WO2002020756A2 - Molécules sécrétoires - Google Patents

Molécules sécrétoires Download PDF

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Publication number
WO2002020756A2
WO2002020756A2 PCT/US2001/027297 US0127297W WO0220756A2 WO 2002020756 A2 WO2002020756 A2 WO 2002020756A2 US 0127297 W US0127297 W US 0127297W WO 0220756 A2 WO0220756 A2 WO 0220756A2
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WO
WIPO (PCT)
Prior art keywords
2000sep08
polynucleotide
polypeptide
nout
seq
Prior art date
Application number
PCT/US2001/027297
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English (en)
Other versions
WO2002020756A3 (fr
Inventor
Stuart E. Jackson
Stephen E. Lincoln
Christina M. Altus
Gerard E. Dufour
Michael S. Chalup
Jennifer L. Jackson
Anissa Lee Jones
Jimmy Y. Yu
Rachel J. Wright
Darryl Gietzen
Tommy F. Liu
Pierre E. Yap
Christopher R. Dahl
Monika G. Momiyama
Diana L. Bradley
Sameer D. Rohatgi
Bernard Harris
Ann M. Roseberry
Edward H. Gerstin, Jr.
Careyna H. Peralta
Marie H. David
Scott R. Panzer
Vincent Flores
Abel Daffo
Rakesh Marwaha
Alice J. Chen
Simon C. Chang
Alan P. Au
Rebekah R. Inman
Original Assignee
Incyte Genomics, Inc.
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
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Publication date
Application filed by Incyte Genomics, Inc. filed Critical Incyte Genomics, Inc.
Priority to AU2001287022A priority Critical patent/AU2001287022A1/en
Priority to CA002419943A priority patent/CA2419943A1/fr
Priority to EP01966516A priority patent/EP1368375A2/fr
Priority to AU8702201A priority patent/AU8702201A/xx
Publication of WO2002020756A2 publication Critical patent/WO2002020756A2/fr
Publication of WO2002020756A3 publication Critical patent/WO2002020756A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

  • the present invention relates to secretory molecules and to the use of these sequences in the diagnosis, study, prevention, and treatment of diseases associated with, as well as effects of exogenous compounds on, the expression of secretory molecules.
  • Protein transport and secretion are essential for cellular function. Protein transport is mediated by a signal peptide located at the amino terminus of the protein to be transported or secreted.
  • the signal peptide is comprised of about ten to twenty hydrophobic amino acids which target the nascent protein from the ribosome to a particular membrane bound compartment such as the 5 endoplasmic reticulum (ER). Proteins targeted to the ER may either proceed through the secretoiy pathway or remain in any of the secretory organelles such as the ER, Golgi apparatus, or lysosomes. Proteins that transit through the secretory pathway are either secreted into the extracellular space or retained in the plasma membrane.
  • Proteins that are retained in the plasma membrane contain one or more transmembrane domains, each comprised of about 20 hydrophobic amino acid residues.
  • Proteins o that are secreted from the cell are generally synthesized as inactive precursors that are activated by post-translational processing events during ttansit through the secretory pathway. Such events include glycosylation, proteolysis, and removal of the signal peptide by a signal peptidase. Other events that may occur during protein transport include chaperone-dependent unfolding and folding of the nascent protein and interaction of the protein with a receptor or pore complex. Examples of secretory proteins 5 with amino terminal signal peptides are discussed below and include proteins with important roles in cell-to-cell signaling.
  • GPCRs G-protein coupled receptors
  • GPCRs include receptors for biogenic amines such as dopamine, epinephrine, histamine, glutamate (metabotropic-type), acetylcholine (muscarinic-type), and serotonin; for lipid mediators of inflammation such as prostaglandins, platelet activating factor, and leukotrienes; for peptide hormones such as
  • l calcitonin C5a anaphylatoxin, follicle stimulating hormone, gonadotropin releasing hormone, neurokinin, oxytocin, and thrombin; and for sensory signal mediators such as retinal ph ⁇ topigments and olfactory stimulatory molecules.
  • the structure of these highly conserved receptors consists of seven hydrophobic transmembrane regions, cysteine disulfide bridges between the second and third 5 extracellular loops, an extracellular N-terminus, and a cytoplasmic C-terminus.
  • the N-terminus interacts, with ligands, the disulfide bridges interact with agonists and antagonists, and the large third intracellular loop interacts with G proteins to activate second messengers such as cyclic AMP, phospholipase C, inositol triphosphate, or ion channels.
  • second messengers such as cyclic AMP, phospholipase C, inositol triphosphate, or ion channels.
  • Other types of receptors include cell surface antigens identified on leukocytic cells of the immune system.
  • antigens have been identified using systematic, monoclonal antibody (mAb)- based "shot gun” techniques. These techniques have resulted in the production of hundreds of mAbs directed against unknown cell surface leukocytic antigens. These antigens have been grouped into 5 "clusters of differentiation” based on common immunocytochemical localization patterns in various differentiated and undifferentiated leukocytic cell types. Antigens in a given cluster are presumed to identify, a single cell surface protein and are assigned a "cluster of differentiation" or "CD” designation. Some of the genes encoding proteins identified by CD antigens have been cloned and verified by standard molecular biology techniques.
  • CD antigens have been characterized as both o transmembrane proteins and cell surface proteins anchored to the plasma membrane via covalent attachment to fatty acid-containing glycolipids such as glycosylphosphatidylinositol (GPI).
  • GPI glycosylphosphatidylinositol
  • MPs Matrix proteins
  • the expression and balance of MPs may be perturbed by biochemical changes that result from congenital, epigenetic, or infectious diseases.
  • MPs affect leukocyte migration, proliferation, differentiation, and activation in the immune response.
  • MPs are frequently characterized by the presence of one or more domains which may include collagen-like o domains, EGF-like domains, immunoglobulin-like domains, and fibronectin-like domains.
  • MPs may be heavily glycosylated and may contain an Arginine-Glycine-Aspartate (RGD) tripeptide motif which may play a role in adhesive interactions.
  • MPs include extracellular proteins such as fibronectin, collagen, galectin, vitronectin and its proteolytic derivative somatomedin B; and cell adhesion receptors such as cell adhesion molecules (CAMs), cadherins, and integrins.
  • Cytokines are secreted by hematopoietic cells in response to injury or infection. Interleukins, nemotrophins, growth factors, interferons, and chemokines all define cytokine families that work in conjunction with cellular receptors to regulate cell proliferation and differentiation. In addition, cytokines effect activities such as leukocyte migration and function, hematopoietic cell proliferation, temperature regulation, acute response to infection, tissue remodeling, and apoptosis.
  • Chemokines are small chemoattractant cytokines involved in inflammation, leukocyte proliferation and migration, angiogenesis and angiostasis, regulation of hematopoiesis, HJN infectivity, and stimulation of cytokine secretion.
  • Chemokines generally contain 70-100 amino acids and are subdivided into four subfamilies based on the presence of conserved cysteine-based motifs. (Callard, R. and Gearing, A. (1994) The Cytokine Facts Book. Academic Press, New York NY, pp. 5 181-190, 210-213, 223-227.)
  • Growth and differentiation factors are secreted proteins which function in intercellular communication. Some factors require oligomerization or association with MPs for activity. Complex interactions among these factors and their receptors trigger intracellular signal ttansduction pathways that stimulate or inhibit cell division, cell differentiation, cell signaling, and cell motility. Most growth o and differentiation factors act on cells in their local environment (paracrine signaling).
  • the first class includes the large polypeptide growth factors such as epidermal growth factor, fibroblast growth factor, transforming growth factor, insulin-like growth factor, and platelet-derived growth factor.
  • the second class includes the hematopoietic growth factors such as the colony stimulating factors (CSFs).
  • CSFs colony stimulating factors
  • Hematopoietic growth 5 factors stimulate the proliferation and differentiation of blood cells such as B-lymphocytes, T- lymphocytes, erythrocytes, platelets, eosinophils, basophils, neutrophils, macrophages, and their stem cell precursors.
  • the third class includes small peptide factors such as bombesin, vasopressin, oxytocin, endothelin, transferrin, angiotensin H, vasoactive intestinal peptide, and bradykinin which function as hormones to regulate cellular functions other than proliferation.
  • o Growth and differentiation factors play critical roles in neoplastic transformation of cells in vitro and in tumor progression in vivo.
  • Inappropriate expression of growth factors by tumor cells may contribute to vascularization and metastasis of tumors.
  • growth factor misregulation can result in anemias, leukemias, and lymphomas.
  • Certain growth factors such as interferon are cytotoxic to tumor cells both in vivo and in vitro.
  • some growth factors and growth factor receptors are related both sxracturally and functionally to oncoproteins.
