, including cosmids and phagemids. Human artificial chromosomes (HACs) may also be employed to deliver larger fragments of DNA than can be contained and expressed in a plasmid.
Particularly suitable expression systems include microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (for example, baculovirus); plant cell systems transformed with virus expression vectors (for example, cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (for example, Ti or pBR322 plasmids); or animal cell systems. Cell-free translation systems can also be employed to produce the polypeptides of the invention.
Introduction of nucleic acid molecules encoding a polypeptide of the present invention into host cells can be effected by methods described in many standard laboratory manuals, such as Davis et al, Basic Methods in Molecular Biology (1986) and Sambrook et al, [supra]. Particularly suitable methods include calcium phosphate transfection, DEAE-dextran mediated transfection, transvection, microinjection, cationic lipid- mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection (see Sambrook et al, 1989 [supra]; Ausubel et al, 1991 [supra]; Spector, Goldman & Leinwald, 1998). In eukaryotic cells, expression systems may either be transient (for example, episomal) or permanent (chromosomal integration) according to the needs of the system.
The encoding nucleic acid molecule may or may not include a sequence encoding a control sequence, such as a signal peptide or leader sequence, as desired, for example, for secretion of the translated polypeptide into the lumen of the endoplasmic reticulum, into the periplasmic space or into the extracellular environment. These signals may be endogenous to the polypeptide or they may be heterologous signals. Leader sequences can be removed by the bacterial host in post-translational processing.
In addition to control sequences, it may be desirable to add regulatory sequences that allow for regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory sequences are those which cause the expression of a gene to be increased or decreased in response to a chemical or physical stimulus, including the presence of a regulatory compound or to various temperature or metabolic conditions. Regulatory sequences are those non-translated regions of the vector, such as enhancers, promoters and 5' and 3' untranslated regions. These interact with host cellular proteins to carry out transcription and translation. Such regulatory sequences may vary in their strength and specificity. Depending on the vector system and host utilised, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the Bluescript phagemid (Stratagene, LaJolla, CA) or pSportl™ plasmid (Gibco BRL) and the like may be used. The baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (for example, heat shock, RUBISCO and storage protein genes) or from plant viruses (for example, viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of the sequence, vectors based on SV40 or EBV may be used with an appropriate selectable marker.
An expression vector is constructed so that the particular nucleic acid coding sequence is located in the vector with the appropriate regulatory sequences, the positioning and orientation of the coding sequence with respect to the regulatory sequences being such that the coding sequence is transcribed under the "control" of the regulatory sequences, i.e., RNA polymerase which binds to the DNA molecule at the control sequences transcribes the coding sequence. In some cases it may be necessary to modify the sequence so that it may be attached to the control sequences with the appropriate orientation; i.e., to maintain the reading frame. The control sequences and other regulatory sequences may be ligated to the nucleic acid coding sequence prior to insertion into a vector. Alternatively, the coding sequence can be cloned directly into an expression vector that already contains the control sequences and an appropriate restriction site.
For long-term, high-yield production of a recombinant polypeptide, stable expression is preferred. For example, cell lines which stably express the polypeptide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells that successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
Mammalian cell lines available as hosts for expression are known in the art and include many immortalised cell lines available from the American Type Culture Collection (ATCC) including, but not limited to, Chinese hamster ovary (CHO), HeLa, baby hamster kidney (BHK), monkey kidney (COS), C127, 3T3, BHK, HEK 293, Bowes melanoma and human hepatocellular carcinoma (for example Hep G2) cells and a number of other cell lines. In the baculovirus system, the materials for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Invitrogen, San Diego CA (the "MaxBac" kit). These techniques are generally known to those skilled in the art and are described fully in Summers and Smith, Texas Agricultural Experiment Station Bulletin No. 1555 (1987). Particularly suitable host cells for use in this system include insect cells such as Drosophila S2 and Spodoptera Sf9 cells.
There are many plant cell culture and whole plant genetic expression systems known in the art. Examples of suitable plant cellular genetic expression systems include those described in US 5,693,506; US 5,659,122; and US 5,608,143. Additional examples of genetic expression in plant cell culture has been described by Zenk, Phytochemistry 30, 3861-3863 (1991). In particular, all plants from which protoplasts can be isolated and cultured to give whole regenerated plants can be utilised, so that whole plants are recovered which contain the transferred gene. Practically all plants can be regenerated from cultured cells or tissues, including but not limited to all major species of sugar cane, sugar beet, cotton, fruit and other trees, legumes and vegetables.
Examples of particularly preferred bacterial host cells include streptococci, staphylococci, E. coli, Streptomyces and Bacillus subtilis cells.
Examples of particularly suitable host cells for fungal expression include yeast cells (for example, S. cerevisiae) and Aspergillus cells. Any number of selection systems are known in the art that may be used to recover transformed cell lines. Examples include the herpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11 :223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1980) Cell 22:817-23) genes that can be employed in tk- or aprt± cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dihydrofolate reductase (DHFR) that confers resistance to methotrexate (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14) and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively. Additional selectable genes have been described, examples of which will be clear to those of skill in the art.
Although the presence or absence of marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed. For example, if the relevant sequence is inserted within a marker gene sequence, transformed cells containing the appropriate sequences can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding a polypeptide of the invention under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well. Alternatively, host cells that contain a nucleic acid sequence encoding a polypeptide of the invention and which express said polypeptide may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassays, for example, fluorescence activated cell sorting (FACS) or immunoassay techniques (such as the enzyme-linked immunosorbent assay [ELISA] and radioimmunoassay [RIA]), that include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein (see Hampton, R. et al (1990) Serological Methods, a Laboratory Manual, APS Press, St Paul, MN) and Maddox, D.E. et al. (1983) J. Exp. Med, 158, 1211-1216).
A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labelled hybridization or PCR probes for detecting sequences related to nucleic acid molecules encoding polypeptides of the present invention include oligolabelling, nick translation, end-labelling or PCR amplification using a labelled polynucleotide. Alternatively, the sequences encoding the polypeptide of the invention may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesise RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3 or SP6 and labelled nucleotides. These procedures may be conducted using a variety of commercially available kits (Pharmacia & Upjohn, (Kalamazoo, MI); Promega (Madison WI); and U.S. Biochemical Corp., Cleveland, OH)).
Suitable reporter molecules or labels, which may be used for ease of detection, include radionuclides, enzymes and fluorescent, chemiluminescent or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
Nucleic acid molecules according to the present invention may also be used to create transgenic animals, particularly rodent animals. Such transgenic animals form a further aspect of the present invention. This may be done locally by modification of somatic cells, or by germ line therapy to incorporate heritable modifications. Such transgenic animals may be particularly useful in the generation of animal models for drug molecules effective as modulators of the polypeptides of the present invention.
The polypeptide can be recovered and purified from recombinant cell cultures by well- known methods including ammonium sulphate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography and lectin chromatography. High performance liquid chromatography is particularly useful for purification. Well known techniques for refolding proteins may be employed to regenerate an active conformation when the polypeptide is denatured during isolation and or purification. Specialised vector constructions may also be used to facilitate purification of proteins, as desired, by joining sequences encoding the polypeptides of the invention to a nucleotide sequence encoding a polypeptide domain that will facilitate purification of soluble proteins. Examples of such purification-facilitating domains include metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilised metals, protein A domains that allow purification on immobilised immunoglobulin, and the domain utilised in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, WA). The inclusion of cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the polypeptide of the invention may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing the polypeptide of the invention fused to several histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification by IMAC (immobilised metal ion affinity chromatography as described in Porath, J. et al. (1992), Prof Exp. Purifi 3: 263-281) while the thioredoxin or enterokinase cleavage site provides a means for purifying the polypeptide from the fusion protein. A discussion of vectors which contain fusion proteins is provided in Kroll, D.J. et al. (1993; DNA Cell Biol. 12:441-453).
If the polypeptide is to be expressed for use in screening assays, generally it is preferred that it be produced at the surface of the host cell in which it is expressed. In this event, the host cells may be harvested prior to use in the screening assay, for example using techniques such as fluorescence activated cell sorting (FACS) or immunoaffinity techniques. If the polypeptide is secreted into the medium, the medium can be recovered in order to recover and purify the expressed polypeptide. If polypeptide is produced intracellularly, the cells must first be lysed before the polypeptide is recovered. The polypeptide of the invention can be used to screen libraries of compounds in any of a variety of drug screening techniques. Such compounds may activate (agonise) or inhibit (antagonise) the level of expression of the gene or the activity of the polypeptide of the invention and form a further aspect of the present invention. Preferred compounds are effective to alter the expression of a natural gene which encodes a polypeptide of the first aspect of the invention or to regulate the activity of a polypeptide of the first aspect of the invention.
Agonist or antagonist compounds may be isolated from, for example, cells, cell-free preparations, chemical libraries or natural product mixtures. These agonists or antagonists may be natural or modified substrates, ligands, enzymes, receptors or structural or functional mimetics. For a suitable review of such screening techniques, see Coligan et al, Current Protocols in Immunology l(2):Chapter 5 (1991).
Compounds that are most likely to be good antagonists are molecules that bind to the polypeptide of the invention without inducing the biological effects of the polypeptide upon binding to it. Potential antagonists include small organic molecules, peptides, polypeptides and antibodies that bind to the polypeptide of the invention and thereby inhibit or extinguish its activity. In this fashion, binding of the polypeptide to normal cellular binding molecules may be inhibited, such that the normal biological activity of the polypeptide is prevented.
The polypeptide of the invention that is employed in such a screening technique may be free in solution, affixed to a solid support, borne on a cell surface or located intracellularly. In general, such screening procedures may involve using appropriate cells or cell membranes that express the polypeptide that are contacted with a test compound to observe binding, or stimulation or inhibition of a functional response. The functional response of the cells contacted with the test compound is then compared with control cells that were not contacted with the test compound. Such an assay may assess whether the test compound results in a signal generated by activation of the polypeptide, using an appropriate detection system. Inhibitors of activation are generally assayed in the presence of a known agonist and the effect on activation by the agonist in the presence of the test compound is observed. A preferred method for identifying an agonist or antagonist compound of a polypeptide of the present invention comprises:
(a) contacting a cell expressing on the surface thereof the polypeptide according to the first aspect of the invention, the polypeptide being associated with a second component capable of providing a detectable signal in response to the binding of a compound to the polypeptide, with a compound to be screened under conditions to permit binding to the polypeptide; and
(b) determining whether the compound binds to and activates or inhibits the polypeptide by measuring the level of a signal generated from the interaction of the compound with the polypeptide. A further preferred method for identifying an agonist or antagonist of a polypeptide of the invention comprises:
(a) contacting a cell expressing on the surface thereof the polypeptide, the polypeptide being associated with a second component capable of providing a detectable signal in response to the binding of a compound to the polypeptide, with a compound to be screened under conditions to permit binding to the polypeptide; and
(b) determining whether the compound binds to and activates or inhibits the polypeptide by comparing the level of a signal generated from the interaction of the compound with the polypeptide with the level of a signal in the absence of the compound.
In further preferred embodiments, the general methods that are described above may further comprise conducting the identification of agonist or antagonist in the presence of labelled or unlabelled ligand for the polypeptide.
In another embodiment of the method for identifying agonist or antagonist of a polypeptide of the present invention comprises: determining the inhibition of binding of a ligand to cells which have a polypeptide of the invention on the surface thereof, or to cell membranes containing such a polypeptide, in the presence of a candidate compound under conditions to permit binding to the polypeptide, and determining the amount of ligand bound to the polypeptide. A compound capable of causing reduction of binding of a ligand is considered to be an agonist or antagonist. Preferably the ligand is labelled.
More particularly, a method of screening for a polypeptide antagonist or agonist compound comprises the steps of: (a) incubating a labelled ligand with a whole cell expressing a polypeptide according to the invention on the cell surface, or a cell membrane containing a polypeptide of the invention,
(b) measuring the amount of labelled ligand bound to the whole cell or the cell membrane; (c) adding a candidate compound to a mixture of labelled ligand and the whole cell or the cell membrane of step (a) and allowing the mixture to attain equilibrium;
(d) measuring the amount of labelled ligand bound to the whole cell or the cell membrane after step (c); and
(e) comparing the difference in the labelled ligand bound in step (b) and (d), such that the compound which causes the reduction in binding in step (d) is considered to be an agonist or antagonist.
The polypeptides may be found to modulate a variety of physiological and pathological processes in a dose-dependent manner in the above-described assays. Thus, the "functional equivalents" of the polypeptides of the invention include polypeptides that exhibit any of the same modulatory activities in the above-described assays in a dose- dependent manner. Although the degree of dose-dependent activity need not be identical to that of the polypeptides of the invention, preferably the "functional equivalents" will exhibit substantially similar dose-dependence in a given activity assay compared to the polypeptides of the invention. In certain of the embodiments described above, simple binding assays may be used, in which the adherence of a test compound to a surface bearing the polypeptide is detected by means of a label directly or indirectly associated with the test compound or in an assay involving competition with a labelled competitor. In another embodiment, competitive drug screening assays may be used, in which neutralising antibodies that are capable of binding the polypeptide specifically compete with a test compound for binding. In this manner, the antibodies can be used to detect the presence of any test compound that possesses specific binding affinity for the polypeptide.
Assays may also be designed to detect the effect of added test compounds on the production of mRNA encoding the polypeptide in cells. For example, an ELISA may be constructed that measures secreted or cell-associated levels of polypeptide using monoclonal or polyclonal antibodies by standard methods known in the art, and this can be used to search for compounds that may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues. The formation of binding complexes between the polypeptide and the compound being tested may then be measured.
Assay methods that are also included within the terms of the present invention are those that involve the use of the genes and polypeptides of the invention in overexpression or ablation assays. Such assays involve the manipulation of levels of these genes/polypeptides in cells and assessment of the impact of this manipulation event on the physiology of the manipulated cells. For example, such experiments reveal details of signaling and metabolic pathways in which the particular genes/polypeptides are implicated, generate information regarding the identities of polypeptides with which the studied polypeptides interact and provide clues as to methods by which related genes and proteins are regulated.
Another technique for drug screening which may be used provides for high throughput screening of compounds having suitable binding affinity to the polypeptide of interest (see International patent application WO84/03564). In this method, large numbers of different small test compounds are synthesised on a solid substrate, which may then be reacted with the polypeptide of the invention and washed. One way of immobilising the polypeptide is to use non-neutralising antibodies. Bound polypeptide may then be detected using methods that are well known in the art. Purified polypeptide can also be coated directly onto plates for use in the aforementioned drug screening techniques.
The polypeptide of the invention may be used to identify membrane-bound or soluble receptors, through standard receptor binding techniques that are known in the art, such as ligand binding and crosslinking assays in which the polypeptide is labelled with a radioactive isotope, is chemically modified, or is fused to a peptide sequence that facilitates its detection or purification, and incubated with a source of the putative receptor (for example, a composition of cells, cell membranes, cell supernatants, tissue extracts, or bodily fluids). The efficacy of binding may be measured using biophysical techniques such as surface plasmon resonance and spectroscopy. Binding assays may be used for the purification and cloning of the receptor, but may also identify agonists and antagonists of the polypeptide, that compete with the binding of the polypeptide to its receptor. Standard methods for conducting screening assays are well understood in the art.
The invention also includes a screening kit useful in the methods for identifying agonists, antagonists, ligands, receptors, substrates, enzymes, that are described above.
The invention includes the agonists, antagonists, ligands, receptors, substrates and enzymes, and other compounds which modulate the activity or antigenicity of the polypeptide of the invention discovered by the methods that are described above.
The invention also provides pharmaceutical compositions comprising a polypeptide, nucleic acid, ligand or compound of the invention in combination with a suitable pharmaceutical carrier. These compositions may be suitable as therapeutic or diagnostic reagents, as vaccines, or as other immunogenic compositions, as outlined in detail below. According to the terminology used herein, a composition containing a polypeptide, nucleic acid, ligand or compound [X] is "substantially free of impurities [herein, Y] when at least 85% by weight of the total X+Y in the composition is X. Preferably, X comprises at least about 90% by weight of the total of X+Y in the composition, more preferably at least about 95%, 98% or even 99% by weight. The pharmaceutical compositions should preferably comprise a therapeutically effective amount of the polypeptide, nucleic acid molecule, ligand, or compound of the invention. The term "therapeutically effective amount" as used herein refers to an amount of a therapeutic agent needed to treat, ameliorate, or prevent a targeted disease or condition, or to exhibit a detectable therapeutic or preventative effect. For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, for example, of neoplastic cells, or in animal models, usually mice, rabbits, dogs, or pigs. The animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
The precise effective amount for a human subject will depend upon the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. This amount can be determined by routine experimentation and is within the judgement of the clinician. Generally, an effective dose will be from 0.01 mg/kg to 50 mg/kg, preferably 0.05 mg/kg to 10 mg/kg. Compositions may be administered individually to a patient or may be administered in combination with other agents, drugs or hormones.
A pharmaceutical composition may also contain a pharmaceutically acceptable carrier, for administration of a therapeutic agent. Such carriers include antibodies and other polypeptides, genes and other therapeutic agents such as liposomes, provided that the carrier does not itself induce the production of antibodies harmful to the individual receiving the composition, and which may be administered without undue toxicity. Suitable carriers may be large, slowly metabolised macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers and inactive virus particles.
Pharmaceutically acceptable salts can be used therein, for example, mineral acid salts such as hydrochlorides, hydrobromides, phosphates, sulphates, and the like; and the salts of organic acids such as acetates, propionates, malonates, benzoates, and the like. A thorough discussion of pharmaceutically acceptable carriers is available in Remington's Pharmaceutical Sciences (Mack Pub. Co., N.J. 1991).
Pharmaceutically acceptable carriers in therapeutic compositions may additionally contain liquids such as water, saline, glycerol and ethanol. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present in such compositions. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
Once formulated, the compositions of the invention can be administered directly to the subject. The subjects to be treated can be animals; in particular, human subjects can be treated.
The pharmaceutical compositions utilised in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra- arterial, intramedullary, intrathecal, intraventricular, transdermal or transcutaneous applications (for example, see WO98/20734), subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, intravaginal or rectal means. Gene guns or hyposprays may also be used to administer the pharmaceutical compositions of the invention. Typically, the therapeutic compositions may be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection may also be prepared. Direct delivery of the compositions will generally be accomplished by injection, subcutaneously, intraperitoneally, intravenously or intramuscularly, or delivered to the interstitial space of a tissue. The compositions can also be administered into a lesion. Dosage treatment may be a single dose schedule or a multiple dose schedule.
If the activity of the polypeptide of the invention is in excess in a particular disease state, several approaches are available. One approach comprises administering to a subject an inhibitor compound (antagonist) as described above, along with a pharmaceutically acceptable carrier in an amount effective to inhibit the function of the polypeptide, such as by blocking the binding of ligands, substrates, enzymes, receptors, or by inhibiting a second signal, and thereby alleviating the abnormal condition. Preferably, such antagonists are antibodies. Most preferably, such antibodies are chimeric and/or humanised to minimise their immunogenicity, as described previously.
In another approach, soluble forms of the polypeptide that retain binding affinity for the ligand, substrate, enzyme, receptor, in question, may be administered. Typically, the polypeptide may be administered in the form of fragments that retain the relevant portions.
In an alternative approach, expression of the gene encoding the polypeptide can be inhibited using expression blocking techniques, such as the use of antisense nucleic acid molecules (as described above), either internally generated or separately administered. Modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA, or PNA) to the control, 5' or regulatory regions (signal sequence, promoters, enhancers and introns) of the gene encoding the polypeptide. Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature (Gee, J.E. et al. (1994) In: Huber, B.E. and B.I. Carr, Molecular and Immunologic Approaches, Futura Publishing Co., Mt. Kisco, NY). The complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes. Such oligonucleotides may be administered or may be generated in situ from expression in vivo.
In addition, expression of the polypeptide of the invention may be prevented by using ribozymes specific to its encoding mRNA sequence. Ribozymes are catalytically active RNAs that can be natural or synthetic (see for example Usman, N, et al, Curr. Opin. Struct. Biol (1996) 6(4), 527-33). Synthetic ribozymes can be designed to specifically cleave mRNAs at selected positions thereby preventing translation of the mRNAs into functional polypeptide. Ribozymes may be synthesised with a natural ribose phosphate backbone and natural bases, as normally found in RNA molecules. Alternatively the ribozymes may be synthesised with non-natural backbones, for example, 2'-O-methyl RNA, to provide protection from ribonuclease degradation and may contain modified bases. RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of non-traditional bases such as inosine, queosine and butosine, as well as acetyl-, methyl-, thio- and similarly modified forms of adenine, cytidine, guanine, thymine and uridine which are not as easily recognised by endogenous endonucleases.
For treating abnormal conditions related to an under-expression of the polypeptide of the invention and its activity, several approaches are also available. One approach comprises administering to a subject a therapeutically effective amount of a compound that activates the polypeptide, i.e., an agonist as described above, to alleviate the abnormal condition. Alternatively, a therapeutic amount of the polypeptide in combination with a suitable pharmaceutical carrier may be administered to restore the relevant physiological balance of polypeptide.
Gene therapy may be employed to effect the endogenous production of the polypeptide by the relevant cells in the subject. Gene therapy is used to treat permanently the inappropriate production of the polypeptide by replacing a defective gene with a corrected therapeutic gene. Gene therapy of the present invention can occur in vivo or ex vivo. Ex vivo gene therapy requires the isolation and purification of patient cells, the introduction of a therapeutic gene and introduction of the genetically altered cells back into the patient. In contrast, in vivo gene therapy does not require isolation and purification of a patient's cells.
The therapeutic gene is typically "packaged" for administration to a patient. Gene delivery vehicles may be non-viral, such as liposomes, or replication-deficient viruses, such as adenovirus as described by Berkner, K.L., in Curr. Top. Microbiol. Immunol., 158, 39-66 (1992) or adeno-associated virus (AAV) vectors as described by Muzyczka, N., in Curr. Top. Microbiol. Immunol., 158, 97-129 (1992) and U.S. Patent No. 5,252,479. For example, a nucleic acid molecule encoding a polypeptide of the invention may be engineered for expression in a replication-defective retroviral vector. This expression construct may then be isolated and introduced into a packaging cell transduced with a retroviral plasmid vector containing RNA encoding the polypeptide, such that the packaging cell now produces infectious viral particles containing the gene of interest. These producer cells may be administered to a subject for engineering cells in vivo and expression of the polypeptide in vivo (see Chapter 20, Gene Therapy and other Molecular Genetic-based Therapeutic Approaches, (and references cited therein) in Human Molecular Genetics (1996), T Strachan and A P Read, BIOS Scientific Publishers Ltd).
Another approach is the administration of "naked DNA" in which the therapeutic gene is directly injected into the bloodstream or muscle tissue.
Assay methods that are also included within the terms of the present invention are those that involve the use of the genes and polypeptides of the invention in overexpression or ablation assays. Such assays involve the manipulation of levels of these genes/polypeptides in cells and assessment of the impact of this manipulation event on the physiology of the manipulated cells. For example, such experiments reveal details of signaling and metabolic pathways in which the particular genes/polypeptides are implicated, generate information regarding the identities of polypeptides with which the studied polypeptides interact and provide clues as to methods by which related genes and proteins are regulated. In situations in which the polypeptides or nucleic acid molecules of the invention are disease-causing agents, the invention provides that they can be used in vaccines to raise antibodies against the disease causing agent. Where the aforementioned polypeptide or nucleic acid molecule is one that is up-regulated, vaccine development can involve the raising of antibodies or T cells against such agents (as described in WO00/29428). Vaccines according to the invention may either be prophylactic (ie. to prevent infection) or therapeutic (ie. to treat disease after infection). Such vaccines comprise immunising antigen(s), immunogen(s), polypeptide(s), protein(s) or nucleic acid, usually in combination with pharmaceutically-acceptable carriers as described above, which include any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Additionally, these carriers may function as immunostimulating agents ("adjuvants"). Furthermore, the antigen or immunogen may be conjugated to a bacterial toxoid, such as a toxoid from diphtheria, tetanus, cholera, H. pylori, and other pathogens.
Since polypeptides may be broken down in the stomach, vaccines comprising polypeptides are preferably administered parenterally (for instance, subcutaneous, intramuscular, intravenous, or intradermal injection). Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the blood of the recipient, and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents.
The vaccine formulations of the invention may be presented in unit-dose or multi-dose containers. For example, sealed ampoules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation.
Genetic delivery of antibodies that bind to polypeptides according to the invention may also be effected, for example, as described in International patent application WO98/55607.
The technology referred to as jet injection (see, for example, www.powderject.com) may also be useful in the formulation of vaccine compositions.
A number of suitable methods for vaccination and vaccine delivery systems are described in International patent application WO00/29428.
This invention also relates to the use of nucleic acid molecules according to the present invention as diagnostic reagents. Detection of a mutated form of the gene characterised by the nucleic acid molecules of the invention which is associated with a dysfunction will provide a diagnostic tool that can add to, or define, a diagnosis of a disease, or susceptibility to a disease, which results from under-expression, over-expression or altered spatial or temporal expression of the gene. Individuals carrying mutations in the gene may be detected at the DNA level by a variety of techniques. Nucleic acid molecules for diagnosis may be obtained from a subject's cells, such as from blood, urine, saliva, tissue biopsy or autopsy material. The genomic DNA may be used directly for detection or may be amplified enzymatically by using PCR, ligase chain reaction (LCR), strand displacement amplification (SDA), or other amplification techniques (see Saiki et al, Nature, 324, 163-166 (1986); Bej, et al, Crit. Rev. Biochem. Molec. Biol., 26, 301-334 (1991); Birkenmeyer et al, J. Virol. Meth., 35, 117-126 (1991); Van Brunt, J., Bio/Technology, 8, 291-294 (1990)) prior to analysis.
In one embodiment, this aspect of the invention provides a method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide according to the invention and comparing said level of expression to a control level, wherein a level that is different to said control level is indicative of disease. The method may comprise the steps of: a)contacting a sample of tissue from the patient with a nucleic acid probe under stringent conditions that allow the formation of a hybrid complex between a nucleic acid molecule of the invention and the probe; b)contacting a control sample with said probe under the same conditions used in step a); c)and detecting the presence of hybrid complexes in said samples; wherein detection of levels of the hybrid complex in the patient sample that differ from levels of the hybrid complex in the control sample is indicative of disease. A further aspect of the invention comprises a diagnostic method comprising the steps of: a)obtaining a tissue sample from a patient being tested for disease; b)isolating a nucleic acid molecule according to the invention from said tissue sample; and c)diagnosing the patient for disease by detecting the presence of a mutation in the nucleic acid molecule which is associated with disease.
To aid the detection of nucleic acid molecules in the above-described methods, an amplification step, for example using PCR, may be included.
Deletions and insertions can be detected by a change in the size of the amplified product in comparison to the normal genotype. Point mutations can be identified by hybridizing amplified DNA to labelled RNA of the invention or alternatively, labelled antisense DNA sequences of the invention. Perfectly-matched sequences can be distinguished from mismatched duplexes by RNase digestion or by assessing differences in melting temperatures. The presence or absence of the mutation in the patient may be detected by contacting DNA with a nucleic acid probe that hybridises to the DNA under stringent conditions to form a hybrid double-stranded molecule, the hybrid double-stranded molecule having an unhybridised portion of the nucleic acid probe strand at any portion corresponding to a mutation associated with disease; and detecting the presence or absence of an unhybridised portion of the probe strand as an indication of the presence or absence of a disease-associated mutation in the corresponding portion of the DNA strand.
Such diagnostics are particularly useful for prenatal and even neonatal testing.
Point mutations and other sequence differences between the reference gene and "mutant" genes can be identified by other well-known techniques, such as direct DNA sequencing or single-strand conformational polymorphism, (see Orita et al, Genomics, 5, 874-879 (1989)). For example, a sequencing primer may be used with double-stranded PCR product or a single-stranded template molecule generated by a modified PCR. The sequence determination is performed by conventional procedures with radiolabelled nucleotides or by automatic sequencing procedures with fluorescent-tags. Cloned DNA segments may also be used as probes to detect specific DNA segments. The sensitivity of this method is greatly enhanced when combined with PCR. Further, point mutations and other sequence variations, such as polymorphisms, can be detected as described above, for example, through the use of allele-specific oligonucleotides for PCR amplification of sequences that differ by single nucleotides. DNA sequence differences may also be detected by alterations in the electrophoretic mobility of DNA fragments in gels, with or without denaturing agents, or by direct DNA sequencing (for example, Myers et al, Science (1985) 230:1242). Sequence changes at specific locations may also be revealed by nuclease protection assays, such as RNase and SI protection or the chemical cleavage method (see Cotton et al, Proc. Natl. Acad. Sci. USA (1985) 85: 4397-4401). In addition to conventional gel electrophoresis and DNA sequencing, mutations such as microdeletions, aneuploidies, translocations, inversions, can also be detected by in situ analysis (see, for example, Keller et al, DNA Probes, 2nd Ed., Stockton Press, New York, N.Y., USA (1993)), that is, DNA or RNA sequences in cells can be analysed for mutations without need for their isolation and/or immobilisation onto a membrane. Fluorescence in situ hybridization (FISH) is presently the most commonly applied method and numerous reviews of FISH have appeared (see, for example, Trachuck et al, Science, 250, 559-562 (1990), and Trask et al, Trends, Genet., 7, 149-154 (1991)).
In another embodiment of the invention, an array of oligonucleotide probes comprising a nucleic acid molecule according to the invention can be constructed to conduct efficient screening of genetic variants, mutations and polymorphisms. Array technology methods are well known and have general applicability and can be used to address a variety of questions in molecular genetics including gene expression, genetic linkage, and genetic variability (see for example: M.Chee et al, Science (1996), Vol 274, pp 610-613). In one embodiment, the array is prepared and used according to the methods described in PCT application WO95/11995 (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). Oligonucleotide pairs may range from two to over 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. In another aspect, an oligonucleotide may be synthesized on the surface of the substrate by using a chemical coupling procedure and an ink jet application apparatus, as described in PCT application W095/25116 (Baldeschweiler et al). In another aspect, 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 or 6144 oligonucleotides, or any other number between two and over one million which lends itself to the efficient use of commercially-available instrumentation. In addition to the methods discussed above, diseases may be diagnosed by methods comprising determining, from a sample derived from a subject, an abnormally decreased or increased level of polypeptide or mRNA. Decreased or increased expression can be measured at the RNA level using any of the methods well known in the art for the quantitation of polynucleotides, such as, for example, nucleic acid amplification, for instance PCR, RT-PCR, RNase protection, Northern blotting and other hybridization methods.
Assay techniques that can be used to determine levels of a polypeptide of the present invention in a sample derived from a host are well-known to those of skill in the art and are discussed in some detail above (including radioimmunoassays, competitive-binding assays, Western Blot analysis and ELISA assays). This aspect of the invention provides a diagnostic method which comprises the steps of: (a) contacting a ligand as described above with a biological sample under conditions suitable for the formation of a ligand- polypeptide complex; and (b) detecting said complex. Protocols such as ELISA, RIA, and FACS for measuring polypeptide levels may additionally provide a basis for diagnosing altered or abnormal levels of polypeptide expression. Normal or standard values for polypeptide expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably humans, with antibody to the polypeptide under conditions suitable for complex formation The amount of standard complex formation may be quantified by various methods, such as by photometric means.
Antibodies which specifically bind to a polypeptide of the invention may be used for the diagnosis of conditions or diseases characterised by expression of the polypeptide, or in assays to monitor patients being treated with the polypeptides, nucleic acid molecules, ligands and other compounds of the invention. Antibodies useful for diagnostic purposes may be prepared in the same manner as those described above for therapeutics. Diagnostic assays for the polypeptide include methods that utilise the antibody and a label to detect the polypeptide in human body fluids or extracts of cells or tissues. The antibodies may be used with or without modification, and may be labelled by joining them, either covalently or non-covalently, with a reporter molecule. A wide variety of reporter molecules known in the art may be used, several of which are described above.
Quantities of polypeptide expressed in subject, control and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease. Diagnostic assays may be used to distinguish between absence, presence, and excess expression of polypeptide and to monitor regulation of polypeptide levels during therapeutic intervention. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials or in monitoring the treatment of an individual patient.
A diagnostic kit of the present invention may comprise: (a) a nucleic acid molecule of the present invention;
(b) a polypeptide of the present invention; or
(c) a ligand of the present invention.
In one aspect of the invention, a diagnostic kit may comprise a first container containing a nucleic acid probe that hybridises under stringent conditions with a nucleic acid molecule according to the invention; a second container containing primers useful for amplifying the nucleic acid molecule; and instructions for using the probe and primers for facilitating the diagnosis of disease. The kit may further comprise a third container holding an agent for digesting unhybridised RNA.
In an alternative aspect of the invention, a diagnostic kit may comprise an array of nucleic acid molecules, at least one of which may be a nucleic acid molecule according to the invention.
To detect polypeptide according to the invention, a diagnostic kit may comprise one or more antibodies that bind to a polypeptide according to the invention; and a reagent useful for the detection of a binding reaction between the antibody and the polypeptide. Such kits will be of use in diagnosing a disease or susceptibility to disease, particularly cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions. Various aspects and embodiments of the present invention will now be described in more detail by way of example, with particular reference to INSP003, INSP004, INSP006, INSP007, INSP007a, INSP007b and INSP008 polypeptides.
It will be appreciated that modification of detail may be made without departing from the scope of the invention.
Brief description of the Figures
Figure 1: The polypeptide sequence of INSP003 (SEQ ID NO: 128 or SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined). Figure 2: Results from BLASTp of INSP003 (SEQ ID NO:128 or SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined) polypeptide sequence against the NCBI nr database.
Figure 3: Alignment generated by results of BLASTp of NCBI nr database between INSP003 (SEQ ID NO: 128 or SEQ ID:2, SEQID:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO: 10, SEQ ID NO: 12 and SEQ ID NO: 14 combined) polypeptide sequence and closest related sequence.
Figure 4: The polypeptide sequence of INSP004 (SEQ ID NO: 130 or SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined).
Figure 5: Results from BLASTp of INSP004 (SEQ ID NO:130 or SEQ ID NO:16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined) polypeptide sequence against the. NCBI nr database.