  • growth factors affect transcriptional regulation of both proto-oncogenes and oncosuppressor genes. (Reviewed in Pimentel, E. (1994) Handbook of Growth Factors. CRC Press, Ann Arbor MI, pp.
  • Proteolytic enzymes or proteases either activate or deactivate proteins by hydrolyzing peptide bonds.
  • Proteases are found in the cytosol, in membrane-bound compartments, and in the extracellular space. The major families are the zinc, serine, cysteine, thiol, and carboxyl proteases.
  • Ion channels, ion pumps, and transport proteins mediate the transport of molecules across cellular membranes.
  • Transport can occur by a passive, concentration-dependent mechanism or can o be linked to an energy source such as ATP hydrolysis.
  • Symporters and antiporters transport ions and small molecules such as amino acids, glucose, and drags.
  • Symporters transport molecules and ions unidirectionally, and antiporters transport molecules and ions bidirectionally.
  • Transporter superfamilies include facilitative transporters and active ATP-binding cassette transporters which are involved in multiple-drug resistance and the targeting of antigenic peptides to MHC Class I molecules.
  • Ion channels are formed by transmembrane proteins which create a lined passageway across the membrane through which water and ions, such as Na + , K + , Ca 2+ , and Cl", enter and exit the cell.
  • chloride channels are involved in the regulation of the membrane electric potential as well as abso ⁇ tion and secretion of ions across the membrane. Chloride channels also regulate the internal pH of membrane-bound organelles.
  • Ion pumps are ATPases which actively maintain membrane gradients. Ion pumps are classified as P, V, or F according to their structure and function. All have one or more binding sites 5 for ATP in their cytosolic domains.
  • the P-class ion pumps include Ca 2+ ATPase and Na + /K + ATPase and function in transporting H + , Na + , K + , and Ca 2+ ions.
  • P-class pumps consist of two ⁇ and two ⁇ transmembrane subunits.
  • the V- and F-class ion pumps have similar structures but transport only H + .
  • F class H + pumps mediate transport across the membranes of mitochondria and chloroplasts, while V- class H + pumps regulate acidity inside lysosomes, endosomes, and plant vacuoles.
  • V- class H + pumps regulate acidity inside lysosomes, endosomes, and plant vacuoles.
  • a family of structurally related intrinsic membrane proteins known as facilitative glucose transporters catalyze the movement of glucose and other selected sugars across the plasma membrane.
  • the proteins in this family contain a highly conserved, large transmembrane domain comprised of 12 ⁇ -helices, and several weakly conserved, cytoplasmic and exoplasmic domains. (Pessin, J.E. and Bell, G.I. (1992) Annu. Rev. Physiol. 54:911-930.)
  • Amino acid transport is mediated by Na + dependent amino acid transporters. These transporters are involved in gastrointestinal and renal uptake of dietary and cellular amino acids and in neuronal reuptake of neurotransmitters. Transport of cationic amino acids is mediated by the system 5 y+ family and the cationic amino acid transporter (CAT) family. Members of the CAT family share a high degree of sequence homology, and each contains 12-14 putative transmembrane domains. (Ito, K. and Groudine, M. (1997) J. Biol. Chem. 272:26780-26786.)
  • Hormones are secreted molecules that travel through the circulation and bind to specific receptors on the surface of, or within, target cells. Although they have diverse biochemical o compositions and mechanisms of action, hormones can be grouped into two categories.
  • One category includes small lipophilic hormones that diffuse through the plasma membrane of target cells, bind to cytosolic or nuclear receptors, and form a complex that alters gene expression. Examples of these molecules include retinoic acid, thyroxine, and the cholesterol-derived steroid hormones such as progesterone, estrogen, testosterone, cortisol, and aldosterone.
  • the second category includes 5 hydrophilic hormones that function by binding to cell surface receptors that transduce signals across the plasma membrane.
  • hormones include amino acid derivatives such as catecholamines and peptide hormones such as glucagon, insulin, gastrin, secretin, cholecystokinin, adrenocorticotropic hormone, follicle stimulating hormone, luteinizing hormone, thyroid stimulating hormone, and vas ⁇ pressin.
  • catecholamines amino acid derivatives
  • peptide hormones such as glucagon, insulin, gastrin, secretin, cholecystokinin, adrenocorticotropic hormone, follicle stimulating hormone, luteinizing hormone, thyroid stimulating hormone, and vas ⁇ pressin.
  • Neuropeptides and vasomediators comprise a large family of endogenous signaling molecules. Included in this family are neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins, urotensin II and related peptides involved in smooth muscle stimulation, vasopressin, vasoactive 5 intestinal peptide, and circulatory system-borne signaling molecules such as angiotensin, complement, calcitonin, endothelins, formyl-methionyl peptides, glucagon, cholecystokinin and gastrin.
  • neuropeptides and neuropeptide hormones such as bombesin, neuropeptide Y, neurotensin, neuromedin N, melanocortins, opioids, galanin, somatostatin, tachykinins
  • NP/NMs can transduce signals directly, modulate the activity or release of other neurotransmitters and hormones, and act as catalytic enzymes in cascades.
  • the effects of ⁇ P/VMs range from extremely brief to long-lasting. (Reviewed in Martin, CR. et al. (1985) Endocrine Physiology. Oxford University Press, o New York, NY, pp. 57-62.)
  • the present invention relates to nucleic acid sequences comprising human polynucleotides 5 encoding secretory polypeptides that contain signal peptides and/or transmembrane domains.
  • human polynucleotides as presented in the Sequence Listing uniquely identify partial or full length genes encoding structural, functional, and regulatory polypeptides involved in cell signaling.
  • the invention provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID 0 NO:l-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184.
  • the polynucleotide comprises at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOX-184; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184; c) a polynucleotide 0 complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d
  • the polynucleotide comprises at least 60 contiguous nucleotides. of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-184; b) a polynucleotide comprising a naturally occurring polynucleotide comprising a 5 polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the invention further provides a composition for the detection of expression of secretory polynucleotides comprising at least one isolated polynucleotide comprising a polynucleotide selected o from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ XD NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d); and a detectable label.
  • a composition for the detection of expression of secretory polynucleotides comprising at least one
  • the invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide sequence of a polyneucleotide selected from the group 5 consisting of a) a polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of SEQ ID NO: 1-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof, and, optionally, if present, the amount thereof.
  • the invention also provides a method for detecting a target polynucleotide in a sample, said target polynucleotide having a polynucleotide sequence of a polynucleotide selected from the group 5 consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ED NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the method 0 comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide, and b) detecting the presence or absence of said hybridization complex, and, optionally, if present, the amount thereof.
  • the 5 invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 30 contiguous nucleotides.
  • the invention provides a composition comprising a target polynucleotide of the method, wherein said probe comprises at least 60 contiguous nucleotides.
  • the invention further provides a recombinant polynucleotide comprising a promoter sequence o operably Mnked to an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ED NOX-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ DD NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the invention provides a cell transformed with the recombinant polynucleotide.
  • the invention provides a transgenic organism comprising the recombinant polynucleotide.
  • the invention also provides a method for producing a secretory polypeptide, the method comprising a) culturing a cell under conditions suitable for expression of the secretory polypeptide, wherein said cell is transformed with a recombinant polynucleotide, said recombinant polynucleotide comprising an isolated polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ DD NOX-184; ii) a 0 polynucleotide comprising a natarally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ED NO:
  • the invention also provides an isolated secretory polypeptide (SPTM) encoded by at least one polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NOX-184.
  • SPTM secretory polypeptide
  • the invention further provides a method of screening for a test compound that specifically binds to the polypeptide having an amino acid sequence selected from the group consisting of SEQ DD 0 NO:l 85-369. The method comprises a) combining the polypeptide having an amino acid sequence.
  • the invention further provides a microarray wherein at least one element of the microarray is an isolated polynucleotide comprising at least 30 contiguous nucleotides of a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ DD NOX-184; b) a polynucleotide comprising a naturally occurring o polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ED NOX-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • the invention also provides a method for generating a transcript image of a sample which contains polynucleotides.
  • the method comprises a) labeling the polynucleotides of the sample, b) contacting the elements of the microarray with the labeled polynucleotides of the sample under conditions suitable for the formation of a hybridization complex, and c) quantifying the expression of the polynucleotides in the sample.
  • the invention provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ DD NO: 1-184; b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1-184; c) a polynucleotide complementary to the polynucleotide of a); d) a polynucleotide complementary to the polynucleotide of b); and e) an RNA equivalent of a) through d).
  • a target polynucleotide comprises a polynucleotide selected from the group consisting of a)
  • the method comprises a) exposing a sample comprising the target polynucleotide to a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.
  • the invention further provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide • comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 1 -184; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a .
  • polynucleotide sequence selected from the group consisting of SEQ DD NO: 1-184; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv).
  • Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide comprising a polynucleotide sequence of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ DD NO: 1-184; ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical to a polynucleotide sequence selected from the group consisting of SEQ DD NOX-184; iii) a polynucleotide complementary to the polynucleotide of i); iv) a polynucleotide complementary to the polynucleotide of ii); and v) an RNA equivalent of i) through iv), and alternatively, the target polynu
  • the invention further provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NOX85-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ED NO: 185-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group o consisting of SEQ ID NO:l 85-369, and d) an immimogenic fragment of a polypeptide having an amino acid sequence selected from.the group consisting of SEQ ID NO:l 85-369.
  • the invention provides an isolated polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NOX85-369.
  • the invention further provides an isolated polynucleotide encoding a polypeptide selected from 5 the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ. DD NO: 185-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, and d) an immunogenic fragment of a o polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 185-
  • polynucleotide encodes a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 185-369.
  • polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO:l-184.
  • the invention provides an isolated antibody which specifically binds to a 5 polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 185-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, and d) an o immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NOX85-369.
  • the invention further provides a composition comprising a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NO: 185-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ DD NOX85- 369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NOX85-369, and d) an immunogenic fragment of a polypeptide having 5 an amino acid sequence selected from the group consisting of SEQ DD NO 185-369, and a pharmaceutically acceptable excipient.
  • the composition comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NOX85-369.
  • the invention additionally provides a method of treating a disease or condition associated with decreased expression of functional SPTM, comprising administering to a patient in need of such treatment the o composition.
  • the invention also provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NOX85-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected 5 from the group consisting of SEQ ID NOX85-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369.
  • the method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting agonist activity in the sample.
  • the o invention provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient.
  • the invention provides a method of treating a disease or condition associated with decreased expression of functional SPTM, comprising administering to a patient in need of such treatment the composition.
  • the invention provides a method for screening a compound for effectiveness as 5 an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ DD NO: 185-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ D o NO: 185-369, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ DD NO:l 85-369.
  • the method comprises a) exposing a sample comprising the polypeptide to a compound, and b) detecting antagonist activity in the sample.
  • the invention provides a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient.
  • the invention provides a method of treating a disease or condition associated with overexpression of functional SPTM, comprising administering to a patient in need of such treatment the composition.
  • the invention further provides a method of screening for a compound that modulates the 5 activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ED NOX85-369, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NOX85-369, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO 185-369, and d) an o immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 185-369.
  • the method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of 5 the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.
  • Table 1 shows the sequence identification numbers (SEQ ID NO:s) and template identification o numbers (template DDs) corresponding to the polynucleotides of the present invention, along with the* sequence identification numbers (SEQ ID NO:s) and open reading frame identification numbers (ORF DDs) corresponding to polypeptides encoded by the template ID.
  • Table 2 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template DDs) corresponding to the polynucleotides of the present invention, along with 5 polynucleotide segments of each template sequence as defined by the indicated “start” and “stop” nucleotide positions.
  • the reading frames of the polynucleotide segments are shown, and the polypeptides encoded by the polynucleotide segments constitute either signal peptide (SP) or transmembrane (TM) domains, as indicated.
  • SP signal peptide
  • TM transmembrane
  • the membrane topology of the encoded polypeptide sequence is indicated, the N-terminus (N) listed as being oriented to either the cytosolic (N in) or non- o cytosolic (N out) side of the cell membrane or organelle.
  • Table 3 shows the sequence identification numbers (SEQ ID NO:s) and template identification numbers (template DDs) corresponding to the polynucleotides of the present invention, along with component sequence identification numbers (component DDs) corresponding to each template.
  • the component sequences, which were used to assemble the template sequences, are defined by the indicated “start” and “stop” nucleotide positions along each template.
  • Table 4 shows the tissue distribution profiles for the templates of the invention.
  • Table 5 shows the sequence identification numbers (SEQ ED NO:s) corresponding to the polypeptides of the present invention, along with the reading frames used to obtain the polypeptide segments, the lengths of the polypeptide segments, the "start" and “stop” nucleotide positions of the polynucleotide sequences used to define the encoded polypeptide segments, the GenBank hits (GI Numbers), probability scores, and functional annotations corresponding to the GenBank hits.
  • Table 6 summarizes the bioinformatics tools which are useful for analysis of the polynucleotides of the present invention.
  • the first column of Table 6 lists analytical tools, programs, and algorithms, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are inco ⁇ orated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
  • sptm refers to a nucleic acid sequence
  • SPTM amino acid sequence encoded by sptm
  • a “full-length” sptm refers to a nucleic acid sequence containing the entire coding region of a gene endogenously expressed in human tissue.
  • Adjuvants are materials such as Freund's adjuvant, mineral gels (aluminum hydroxide), and surface active substances (lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol) which may be administered to increase a host's immunological response.
  • mineral gels aluminum hydroxide
  • surface active substances lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol
  • Alleles refers to an alternative form of a nucleic acid sequence. Alleles result from a “mutation,” a change or an alternative reading of the genetic code. Any given gene may have none, one, or many allelic forms. Mutations which give rise to alleles include deletions, additions, or substitutions of nucleotides. Each of these changes may occur alone, or in combination with the others, one or more times in a given nucleic acid sequence.
  • the present invention encompasses allelic sptm.
  • amino acid sequence refers to a peptide, a polypeptide, or a protein of either natural or synthetic origin.
  • the amino acid sequence is not limited to the complete, endogenous amino acid sequence and may be a fragment, epitope, variant, or derivative of a protein expressed by a nucleic acid sequence.
  • Amplification refers to the production of additional copies of a sequence and is carried out using polymerase chain reaction (PCR) technologies well known in the art.
  • PCR polymerase chain reaction
  • Antibody refers to intact molecules as well as to fragments thereof, such as Fab, F(ab') 2> and Fv fragments, which are capable of binding the epitopic determinant.
  • Antibodies that bind SPTM polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen.
  • the polypeptide or peptide used to immunize an animal e.g., a mouse, a rat, or a rabbit
  • an animal e.g., a mouse, a rat, or a rabbit
  • RNA e.g., a mouse, a rat, or a rabbit
  • Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence may include DNA, RNA, or any nucleic acid mimic or analog such as peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'-deoxyguanosine.
  • PNA peptide nucleic acid
  • Antisense sequence refers to a sequence capable of specifically hybridizing to a target sequence.
  • the antisense sequence can be DNA, RNA, or any nucleic acid mimic or analog.
  • Antisense technology refers to any technology which relies on the specific hybridization of an antisense sequence to a target sequence.
  • a “bin” is a portion of computer memory space used by a computer program for storage of data, and bounded in such a manner that data stored in a bin may be retrieved by the program.
  • “Biologically active” refers to an amino acid sequence having a structural, regulatory, or biochemical function of a naturally occurring amino acid sequence.
  • “Clone joining” is a process for combining gene bins based upon the bins' containing sequence information from the same clone.
  • the sequences may assemble into a primary gene transcript as well as one or more splice variants.
  • “Complementary” describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing (5'-A-G-T-3' pairs with its complement 3'-T-C-A-5').
  • a “component sequence” is a nucleic acid sequence selected by a computer program such as PHRED and used to assemble a consensus or template sequence from one or more component sequences.
  • a “consensus sequence” or “template sequence” is a nucleic acid sequence which has been assembled from overlapping sequences, using a computer program for fragment assembly such as the GELVTEW fragment assembly system (Genetics Computer Group (GCG), Madison WI) or using a relational database management system (RDMS).
  • GCG Genetics Computer Group
  • RDMS relational database management system
  • Constant amino acid substitutions are those substitutions that, when made, least interfere with the properties of the original protein, i.e., the stracture and especially the function of the protein is conserved and not significantly changed by such substitutions.
  • the table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative substitutions.
  • Conservative substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain.
  • “Deletion” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or amino acid residue, respectively, is absent.
  • “Derivative” refers to the chemical modification of a nucleic acid sequence, such as by replacement of hydrogen by an alkyl, acyl, amino, hydroxyl, or other group.
  • “Differential expression” refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons may be carried out between, for example, a treated and an untreated sample, or a 0 diseased and a normal sample.
  • array element refers to a polynucleotide, polypeptide, or other chemical compound having a unique and defined position on a microarray.
  • E-value refers to the statistical probability that a match between two sequences occurred by chance.
  • Exon shuffling refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortinent of stable substructures, thus allowing acceleration of the evolution of new protein functions.
  • a “fragment” is a unique portion of sptm or SPTM which is identical in sequence to but o shorter in length than the parent sequence.
  • a fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue.
  • a fragment may comprise from 10 to 1000 contiguous amino acid residues or nucleotides.