Figure 6: Alignment generated by results of BLASTp of NCBI nr database between INSP004 (SEQ ID NO: 130 or SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 combined) polypeptide sequence and closest related sequence.
Figure 7: The polypeptide sequence of INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined). Figure 8: Results from BLASTp of INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined) polypeptide sequence against the NCBI nr database.
Figure 9: Alignment generated by results of BLASTp of NCBI nr database between INSP006 (SEQ ID NO:134 or SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 combined) polypeptide sequence and closest related sequence. Figure 10: The polypeptide sequence of INSP007 (SEQ ID NO: 136 or SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:l 10 combined).
Figure 11: Results from BLASTp of INSP007 (SEQ ID NO: 136 or SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:1 10 combined) polypeptide sequence against the NCBI nr database. Figure 12: Alignment generated by results of BLASTp of NCBI nr database between INSP007 (SEQ ID NO: 136 or SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:110 combined) polypeptide sequence and closest related sequence.
Figure 13: Predicted nucleotide sequence and translation of the full length, INSP007a polypeptide.
Figure 14: Alignment of INSP007a with Image 2957838 translation.
Figure 15: Alignment of INSP007, INSP007a, and INSP007b with KIAA1950 .
Figure 16: The polypeptide sequence of INSP008 (SEQ ID NO:138 or SEQ ID NO: 112, SEQ ID NO:l 14, SEQ ID NO: 116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 combined)
Figure 17: Results from BLASTp of INSP008 (SEQ ID NO:138 or SEQ ID NO:l 12, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124 and SEQ ID NO: 126 combined) polypeptide sequence against the NCBI nr database. Figure 18: Alignment generated by results of BLASTp of NCBI nr database between INSP008 (SEQ ID NO:138 or SEQ ID NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 combined) polypeptide sequence and closest related sequence.
Examples
Example 1 INSP003
The polypeptide sequence derived from combining SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14 is SEQ ID NO: 128 which represents the translation of consecutive exons from INSP003 and is given in Figure 1. The polypeptide sequence derived from combining SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12 and SEQ ID NO:14 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 2). Figure 3 shows the alignment of the INSP003 query sequence to the sequence of Matrix Metalloproteinase-21 (Cynops pyrrhogaster) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
Example 2 INSP004 The polypeptide sequence derived from combining SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 is SEQ ID NO: 130 which represents the translation of consecutive exons from INSP004 and is given in Figure 4. The polypeptide sequence derived from combining SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:26, SEQ ID NO:28, SEQ ID NO:30, SEQ ID NO:32, SEQ ID NO:34, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:42 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 5). Figure 6 shows the alignment of the INSP04 query sequence to the sequence of ADAMTS-12 (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance. Example 3: INSP006
The polypeptide sequence derived from combining SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 is SEQ ID NO: 134 which represents the translation of consecutive exons from INSP006 and is given in Figure 7. The polypeptide sequence derived from combining SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:70, SEQ ID NO:72, SEQ ID NO:74, SEQ ID NO:76, SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:86, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:94, SEQ ID NO:96, SEQ ID NO:98, SEQ ID NO: 100, SEQ ID NO: 102 and SEQ ID NO: 104 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 8). Figure 9 shows the alignment of the INSP006 query sequence to the sequence of ADAMTS-9 Precursor (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
Example 4a: INSP007
The polypeptide sequence derived from combining SEQ ID NO: 106, SEQ ID NO: 108 and SEQ ID NO:l 10 is SEQ ID NO: 136 which represents the translation of consecutive exons from INSP007 and is given in Figure 10. The polypeptide sequence derived from combining SEQ ID NO:106, SEQ ID NO:108 and SEQ ID NO:110 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 11). Figure 12 shows the alignment of the INSP007 query sequence to the sequence of Matrix Metalloproteinase 11 Preproprotein (Homo sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
Example 4b: Summary of INSP007 cloning
The full length INSP007a polypeptide is a full length prediction for a novel metalloprotease related to stromelysin 1 (see Figure 13).
Blast analysis using the partial predicted sequence INSP007 identified a cloned cDNA from brain, KIAA1950 (GenBank Ace: AB075830 - 26/02/2002) that subsumes all 3 exons of INSP007. KIAA1950 also lacks a predicted start methionine and signal peptide.
KIAA1950 appears to be a true representative of the INSP007 metalloproteinase. All efforts to repredict KIAA1950, so as to identify both a start methionine and a signal peptide, have failed. However, a candidate start methionine has been identified that does not result in a signal peptide. The candidate methionine resides in exonl of KIAA1950 and is the first available in the largest ORF. The resultant protein is herein referred to as INSP007a.
A 5'EST, BI260666, predicts an alternative first non-coding exon to KIAA1950 that splices to exon2. BI260666 comes from a cervical carcinoma cell line.
An image clone (GenBank Ace: BE336821) from a renal cell adenocarcinoma library may represent an alternative splice variant of INSP007 that splices directly from exon 1 to 3, missing exon2. This corresponds to exons 4-6 of KIAA1950. The image clone contains an extra base at the boundary of the deleted exon. In the absence of the exon, this single nucleotide insertion leads to a frame shift and creates a downstream premature stop codon. This creates an alternative protein product that does not contain the active site residues and is predicted to be inactive. This protein is referred to herein as INSP007b.
INSP007b is backed up by an additional cDNA clone (GenBack Ace: AK092107.1 - deposited 15/7/2002) from differentiated NT2 neuronal precursor cells. AK092107.1 does not have a corresponding protein entry in GenBank and is not annotated. However, a translation of AK092107.1 matches INSP007b.
Considering these splice variations it is possible to predict 4 cDNAs based on the original KIAA1950 sequence (i.e. the original and three novel sequences). This corresponds to just two different protein predictions: INSP007a and INSP007b. Example 5: INSP008
The polypeptide sequence derived from combining SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO:116, SEQ ID NO:l 18, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO: 126 is SEQ ID NO: 138 which represents the translation of consecutive exons from INSP008 and is given in Figure 16. The polypeptide sequence derived from combining SEQ ID NO:112, SEQ ID NO:114, SEQ ID NO:116, SEQ ID NO:118, SEQ ID NO:120, SEQ ID NO:122, SEQ ID NO:124 and SEQ ID NO:126 was used as a query for a BLASTp of the NCBI non-redundant database. The top ten matches represent sequences of the metalloprotease family members, all of which align to the query sequence with high sequence identity (Figure 17). Figure 18 shows the alignment of the INSP008 query sequence to the sequence of ADAMTS-7 Preproprotein (Homo Sapiens) a member of the matrix metalloproteinase family. Members of the matrix metalloproteinase family of secreted proteins are of therapeutic importance.
Sequence Listing
SEQ ID NO 1 (INSP003 Nucleotide sequence exon 1)
1 ATGCTCGCCG CCTCCATCTT CCGTCCGACA CTGCTGCTCT GCTGGCTGGC 51 TGCTCCCTGG CCCACCCAGC CCGAGAGTCT CTTCCACAGC CGGGACCGCT 101 CGGACCTGGA GCCGTCCCCA CTGCGCCAGG CCAAGCCCAT TGCCGACCTC 151 CACGCTGCTC AG SEQ ID NO 2 (INSP003 Protein sequence exon 1)
1 MLAASIF PT LLCW AAP PTQPESLFHS RDRSDLEPSP LRQAKPIADL 51 HAAQ
SEQ ID NO 3 (1NSP003 Nucleotide sequence exon 2)
1 CGGTTCCTGT CCAGATACGG CTGGTCAGGG GTGTGGGCGG CCTGGGGGCC 51 CAGTCCCGAG GGGCCGCCGG AGACCCCCAA GGGCGCCGCC CTGGCCGAGG 101 CGGTGCGCAG GTTCCAGCGG GCGAACGCGC TGCCGGCCAG CGGGGAGCTG 151 GACGCGGCCA CCCTAGCGGC CATGAACCGG CCGCGCTGCG GGGTCCCGGA 201 CATGCGCCCA CCGCCCCCCT CCGCCCCGCC TTCGCCCCCG GGCCCGCCCC 251 CCAGAGCCCG CTCCAGGCGC TCCCCGCGGG CGCCGCTGTC CTTGTCCCGG 301 CGGGGTTGGC AGCCCCGGGG CTACCCCGAC GGCGGAGCTG CCCAGGCCTT 351 CTCCAAGAGG ACGCTGAGCT GGCGGCTGCT GGGCGAGGCC CTGAGCAGCC 401 AACTGTCCGT GGCCGACCAG CGGCGCATTG TGGCGCTGGC CTTCAGGATG 451 TGGAGCGAGG TGACGCCGCT GGACTTCCGC GAGGACCTGG CCGCCCCCGG 501 GGCCGCGGTC GACATCAAGC TGGGCTTTGG GAGAG SEQ ID NO 4 (INSP003 Protein sequence exon 2)
1 RFLSRYGWSG V AAWGPSPE GPPETPKGAA LAEAVRRFQR ANALPASGEL 51 DAAT AAM R PRCGVPDMRP PPPSAPPSPP GPPPRARSRR SPRAPLSLΞR 101 RG QPRGYPD GGAAQAFSKR TLSWRLLGEA SSQLSVADQ RRIVALAFRM 151 WSEVTPLDFR EDLAAPGAAV DIKLGFGRG SEQ IDNO 5 (INSP003 Nucleotide sequence exon 3)
1 GCCGGCACCT GGGCTGTCCG CGGGCCTTCG ATGGGAGCGG GCAGGAGTTT 51 GCACACGCCT GGCGCCTAGG TGACATTCAC TTTGACGACG ACGAGCACTT 101 CACACCTCCC ACCAGTGACA CGGGCATCAG CCTTCTCAAG SEQ ID NO 6 (INSP003 Protein sequence exon 3)
1 RH GCPRAFD GSGQEFAHAW RLGDIHFDDD EHFTPPTSDT GISLLK SEQ IDNO 7 (INSP003 Nucleotide sequence exon 4) 1 GTGGCCGTCC ATGAAATTGG CCATGTCCTG GGCTTGCCTC ACACCTACAG 51 GACGGGATCC ATAATGCAAC CAAATTACAT TCCCCAGGAG CCTGCCTTTG 101 AGTTGGACTG GTCAGACAGG AAAGCAATTC AAAAGCTGTA TG SEQ IDNO 8 (INSP003 Protein sequence exon 4)
1 VAVHEIGHVL GLPHTYRTGΞ IMQPNYIPQE PAFELDWΞDR KAIQKLYG SEQ ID NO 9 (INSP003 Nucleotide sequence exon 5)
1 GCTCCTGTGA GGGATCATTT GATACTGCGT TTGACTGGAT TCGCAAAGAG 51 AGAAACCAAT ATGGAGAGGT GATGGTGAGA TTTAGCACAT ATTTCTTCCG 101 TAACAGCTGG TACTGGCTTT ATGAAAATCG AAACAATAGG ACACGCTATG 151 GGGACCCTAT CCAAATCCTC ACTGGCTGGC CTGGAATCCC AACACACAAC 201 ATAGATGCCT TTGTTCACAT CTGGACATGG AAAAGAGATG AACGTTATTT 251 TTTTCAAG SEQ IDNO 10 (INSP003 Protein sequence exon 5)
1 SCEGSFDTAF DWIRKERNQY GEVMVRFSTY FFRNS Y LY ENRNNRTRYG 51 DPIQILTGWP GIPTHNIDAF VHIWTWKRDE RYFFQG SEQ ID NO 11 (INSP003 Nucleotide sequence exon 6)
1 GAAATCAATA CTGGAGATAT GACAGTGACA AGGATCAGGC CCTCACAGAA 51 GATGAACAAG GAAAAAGCTA TCCCAAATTG ATTTCAGAAG GATTTCCTGG 101 CATCCCAAGT CCCCTAGACA CGGCGTTTTA TGACCGAAGA CAGAAGTTAA 151 TTTACTTCTT CAAGGAGTCC CTT SEQ ID NO 12 (INSP003 Protein sequence exon 6)
1 NQYWRYDSDK DQALTEDEQG KΞYPKLISEG FPGIPSPLDT AFYDRRQKLI 51 YFFKESL SEQ IDNO 13 (INSP003 Nucleotide sequence exon 7)
1 GTATTTGCAT TTGATGTCAA CAGAAATCGA GTACTTAATT CTTATCCAAA 51 GAGGATTACT GAAGTTTTTC CAGCAGTAAT ACCACAAAAT CATCCTTTCA 101 GAAATATAGA TTCCGCTTAT TACTCCTATG CATACAACTC CATTTTCTTT 151 TTCAAAGGCA ATGCATACTG GAAGGTAGTT AATGACAAGG ACAAACAACA 201 GAATTCCTGG CTTCCTGCTA ATGGCTTATT TCCAAAAAAG TTTATTTCAG 251 AGAAGTGGTT TGATGTTTGT GACGTCCATA TCTCCACACT GAACATGTAA SEQ ID NO 14 (INSP003 Protein sequence exon 7)
1 VFAFDVNRNR VLNSYPKRIT EVFPAVIPQN HPFRNIDSAY YSYAYNSIFF 51 FKGNAYWKVV NDKDKQQNSW LPANGLFPKK FISEK FDVC DVHISTLNM SEQ ID NO 15 (INSP004 Nucleotide sequence exon 1)
1 ATGCTAGCTT TCCTACTTAC TATCTTAGCT TCAATTTTCT CCTTTGTAAA 51 TGGGGGTGGT GATAATAGCA ACTTGTCCAG CCAG SEQ ID NO 16 (INSP004 Protein sequence exon 1) 1 MLAFLLTI A SIFSFVNGGG DNSNLSSQ SEQ TD NO 17 (INSP004 Nucleotide sequence exon 2)
1 CTTCTGGCCC AGGAACACAA CTACAGCTCC CCTGCGGGTC ACCATCCTCA 51 CGTACTGTAC AAAAGGACAG CAGAGGAGAA GATCCAGCGG TACCGTGGCT 101 ACCCCGGCTC TGGCCGGAAT TATCCTGGTT ACTCCCCAAG TCACATTCCC lbl CATGCATCTC AGAGTCGAGA GACAGAGTAT CACCATCGAA GGTTGCAAAA 201 GCAGCATTTT TGTGGACGAC GCAAGAAATG TAT SEQ ID NO 18 (INSP004 Protein sequence exon 2)
1 LLAQEHNYSS PAGHHPHVLY KRTAEEKIQR YRGYPGSGRN YPGYSPSHIP 51 HASQSRETEY HHRRLQKQHF CGRRKKCI SEQ ID NO 19 (INSP004 Nucleotide sequence exon 3)
1 ATATTCTCTA ATATCCCTTC CAAATGCTCT TCTGTTCATC GTAGATGCTC
51 CCAAGCCTCC CACAGAGGAC ACCTATCTAA GGTTTGATGA ATATGGGAGC
101 TCTGGGCGAC CCAGAAGATC AGCTGGAAAA TCACAAAAGG GCCTCAATGT
151 GGAAACCCTC GTGGTGGCAG ACAAGAAAAT GGTGGAAAAG CATGGCAAGG 201 GAAATGTCAC CACATACATT CTCACAGTAA TGAACATG
SEQ ID NO 20 (INSP004 Protein sequence exon 3)
1 YΞLIS PNAL LFIVDAPKPP TEDTYLRFDE YGSSGRPRRS AGKSQKGLNV 51 ETLWADKKM VEKHGKGNVT TYILTVMNM SEQ ID NO 21 (INSP004 Nucleotide sequence exon 4) 1 GTTTCTGGCC TATTTAAAGA TGGGACTATT GGAAGTGACA TAAACGTGGT
51 TGTGGTGAGC CTAATTCTTC TGGAACAAGA ACCT SEQ ID NO 22 (INSP004 Protein sequence exon 4) 1 VSG FKDGTI GSDINVWVS LI EQEP SEQ ID NO 23 ( MSP004 Nucleotide sequence exon 5) 1 GGAGGATTAT TGATCAACCA TCATGCAGAC CAGTCTCTGA ATAGTTTTTG
51 TCAATGGCAG TCTGCCCTCA TTGGAAAGAA TGGCAAGAGA CATGATCATG 101 CCATCTTACT AACAGGATTT GATATTTGTT CTTGGAAGAA TGAACCATGT 151 GACACTCTAG SEQ ID NO 24 (INSP004 Protein sequence exon 5) 1 GGLLINHHAD QSLNSFCQ Q SALIGKNGKR HDHAI LTGF DICS KNEPC
51 DTLG SEQ ID NO 25 (INSP004 Nucleotide sequence exon 6)
1 GGTTTGCCCC CATCAGTGGA ATGTGCTCTA AGTACCGAAG TTGTACCATC 51 AATGAGGACA CAGGACTTGG CCTTGCCTTC ACCATCGCTC ATGAGTCAGG 101 GCACAA
SEQ ID NO 26 (INSP004 Protein sequence exon 6)
1 FAPISGMCSK YRSCTINEDT GLGLAFT1AH ESGHN SEQ IDNO 27 (INSP004 Nucleotide sequence exon 7)
1 CTTTGGTATG ATTCACGATG GAGAAGGGAA TCCCTGCAGA AAGGCTGAAG 51 GCAATATCAT GTCTCCCACA CTGACCGGAA ACAATGGAGT GTTTTCATGG 101 TCTTCCTGCA GCCGCCAGTA TCTCAAGAAA TTCCTCAG SEQ IDNO 28 (Protein sequence exon 7)
1 FGMIHDGEGN PCRKAEGNI SPTLTGNNGV FSWSSCSRQY LKKF S SEQ IDNO 29 (INSP004 Nucleotide sequence exon 8) 1 CACACCTCAG GCGGGGTGTC TAGTGGATGA GCCCAAGCAA GCAGGACAGT 51 A AAATATCC GGACAAACTA CCAGGACAGA TTTATGATGC TGACACACAG 101 TGTAAATGGC AATTTGGAGC AAAAGCCAAG TTATGCAGCC TTGGTTTTGT 151 GAAG SEQ IDNO 30 (INSP004 Protein sequence exon 8) 1 TPQAGCLVDE PKQAGQYKYP DKLPGQIYDA DTQCK QFGA KAKLCSLGFV 51 K SEQ IDNO 31 (INSP004 Nucleotide sequence exon 9)
1 GATATTTGCA AATCACTTTG GTGCCACCGA GTAGGCCACA GGTGTGAGAC 51 CAAGTTTATG CCCGCAGCAG AAGGGACCGT TTGTGGCTTG AGTATG SEQ IDNO 32 (INSP004 Protein sequence exon 9)
1 DICKSLWCHR VGHRCETKFM PAAEGTVCGL SM SEQ ID NO 33 (INSP004 Nucleotide sequence exon 10)
1 TGGTGTCGGC AAGGCCAGTG CGTAAAGTTT GGGGAGCTCG GGCCCCGGCC 51 CATCCACGGC CAGTGGTCCG CCTGGTCGAA GTGGTCAGAA TGTTCCCGGA 101 CATGTGGTGG AGGAGTCAAG TTCCAGGAGA GACACTGCAA TAACCCCAA SEQ IDNO 34 (INSP004 Protein sequence exon 10)
1 CRQGQCVKF GELGPRPIHG QWSAWSKWSE CSRTCGGGVK FQERHCNNPK SEQ IDNO 35 (INSP004 NuclcoUde sequence exon 11)
1 GCCTCAGTAT GGTGGCTTAT TCTGTCCAGG TTCTAGCCGT ATTTATCAGC 51 TGTGCAATAT TAACCCTTGC AATGAAAATA GCTTGGATTT TCGGGCTCAA 101 CAGTGTGCAG AATATAACAG CAAACCTTTC CGTGGATGGT TCTACCAGTG 151 GAAACCCTAT ACAAAAGTGG AAG SEQ ID NO 36 (INSP004 Protein sequence exon 11)
1 PQYGG FCPG SSRIYQLCNI NPCNENSLDF RAQQCAEYNS KPFRGWFYQW 51 KPYTKVEE
SEQ ID NO 37 (INSP004 Nucleotide sequence exon 12)
1 AGGAAGATCG ATGCAAACTG TACTGCAAGG CTGAGAACTT TGAATTTTTT 51 TTTGCAATGT CCGGCAAAGT GAAAGATGGA ACTCCCTGCT CCCCAAACAA 101 AAATGATGTT TGTATTGACG GGGTTTGTGA A SEQ ID NO 38 (INSP004 Protein sequence exon 12)
1 EDRCKLYCKA ENFEFFFAMS GKVKDGTPCS PNKNDVCIDG VCE SEQ ID NO 39 (INSP004 Nucleotide sequence exon 13)
1 CTAGTGGGAT GTGATCATGA ACTAGGCTCT AAAGCAGTTT CAGATGCTTG 51 TGGCGTTTGC AAAGGTGATA ATTCAACTTG CAAGTTTTAT AAAGGCCTGT 101 ACCTCAACCA GCATAAAGCA AATG
SEQ ID NO 40 (INSP004 Protein sequence exon 13)
1 LVGCDHELGS KAVSDACGVC KGDNSTCKFY KGLYLNQHKA NE SEQ ID NO 41 (INSP004 Nucleotide sequence exon 14)
1 AATATTATCC GGTGGTCCTC ATTCCAGCTG GCGCCCGAAG CATCGAAATC 51 CAGGAGCTGC AGGTTTCCTC CAGTTACCTC GCAGTTCGAA GCCTCAGTCA 101 AAAGTATTAC CTCACCGGGG GCTGGAGCAT CGACTGGCCT GGGGAGTTCC 151 CCTTCGCTGG GACCACGTTT GAATACCAGC GCTCTTTCAA CCGCCCGGAA 201 CGTCTGTACG CGCCAGGGCC CACAAATGAG ACGCTGGTCT TTGAAGTAAG 251 CCCCTTCTGT GTATTCAGTT CTCAGTGCTT CTTGCTACAT TTATATCGTT 301 GA SEQ ID NO 42 (INSP004 Protein sequence exon 14) 1 YYPVVLIPAG ARSIEIQELQ VSSSYLAVRS LSQKYYLTGG WSIDWPGEFP 51 FAGTTFEYQR SFNRPERLYA PGPTNETLVF EVSPFCVFSS QCFL H YR SEQ ID NO 53 (INSP006 Nucleotide sequence exon 1) Note Frame +3 (i e Starttranslation at position 3 nucleotide )
1 AAGCCCTGGT GAGGACACTG ACCTCCTACG AAGTAGTGAT CCCCGAGCGG 51 GTCAATGAGT TTGGAGAAGT GTTCCCTCAG AGCCACCACT TCAGCCGGCA 101 GAAACGCAGC TCCGAGGCGC TGGAACCCAT GCCGTTCCGA ACCCACTATC 151 GCTTCACTGC CTACGGGCAG CTCTTCCAGC TGAACCTGAC CGCCGATGCA 201 TCCTTTCTGG CCGCCGGCTA CACCGAGGTG CACTTGGGAA CCCCGGAGCG 251 CGGGGCCTGG GAGAGCGACG CAGGGCCCTC GGACCTGCGC CACTGCTTCT 301 ACCGCGGCCA GGTCAACTCA CAGGAGGATT ACAAGGCCGT CGTCAGCTTA 351 TGCGGAGGCC TG SEQ ID NO 54 (INSP006 Protein sequence exon 1)
1 ALVRTLTSYE VVIPERVNEF GEVFPQSHHF SRQKRSSEAL EPMPFRTHYR 51 FTAYGQLFQL NLTADASFLA AGYTEVHLGT PERGAWESDA GPSDLRHCFY 101 RGQVNSQEDY KAVVSLCGGL
SEQ ID NO 55 (INSP006 Nucleotide sequence exon 2)
1 ACGGGAACAT TTAAAGGACA GAACGGTGAA TATTTCTTAG AACCTATAAT 51 GAAGGCAGAT GGGAATGAAT ATGAAGATGG TCACAACAAG CCACATCTTA 101 TATACAGACA AGACTTAAAT AACTCTTTTC TGCAGACTCT GAAGTATTGC 151 AGTGTGTCAG
SEQ ID NO 56 (INSP006 Protein sequence exon 2)
1 TGTFKGQNGE YFLEPIMKAD GNEYEDGHNK PHLIYRQDLN NSFLQTLKYC 51 SVSE SEQ IDNO 57 (INSP006 Nucleotide sequence exon 3) 1 AAAGTCAAAT AAAGGAAACC AGTTTACCCT TTCATACCTA CAGCAACATG 51 AATGAAGATC TTAATGTAAT GAAAGAAAGA GTTTTAGGAC ACACATCAAA 101 AAATGTACCA TTGAAAGATG AAAGAAGACA TTCCAGGAAA AAACGTCTTA 151 TATCATATCC AAGATACATT GAAATTATGG TTACAGCTGA TGCTAAAGTG 201 GTTTCTGCTC ATGGATCGAA TTTGCAAAAC TATATACTGA CTCTAATGTC 251 AATT
SEQ ID NO 58 (INSP006 Protein sequence exon 3)
1 SQIKETSLPF HTYSN NEDL NVMKERVLGH TSKNVPLKDE RRHSRKKRLI 51 SYPRYIEIMV TADAKVVSAH GSNLQNYILT LMSI SEQ ID NO 59 (INSP006 Nucleotide sequence exon 4) 1 GTTGCAACAA TCTACAAAGA TCCAAGTATT GGAAATTTGA TACACATAGT
51 AGTGGTAAAA TTAGTTATGA TTCACCGTGA GGAG SEQ ID NO 60 (INSP006 Protein sequence exon 4) 1 VATIYKDPSI GN IHIVVVK LV IHREE SEQ ID NO 61 (INSP006 Nucleotide sequence exon 5) 1 GAAGGACCAG TCATTAATTT TGATGGTGCT ACCACATTAA AGAACTTTTG
51 TTCATGGCAA CAAACTCAGA ATGACCTTGA TGATGTTCAC CCTTCCCACC 101 ATGACACTGC TGTTCTTATC ACTAG SEQ ID NO 62 (INSP006 Protein sequence exon 5)
1 EGPVINFDGA TTLKNFCS Q QTQNDLDDVH PSHHDTAVLI TR SEQ ID NO 63 (INSP006 Nucleotide sequence exon 6)
1 GGAAGACATT TGTTCATCTA AAGAGAAATG TAACATGTTA G SEQ ID NO 64 (INSP006 Protein sequence exon 6)
1 EDICSSKEKC NMLG SEQ ID NO 65 (INSP006 Nucleotide sequence exon 7) 1 GTTTATCATA TTTAGGTACC ATATGTGATC CTTTACAAAG CTGCTTTATT
51 AATGAAGAAA AAGGACTCAT TTCTGCTTTT ACTATAGCCC ATGAGCTTGG 101 GCACAC SEQ ID NO 66 (INSP006 Protein sequence exon 7)
1 LSYLGTICDP LQSCFINEEK GLISAFTIAH ELGHT SEQ ID NO 67 (INSP006 Nucleotide sequence exon 8)
1 ACTTGGTGTT CAACATGATG ATAATCCTAG ATGTAAAGAA ATGAAAGTTA 51 CAAAGTATCA TGTAATGGCC CCTGCTTTAA GTTTTCACAT GAGTCCTTGG 101 AGCTGGTCAA ACTGTAGTCG GAAATATGTT ACTGAATTCC TAGA SEQ ID NO 68 (INSP006 Protein sequence exon 8) 1 GVQHDDNPR CKEMKVTKYH VMAPALSFHM SPWSWSNCSR KYVTEFLD
SEQ ID NO 69 (INSP006 Nucleotide sequence exon 9)
1 TACTGGTTAC GGGGAATGTC TTCTTGACAA ACCAGATGAA GAAATATATA 51 ATCTGCCTTC AGAACTTCCT GGATCACGAT ATGATGGAAA CAAGCAGTGT 101 GAGCTTGCGT TTGGTCCTGG GTCACAAATG TGTCCCCATA TA SEQ ID NO 70 (INSP006 Protein sequence exon 9)
1 TGYGECLLDK PDEEIYN PS ELPGSRYDGN KQCELAFGPG SQMCPHI SEQ ID NO 71 (INSP006 Nucleotide sequence exon 10) 1 GAGAATATAT GCATGCATCT GTGGTGCACA AGCACAGAAA AGCTTCACAA 51 AGGCTGTTTC ACTCAACACG TGCCACCAGC AGATGGAACA GACTGCGGTC 101 CTGGAATG SEQ ID NO 72 (INSP006 Protein sequence exon 10) 1 ENICMHLWCT STEKLHKGCF TQHVPPADGT DCGPGM
SEQ ID NO 73 (INSP006 Nucleotide sequence exon 1 1 )
1 CATTGCCGTC ATGGGCTATG TGTAAACAAA GAAACGGAAA CACGTCCTGT 51 AAATGGTGAA TGGGGACCAT GGGAACCTTA CAGTTCTTGT TCAAGAACAT 101 GTGGAGGCGG AATCGAAAGT GCAACCAGGC GCTGTAATCG TCCTGA SEQ ID NO 74 (INSP006 Protein sequence exon 11 )
1 HCRHGLCVNK ETETRPVNGE WGPWEPYSSC ΞRTCGGGIES ATRRCNRPE SEQ ID NO 75 (1NSP006 Nucleotide sequence exon 12)
1 GCCAAGAAAC GGAGGAAATT ACTGTGTGGG CCGCAGGATG AAATTTCGAT 51 CATGTAATAC TGATTCATGT CCAAAAGGCA CACAAGACTT TCGAGAGAAG 101 CAGTGCTCTG ATTTTAATGG TAAACATTTG GACATCAGTG GCATTCCCTC
151 TAATGTGAGG TGGCTTCCAA GATACAGTGG CA SEQ ID NO 76 (INSP006 Protein sequence exon 12)
1 PRNGGNYCVG RRMKFRSCNT DSCPKGTQDF REKQCSDFNG KHLDISGIPS 51 NVR LPRYSG I SEQ ID NO 77 (INSP006 Nucleotide sequence exon 13)
1 TTGGCACAAA GGATCGTTGT AAACTCTATT GTCAGGTTGC TGGAACCAAT 51 TATTTCTACC TATTGAAGGA TATGGTTGAA GATGGTACTC CTTGTGGAAC 101 TGAAACTCAT GACATCTGTG TTCAAGGCCA GTGTATG SEQ ID NO 78 (INSP006 Protein sequence exon 13) 1 GTKDRCKLYC QVAGTNYFYL LKDMVEDGTP CGTETHDICV QGQC
SEQ ID NO 79 (INSP006 Nucleotide sequence exon 14)
1 GCAGCTGGTT GTGATCACGT GTTAAACTCC AGTGCCAAGA TAGACAAATG 51 TGGAGTGTGT GGTGGGGACA ACTCTTCATG CAAGACAATA ACAGGTGTCT 101 TCAACAGTTC TCATTATG SEQ ID NO 80 (INSP006 Protein sequence exon 14)
1 AAGCDHVLNS SAKIDKCGVC GGDNSSCKTI TGVFNSSHYG SEQ ID NO 81 (INSP006 Nucleotide sequence exon 15)
1 GTTATAATGT TGTTGTAAAG ATTCCCGCAG GAGCAACAAA CGTTGACATT 51 CGTCAGTACA GCTATTCTGG ACAACCAGAT GACAGTTACC TTG SEQ ID NO 82 (INSP006 Protein sequence exon 15)
1 YNVVVKI PAG ATNVDIRQYS YΞGQPDDSY A SEQ ID NO 83 (INSP006 Nucleotide sequence exon 16)
1 CATTATCTGA CGCTGAAGGG AATTTTCTTT TCAATGGAAA TTTTCTTCTA 51 AGTACGTCAA AAAAAGAAAT CAATGTGCAA GGAACAAGAA CTGTTATTGA 101 ATACAGTGGA TCAAATAACG CAGTTGAAAG AATTAATAGT ACTAATCGAC