  • a fragment used as a probe, primer, antigen, therapeutic molecule, or for other pmposes may be at least 5, 10, 15, 16, 20, 25, 30, 40, 50, 60, 75, 100, 150, 250 or at least 500 contiguous amino acid residues or nucleotides in length. Fragments 5 may be preferentially selected from certain regions of a molecule.
  • a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence.
  • these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing and the figures, may be encompassed by the present embodiments.
  • a fragment of sptm comprises a region of unique polynucleotide sequence that specifically 5 identifies sptm, for example, as distinct from any other sequence in the same genome.
  • a fragment of sptm is useful, for example, in hybridization and amplification technologies and in analogous methods that distinguish sptm from related polynucleotide sequences.
  • the precise length of a fragment of sptm and the region of sptm to which the fragment corresponds are routinely determinable by one of ordinary skill in the ait based on the intended pmpose for the fragment. o
  • a fragment of SPTM is encoded by a fragment of sptm.
  • a fragment of SPTM comprises a region of unique amino acid sequence that specifically identifies SPTM.
  • a fragment of SPTM is useful as an immunogenic peptide for the development of antibodies that specifically recognize SPTM.
  • the precise length of a fragment of SPTM and the region of SPTM to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the 5 intended pmpose for the fragment.
  • a “full length” nucleotide sequence is one containing at least a start site for translation to a protein sequence, followed by an open reading frame and a stop site, and encoding a "full length” polypeptide.
  • “Hit” refers to a sequence whose annotation will be used to describe a given template. o Criteria for selecting the top hit are as follows: if the template has one or more exact nucleic acid matches, the top hit is the exact match with highest percent identity. If the template has no exact matches but has significant protein hits, the top hit is the protein hit with the lowest E- value. If the template has no significant protein hits, but does have significant non-exact nucleotide hits, the top hit is the nucleotide hit with the lowest E-value. 5 "Homology” refers to sequence similarity either between a reference nucleic acid sequence and at least a fragment of an sptm or between a reference amino acid sequence and a fragment of an SPTM.
  • Hybridization refers to the process by which a stiand of nucleotides anneals with a complementary strand through base pairing. Specific hybridization is an indication that two nucleic o acid sequences share a high degree of identity. Specific hybridization complexes form under defined annealing conditions, and remain hybridized after the "washing" step.
  • the defined hybridization conditions include the annealing conditions and the washing step(s), the latter of which is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific binding, i.e., binding between pairs of nucleic acid probes that are not perfectly matched.
  • Permissive conditions for annealing of nucleic acid sequences are routinely determinable and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency.
  • stringency of hybridization is expressed with reference to the temperature under which the wash step is carried out.
  • wash temperatures are selected to be about 5°C to 20°C lower than the thermal melting point (T ⁇ for the specific sequence at a defined ionic strength and pH.
  • T m is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe.
  • High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0.1 % SDS, for 1 hour. 5 Alternatively, temperatures of about 65°C, 60°C, or 55°C may be used. SSC concentration may be varied from about 0.2 to 2 x SSC, with SDS being present at about 0.1%.
  • blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, denatured salmon sperm DNA at about 100-200 ⁇ g/ml. Useful variations on these conditions will be readily apparent to those skilled in the art.
  • Hybridization, particularly under high stringency conditions may be o suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their resultant proteins.
  • RNA:DNA 5 hybridizations RNA:DNA 5 hybridizations. Appropriate hybridization conditions are routinely determinable by one of ordinary skill in the art.
  • Immunologically active or “immunogenic” describes the potential for a natural, recombinant, or synthetic peptide, epitope, polypeptide, or protein to induce antibody production in appropriate animals, cells, or cell lines.
  • “Insertion” or “addition” refers to a change in either a nucleic or amino acid sequence in which at least one nucleotide or residue, respectively, is added to the sequence.
  • Labeling refers to the covalent or noncovalent joining of a polynucleotide, polypeptide, or antibody with a reporter molecule capable of producing a detectable or measurable signal.
  • “Microarray” is any arrangement of nucleic acids, amino acids, antibodies, etc., on a substrate.
  • the substrate may be a solid support such as beads, glass, paper, nitrocellulose, nylon, or an appropriate membrane.
  • Linkers are short stretches of nucleotide sequence which may be added to a vector or an sptm to create restriction endonuclease sites to facilitate cloning.
  • Polylinkers are engineered to inco ⁇ orate multiple restriction enzyme sites and to provide for the use of enzymes which leave 5' or 3' overhangs (e.g., BamHI, EcoRI, and HindlH) and those which provide blunt ends (e.g., EcoRV, SnaBI, and Stul).
  • Naturally occurring refers to an endogenous polynucleotide or polypeptide that may be isolated from viruses or prokaryotic or eukaryotic. cells.
  • Nucleic acid sequence refers to the specific order of nucleotides joined by phosphodiester bonds in a linear, polymeric arrangement. Depending on the number of nucleotides, the nucleic acid sequence can be considered an oligomer, oligonucleotide, or polynucleotide.
  • the nucleic acid can be DNA, RNA, or any nucleic acid analog, such as PNA, may be of genomic or synthetic origin, may be either double-stranded or single-stranded, and can represent either the sense or antisense (complementary) strand.
  • Oligomer refers to a nucleic acid sequence of at least about 6 nucleotides and as many as about 60 nucleotides, preferably about 15 to 40 nucleotides, and most preferably between about 20 and 30 nucleotides, that may be used in hybridization or amplification technologies. Oligomers may be used as, e.g., primers for PCR, and are usually chemically synthesized.
  • operably linked refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
  • a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
  • operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.
  • PNA protein nucleic acid
  • PNAs refers to a DNA mimic in which nucleotide bases are attached to a pseudopeptide backbone to increase stability. PNAs, also designated antigene agents, can prevent gene expression by targeting complementary messenger RNA.
  • Percent identity and “% identity”, as applied to polynucleotide sequences refer to the percentage of residue matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences. Percent identity between polynucleotide sequences may be determined using the default parameters of the CLUSTAL V algorithm as inco ⁇ orated into the MEGALIGN version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison WT).
  • CLUSTAL V is described in 5 Higgins, D.G. and Sha ⁇ , P.M. (1989) CABIOS 5:151-153 and in Higgins, D.G. et al. (1992) CABIOS 8:189-191.
  • the "weighted” residue weight table is selected as the default. Percent identity is reported by CLUSTAL V as the "percent similarity" between aligned polynucleotide sequence pairs.
  • NCBI National Center for Biotechnology Information
  • BLAST Basic Local Alignment Search Tool
  • NCBI National Center for Biotechnology Information
  • BLAST Basic Local Alignment Search Tool
  • the BLAST software suite includes various sequence analysis 5 programs including "blastn,” that is used to determine alignment between a known polynucleotide sequence and other sequences on a variety of databases.
  • BLAST 2 Sequences are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) set at default parameters. Such default parameters may be, for example: Matrix: BLOSUM62 Reward for match: I 5 Penalty for mismatch: -2
  • Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ DD number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides.
  • Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
  • Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.
  • Percent identity and “% identity”, as applied to polypeptide sequences refer to the percentage of residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence ahgnment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the hydrophobicity and acidity of the substituted residue, thus preserving the structure (and therefore function) of the folded polypeptide. Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as inco ⁇ orated into the MEGALIGN version 3.12e sequence alignment program (described and referenced above).
  • NCBI BLAST software suite may be used.
  • BLAST 2 Sequences Version 2.0.9 (May-07-1999) with blastp set at default parameters.
  • Such default parameters may be, for example: Matrix: BLOSUM62
  • Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ DD number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues.
  • Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in figures or Sequence Listings, may be used to describe a length over which percentage identity may be measured.
  • Post-translational modification of an SPTM may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu and the SPTM.
  • Probe refers to sptm or fragments thereof, which are used to detect identical, allelic or o related nucleic acid sequences.
  • Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes.
  • Primmers are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. 5 Primer pairs can be used for amplification (and identification) of a nucleic acid sequence, e.g., by the polymerase chain reaction (PCR).
  • PCR polymerase chain reaction
  • Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20, 30, 40, 50, 60, 70, 80, 90, 100, or at o least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the figures and Sequence Listing, may be used.
  • PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that pmpose such as Primer (Version 0.5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).
  • Oligonucleotides for use as primers are selected using software known in the art for such pmpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have inco ⁇ orated additional features for expanded capabilities. For example, the PrimOU primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome- wide scope.
  • the Primer3 primer selection program (available to the public from the Whitehead Institate/MiT Center for Genome Research, Cambridge MA) allows the user to input a "mispriming library," in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs.)
  • the PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences.
  • this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments.
  • the oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.
  • “Purified” refers to molecules, either polynucleotides or polypeptides that are isolated or separated from their natural environment and are at least 60% free, preferably at least 75% free, and most preferably at least 90% free from other compounds with which they are naturally associated.
  • a "recombinant nucleic acid” is a sequence that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques such as those described in Sambrook, supra.
  • the term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid.
  • a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.
  • such recombinant nucleic acids may be part of a viral vector, e.g., based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.
  • Regulatory element refers to a nucleic acid sequence from nontranslated regions of a gene, and includes enhancers, promoters, introns, and 3' untranslated regions, which interact with host proteins to carry out or regulate transcription or translation.
  • Reporter molecules are chemical or biochemical moieties used for labeling a nucleic acid, an amino acid, or an antibody. They include radionuclides; enzymes; fluorescent, chemiluminescent, or cfiromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.
  • RNA equivalent in reference to a DNA sequence, is composed of the same linear sequence of nucleotides as the reference DNA sequence with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.
  • Samples may contain nucleic or amino acids, antibodies, or other materials, and may be derived from any source (e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots or imprints from such cells or tissues).
  • source e.g., bodily fluids including, but not limited to, saliva, blood, and urine; chromosome(s), organelles, or membranes isolated from a cell; genomic DNA, RNA, or cDNA in solution or bound to a substrate; and cleared cells or tissues or blots or imprints from such cells or tissues).
  • Specific binding or “specifically binding” refers to the interaction between a protein or peptide and its agonist, antibody, antagonist, or other binding partner. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A,” the presence of a polypeptide containing epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
  • substitution refers to the replacement of at least one nucleotide or amino acid by a different nucleotide or amino acid.
  • Substrate refers to any suitable rigid or semi-rigid support including, e.g., membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles or capillaries.
  • the substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
  • a “transcript image” refers to the collective pattern of gene expression by a particular tissue or cell type under given conditions at a given time.
  • Transformation refers to a process by which exogenous DNA enters a recipient cell. Transformation may occur under natural or artificial conditions using various methods well known in the art. Transformation may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method is selected based on the host cell being transformed.
  • Transformants include stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as cells which transiently express inserted DNA or RNA.
  • a "transgenic organism,” as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art.
  • the nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus.
  • the term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule.
  • the transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, and plants and animals.
  • the isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al. (1989), supra.
  • a "variant" of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 25% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the "BLAST 2 Sequences" tool Version 2.0.9 (March-07- 1999) set at default parameters.
  • Such a pair of nucleic acids may show, for example, at least 30%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length.
  • the variant may result in "conservative" amino acid changes which do not affect structural and/or chemical properties.
  • a variant may be described as, for example, an "allelic” (as defined above), “splice,” “species,” or “polymo ⁇ hic” variant.
  • a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing.
  • the corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule.
  • Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other.
  • a polymo ⁇ hic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
  • Polymo ⁇ hic variants also may encompass "single nucleotide polymo ⁇ hisms'' (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
  • variants of the polynucleotides of the present invention may be generated through recombinant methods.
  • One possible method is a DNA shuffling technique such as MOLECULARBREEDING (Maxygen Inc., Santa Clara CA; described in U.S.
  • DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties.
  • a “variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40-% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07- 1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%,
  • a “variant" of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the "BLAST 2 Sequences" tool Version 2.0.9 (May-07-1999) set at default parameters.
  • Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93 %, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length of one of the polypeptides. sequence identity over a certain defined length of one of the polypeptides.
  • cDNA sequences derived from human tissues and cell lines were aligned based on nucleotide sequence identity and assembled into "consensus" or "template” sequences which are designated by the template identification numbers (template IDs) in column 2 of 5 Table 2.
  • the sequence identification numbers (SEQ DD NO:s) corresponding to the template EDs are shown in column 1. Segments of the template sequences are defined by the "start” and “stop” nucleotide positions listed in columns 3 and 4. These segments, when translated in the reading frames indicated in column 5, have similarity to signal peptide (SP) or transmembrane (TM) domain consensus sequences, as indicated in column 6. o
  • SP signal peptide
  • TM transmembrane domain consensus sequences
  • sequences of the present invention are used to develop a transcript image for a particular cell or tissue.
  • cDNA was isolated from libraries constructed using RNA derived from normal and diseased o human tissues and cell lines.
  • the human tissues and cell lines used for cDNA library construction were selected from a broad range of sources to provide a diverse population of cDNAs representative of gene transcription throughout the human body. Descriptions of the human tissues and cell lines used for cDNA library construction are provided in the LIFESEQ database (Incyte Genomics, Inc. (Incyte), Palo Alto CA).
  • Human tissues were broadly selected from, for example, cardiovascular, 5 dermatologic, endocrine, gastrointestinal, hematopoietic/immune system, musculoskeletal, neural, reproductive, and urologic sources.
  • Cell lines used for cDNA library construction were derived from, for example, leukemic cells, teratocarcinomas, neuroepitheliomas, cervical carcinoma, lung fibroblasts, and endothelial cells. Such cell lines include, for example, THP-1, Jurkat, HUVEC, hNT2, WI38, HeLa, and other cell lines o commonly used and available from public depositories (American Type Culture Collection, Manassas).
  • Chain termination reaction products may be electrophoresed on urea- polyacrylamide gels and detected either by autoradiography (for radioisotope-labeled nucleotides) or by fluorescence (for fluorophore-labeled nucleotides).
  • Automated methods for mechanized reaction preparation, sequencing, and analysis using fluorescence detection methods have been developed.
  • Machines used to prepare cDNAs for sequencing can include the MICROLAB 2200 liquid transfer system (Hamilton Company (Hamilton), Reno NV), Peltier thermal cycler (PTC200; MJ Research, Inc.
  • Sequencing can be carried out using, for example, the ABI 373 or 377 (Applied Biosystems) or MEGABACE 1000 (Molecular Dynamics, Inc. (Molecular Dynamics), Sunnyvale CA) DNA sequencing systems, or other automated and manual sequencing systems well known in the art.
  • nucleotide sequences of the Sequence Listing have been prepared by current, state-of- the-art, automated methods and, as such, may contain occasional sequencing errors or unidentified nucleotides. Such unidentified nucleotides are designated by an N. These infrequent unidentified bases do not represent a hindrance to practicing the invention for those skilled in the art.
  • Several methods employing standard recombinant techniques may be used to correct errors and complete the missing sequence information. (See, e.g., those described in Ausubel, F.M. et al. (1997) Short Protocols in Molecular Biology. John Wiley & Sons, New York NY; and Sambrook, J. et al. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Plainview NY.)
  • Human polynucleotide sequences may be assembled using programs or algorithms well known in the art. Sequences to be assembled are related, wholly or in part, and may be derived from a single or many different transcripts. Assembly of the sequences can be performed using such programs as PHRAP (Phils Revised Assembly Program) and the GELVD ⁇ W fragment assembly system (GCG), or other methods known in the art.
  • PHRAP Phils Revised Assembly Program
  • GCG GELVD ⁇ W fragment assembly system
  • cDNA sequences are used as "component" sequences that are assembled into 5 "template” or “consensus” sequences as follows. Sequence chromatograms are processed, verified, and quality scores are obtained using PHRED. Raw sequences are edited using an editing pathway known as Block 1 (See, e.g., the LDFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA). A series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucleotide repeats, Alu repeats, etc.) are replaced by "n's", or masked, to prevent spurious o matches. Mitochondrial and ribosomal RNA sequences are also removed.
  • Block 1 See, e.g., the LDFESEQ Assembled User Guide, Incyte Genomics, Palo Alto, CA).
  • a series of BLAST comparisons is performed and low-information segments and repetitive elements (e.g., dinucle
  • the processed sequences are then loaded into a relational database management system (RDMS) which assigns edited sequences to existing templates, if available.
  • RDMS relational database management system
  • a process is initiated which modifies existing templates or creates new templates from works in progress (i.e., nonfinal assembled sequences) containing queued sequences or the sequences themselves.
  • the templates can be merged into bins. If multiple templates exist in one bin, the bin can be split and the templates reannotated.
  • bins are "clone joined" based upon clone information. Clone joining occurs when the 5' sequence of one clone is present in one bin and the 3' sequence from the same clone is present in a different bin, indicating that the two o bins should be merged into a single bin. Only bins which share at least two different clones are merged.
  • a resultant template sequence may contain either a partial or a full length open reading frame, or all or part of a genetic regulatory element. This variation is due in part to the fact that the full length cDNAs of many genes are several hundred, and sometimes several thousand, bases in length. 5 With current technology, cDNAs comprising the coding regions of large genes cannot be cloned because of vector limitations, incomplete reverse transcription of the mRNA, or incomplete "second strand" synthesis. Template sequences may be extended to include additional contiguous sequences derived from the parent RNA transcript using a variety of methods known to those of skill in the art. Extension may thus be used to achieve the full length coding sequence of a gene. 0
  • cDNA sequences are analyzed using a variety of programs and algorithms which are well known in the art. (See, e.g., Ausubel, 1997, supra. Chapter 7.7; Meyers, R.A. (Ed.) (1995) Molecular Biology and Biotechnology. Wiley VCH, New York NY, pp. 856-853; and Table 6.) These analyses comprise both reading frame determinations, e.g., based on triplet codon periodicity for particular organisms (Fickett, J.W. (1982) Nucleic Acids Res. 10:5303-5318); analyses of potential start and stop codons; and homology searches.