151 AAGAGAAAGA ACTTATTTTG CAG SEQ ID NO 84 (INSP006 Protein sequence exon 16)
1 LSDAEGNFLF NGNFLLSTSK KEINVQGTRT VIEYSGSNNA VERINSTNRQ 51 EKELILQ SEQ ID NO 85 (1NSP006 Nucleotide sequence exon 17)
1 GTGTTGTGTG TGGGTAATTT ATACAACCCT GATGTACATT ATTCCTTCAA 51 TATCCCTTTG GAAGAGAGGA GTGACATGTT CACATGGGAC CCCTATGGAC 101 CATGGGAAGG CTGTACCAAA ATGTGTCAAG SEQ ID NO 86 (1NSP006 Protein sequence exon 17) 1 V CVGNLYNP DVHYSFNI PL EERSD FTWD PYGPWEGCTK MCQG
SEQ ID NO 87 (INSP006 Nucleotide sequence exon 18)
1 GTCTTCAGCG AAGAAACATA ACTTGCATAC ATAAGAGTGA TCATAGTGTT 51 GTGTCTGATA AAGAATGTGA CCACTTGCCA CTTCCATCAT TTGTTACTCA 101 AAGTTGCAAT ACAGACTGTG AACTAAG SEQ ID NO 88 (INSP006 Protein sequence exon 18)
1 LQRRNITCIH KSDHSVVSDK ECDHLPLPSF VTQSCNTDCE LR SEQ ID NO 89 (INSP006 Nucleotide sequence exon 19)
1 GTGGCATGTT ATTGGCAAAA GTGAATGTTC ATCCCAATGT GGTCAAGGAT 51 ATAGAACCTT GGACATCCAT TGCATGAAGT ATTCCATTCA TGAAGGACAG 101 ACTGTTCAAG TTGATGACCA CTACTGTGGT GACCAGCTTA AACCTCCTAC
151 CCAAGAACTA TGCCATGGTA ACTGTGTCTT CACAAGATGG CATTATTCAG 201 AATGGTCTCA G SEQ ID NO 90 (INSP006 Protein sequence exon 1 )
1 WHVIGKSECS SQCGQGYRT DIHCMKYSIH EGQTVQVDDH YCGDQLKPPT 51 QELCHGNCVF TRWHYSE SQ
SEQ ID NO 91 (INSP006 Nucleotide sequence exon 20)
1 TGTTCCAGGA GTTGTGGAGG AGGGGAAAGG TCTCGAGAAT CTTATTGTAT 51 GAATAACTTT GGCCATCGTC TTGCTGACAA TGAATGCCAA GAACTGTCCC 101 GAGTGACGAG AGAGAATTGC AATGAATTTT CCTGTCCCAG TTGGGCTGCT 151 AGTGAATGGA GCGAG
SEQ ID NO 92 (INSP006 Protein sequence exon 20)
1 CSRSCGGGER SRESYCMNNF GHRLADNECQ ELSRVTRENC NEFSCPSWAA 51 SEWSE SEQ ID NO 93 (INSP006 Nucleotide sequence exon 21) 1 TGCCTTGTTA CATGTGGTAA AGGAACAAAG CAGCGGCAGG TATGGTGTCA
51 GCTGAATGTA GATCACTTGA GTGATGGCTT CTGTAATTCA AGTACCAAAC 101 CTGAATCTCT GAGTCCATGT GAACTTCATA CATGTGCTTC CTGGCAAGTA 151 GGACCATGGG GTCCT SEQ ID NO 94 (INSP006 Protein sequence exon 21)
1 CLVTCGKGTK QRQV CQLNV DH SDGFCNS STKPESLSPC E HTCASWQV 51 GPWGP SEQ ID NO 95 (INSP006 Nucleotide sequence exon 22)
1 TGCACAACCA CATGTGGACA TGGGTATCAG ATGCGAGATG TTAAATGTGT 51 CAATGAGCTA GCTAGTGCAG TGTTAGAGGA CACAGAATGC CATGAAGCTA 101 GTCGCCCCAG TGACAGACAG SEQ ID NO 96 (INSP006 Protein sequence exon 22) 1 CTTTCGHGYQ MRDVKCVNEL ASAVLEDTEC HEASRPSDRQ SEQ ID NO 97 (INSP006 Nucleotide sequence exon 23)
1 TGCTCCGTAT CTTGTGGAAG AGGTACTCAA GCCCGCTATG TAAGCTGTCG 51 TGATGCTCTT GATAGAATAG CAGATGAATC ATATTGTGCC CACTTACCCC 101 GACCTGCTGA AATATGGGAC TGTTTTACCC CTTGTGGAGA GTGGCAAGCA 151 GGGGATTGGT CACCC
SEQ ID NO 98 (INSP006 Protein sequence exon 23)
1 CSVSCGRGTQ ARYVSCRDAL DRIADESYCA HLPRPAEI D CFTPCGEWQA 51 GD SP SEQ IDNO 99 (INSP006 Nucleotide sequence exon24) 1 TGTTCAGCTT CCTGTGGCCA TGGAAAAACA ACTCGACAAG TTTTATGCAT 51 GAACTACCAT CAGCCAATTG ATGAGAATTA CTGTGATCCT GAAGTTCGCC 101 CTTTGATGGA ACAGGAATGT AGCCTGGCAG CCTGCCCTCC TGCACACAGC 151 CACTTTCCTA GTTCCCCTGT GCAGCCAAGC TATTATCTAA GCACGAATTT 201 GCCATTAACT CAAAAACTTG AAGATAATGA AAATCAGGTG GTCCATCCAT 251 CAGTCAGAGG AAACCAGTGG AGAACCGGAC CATGGGGATC A SEQ ID NO 100 (INSP006 Protein sequence exon 24)
1 CSASCGHGKT TRQV CMNYH QPIDENYCDP EVRPLMEQEC SLAACPPAHS 51 HFPSSPVQPS YYLSTNLPLT QKLEDNENQV VHPSVRGNQW RTGP GS SEQ IDNO 101 (INSP006 Nucleotide sequence exon 25) 1 TGCTCCAGCA GTTGTTCTGG AGGTCTTCAG CATAGGGCTG TGGTCTGCCA 51 GGATGAAAAT GGACAAAGTG CTAGTTACTG CGATGCAGCC TCCAAGCCTC 101 CAGAGTTACA GCAATGTGGT CCAGGGCCTT GTCCACAGTG GAACTACGGA 151 AATTGGGGAG AA SEQ ID NO 102 (INSP006 Protein sequence exon 25) 1 CSSSCSGG Q HRAVVCQDEN GQSASYCDAA SKPPELQQCG PGPCPQ NYG 51 N GE SEQ ID NO 103 (INSP006 Nucleotide sequence exon26)
1 TGTTCACAAA CATGTGGAGG AGGAATAAAA TCAAGACTTG TAATATGTCA 51 ATTTCCCAAT GGCCAAATAT TAGAAGATCA CAACTGTGAA ATTGTAAACA 101 AGCCACCTAG CGTAATACAG TGTCATATGC ATGCTTGCCC TGCTGATGTG 151 TCATGGCATC AGGAACCATG GACATCGGTA TGA SEQ ID NO 104 (INSP006 Protein sequence exon 26)
1 CΞQTCGGGIK SRLVICQFPN GQILEDHNCE IVNKPPSVIQ CH HACPADV 51 SWHQEPWTSV SEQ IDNO 105 (INSP007 Nucleotide sequence exon 1)
1 CTGTCTGACC TGTACCCCCA TGAGGCCTGG AGCTTCACCT TCAGCAAGTT 51 CCTTCCAGGG CACG SEQ IDNO 106 (INSP007 Protein sequence exon 1) 1 LSDLYPHEAW SFTFSKFLPG HE SEQ ID NO 107 (INSP007 Nucleotide sequence exon 2)
1 AAGTGGGCGT CTGCAGCTTC GCCCGGTTCT CAGGGGAATT CCCGAAGTCG 51 GGGCCCAGCG CCCCTGATCT GGCCCTGGTA GAGGCAGCAG CAGACGGCCC 101 CGAGGCCCCC CTGCAGGACA GGGGCTGGGC CCTGTGCTTC AGTGCCCTGG 151 GGATGGTTCA GTGCTGCAAG SEQ ID NO 108 (INSP007 Protein sequence exon 2)
1 VGVCSFARFS GEFPKSGPSA PDLALVEAAA DGPEAPLQDR GWA CFSALG 51 MVQCCK SEQ ID NO 109 (INSP007 Nucleotide sequence exon 3)
1 GTCACGTGCC ACGAGCTCTG CCACCTTCTG GGCCTGGGGA ACTGCCGCTG 51 GCTCCGCTGC CTCATGCAGG GTGCGCTCAG CCTGGACGAG GCCCTGCGGC 101 GGCCCCTGGA CCTCTGTCCC ATCTGCCTGA GGAAGCTGCA GCATGTCCTG 151 GGTTTCAGGC TCATCGAGAG GTACCAG SEQ ID NO 110 (INSP007 Protein sequence exon 3)
1 VTCHELCHLL GLGNCR LRC LMQGALSLDE ALRRPLDLCP ICLRK QHV 51 GFRLIERYQ
SEQ ID NO 11 1 (INSP008 Nucleotide sequence exon 1)
1 GGAATTGCTT ACTTAGGAGG TGTGTGCAGT GCTAAGAGGA AGTGTGTGCT 51 TGCCGAAGAC AATGGTCTCA ATTTGGCCTT TACCATCGCC CATGAGCTGG 101 GCCACAA
SEQ ID NO 112 (1NSP008 Protein sequence exon 1)
1 GIAYLGGVCS AKRKCV AED NGLN AFTIA HELGHN SEQ ID NO 113 (1NSP008 Nucleotide sequence exon 2) 1 CTTGGGCATG AACCACGACG ATGACCACTC ATCTTGCGCT GGCAGGTCCC 51 ACATCATGTC AGGAGAGTGG GTGAAAGGCC GGAACCCAAG TGACCTCTCT
101 TGGTCCTCCT GCAGCCGAGA TGACCTTGAA AACTTCCTCA A SEQ ID NO 114 (INSP008 Protein sequence exon 2) 1 LGMNHDDDHS SCAGRSHIMS GEWVKGR PS DLSWSSCSRD DLENFLK SEQ ID NO 115 (INSP008 Nucleotide sequence exon 3)
1 GTCAAAAGTC AGCACCTGCT TGCTAGTCAC GGACCCCAGA AGCCAGCACA 51 CAGTACGCCT CCCGCACAAG CTGCCGGGCA TGCACTACAG TGCCAACGAG 101 CAGTGCCAGA TCCTGTTTGG CATGAATGCC ACCTTCTGCA GAAACATGGA 151 G SEQ ID NO 116 (INSP008 Protein sequence exon 3)
1 SKVSTCLLVT DPRSQHTVRL PHKLPGMHYS ANEQCQILFG MNATFCRNME SEQ ID NO 117 (INSP008 Nucleotide sequence exon 4) 1 CATCTAATGT GTGCTGGACT GTGGTGCCTG GTAGAAGGAG ACACATCCTG 51 CAAGACCAAG CTGGACCCTC CCCTGGATGG CACCGAGTGT GGGGCAGACA 101 AG SEQ IDNO 118 (INSP008 Protein sequence exon 4)
1 HLMCAGLWCL VEGDTSCKTK LDPP DGTEC GADK SEQ IDNO 119 (INSP008 Nucleotide sequence exon 5)
1 TGGTGCCGCG CGGGGGAGTG CGTGAGCAAG ACGCCCATCC CGGAGCATGT 51 GGACGGAGAC TGGAGCCCGT GGGGCGCCTG GAGCATGTGC AGCCGAACAT 101 GTGGGACGGG AGCCCGCTTC AGGCAGAGGA AATGTGACAA CCCCCC SEQ ID NO 120 (HNSP008 Protein sequence exon 5) 1 WCRAGECVSK TPIPEHVDGD WSPWGAWSMC SRTCGTGARF RQRKCDNPP SEQ IDNO 121 (INSP008 Nucleotide sequence exon 6)
1 CCCTGGGCCT GGAGGCACAC ACTGCCCGGG TGCCAGTGTA GAACATGCGG 51 TCTGCGAGAA CCTGCCCTGC CCCAAGGGTC TGCCCAGCTT CCGGGACCAG 101 CAGTGCCAGG CACACGACCG GCTGAGCCCC AAGAAGAAAG GCCTGCTGAC 151 AGCCGTGGTG GTTGACG
SEQ ID NO 122 ( NSP008 Protein sequence exon 6)
1 PGPGGTHCPG ASVEHAVCEN PCPKGLPSF RDQQCQAHDR LΞPK KGL T 51 AVWDD SEQ ID NO 123 (INSP008 Nucleotide sequence exon 7) 1 ATAAGCCATG TGAACTCTAC TGCTCGCCCC TCGGGAAGGA GTCCCCACTG 51 CTGGTGGCCG ACAGGGTCCT GGACGGTACA CCCTGCGGGC CCTACGAGAC 101 TGATCTCTGC GTGCACGGCA AGTGCCAG SEQIDNO 124 (INSP008 Protein sequence exon 7)
1 KPCELYCSPL GKESPLLVAD RVLDGTPCGP YETDLCVHGK CQ SEQ ID NO 125 (INSP008 Nucleotide sequence exon 8)
1 AAAATCGGCT GTGACGGCAT CATCGGGTCT GCAGCCAAAG AGGACAGATG 51 CGGGGTCTGC AGCGGGGACG GCAAGACCTG CCACTTGGTG AAGGGCGACT 101 TCAGCCACGC C SEQ ID NO 126 (NSP008 Protein sequence exon 8) 1 KIGCDGIIGΞ AAKEDRCGVC SGDGKTCHLV KGDFΞHA SEQ ID NO 127 (INSP003 nucleotide sequence)
1 ATGCTCGCCG CCTCCATCTT CCGTCCGACA CTGCTGCTCT GCTGGCTGGC 51 TGCTCCCTGG CCCACCCAGC CCGAGAGTCT CTTCCACAGC CGGGACCGCT 101 CGGACCTGGA GCCGTCCCCA CTGCGCCAGG CCAAGCCCAT TGCCGACCTC 151 CACGCTGCTC AGCGGTTCCT GTCCAGATAC GGCTGGTCAG GGGTGTGGGC 201 GGCCTGGGGG CCCAGTCCCG AGGGGCCGCC GGAGACCCCC AAGGGCGCCG 251 CCCTGGCCGA GGCGGTGCGC AGGTTCCAGC GGGCGAACGC GCTGCCGGCC 301 AGCGGGGAGC TGGACGCGGC CACCCTAGCG GCCATGAACC GGCCGCGCTG 351 CGGGGTCCCG GACATGCGCC CACCGCCCCC CTCCGCCCCG CCTTCGCCCC 401 CGGGCCCGCC CCCCAGAGCC CGCTCCAGGC GCTCCCCGCG GGCGCCGCTG 451 TCCTTGTCCC GGCGGGGTTG GCAGCCCCGG GGCTACCCCG ACGGCGGAGC 501 TGCCCAGGCC TTCTCCAAGA GGACGCTGAG CTGGCGGCTG CTGGGCGAGG 551 CCCTGAGCAG CCAACTGTCC GTGGCCGACC AGCGGCGCAT TGTGGCGCTG 601 GCCTTCAGGA TGTGGAGCGA GGTGACGCCG CTGGACTTCC GCGAGGACCT 651 GGCCGCCCCC GGGGCCGCGG TCGACATCAA GCTGGGCTTT GGGAGAGGCC 701 GGCACCTGGG CTGTCCGCGG GCCTTCGATG GGAGCGGGCA GGAGTTTGCA 751 CACGCCTGGC GCCTAGGTGA CATTCACTTT GACGACGACG AGCACTTCAC 801 ACCTCCCACC AGTGACACGG GCATCAGCCT TCTCAAGGTG GCCGTCCATG 851 AAATTGGCCA TGTCCTGGGC TTGCCTCACA CCTACAGGAC GGGATCCATA 901 ATGCAACCAA ATTACATTCC CCAGGAGCCT GCCTTTGAGT TGGACTGGTC 951 AGACAGGAAA GCAATTCAAA AGCTGTATGG CTCCTGTGAG GGATCATTTG 1001 ATACTGCGTT TGACTGGATT CGCAAAGAGA GAAACCAATA TGGAGAGGTG 1051 ATGGTGAGAT TTAGCACATA TTTCTTCCGT AACAGCTGGT ACTGGCTTTA 1101 TGAAAATCGA AACAATAGGA CACGCTATGG GGACCCTATC CAAATCCTCA 1151 CTGGCTGGCC TGGAATCCCA ACACACAACA TAGATGCCTT TGTTCACATC 1201 TGGACATGGA AAAGAGATGA ACGTTATTTT TTTCAAGGAA ATCAATACTG 1251 GAGATATGAC AGTGACAAGG ATCAGGCCCT CACAGAAGAT GAACAAGGAA 1301 AAAGCTATCC CAAATTGATT TCAGAAGGAT TTCCTGGCAT CCCAAGTCCC 1351 CTAGACACGG CGTTTTATGA CCGAAGACAG AAGTTAATTT ACTTCTTCAA 1401 GGAGTCCCTT GTATTTGCAT TTGATGTCAA CAGAAATCGA GTACTTAATT 1451 CTTATCCAAA GAGGATTACT GAAGTTTTTC CAGCAGTAAT ACCACAAAAT 1501 CATCCTTTCA GAAATATAGA TTCCGCTTAT TACTCCTATG CATACAACTC 1551 CATTTTCTTT TTCAAAGGCA ATGCATACTG GAAGGTAGTT AATGACAAGG 1601 ACAAACAACA GAATTCCTGG CTTCCTGCTA ATGGCTTATT TCCAAAAAAG 1651 TTTATTTCAG AGAAGTGGTT TGATGTTTGT GACGTCCATA TCTCCACACT 1701 GAACATGTAA SEQ ID NO 128 (INSP003 protein sequence)
1 M AASIFRPT LLCWLAAPW PTQPESLFHS RDRSD EPSP LRQAKPIADL 51 HAAQRFLSRY GWSGVWAAWG PSPEGPPETP KGAALAEAVR RFQRANALPA 101 SGE DAATLA AMNRPRCGVP DMRPPPPSAP PSPPGPPPRA RSRRSPRAPL 151 SLSRRGWQPR GYPDGGAAQA FSKRT SWR GEALSSQLΞ VADQRRIVAL 201 AFRM SEVTP LDFREDLAAP GAAVDIKLGF GRGRHLGCPR AFDGSGQEFA 251 HA RLGDIHF DDDEHFTPPT SDTGISLLKV AVHEIGHVLG LPHTYRTGSI 301 MQPNYIPQEP AFE D SDRK AIQK YGSCE GSFDTAFDWI RKERNQYGEV 351 MVRFSTYFFR NSWYW YENR NNRTRYGDPI QILTG PGIP THNIDAFVHI 401 TWKRDERYF FQGNQYWRYD SDKDQALTED EQGKSYPKLI SEGFPGIPSP 451 LDTAFYDRRQ K IYFFKESL VFAFDVNRNR VLNSYPKRIT EVFPAVIPQN 501 HPFRNIDSAY YSYAYNSIFF FKGNAYWKW NDKDKQQNSW LPANGLFPKK 551 FISEKWFDVC DVHISTLNM SEQ ID NO 129 (INSP004 nucleotide sequence)
1 ATGCTAGCTT TCCTACTTAC TATCTTAGCT TCAATTTTCT CCTTTGTAAA 51 TGGGGGTGGT GATAATAGCA ACTTGTCCAG CCAGCTTCTG GCCCAGGAAC 101 ACAACTACAG CTCCCCTGCG GGTCACCATC CTCACGTACT GTACAAAAGG 151 ACAGCAGAGG AGAAGATCCA GCGGTACCGT GGCTACCCCG GCTCTGGCCG
201 GAATTATCCT GGTTACTCCC CAAGTCACAT TCCCCATGCA TCTCAGAGTC 251 GAGAGACAGA GTATCACCAT CGAAGGTTGC AAAAGCAGCA TTTTTGTGGA 301 CGACGCAAGA AATGTATATA TTCTCTAATA TCCCTTCCAA ATGCTCTTCT 351 GTTCATCGTA GATGCTCCCA AGCCTCCCAC AGAGGACACC TATCTAAGGT 401 TTGATGAATA TGGGAGCTCT GGGCGACCCA GAAGATCAGC TGGAAAATCA 451 CAAAAGGGCC TCAATGTGGA AACCCTCGTG GTGGCAGACA AGAAAATGGT 501 GGAAAAGCAT GGCAAGGGAA ATGTCACCAC ATACATTCTC ACAGTAATGA 551 ACATGGTTTC TGGCCTATTT AAAGATGGGA CTATTGGAAG TGACATAAAC