  • BLAST Basic Local Ahgnment Search Tool
  • BLAST is especially useful in determining exact matches and comparing two sequence fragments of arbitrary but equal lengths, whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user
  • Protein hierarchies can be assigned to the putative encoded polypeptide based on, e.g., motif, BLAST, or biological analysis. Methods for assigning these hierarchies are described, for example, in "Database System Employing Protein Function Hierarchies for Viewing Biomolecular Sequence Data," U.S.S.N. 08/812,290, filed March 6, 1997, inco ⁇ orated herein by reference.
  • the sptm of the present invention may be used for a variety of diagnostic and therapeutic pu ⁇ oses.
  • an sptm may be used to diagnose a particular condition, disease, or disorder associated with cell signaling.
  • Such conditions, diseases, and disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, a cancer of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix
  • the sptm can be used to detect the presence of, or to quantify the amount of, an sptm- related polynucleotide in a sample. This information is then compared to information obtained from appropriate reference samples, and a diagnosis is established.
  • a polynucleotide complementary to a given sptm can inhibit or inactivate a therapeutically relevant gene related to the sptm.
  • the expression of sptm may be routinely assessed by hybridization-based methods to determine, for example, the tissue-specificity, disease-specificity, or developmental stage-specificity of sptm expression.
  • the level of expression of sptm may be compared among different cell types or tissues, among diseased and normal cell types or tissues, among cell types or tissues at different developmental stages, or among cell types or tissues undergoing various treatments.
  • This type of analysis is useful, for example, to assess the relative levels of sptm expression in fully or partially differentiated cells or tissues, to determine if changes in sptm expression levels are correlated with the development or progression of specific disease states, and to assess the response of a cell or tissue to a specific therapy, for example, in pharmacological or toxicological studies.
  • Methods for the analysis of sptm expression are based on hybridization and amplification technologies and include membrane-based procedures such as northern blot analysis, high-throughput procedures that utilize, for example, microarrays, and PCR-based procedures.
  • the sptm, their fragments, or complementary sequences may be used to identify the presence of and/or to determine the degree of similarity between two (or more) nucleic acid sequences.
  • the sptm may be hybridized to naturally occurring or recombinant nucleic acid sequences under appropriately selected temperatmes and salt concentrations. Hybridization with a probe based on the nucleic acid sequence of at least one of the sptm allows for the detection of nucleic acid sequences, including genomic sequences, which are identical or related to the sptm of the Sequence Listing.
  • Probes may be selected from non-conserved or unique regions of at least one of the polynucleotides of SEQ DD NOX-184 and tested for their abihty to identify or amplify the target nucleic acid sequence using standard protocols.
  • Polynucleotide sequences that are capable of hybridizing, in particular, to those shown in SEQ DD NO: 1-184 and fragments thereof, can be identified using various conditions of stringency. (See, e.g., Wahl, G.M. and S.L. Berger (1987) Methods Enzymol. 152:399-407; Kimmel, A.R. (1987) Methods Enzymol. 152:507-511.) Hybridization conditions are discussed in "Definitions.”
  • a probe for use in Southern or northern hybridization may be derived from a fragment of an sptm sequence, or its complement, that is up to several hundred nucleotides in length and is either single-stranded or double-stranded. Such probes may be hybridized in solution to biological materials such as plasmids, bacterial, yeast, or human artificial chromosomes, cleared or sectioned tissues, or to artificial substrates containing sptm. Microarrays are particularly suitable for identifying the presence of and detecting the level of expression for multiple genes of interest by examining gene expression correlated with, e.g., various stages of development, treatment with a drug or compound, or disease progression.
  • An array analogous to a dot or slot blot may be used to arrange and link polynucleotides to the surface of a substrate using one or more of the following: mechanical (vacuum), chemical, thermal, or UV bonding procedures.
  • Such an array may contain any number of sptm and may be produced by hand or by using available devices, materials, and machines.
  • Microarrays may be prepared, used, and analyzed using methods known in the art.
  • methods known in the art See, e.g., Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93:10614-10619; Baldeschweiler et al. (1995) PCT appUcation W095/251116; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R.A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.
  • Probes may be labeled by either PCR or enzymatic techniques using a variety of commercially available reporter molecules.
  • commercial kits are available for radioactive and chemiluminescent labeling (Amersham Pharmacia Biotech) and for alkaline phosphatase labeling (Life Technologies).
  • sptm may be cloned into commercially available vectors for the production of RNA probes.
  • Such probes may be transcribed in the presence of at least one labeled nucleotide (e.g., 32 P-ATP, Amersham Pharmacia Biotech).
  • polynucleotides of SEQ ID NOX-184 or suitable fragments thereof can be used to isolate full length cDNA sequences utilizing hybridization and/or amplification procedures well known in the art, e.g., cDNA library screening, PCR amplification, etc.
  • the molecular cloning of such full length cDNA sequences may employ the method of cDNA library screening with probes using the hybridization, stringency, washing, and probing strategies described above and in Ausubel, supra. Chapters 3, 5, and 6.
  • These procedures may also be employed with genomic libraries to isolate genomic sequences of sptm in order to analyze, e.g., regulatory elements.
  • Gene identification and mapping are important in the investigation and treatment of almost all conditions, diseases, and disorders. Cancer, cardiovascular disease, Alzheimer's disease, arthritis, diabetes, and mental illnesses are of particular interest. Each of these conditions is more complex than the single gene defects of sickle cell anemia or cystic fibrosis, with select groups of genes being predictive of predisposition for a particular condition, disease, or disorder. For example, 5 cardiovascular disease may result from malfunctioning receptor molecules that fail to clear cholesterol from the bloodstream, and diabetes may result when a particular individual's immune system is activated by an infection and attacks the insulin-producing cells of the pancreas. In some studies, Alzheimer's disease has been linked to a gene on chromosome 21 ; other studies predict a different gene and location. Mapping of disease genes is a complex and reiterative process and generally 0 proceeds from genetic linkage analysis to physical mapping.
  • a genetic linkage map traces parts of chromosomes that are inherited in the same pattern as the condition.
  • Statistics link the inheritance of particular conditions to particular regions of chromosomes, as defined by RFLP or other markers.
  • RFLP radio frequency polypeptide
  • markers and their locations are known from previous studies. More often, however, the markers are simply stretches of DNA that differ among individuals. Examples of genetic linkage maps can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site.
  • sptm sequences may be used to generate o hybridization probes useful in chromosomal mapping of naturally occmring genomic sequences. Either coding or noncoding sequences of sptm may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of an sptm coding sequence among members of a multi-gene family may potentially cause xindesired cross hybridization during chromosomal mapping.
  • sequences may be mapped to a particular chromosome, to a specific 5 region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDNA libraries.
  • HACs human artificial chromosomes
  • YACs yeast artificial chromosomes
  • BACs bacterial artificial chromosomes
  • PI constructions or single chromosome cDNA libraries.
  • o Fluorescent in situ hybridization may be correlated with other physical chromosome mapping techniques and genetic map data.
  • FISH Fluorescent in situ hybridization
  • Correlation between the location of sptm on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder.
  • the sptm sequences may also be used to detect polymo ⁇ hisms that are genetically linked to the inheritance of a particular condition, disease, or disorder.
  • In situ hybridization of chromosomal preparations and genetic mapping techniques may be used for extending existing genetic 5 maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of the corresponding human chromosome is not known. These new marker sequences can be mapped to human chromosomes and may provide valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques.
  • any sequences mapping to that area may represent associated or regulatory genes for further investigation.
  • the nucleotide sequences of the subject invention may also be used to detect differences in chromosomal architecture due to translocation, inversion, etc., among normal, carrier, or affected individuals.
  • a disease-associated gene is mapped to a chromosomal region, the gene must be cloned in order to identify mutations or other alterations (e.g., translocations or inversions) that may be correlated with disease.
  • This process requires a physical map of the chromosomal region containing the disease-gene of interest along with associated markers. A physical map is necessary for determining the nucleotide sequence of and order of marker genes on a particular chromosomal o region. Physical mapping techniques are well known in the art and require the generation of overlapping sets of cloned DNA fragments from a particular organelle, chromosome, or genome. These clones are analyzed to reconstruct and catalog their order. Once the position of a marker is determined, the DNA from that region is obtained by consulting the catalog and selecting clones from that region. The gene of interest is located through positional cloning techniques using hybridization or 5 similar methods.
  • the sptm of the present invention may be used to design probes useful in diagnostic assays. Such assays, well known to those skilled in the art, may be used to detect or confirm conditions, o disorders, or diseases associated with abnormal levels of sptm expression. Labeled probes developed from spun sequences are added to a sample under hybridizing conditions of desired stringency. In some instances, sptm, or fragments or oligonucleotides derived from sptm, may be used as primers in amplification steps prior to hybridization. The amount of hybridization complex formed is quantified and compared with standards for that cell or tissue. If sptm expression varies significantly from the standard, the assay indicates the presence of the condition, disorder, or disease.
  • Qualitative or quantitative diagnostic methods may include northern, dot blot, or other membrane or dip-stick based technologies or multiple-sample format technologies such as PCR, enzyme-linked immunosorbent 5 assay (ELISA)-like, pin, or chip-based assays.
  • PCR enzyme-linked immunosorbent 5 assay
  • the probes described above may also be used to monitor the progress of conditions, disorders, or diseases associated with abnormal levels of sptm expression, or to evaluate the efficacy of a particular therapeutic treatment.
  • the candidate probe may be identified from the sptm that are specific to a given human tissue and have not been observed in GenBank or other genome databases. 0 Such a probe may be used in animal studies, preclinical tests, clinical trials, or in monitoring the treatment of an individual patient. In a typical process, standard expression is established by methods well known in the art for use as a basis of comparison, samples from patients affected by the disorder or disease are combined with the probe to evaluate any deviation from the standard profile, and a therapeutic agent is administered and effects are monitored to generate a treatment profile.
  • Efficacy 5 is evaluated by determining whether the expression progresses toward or returns to the standard normal pattern. Treatment profiles may be generated over a period of several days or several months. Statistical methods well known to those skilled in the art may be use to determine the significance of " such therapeutic agents.
  • the polynucleotides are also useful for identifying individuals from minute biological samples, o for example, by matching the RFLP pattern of a sample' s DNA to that of an individual' s DNA.
  • the polynucleotides of the present invention can also be used to determine the actual base-by-base DNA sequence of selected portions-of an individual's genome. These sequences can be used to prepare PCR primers for amplifying and isolating such selected DNA, which can then be sequenced. Using this technique, an individual can be identified through a unique set of DNA sequences. Once a unique 5 DD database is established for an individual, positive identification of that individual can be made from extremely small tissue samples.
  • oligonucleotide primers derived from the sptm of the invention may be used to detect single nucleotide polymo ⁇ hisms (SNPs).
  • SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans.
  • Methods of o SNP detection include, but are not limited to, single-stranded conformation polymo ⁇ hism (SSCP) and fluorescent SSCP (fSSCP) methods.
  • SSCP single-stranded conformation polymo ⁇ hism
  • fSSCP fluorescent SSCP
  • oligonucleotide primers derived from sptm are used to amplify DNA using the polymerase chain reaction (PCR).
  • the DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like.
  • SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels.
  • the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high- throughput equipment such as DNA sequencing machines.
  • sequence database analysis 5 methods termed in sihco SNP (isSNP) are capable of identifying polymo ⁇ hisms by comparing the sequences of individual overlapping DNA fragments which assemble into a common consensus sequence.
  • DNA-based identification techniques are critical in forensic technology. DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, semen, etc., can be amplified using, e.g., PCR, to identify individuals. (See, e.g., Erlich, H. (1992) PCR Technology. Freeman and Co., New York, NY). Similarly, polynucleotides of the present 5 invention can be used as polymo ⁇ hic markers.
  • reagents capable of identifying the source of a particular tissue.
  • Appropriate reagents can comprise, for example, DNA probes or primers prepared from the sequences of the present invention that are specific for particular tissues. Panels of such reagents can identify tissue by species and/or by organ type. In a similar fashion, these reagents can be used to o screen tissue cultures for contamination.
  • polynucleotides of the present invention can also be used as molecular weight markers on nucleic acid gels or Southern blots, as diagnostic probes for the presence of a specific mRNA in a ' particular cell type, in the creation of subtracted cDNA libraries which aid in the discovery of novel polynucleotides, in selection and synthesis of oligomers for attachment to an array or other support, 5 and as an antigen to elicit an immune response.
  • the polynucleotides encoding SPTM or their mammalian homologs may be "knocked out" in an animal model system using homologous recombination in embryonic stem (ES) cells.
  • ES embryonic stem
  • Such o techniques are weU known in the art and are useful for the generation of animal models of human disease. (See, e.g., U.S. Patent Number 5,175,383 and U.S. Patent Number 5,767,337.)
  • mouse ES cells such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture.
  • the ES cells are transformed with a vector containing the gene of interest disrupted by a marker gene, e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292).
  • a marker gene e.g., the neomycin phosphotransferase gene (neo; Capecchi, M.R. (1989) Science 244:1288-1292).
  • the vector integrates into the corresponding region of the host genome by homologous recombination.
  • homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue- or developmental stage-specific manner (Marth, J.D. 5 (1996) Clin. Invest. 97:1999-2002; Wagner, K.U. et al. (1997) Nucleic Acids Res. 25:4323-4330).
  • Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain.
  • the blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains.
  • Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.
  • the polynucleotides encoding SPTM may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types.
  • the polynucleotides encoding SPTM of the invention can also be used to create "knockin" humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of sptm is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above.
  • Transgenic progeny or inbred lines are studied and treated with potential o pharmaceutical agents to obtain information on treatment of a human disease.
  • a mammal inbred to overexpress sptm resulting, e.g., in the secretion of SPTM in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4:55-74).
  • Screening Assays 5 SPTM encoded by polynucleotides of the present invention may be used to screen for molecules that bind to or are bound by the encoded polypeptides.
  • the binding of the polypeptide and the molecule may activate (agonist), increase, inhibit (antagonist), or decrease activity of the polypeptide or the bound molecule.
  • Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.
  • the molecule is closely related to the natural ligand of the polypeptide, e.g., a ligand or fragment thereof, a natural substrate, or a structural or functional mimetic.
  • the molecule can be closely related to the natural receptor to which the polypeptide binds, or to at least a fragment of the receptor, e.g., the active site. In either case, the molecule can be rationally designed using known techniques.
  • the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane.
  • Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide or cell membrane fractions 5 which contain the expressed polypeptide are then contacted with a test compound and binding, stimulation, or inhibition of activity of either the polypeptide or the molecule is analyzed.
  • An assay may simply test binding of a candidate compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. Alternatively, the assay may assess binding in the presence of a labeled competitor. 0 Additionally, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtares. The assay may also simply comprise the steps of mixing a candidate compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.
  • an ELISA assay using, e.g., a monoclonal or polyclonal antibody can measure polypeptide level in a sample.
  • the antibody can measure polypeptide level by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.
  • All of the above assays can be used in a diagnostic or prognostic context.
  • the molecules discovered using these assays can be used to treat disease or to bring about a particular result in a 0 patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule.
  • the assays can discover agents which may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.
  • Transcript Imaging and Toxicological Testing 5 Another embodiment relates to the use of sptm to develop a transcript image of a tissue or cell type.
  • a transcript image represents the global pattern of gene expression by a particular tissue or ceU type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at a given time. (See Seilhamer et al, "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, expressly inco ⁇ orated by o reference herein.)
  • a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type.
  • the hybridization takes place in high-throughput . format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray.
  • the resultant transcript image would provide a profile of gene activity pertaining to cell signaling.
  • Transcript images which profile sptm expression may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples.
  • the transcript image may thus reflect 5 sptm expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.
  • Transcript images which profile sptm expression may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic 0 gene expression patterns, frequently termed molecular finge ⁇ rints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24:153- 159; Steiner, S. and Anderson, N. L. (2000) Toxicol. Lett. 112-113:467-71, expressly inco ⁇ orated by reference herein). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties.
  • finge ⁇ rints or signatures are most useful and 5 refined when they contain expression information from a large number of genes and gene families. Ideally, a genome- wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data. The normalization procedure is useful for comparison of expression data after treatment with different compounds. o While the assignment of gene function to elements of a toxicant signature aids in inte ⁇ retation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity.
  • the toxicity of a test compound is assessed by treating a biological sample containing nucleic acids with the test compound.
  • Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be o quantified.
  • the transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.
  • proteome refers to the global pattern of protein expression in a particular tissue or cell type.
  • proteome expression patterns, or profiles are analyzed by quantifying the number of expressed proteins and their relative abundance under 5 given conditions and at a given time.
  • a profile of a ceU's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type.
  • the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, 0 supra).
  • the proteins are visuaMzed in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains.
  • the optical density of each protein spot is generally proportional to the level of the protein in the sample.