601 GTGGTTGTGG TGAGCCTAAT TCTTCTGGAA CAAGAACCTG GAGGATTATT 651 GATCAACCAT CATGCAGACC AGTCTCTGAA TAGTTTTTGT CAATGGCAGT 701 CTGCCCTCAT TGGAAAGAAT GGCAAGAGAC ATGATCATGC CATCTTACTA
751 ACAGGATTTG ATATTTGTTC TTGGAAGAAT GAACCATGTG ACACTCTAGG 801 GTTTGCCCCC ATCAGTGGAA TGTGCTCTAA GTACCGAAGT TGTACCATCA 851 ATGAGGACAC AGGACTTGGC CTTGCCTTCA CCATCGCTCA TGAGTCAGGG 901 CACAACTTTG GTATGATTCA CGATGGAGAA GGGAATCCCT GCAGAAAGGC 951 TGAAGGCAAT ATCATGTCTC CCACACTGAC CGGAAACAAT GGAGTGTTTT 1001 CATGGTCTTC CTGCAGCCGC CAGTATCTCA AGAAATTCCT CAGCACACCT 1051 CAGGCGGGGT GTCTAGTGGA TGAGCCCAAG CAAGCAGGAC AGTATAAATA 1101 TCCGGACAAA CTACCAGGAC AGATTTATGA TGCTGACACA CAGTGTAAAT 1151 GGCAATTTGG AGCAAAAGCC AAGTTATGCA GCCTTGGTTT TGTGAAGGAT 1201 ATTTGCAAAT CACTTTGGTG CCACCGAGTA GGCCACAGGT GTGAGACCAA 1251 GTTTATGCCC GCAGCAGAAG GGACCGTTTG TGGCTTGAGT ATGTGGTGTC 1301 GGCAAGGCCA GTGCGTAAAG TTTGGGGAGC TCGGGCCCCG GCCCATCCAC 1351 GGCCAGTGGT CCGCCTGGTC GAAGTGGTCA GAATGTTCCC GGACATGTGG 1401 TGGAGGAGTC AAGTTCCAGG AGAGACACTG CAATAACCCC AAGCCTCAGT 1451 ATGGTGGCTT ATTCTGTCCA GGTTCTAGCC GTATTTATCA GCTGTGCAAT 1501 ATTAACCCTT GCAATGAAAA TAGCTTGGAT TTTCGGGCTC AACAGTGTGC 1551 AGAATATAAC AGCAAACCTT TCCGTGGATG GTTCTACCAG TGGAAACCCT 1601 ATACAAAAGT GGAAGAGGAA GATCGATGCA AACTGTACTG CAAGGCTGAG 1651 AACTTTGAAT TTTTTTTTGC AATGTCCGGC AAAGTGAAAG ATGGAACTCC 1701 CTGCTCCCCA AACAAAAATG ATGTTTGTAT TGACGGGGTT TGTGAACTAG 1751 TGGGATGTGA TCATGAACTA GGCTCTAAAG CAGTTTCAGA TGCTTGTGGC 1801 GTTTGCAAAG GTGATAATTC AACTTGCAAG TTTTATAAAG GCCTGTACCT 1851 CAACCAGCAT AAAGCAAATG AATATTATCC GGTGGTCCTC ATTCCAGCTG 1901 GCGCCCGAAG CATCGAAATC CAGGAGCTGC AGGTTTCCTC CAGTTACCTC 1951 GCAGTTCGAA GCCTCAGTCA AAAGTATTAC CTCACCGGGG GCTGGAGCAT 2001 CGACTGGCCT GGGGAGTTCC CCTTCGCTGG GACCACGTTT GAATACCAGC 2051 GCTCTTTCAA CCGCCCGGAA CGTCTGTACG CGCCAGGGCC CACAAATGAG 2101 ACGCTGGTCT TTGAAGTAAG CCCCTTCTGT GTATTCAGTT CTCAGTGCTT 2151 CTTGCTACAT TTATATCGTT GA SEQ ID NO 130 (INSP004 protein sequence)
1 MLAF LTILA SIFSFVNGGG DNSN ΞSQL AQEHNYSSPA GHHPHVLYKR 51 TAEEKIQRYR GYPGSGRNYP GYSPSHIPHA SQSRETEYHH RR QKQHFCG 101 RRKKCIYS I SLPNALLFIV DAPKPPTEDT YLRFDEYGSS GRPRRSAGKS 151 QKGLNVETLV VADKKMVEKH GKGNVTTYIL TVM MVSGLF KDGTIGSDIN 201 WWSLILLE QEPGGLLINH HADQSLNSFC Q QSALIGKN GKRHDHAILL 251 TGFDICS KN EPCDTLGFAP ISGMCSKYRS CTINEDTGLG LAFTIAHESG 301 HNFGMIHDGE GNPCRKAEGN IMSPTLTGNN GVFS SΞCSR QYLKKFLSTP 351 QAGC VDEPK QAGQYKYPDK PGQIYDADT QCKWQFGAKA KLCS GFVKD 401 ICKSLWCHRV GHRCETKFMP AAEGTVCGLS MWCRQGQCVK FGELGPRPIH 451 GQWSAWSKWS ECSRTCGGGV KFQERHCNNP KPQYGG FCP GSSRIYOLCN 501 INPCNENSLD FRAQQCAEYN SKPFRGWFYQ KPYTKVEEE DRCKLYCKAE 551 NFEFFFAMSG KVKDGTPCSP NKNDVCIDGV CELVGCDHE GSKAVSDACG 601 VCKGDNSTCK FYKGLYLNQH KANEYYPWL IPAGARSIEI QELQVSSSYL 651 AVRS SQKYY TGGWSID P GEFPFAGTTF EYQRSFNRPE RLYAPGPTNE 701 TLVFEVSPFC VFSSQCF LH YR SEQ ID NO 133 (INSP006 nucleotide sequence)
1 AAGCCCTGGT GAGGACACTG ACCTCCTACG AAGTAGTGAT CCCCGAGCGG 51 GTCAATGAGT TTGGAGAAGT GTTCCCTCAG AGCCACCACT TCAGCCGGCA 101 GAAACGCAGC TCCGAGGCGC TGGAACCCAT GCCGTTCCGA ACCCACTATC 151 GCTTCACTGC CTACGGGCAG CTCTTCCAGC TGAACCTGAC CGCCGATGCA 201 TCCTTTCTGG CCGCCGGCTA CACCGAGGTG CACTTGGGAA CCCCGGAGCG 251 CGGGGCCTGG GAGAGCGACG CAGGGCCCTC GGACCTGCGC CACTGCTTCT 301 ACCGCGGCCA GGTCAACTCA CAGGAGGATT ACAAGGCCGT CGTCAGCTTA 351 TGCGGAGGCC TGACGGGAAC ATTTAAAGGA CAGAACGGTG AATATTTCTT 401 AGAACCTATA ATGAAGGCAG ATGGGAATGA ATATGAAGAT GGTCACAACA 451 AGCCACATCT TATATACAGA CAAGACTTAA ATAACTCTTT TCTGCAGACT 501 CTGAAGTATT GCAGTGTGTC AGAAAGTCAA ATAAAGGAAA CCAGTTTACC 551 CTTTCATACC TACAGCAACA TGAATGAAGA TCTTAATGTA ATGAAAGAAA 601 GAGTTTTAGG ACACACATCA AAAAATGTAC CATTGAAAGA TGAAAGAAGA 651 CATTCCAGGA AAAAACGTCT TATATCATAT CCAAGATACA TTGAAATTAT 701 GGTTACAGCT GATGCTAAAG TGGTTTCTGC TCATGGATCG AATTTGCAAA 751 ACTATATACT GACTCTAATG TCAATTGTTG CAACAATCTA CAAAGATCCA 801 AGTATTGGAA ATTTGATACA CATAGTAGTG GTAAAATTAG TTATGATTCA 851 CCGTGAGGAG GAAGGACCAG TCATTAATTT TGATGGTGCT ACCACATTAA 901 AGAACTTTTG TTCATGGCAA CAAACTCAGA ATGACCTTGA TGATGTTCAC 951 CCTTCCCACC ATGACACTGC TGTTCTTATC ACTAGGGAAG ACATTTGTTC 1001 ATCTAAAGAG AAATGTAACA TGTTAGGTTT ATCATATTTA GGTACCATAT 1051 GTGATCCTTT ACAAAGCTGC TTTATTAATG AAGAAAAAGG ACTCATTTCT 1101 GCTTTTACTA TAGCCCATGA GCTTGGGCAC ACACTTGGTG TTCAACATGA 1151 TGATAATCCT AGATGTAAAG AAATGAAAGT TACAAAGTAT CATGTAATGG 1201 CCCCTGCTTT AAGTTTTCAC ATGAGTCCTT GGAGCTGGTC AAACTGTAGT 1251 CGGAAATATG TTACTGAATT CCTAGATACT GGTTACGGGG AATGTCTTCT 1301 TGACAAACCA GATGAAGAAA TATATAATCT GCCTTCAGAA CTTCCTGGAT 1351 CACGATATGA TGGAAACAAG CAGTGTGAGC TTGCGTTTGG TCCTGGGTCA 1401 CAAATGTGTC CCCATATAGA GAATATATGC ATGCATCTGT GGTGCACAAG 1451 CACAGAAAAG CTTCACAAAG GCTGTTTCAC TCAACACGTG CCACCAGCAG 1501 ATGGAACAGA CTGCGGTCCT GGAATGCATT GCCGTCATGG GCTATGTGTA 1551 AACAAAGAAA CGGAAACACG TCCTGTAAAT GGTGAATGGG GACCATGGGA 1601 ACCTTACAGT TCTTGTTCAA GAACATGTGG AGGCGGAATC GAAAGTGCAA 1651 CCAGGCGCTG TAATCGTCCT GAGCCAAGAA ACGGAGGAAA TTACTGTGTG 1701 GGCCGCAGGA TGAAATTTCG ATCATGTAAT ACTGATTCAT GTCCAAAAGG 1751 CACACAAGAC TTTCGAGAGA AGCAGTGCTC TGATTTTAAT GGTAAACATT 1801 TGGACATCAG TGGCATTCCC TCTAATGTGA GGTGGCTTCC AAGATACAGT 1851 GGCATTGGCA CAAAGGATCG TTGTAAACTC TATTGTCAGG TTGCTGGAAC 1901 CAATTATTTC TACCTATTGA AGGATATGGT TGAAGATGGT ACTCCTTGTG 1951 GAACTGAAAC TCATGACATC TGTGTTCAAG GCCAGTGTAT GGCAGCTGGT 2001 TGTGATCACG TGTTAAACTC CAGTGCCAAG ATAGACAAAT GTGGAGTGTG 2051 TGGTGGGGAC AACTCTTCAT GCAAGACAAT AACAGGTGTC TTCAACAGTT 2101 CTCATTATGG TTATAATGTT GTTGTAAAGA TTCCCGCAGG AGCAACAAAC 2151 GTTGACATTC GTCAGTACAG CTATTCTGGA CAACCAGATG ACAGTTACCT 2201 TGCATTATCT GACGCTGAAG GGAATTTTCT TTTCAATGGA AATTTTCTTC 2251 TAAGTACGTC AAAAAAAGAA ATCAATGTGC AAGGAACAAG AACTGTTATT 2301 GAATACAGTG GATCAAATAA CGCAGTTGAA AGAATTAATA GTACTAATCG 2351 ACAAGAGAAA GAACTTATTT TGCAGGTGTT GTGTGTGGGT AATTTATACA 2401 ACCCTGATGT ACATTATTCC TTCAATATCC CTTTGGAAGA GAGGAGTGAC 2451 ATGTTCACAT GGGACCCCTA TGGACCATGG GAAGGCTGTA CCAAAATGTG 2501 TCAAGGTCTT CAGCGAAGAA ACATAACTTG CATACATAAG AGTGATCATA 2551 GTGTTGTGTC TGATAAAGAA TGTGACCACT TGCCACTTCC ATCATTTGTT 2601 ACTCAAAGTT GCAATACAGA CTGTGAACTA AGGTGGCATG TTATTGGCAA 2651 AAGTGAATGT TCATCCCAAT GTGGTCAAGG ATATAGAACC TTGGACATCC 2701 ATTGCATGAA GTATTCCATT CATGAAGGAC AGACTGTTCA AGTTGATGAC 2751 CACTACTGTG GTGACCAGCT TAAACCTCCT ACCCAAGAAC TATGCCATGG 2801 TAACTGTGTC TTCACAAGAT GGCATTATTC AGAATGGTCT CAGTGTTCCA 2851 GGAGTTGTGG AGGAGGGGAA AGGTCTCGAG AATCTTATTG TATGAATAAC 2901 TTTGGCCATC GTCTTGCTGA CAATGAATGC CAAGAACTGT CCCGAGTGAC 2951 GAGAGAGAAT TGCAATGAAT TTTCCTGTCC CAGTTGGGCT GCTAGTGAAT 3001 GGAGCGAGTG CCTTGTTACA TGTGGTAAAG GAACAAAGCA GCGGCAGGTA 3051 TGGTGTCAGC TGAATGTAGA TCACTTGAGT GATGGCTTCT GTAATTCAAG 3101 TACCAAACCT GAATCTCTGA GTCCATGTGA ACTTCATACA TGTGCTTCCT 3151 GGCAAGTAGG ACCATGGGGT CCTTGCACAA CCACATGTGG ACATGGGTAT 3201 CAGATGCGAG ATGTTAAATG TGTCAATGAG CTAGCTAGTG CAGTGTTAGA 3251 GGACACAGAA TGCCATGAAG CTAGTCGCCC CAGTGACAGA CAGTGCTCCG 3301 TATCTTGTGG AAGAGGTACT CAAGCCCGCT ATGTAAGCTG TCGTGATGCT 3351 CTTGATAGAA TAGCAGATGA ATCATATTGT GCCCACTTAC CCCGACCTGC 3401 TGAAATATGG GACTGTTTTA CCCCTTGTGG AGAGTGGCAA GCAGGGGATT 3451 GGTCACCCTG TTCAGCTTCC TGTGGCCATG GAAAAACAAC TCGACAAGTT 3501 TTATGCATGA ACTACCATCA GCCAATTGAT GAGAATTACT GTGATCCTGA 3551 AGTTCGCCCT TTGATGGAAC AGGAATGTAG CCTGGCAGCC TGCCCTCCTG 3601 CACACAGCCA CTTTCCTAGT TCCCCTGTGC AGCCAAGCTA TTATCTAAGC 3651 ACGAATTTGC CATTAACTCA AAAACTTGAA GATAATGAAA ATCAGGTGGT 3701 CCATCCATCA GTCAGAGGAA ACCAGTGGAG AACCGGACCA TGGGGATCAT 3751 GCTCCAGCAG TTGTTCTGGA GGTCTTCAGC ATAGGGCTGT GGTCTGCCAG 3801 GATGAAAATG GACAAAGTGC TAGTTACTGC GATGCAGCCT CCAAGCCTCC 3851 AGAGTTACAG CAATGTGGTC CAGGGCCTTG TCCACAGTGG AACTACGGAA 3901 ATTGGGGAGA ATGTTCACAA ACATGTGGAG GAGGAATAAA ATCAAGACTT 3951 GTAATATGTC AATTTCCCAA TGGCCAAATA TTAGAAGATC ACAACTGTGA 4001 AATTGTAAAC AAGCCACCTA GCGTAATACA GTGTCATATG CATGCTTGCC 4051 CTGCTGATGT GTCATGGCAT CAGGAACCAT GGACATCGGT ATGA SEQ ID NO 134 (INSP006 protein sequence)
1 ALVRTLTSYE WIPERVNEF GEVFPQSHHF SRQKRSSEAL EP PFRTHYR
51 FTAYGQLFQL NLTADASFLA AGYTEVHLGT PERGAWESDA GPSDLRHCFY
101 RGQVNSQEDY KAVVS CGGL TGTFKGQNGE YFLEPI KAD GNEYEDGHNK 151 PHL1YRQDLN NSFLQT KYC SVSESQIKET SLPFHTYSNM NEDLNVMKER 201 V GHTSKNVP LKDERRHSRK KRLISYPRYI EIMVTADAKV VSAHGSNLQN 251 YI TLMSIVA TIYKDPSIGN LIHIVWKLV MIHREEEGPV INFDGATTLK 301 NFCSWQQTQN D DDVHPSHH DTAVLITRED ICSSKEKCNM GLSYLGTIC 351 DPLQSCFINE EKGLISAFTI AHE GHT GV QHDDNPRCKE KVTKYHV A 401 PALSFHMSPW SWSNCSRKYV TEF DTGYGE CLLDKPDEEI YNLPSELPGS
451 RYDGNKQCE AFGPGSQMCP HIENICMHLW CTSTEKLHKG CFTQHVPPAD 501 GTDCGPGMHC RHGLCV KET ETRPVNGEWG PWEPYSSCSR TCGGGIESAT 551 RRCNRPEPRN GGNYCVGRR KFRSCNTDSC PKGTQDFREK QCSDFNGKHL 601 DISGIPSNVR LPRYSGIGT KDRCK YCQV AGTNYFY LK DMVEDGTPCG 651 TETHDICVQG QCMAAGCDHV LNSSAKIDKC GVCGGDNSSC KTITGVFNSS
701 HYGYNVVVKI PAGATNVDIR QYSYSGQPDD SY ALSDAEG NFLFNGNF L 751 STSKKEINVQ GTRTVIEYSG SNNAVERINS TNRQEKELIL QVLCVGNLYN 801 PDVHYSFNIP LEERSDMFT DPYGP EGCT KMCQGLQRRN ITCIHKSDHS 851 WSDKECDHL PLPSFVTQSC NTDCE RWHV IGKSECSSQC GQGYRTLDIH 901 CMKYSIHEGQ TVQVDDHYCG DQLKPPTQEL CHGNCVFTRW HYSE SQCSR
951 SCGGGERSRE SYCMNNFGHR LADNECQELS RVTRENCNEF SCPSWAASEW 1001 SECLVTCGKG TKQRQV CQL NVDHLSDGFC NSSTKPESLS PCELHTCAS 1051 QVGPWGPCTT TCGHGYQMRD VKCVNELASA VLEDTECHEA SRPSDRQCSV 1101 SCGRGTQARY VSCRDALDRI ADESYCAHLP RPAEI DCFT PCGE QAGDW 1151 SPCSASCGHG KTTRQV CMN YHQPIDENYC DPEVRP MEQ ECSLAACPPA
1201 HSHFPSSPVQ PSYYLSTNLP LTQKLEDNEN QWHPSVRGN Q RTGPWGSC 1251 SΞSCSGGLQH RAWCQDENG QSASYCDAAS KPPELQQCGP GPCPQ YGN 1301 WGECSQTCGG GIKSRLVICQ FPNGQILEDH NCEIV KPPS VIQCH HACP 1351 ADVSWHQEP TSV SEQ ID NO 135 (INSP007 nucleotide sequence)
1 CTGTCTGACC TGTACCCCCA TGAGGCCTGG AGCTTCACCT TCAGCAAGTT 51 CCTTCCAGGG CACGAAGTGG GCGTCTGCAG CTTCGCCCGG TTCTCAGGGG 101 AATTCCCGAA GTCGGGGCCC AGCGCCCCTG ATCTGGCCCT GGTAGAGGCA 151 GCAGCAGACG GCCCCGAGGC CCCCCTGCAG GACAGGGGCT GGGCCCTGTG 201 CTTCAGTGCC CTGGGGATGG TTCAGTGCTG CAAGGTCACG TGCCACGAGC
251 TCTGCCACCT TCTGGGCCTG GGGAACTGCC GCTGGCTCCG CTGCCTCATG 301 CAGGGTGCGC TCAGCCTGGA CGAGGCCCTG CGGCGGCCCC TGGACCTCTG 351 TCCCATCTGC CTGAGGAAGC TGCAGCATGT CCTGGGTTTC AGGCTCATCG 401 AGAGGTACCA G SEQ ID NO 136 (INSP007 protein sequence)
1 SD YPHEAW SFTFSKFLPG HEVGVCSFAR FSGEFPKSGP SAPDLALVEA 51 AADGPEAPLQ DRGWALCFSA LGMVQCCKVT CHELCHL GL GNCRWLRCLM 101 QGALSLDEAL RRPLDLCPIC LRKLQHVLGF RLIERYQ SEQ ID NO 137 (INSP008 nucleotide sequence) 1 GGAATTGCTT ACTTAGGAGG TGTGTGCAGT GCTAAGAGGA AGTGTGTGCT
51 TGCCGAAGAC AATGGTCTCA ATTTGGCCTT TACCATCGCC CATGAGCTGG
101 GCCACAACTT GGGCATGAAC CACGACGATG ACCACTCATC TTGCGCTGGC
151 AGGTCCCACA TCATGTCAGG AGAGTGGGTG AAAGGCCGGA ACCCAAGTGA
201 CCTCTCTTGG TCCTCCTGCA GCCGAGATGA CCTTGAAAAC TTCCTCAAGT 251 CAAAAGTCAG CACCTGCTTG CTAGTCACGG ACCCCAGAAG CCAGCACACA
301 GTACGCCTCC CGCACAAGCT GCCGGGCATG CACTACAGTG CCAACGAGCA 351 GTGCCAGATC CTGTTTGGCA TGAATGCCAC CTTCTGCAGA AACATGGAGC 401 ATCTAATGTG TGCTGGACTG TGGTGCCTGG TAGAAGGAGA CACATCCTGC 451 AAGACCAAGC TGGACCCTCC CCTGGATGGC ACCGAGTGTG GGGCAGACAA 501 GTGGTGCCGC GCGGGGGAGT GCGTGAGCAA GACGCCCATC CCGGAGCATG
551 TGGACGGAGA CTGGAGCCCG TGGGGCGCCT GGAGCATGTG CAGCCGAACA 601 TGTGGGACGG GAGCCCGCTT CAGGCAGAGG AAATGTGACA ACCCCCCCCC 651 TGGGCCTGGA GGCACACACT GCCCGGGTGC CAGTGTAGAA CATGCGGTCT 701 GCGAGAACCT GCCCTGCCCC AAGGGTCTGC CCAGCTTCCG GGACCAGCAG 751 TGCCAGGCAC ACGACCGGCT GAGCCCCAAG AAGAAAGGCC TGCTGACAGC
801 CGTGGTGGTT GACGATAAGC CATGTGAACT CTACTGCTCG CCCCTCGGGA 851 AGGAGTCCCC ACTGCTGGTG GCCGACAGGG TCCTGGACGG TACACCCTGC 901 GGGCCCTACG AGACTGATCT CTGCGTGCAC GGCAAGTGCC AGAAAATCGG 951 CTGTGACGGC ATCATCGGGT CTGCAGCCAA AGAGGACAGA TGCGGGGTCT 1001 GCAGCGGGGA CGGCAAGACC TGCCACTTGG TGAAGGGCGA CTTCAGCCAC
1051 GCC SEQ ID NO 138 (INSP008 protein sequence)
1 GIAYLGGVCS AKRKCV AED NGLN AFTIA HE GHNLGMN HDDDHSSCAG 51 RSHIMSGEWV KGRNPSDLSW SΞCΞRDDLEN FLKSKVSTCL VTDPRSQHT 101 VRLPHKLPGM HYSANEQCQI LFGMNATFCR NMEHLMCAG WCLVEGDTSC
151 KTKLDPPLDG TECGADK CR AGECVSKTPI PEHVDGDWSP WGAWSMCSRT 201 CGTGARFRQR KCDNPPPGPG GTHCPGASVE HAVCENLPCP KGLPSFRDQQ 251 CQAHDRLΞPK KKGLLTAWV DDKPCELYCS PLGKESPL V ADRVLDGTPC 301 GPYETDLCVH GKCQKIGCDG IIGSAAKEDR CGVCSGDGKT CHLVKGDFSH 351 A
INSP007a
SEQ ID NO: 139 (INSP007A nucleotide sequence exon 1)
1 ATGCTGCAGT GTAGACCCGC ACAGGAGTTC AGCTTCGGGC CCCGGGCCTT
51 GAAGGACGCT CTGGTCTCCA CTGACGCAGC CCTGCAGCAG CTGTATGTGT 101 CCGCCTTCTC CCCTGCCGAG CGGCTCTTCC TGGCCGAGGC CTACAACCCG
151 CAGAGGACGC TCTTCTGCAC CCTGCTCATC CGCACGGGCT TCGACTGGCT
201 CCTGAGCCGA CCCGAGGCTC CCGAGGACTT CCAGACCTTC CACGCCTCCC 251 TGCAGCACCG GAAGCCCCGC CTGGCTCGGA AGCACATCTA CCTACAGCCG 301 ATAG
SEQ ID NO: 140 (INSP007A protein sequence exon 1) 1 MLQCRPAQEF SFGPRALKDA LVSTDAALQQ LYVSAFSPAE RLFLAEAYNP 51 QRTLFCTLLI RTGFDWLLSR PEAPEDFQTF HASLQHRKPR LARKHIYLQP 101 ID
SEQ ID NO: 141 (INSP007A nucleotide sequence exon 2) 1 ACCTGAGCGA GGAGCCGGTG GGAAGCTCCC TGCTGCACCA GCTGTGCAGC 51 TGCACAGAGG CCTTCTTCCT GGGCCTGCGC GTCAAGTGCC TGCCGTCGGT 101 GGCAGCCGCG TCCATCCGCT GCTCCTCGCG GCCCAGCCGG GACTCTGACA 151 GGCTCCAGCT CCACACAG SEQ ID NO: 142 (INSP007A protein sequence exon 2)
1 LSEEPVGSSL LHQLCSCTEA FFLGLRVKCL PSVAAASIRC SSRPSRDSDR 51 LQLHTD
SEQ ID NO: 143 (INSP007A nucleotide sequence exon 3) 1 ACGGCATCCT GTCCTTCTTG AAGAACAACA AGCCAGGGGA CGCGCTGTGT 51 GTGCTGGGCC TCACACTGTC TGACCTGTAC CCCCATGAGG CCTGGAGCTT 101 CACCTTCAGC AAGTTCCTTC CAGGGCACG
SEQ ID NO: 144 (INSP007A protein sequence exon 3) 1 GILSFLKNNK PGDALCVLGL TLSDLYPHEA WSFTFSKFLP GHE
SEQ ID NO: 145 (INSP007A nucleotide sequence exon 4)
1 AAGTGGGCGT CTGCAGCTTC GCCCGGTTCT CAGGGGAATT CCCGAAGTCG 51 GGGCCCAGCG CCCCTGATCT GGCCCTGGTA GAGGCAGCAG CAGACGGCCC 101 CGAGGCCCCC CTGCAGGACA GGGGCTGGGC CCTGTGCTTC AGTGCCCTGG 151 GGATGGTTCA GTGCTGCAAG
SEQ ID NO: 146 (INSP007A protein sequence exon 4)
1 VGVCSFARFS GEFPKSGPSA PD ALVEAAA DGPEAPLQDR G ALCFSALG 51 MVQCCK
SEQ ID NO: 147 (INSP007A nucleotide sequence exon 5)
1 GTCACGTGCC ACGAGCTCTG CCACCTTCTG GGCCTGGGGA ACTGCCGCTG 51 GCTCCGCTGC CTCATGCAGG GTGCGCTCAG CCTGGACGAG GCCCTGCGGC 101 GGCCCCTGGA CCTCTGTCCC ATCTGCCTGA GGAAGCTGCA GCATGTCCTG 151 GGTTTCAGGC TCATCGAGAG GTACCAG
SEQ ID NO: 148 (INSP007A protein sequence exon 5)
1 VTCHELCHLL GLGNCR LRC LMQGALSLDE ALRRPLDLCP ICLRKLQHVL 51 GFRLIERYQ
SEQ ID NO: 149 (INSP007A nucleotide sequence exon 6)
1 AGACTCTACA CCTGGACTCA GGCGGTGGTG GGGACGTGGC CCAGCCAGGA
51 GGCGGGGGAG CCGTCAGTGT GGGAGGACAC CCCGCCTGCC AGCGCCGACT 101 CGGGCATGTG CTGTGAGAGT GACTCGGAGC CCGGCACCAG TGTGTCGGAG
151 CCCCTCACCC CTGATGCCGG GAGTCACACC TTCGCCTCAG GGCCAGAGGA
201 AGGGCTGAGC TACCTGGCAG CCTCAGAGGC TCCGCTGCCA CCTGGGGGCC
251 CTGCGGAGGC CATCAAGGAG CATGAACGGT GGCTGGCCAT GTGCATCCAG
301 GCCCTGCAGC GGGAAGTGGC AGAGGAGGAC CTGGTGCAGG TGGACAGAGC 351 CGTGGACGCC CTCGACCGCT GGGAGATGTT CACGGGCCAG CTCCCGGCCA
401 CCAGGCAGGA CCCACCCAGC AGCAGGGACA GCGTGGGGCT GCGCAAGGTG
451 CTGGGGGACA AGTTCTCCTC CCTGAGGAGG AAGCTGAGTG CCCGAAAACT 501 CGCCAGAGCA GAGTCGGCCC CCCGTCCCTG GGATGGGGAA GAGAGT
SEQ ID NO: 150 (INSP007A protein sequence exon 6)
1 RLYT TQAVV GT PSQEAGE PSVWEDTPPA SADSGMCCES DSEPGTSVSE 51 PLTPDAGSHT FASGPEEGLS YLAASEAPLP PGGPAEAIKE HERWLAMCIQ 101 ALQREVAEED LVQVDRAVDA LDR EMFTGQ LPATRQDPPS SRDSVGLRKV 151 LGDKFSSLRR KLSARKLARA ESAPRP DGE ES
SEQ ID NO: 151 (INSP007A full nucleotide sequence)
1 ATGCTGCAGT GTAGACCCGC ACAGGAGTTC AGCTTCGGGC CCCGGGCCTT
51 GAAGGACGCT CTGGTCTCCA CTGACGCAGC CCTGCAGCAG CTGTATGTGT
101 CCGCCTTCTC CCCTGCCGAG CGGCTCTTCC TGGCCGAGGC CTACAACCCG
151 CAGAGGACGC TCTTCTGCAC CCTGCTCATC CGCACGGGCT TCGACTGGCT 201 CCTGAGCCGA CCCGAGGCTC CCGAGGACTT CCAGACCTTC CACGCCTCCC
251 TGCAGCACCG GAAGCCCCGC CTGGCTCGGA AGCACATCTA CCTACAGCCG
301 ATAGACCTGA GCGAGGAGCC GGTGGGAAGC TCCCTGCTGC ACCAGCTGTG
351 CAGCTGCACA GAGGCCTTCT TCCTGGGCCT GCGCGTCAAG TGCCTGCCGT
401 CGGTGGCAGC CGCGTCCATC CGCTGCTCCT CGCGGCCCAG CCGGGACTCT 451 GACAGGCTCC AGCTCCACAC AGACGGCATC CTGTCCTTCT TGAAGAACAA
501 CAAGCCAGGG GACGCGCTGT GTGTGCTGGG CCTCACACTG TCTGACCTGT
551 ACCCCCATGA GGCCTGGAGC TTCACCTTCA GCAAGTTCCT TCCAGGGCAC
601 GAAGTGGGCG TCTGCAGCTT CGCCCGGTTC TCAGGGGAAT TCCCGAAGTC
651 GGGGCCCAGC GCCCCTGATC TGGCCCTGGT AGAGGCAGCA GCAGACGGCC 701 CCGAGGCCCC CCTGCAGGAC AGGGGCTGGG CCCTGTGCTT CAGTGCCCTG
751 GGGATGGTTC AGTGCTGCAA GGTCACGTGC CACGAGCTCT GCCACCTTCT
801 GGGCCTGGGG AACTGCCGCT GGCTCCGCTG CCTCATGCAG GGTGCGCTCA
851 GCCTGGACGA GGCCCTGCGG CGGCCCCTGG ACCTCTGTCC CATCTGCCTG
901 AGGAAGCTGC AGCATGTCCT GGGTTTCAGG CTCATCGAGA GGTACCAGAG 951 ACTCTACACC TGGACTCAGG CGGTGGTGGG GACGTGGCCC AGCCAGGAGG
1001 CGGGGGAGCC GTCAGTGTGG GAGGACACCC CGCCTGCCAG CGCCGACTCG
1051 GGCATGTGCT GTGAGAGTGA CTCGGAGCCC GGCACCAGTG TGTCGGAGCC
1101 CCTCACCCCT GATGCCGGGA GTCACACCTT CGCCTCAGGG CCAGAGGAAG
1151 GGCTGAGCTA CCTGGCAGCC TCAGAGGCTC CGCTGCCACC TGGGGGCCCT 1201 GCGGAGGCCA TCAAGGAGCA TGAACGGTGG CTGGCCATGT GCATCCAGGC
1251 CCTGCAGCGG GAAGTGGCAG AGGAGGACCT GGTGCAGGTG GACAGAGCCG
1301 TGGACGCCCT CGACCGCTGG GAGATGTTCA CGGGCCAGCT CCCGGCCACC
1351 AGGCAGGACC CACCCAGCAG CAGGGACAGC GTGGGGCTGC GCAAGGTGCT
1401 GGGGGACAAG TTCTCCTCCC TGAGGAGGAA GCTGAGTGCC CGAAAACTCG 1451 CCAGAGCAGA GTCGGCCCCC CGTCCCTGGG ATGGGGAAGA GAGT
SEQ ID NO: 152 (INSP007A full protein sequence)
1 MLQCRPAQEF SFGPRALKDA LVSTDAALQQ LYVSAFSPAE RLFLAEAYNP
51 QRTLFCTLLI RTGFDWLLSR PEAPEDFQTF HASLQHRKPR LARKHIYLQP 101 IDLSEEPVGS SLLHQLCSCT EAFFLGLRVK CLPSVAAASI RCSSRPSRDS
151 DRLQLHTDGI LSFLKNNKPG DALCVLGLTL SDLYPHEAWS FTFSKFLPGH
201 EVGVCSFARF SGEFPKSGPS APDLALVEAA ADGPEAPLQD RGWALCFSAL
251 GMVQCCKVTC HELCHLLGLG NCRWLRCLMQ GALSLDEALR RPLDLCPICL
301 RKLQHVLGFR LIERYQRLYT WTQAVVGTWP SQEAGEPSVW EDTPPASADS 351 GMCCESDSEP GTSVSEPLTP DAGSHTFASG PEEGLSYLAA SEAPLPPGGP
401 AEAIKEHERW LAMCIQALQR EVAEEDLVQV DRAVDALDRW EMFTGQLPAT
451 RQDPPSSRDS VGLRKVLGDK FSSLRRKLSA RKLARAESAP RPWDGEES
INSP007b
SEQ ID NO: 153 (INSP007B nucleotide sequence exon 1)
1 ATGCTGCAGT GTAGACCCGC ACAGGAGTTC AGCTTCGGGC CCCGGGCCTT
51 GAAGGACGCT CTGGTCTCCA CTGACGCAGC CCTGCAGCAG CTGTATGTGT 101 CCGCCTTCTC CCCTGCCGAG CGGCTCTTCC TGGCCGAGGC CTACAACCCG 151 CAGAGGACGC TCTTCTGCAC CCTGCTCATC CGCACGGGCT TCGACTGGCT
201 CCTGAGCCGA CCCGAGGCTC CCGAGGACTT CCAGACCTTC CACGCCTCCC
251 TGCAGCACCG GAAGCCCCGC CTGGCTCGGA AGCACATCTA CCTACAGCCG
301 ATAG
SEQ ID NO: 154 (INSP007B protein sequence exon 1)
1 MLQCRPAQEF SFGPRALKDA LVSTDAALQQ LYVSAFSPAE RLFLAEAYNP
51 QRTLFCTLLI RTGFDWLLSR PEAPEDFQTF HASLQHRKPR LARKHIYLQP
101 ID
SEQ ID NO: 155 (INSP007B nucleotide sequence exon 2)
1 ACCTGAGCGA GGAGCCGGTG GGAAGCTCCC TGCTGCACCA GCTGTGCAGC 51 TGCACAGAGG CCTTCTTCCT GGGCCTGCGC GTCAAGTGCC TGCCGTCGGT 101 GGCAGCCGCG TCCATCCGCT GCTCCTCGCG GCCCAGCCGG GACTCTGACA 151 GGCTCCAGCT CCACACAG
SEQ ID NO: 156 (INSP007B protein sequence exon 2)
1 LSEEPVGSSL LHQLCSCTEA FFLGLRVKCL PSVAAASIRC SSRPSRDSDR 51 LQLHTD
SEQ ID NO: 157 (INSP007B nucleotide sequence exon 3)
1 ACGGCATCCT GTCCTTCTTG AAGAACAACA AGCCAGGGGA CGCGCTGTGT 51 GTGCTGGGCC TCACACTGTC TGACCTGTAC CCCCATGAGG CCTGGAGCTT 101 CACCTTCAGC AAGTTCCTTC CAGGGCACG
SEQ ID NO: 158 (INSP007B protein sequence exon 3) 1 GILSFLKNNK PGDALCVLGL TLSDLYPHEA WSFTFSKFLP GHG
SEQ ID NO: 159 (INSP007B nucleotide sequence exon 4) 1 GTCACGTGCC ACGAGCTCTG CCACCTTCTG GGCCTGGGGA ACTGCCGCTG 51 GCTCCGCTGC CTCATGCAGG GTGCGCTCAG CCTGGACGAG GCCCTGCGGC 101 GGCCCCTGGA CCTCTGTCCC ATCTGCCTGA GGAAGCTGCA GCATGTCCTG 151 GGTTTCAGGC TCATCGAGAG GTACCAG SEQ ID NO: 160 (INSP007B protein sequence exon 4)
1 HVPRALPPSG PGELPLAPLP HAGCAQPGRG PAAAPGPLSH LPEEAAACPG 51 FQAHREVPE
SEQ ID NO: 161 (INSP007B nucleotide sequence exon 5) 1 AGACTCTACA CCTGGACTCA GGCGGTGGTG GGGACGTGGC CCAGCCAGGA 51 GGCGGGGGAG CCGTCAGTGT GGGAGGACAC CCCGCCTGCC AGCGCCGACT 101 CGGGCATGTG CTG
SEQ ID NO: 162 (INSP007B protein sequence exon 5) 1 TLHLDSGGGG DVAQPGGGGA VSVGGHPACQ RRLGHVL
SEQ ID NO: 163 (INSP007B full nucleotide sequence)
1 ATGCTGCAGT GTAGACCCGC ACAGGAGTTC AGCTTCGGGC CCCGGGCCTT
51 GAAGGACGCT CTGGTCTCCA CTGACGCAGC CCTGCAGCAG CTGTATGTGT 101 CCGCCTTCTC CCCTGCCGAG CGGCTCTTCC TGGCCGAGGC CTACAACCCG
151 CAGAGGACGC TCTTCTGCAC CCTGCTCATC CGCACGGGCT TCGACTGGCT
201 CCTGAGCCGA CCCGAGGCTC CCGAGGACTT CCAGACCTTC CACGCCTCCC
251 TGCAGCACCG GAAGCCCCGC CTGGCTCGGA AGCACATCTA CCTACAGCCG
301 ATAGACCTGA GCGAGGAGCC GGTGGGAAGC TCCCTGCTGC ACCAGCTGTG 351 CAGCTGCACA GAGGCCTTCT TCCTGGGCCT GCGCGTCAAG TGCCTGCCGT
401 CGGTGGCAGC CGCGTCCATC CGCTGCTCCT CGCGGCCCAG CCGGGACTCT
451 GACAGGCTCC AGCTCCACAC AGACGGCATC CTGTCCTTCT TGAAGAACAA 501 CAAGCCAGGG GACGCGCTGT GTGTGCTGGG CCTCACACTG TCTGACCTGT
551 ACCCCCATGA GGCCTGGAGC TTCACCTTCA GCAAGTTCCT TCCAGGGCAC
601 GGTCACGTGC CACGAGCTCT GCCACCTTCT GGGCCTGGGG AACTGCCGCT
651 GGCTCCGCTG CCTCATGCAG GGTGCGCTCA GCCTGGACGA GGCCCTGCGG
701 CGGCCCCTGG ACCTCTGTCC CATCTGCCTG AGGAAGCTGC AGCATGTCCT
751 GGGTTTCAGG CTCATCGAGA GGTACCAGAG ACTCTACACC TGGACTCAGG
801 CGGTGGTGGG GACGTGGCCC AGCCAGGAGG CGGGGGAGCC GTCAGTGTGG
851 GAGGACACCC CGCCTGCCAG CGCCGACTCG GGCATGTGCT G
SEQ ID NO: 164 (INSP007B full protein sequence)
1 MLQCRPAQEF SFGPRALKDA LVSTDAALQQ LYVSAFSPAE RLFLAEAYNP
51 QRTLFCTLLI RTGFDWLLSR PEAPEDFQTF HASLQHRKPR LARKHIYLQP
101 IDLSEEPVGS SLLHQLCSCT EAFFLGLRVK CLPSVAAASI RCSSRPSRDS
151 DRLQLHTDGI LSFLKNNKPG DALCVLGLTL SDLYPHEAWS FTFSKFLPGH
201 GHVPRALPPS GPGELPLAPL PHAGCAQPGR GPAAAPGPLS HLPEEAAACP
251 GFQAHREVPE TLHLDSGGGG DVAQPGGGGA VSVGGHPACQ RRLGHVL

Claims

1. A polypeptide, which polypeptide is a secreted polypeptide and which: i. comprises the amino acid sequence as recited in SEQ ID NO: 152; ii. is a fragment thereof which functions as a secreted protein of the metalloprotease class or has an antigenic determinant in common with the polypeptides of (i); or iii. is a functional equivalent of (i) or (ii).
2. A polypeptide according to claim 1 which consists of the sequence recited in SEQ ID NO: 152 or is a functional equivalent thereof.
3. A polypeptide which is a functional equivalent according to claim 1 or 2, which is homologous to the amino acid sequence as recited in SEQ ID NO: 152, and has metalloprotease activity.
4. A fragment or functional equivalent according to any one of the preceding claims, which has greater than 90% sequence identity with the amino acid sequence recited in SEQ ID NO: 152 or with active fragments thereof, preferably greater than 95%, 98% or 99% sequence identity.
5. A purified nucleic acid molecule which encodes a polypeptide according to any one of the preceding claims.
6. A purified nucleic acid molecule according to claim 5, which has the nucleic acid sequence as recited in SEQ ID NO: 139 or is a redundant equivalent or fragment thereof.
7. A purified nucleic acid molecule which hydridizes under high stringency conditions with a nucleic acid molecule according to claim 5 or claim 6.
8. A vector comprising a nucleic acid molecule as recited in any one of claims 5-7.
9. A host cell transformed with a vector according to claim 8.
10. A ligand which binds specifically to, and which preferably inhibits the metalloprotease activity of, a polypeptide according to any one of claims 1-5.
11. A ligand according to claim 10, which is an antibody.
12. A compound that either increases or decreases the level of expression or activity of a polypeptide according to any one of claims 1-4.
13. A compound according to claim 12 that binds to a polypeptide according to any one of claims 1-4 without inducing any of the biological effects of the polypeptide.
14. A compound according to claim 13, which is a natural or modified substrate, ligand, enzyme, receptor or structural or functional mimetic.
15. A polypeptide according to any one of claim 1-4, a nucleic acid molecule according to any one of claims 5-7, a vector according to claim 8, a host cell according to claim 9, a ligand according to claim 10 or 11, or a compound according to any one of claims 12-14, for use in therapy or diagnosis of disease.
16. A method of diagnosing a disease in a patient, comprising assessing the level of expression of a natural gene encoding a polypeptide according to any one of claim
1-4, or assessing the activity of a polypeptide according to any one of claim 1-4, in tissue from said patient and comparing said level of expression or activity to a control level, wherein a level that is different to said control level is indicative of disease.
17. A method according to claim 16 that is carried out in vitro.
18. A method according to claim 16 or claim 17, which comprises the steps of: (a) contacting a ligand according to claim 10 or claim 1 1 with a biological sample under conditions suitable for the formation of a ligand-polypeptide complex; and (b) detecting said complex.
19. A method according to claim 16 or claim 17, comprising the steps of: a) contacting a sample of tissue from the patient with a nucleic acid probe under stringent conditions that allow the formation of a hybrid complex between a nucleic acid molecule according to any one of claims 5-7 and the probe; b) contacting a control sample with said probe under the same conditions used in step a); and c) detecting the presence of hybrid complexes in said samples; wherein detection of levels of the hybrid complex in the patient sample that differ from levels of the hybrid complex in the control sample is indicative of disease.
20. A method according to claim 16 or claim 17, comprising: a) contacting a sample of nucleic acid from tissue of the patient with a nucleic acid primer under stringent conditions that allow the formation of a hybrid complex between a nucleic acid molecule according to any one of claims 6-8 and the primer; b) contacting a control sample with said primer under the same conditions used in step a); and c) amplifying the sampled nucleic acid; and d) detecting the level of amplified nucleic acid from both patient and control samples; wherein detection of levels of the amplified nucleic acid in the patient sample that differ significantly from levels of the amplified nucleic acid in the control sample is indicative of disease.
21. A method according to claim 16 or claim 17 comprising: a) obtaining a tissue sample from a patient being tested for disease; b) isolating a nucleic acid molecule according to any one of claims 5-7 from said tissue sample; and c) diagnosing the patient for disease by detecting the presence of a mutation which is associated with disease in the nucleic acid molecule as an indication of the disease.
22. The method of claim 21 , further comprising amplifying the nucleic acid molecule to form an amplified product and detecting the presence or absence of a mutation in the amplified product.
23. The method of either claim 21 or 22, wherein the presence or absence of the mutation in the patient is detected by contacting said nucleic acid molecule with a nucleic acid probe that hybridises to said nucleic acid molecule under stringent conditions to form a hybrid double-stranded molecule, the hybrid double-stranded molecule having an unhybridised portion of the nucleic acid probe strand at any portion corresponding to a mutation associated with disease; and detecting the presence or absence of an unhybridised portion of the probe strand as an indication of the presence or absence of a disease-associated mutation.
24. A method according to any one of claims 16-23, wherein said disease is a cell proliferative disorder, autoimmune/inflammatory disorder, cardiovascular disorder, neurological disorder, developmental disorder, metabolic disorder, infection or another pathological condition.
25. Use of a polypeptide according to any one of claims 1-4 as a secreted protein, preferably as a metalloprotease.
26. A pharmaceutical composition comprising polypeptide according to any one of claim 1-4, a nucleic acid molecule according to any one of claims 5-7, a vector according to claim 8, a host cell according to claim 9, a ligand according to claim 10 or 1 1, or a compound according to any one of claims 12-14.
27. A vaccine composition comprising a polypeptide according to any one of claims 1-4 or a nucleic acid molecule according to any one of claims 5-7.
28. A polypeptide according to any one of claim 1-4, a nucleic acid molecule according to any one of claims 5-7, a vector according to claim 8, a host cell according to claim 9, a ligand according to claim 10 or 1 1 , or a compound according to any one of claims 12-14, or a pharmaceutical composition according to claim 26, for use in the manufacture of a medicament for the treatment of cell proliferative disorders, autoimmune/inflammatory disorders, cardiovascular disorders, neurological disorders, developmental disorders, metabolic disorders, infections and other pathological conditions.
29. A method of treating a disease in a patient, comprising administering to the patient polypeptide according to any one of claim 1-4, a nucleic acid molecule according to any one of claims 5-7, a vector according to claim 8, a host cell according to claim 9, a ligand according to claim 10 or 11, or a compound according to any one of claims 12-14, or a pharmaceutical composition according to claim 26.
30. A method according to claim 29, wherein, for diseases in which the expression of the natural gene or the activity of the polypeptide is lower in a diseased patient when compared to the level of expression or activity in a healthy patient, the polypeptide, nucleic acid molecule, vector, ligand, compound or composition administered to the patient is an agonist.
31. A method according to claim 29, wherein, for diseases in which the expression of the natural gene or activity of the polypeptide is higher in a diseased patient when compared to the level of expression or activity in a healthy patient, the polypeptide, nucleic acid molecule, vector, ligand, compound or composition administered to the patient is an antagonist.
32. A method of monitoring the therapeutic treatment of disease in a patient, comprising monitoring over a period of time the level of expression or activity of a polypeptide according to any one of claims 1 -4, or the level of expression of a nucleic acid molecule according to any one of claims 5-7 in tissue from said patient, wherein altering said level of expression or activity over the period of time towards a control level is indicative of regression of said disease.
33. A method for the identification of a compound that is effective in the treatment and/or diagnosis of disease, comprising contacting a polypeptide according to any one of claims 1-4, or a nucleic acid molecule according to any one of claims 5-7 with one or more compounds suspected of possessing binding affinity for said polypeptide or nucleic acid molecule, and selecting a compound that binds specifically to said nucleic acid molecule or polypeptide.
34. A kit useful for diagnosing disease comprising a first container containing a nucleic acid probe that hybridises under stringent conditions with a nucleic acid molecule according to any one of claims 5-7; a second container containing primers useful for amplifying said nucleic acid molecule; and instructions for using the probe and primers for facilitating the diagnosis of disease.
35. The kit of claim 34, further comprising a third container holding an agent for digesting unhybridised RNA.
36. A kit comprising an array of nucleic acid molecules, at least one of which is a nucleic acid molecule according to any one of claims 5-7.
37. A kit comprising one or more antibodies that bind to a polypeptide as recited in any one of claims 1-4; and a reagent useful for the detection of a binding reaction between said antibody and said polypeptide.
38. A transgenic or knockout non-human animal that has been transformed to express higher, lower or absent levels of a polypeptide according to any one of claims 1-4.
39. A method for screening for a compound effective to treat disease, by contacting a non-human transgenic animal according to claim 38 with a candidate compound and determining the effect of the compound on the disease of the animal.
PCT/GB2002/005866 2001-12-20 2002-12-20 Metalloprotease proteins WO2003054178A2 (en)

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US7285633B2 (en) 2001-04-26 2007-10-23 Bristol-Myers Squibb Company Metalloprotease highly expressed in the testis, MMP-29

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