  • the optical densities of equivalently positioned protein spots from different samples are 5 compared to identify any changes in protein spot density related to the treatment.
  • the proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry.
  • the identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of the present invention. In some cases, further sequence data may be o obtained for definitive protein identification.
  • a proteomic profile may also be generated using antibodies specific for SPTM to quantify the levels of SPTM expression.
  • the antibodies are used as elements on a microarray, and protein expression levels are quantified by exposing the microarray to the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal. Biochem. 270:103- 5 11; Mendoze, L. G. et al. (1999) Biotechniques 27:778-88). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol- or amino- reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.
  • Toxicant signatures at the proteome level are also useful for toxicological screening, and o should be analyzed in paraUel with toxicant signatures at the transcript level.
  • There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and Seilhamer, J. (1997) Electrophoresis 18:533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile.
  • the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiMng may be more reMable and informative in such cases.
  • the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated 5 biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the SPTM encoded by 0 polynucleotides of the present invention.
  • the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the SPTM encoded by polynucleotides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated 5 biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.
  • Transcript images may be used to profile sptm expression in distinct tissue types. This process can be used to determine ceU signaUng activity in a particular tissue type relative to this o activity in a different tissue type. Transcript images may be used to generate a profile of sptm expression characteristic of diseased tissue. Transcript images of tissues before and after treatment may be used for diagnostic pmposes, to monitor the progression of disease, and to monitor the efficacy of drug treatments for diseases which affect ceU signaMng activity.
  • Transcript images of cell Mnes can be used to assess ceU signaMng activity and/or to identify 5 cell Mnes that lack or misregulate this activity. Such cell Mnes may then be treated with pharmaceutical agents, and a transcript image fohowing treatment may indicate the efficacy of these agents in restoring desired levels of this activity.
  • a similar approach may be used to assess the toxicity of pharmaceutical agents as reflected by undesirable changes in cell signaMng activity.
  • Candidate pharmaceutical agents may be evaluated by comparing their associated transcript images with those of o pharmaceutical agents of known effectiveness.
  • the polynucleotides of the present invention are useful in antisense technology.
  • Antisense technology or therapy reMes on the modulation of expression of a target protein through the specific binding of an antisense sequence to a target sequence encoding the target protein or directing its expression.
  • Agrawal, S., ed. 1996 Antisense Therapeutics, Humana Press Inc., Totawa NJ; Alama, A. et al. (1997) Pharmacol. Res. 36(3):171-178; Crooke, S.T. (1997) Adv. Pharmacol. 40:1-49; Sharma, H.W. and R. Narayanan (1995) Bioessays 17(12):1055-1063; and Lavrosky, Y.
  • An antisense sequence is a polynucleotide sequence capable of specifically hybridizing to at least a portion of the target sequence. Antisense sequences bind to ceUular mRNA and/or genomic DNA, affecting translation and/or transcription. Antisense sequences can be DNA, RNA, or nucleic acid mimics and analogs. (See, e.g., Rossi, J.J. et al. (1991) Antisense Res. Dev. 1 (3):285-288; Lee, R. et al. (1998) Biochemistry 37(3):900-1010; Pardridge, W.M. et al. (1995) Proc. Natl. Acad.
  • Antisense sequences can also bind to DNA duplexes through specific interactions in the major groove of the double heMx.
  • the polynucleotides of the present invention and fragments thereof can be used as antisense sequences to modify the expression of the polypeptide encoded by sptm.
  • the antisense sequences can be produced ex vivo, such as by using any of the ABI nucleic acid synthesizer series (AppMed Biosystems) or other automated systems known in the art. Antisense sequences can also be produced *. biologically, such as by transforming an appropriate host cell with an expression vector containing the sequence of interest. (See, e.g., Agrawal, supra.)
  • any gene deMvery system suitable for introduction of the antisense sequences into appropriate target ceMs can be used.
  • Antisense sequences can be dehvered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the ceMular sequence encoding the target protein.
  • Antisense sequences can also be introduced intracehularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors.
  • viral vectors such as retrovirus and adeno-associated virus vectors.
  • viral vectors such as retrovirus and adeno-associated virus vectors.
  • Other gene deMvery mechanisms include Mposome-derived systems, artificial viral envelopes, and other systems known in the art.
  • the nucleotide sequences encoding SPTM or fragments thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
  • an appropriate expression vector i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
  • a variety of expression vector/host systems may be utiMzed to contain and express sequences encoding SPTM.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect ceU systems infected with viral expression vectors (e.g., baculovirus); plant ceU systems transformed with viral expression vectors (e.g., cauMflower mosaic viras, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal (mammaMan) cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect ceU systems infected with viral expression vectors (e.g., baculovirus); plant ceU systems transformed with viral expression vectors (e.g., cauMflower mosaic viras, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vector
  • Expression vectors derived from retroviruses, adenoviruses, or he ⁇ es or vaccinia viruses, or from various bacterial plasmids may be used for deMvery of nucleotide sequences to the targeted organ, tissue, or ceU population.
  • the invention is not Mmited by the host cell employed.
  • sequences encoding SPTM can be transformed into cell Mnes using expression vectors which may contain viral origins of repMcation and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Any number of selection systems may be used to recover transformed ceU Mnes.
  • the polynucleotides encoding SPTM of the invention may be used for somatic or germMne o gene therapy.
  • Gene therapy may be performed to (i) correct a genetic deficiency (e.g., in the cases of severe combined immunodeficiency (SCID)-Xl disease characterized by X-Mnked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288:669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R.M. et al. (1995) Science 270:475-480; Bordignon, C. et al.
  • SCID severe combined immunodeficiency
  • ADA adenosine deaminase
  • hepatitis B or C viras HBV, HCV
  • fungal parasites such as Candida albicans and Paracoccidioides brasiMensis
  • protozoan parasites such as Plasmodium falciparum and Trypanosoma cruzi.
  • the expression of sptm from an appropriate population of transduced ceUs may alleviate the cMnical manifestations caused by the genetic deficiency.
  • diseases or disorders caused by deficiencies in sptm are treated by constructing mammaMan expression vectors comprising sptm and introducing these o vectors by mechanical means into sptm-deficient ceUs.
  • Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual ceUs, (ii) ballistic gold particle deMvery, (Mi) Mposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R.A. and Anderson, W.F. (1993) Annu. Rev. Biochem. 62:191- 217; Ivies, Z. (1997) Cell 91:501-510; Boulay, J-L. and Recipon, H. (1998) Curr. Opin. Biotechnol. 9:445-450).
  • Expression vectors that may be effective for the expression of sptm include, but are not Mmited to, the PCDNA 3.1, EPiTAG, PRCCMV2, PREP, PVAX vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La JoUa CA), and PTET-OFF,
  • the sptm of the invention may be expressed using (i) a constitutively active promoter, (e.g., from cytomegalovirus (CMV), Rous sarcoma viras (RSV), SV40 viras, thymidine kinase (TK), or ⁇ -actin genes), (ii) an inducible promoter (e.g., the tetracycMne-regulated promoter (Gossen, M. and Bujard, H. (1992) Proc. Natl. Acad. Sci. U.S.A.
  • a constitutively active promoter e.g., from cytomegalovirus (CMV), Rous sarcoma viras (RSV), SV40 viras, thymidine kinase (TK), or ⁇ -actin genes
  • an inducible promoter e.g., the tetracycMne-regulated promoter (Gossen, M.
  • Mposome transformation kits e.g., the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen
  • PERFECT LIPID TRANSFECTION KIT available from Invitrogen
  • transformation is performed using the calcium phosphate method (Graham, F.L. and Eb, A.J. (1973) Virology 52:456-467), or by electroporation (Neumann, E. et al. (1982) EMBO J. 1:841-845).
  • the introduction of DNA to primary ceUs requires modification of these standardized mammaMan transfection protocols.
  • diseases or disorders caused by genetic defects with respect to sptm expression are treated by constructing a retrovirus vector consisting of (i) sptm under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (n) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus s-acting RNA sequences and coding sequences required for efficient vector propagation.
  • Retrovirus vectors e.g., PFB and PFBNEO
  • Retrovirus vectors are commercially available (Stratagene) and are based onpubMshed data (Riviere, I. et al. (1995) Proc. Natl. Acad. Sci. U.S.A.
  • the vector is propagated in an appropriate vector producing ceU Mne (VPCL) that expresses an envelope gene with a tropism for receptors on the target ceUs or a promiscuous envelope protein such as VSVg (Armentano, D. et al. (1987) J. Virol. 61:1647-1650; Bender, M.A. et al. (1987) J. Virol. 61:1639-1646; Adam, M.A. and MiUer, A.D. (1988) J. Virol. 62:3802-3806; DuU, T. et al. (1998) J. Virol. 72:8463-8471; Zufferey, R.
  • VPCL ceU Mne
  • U.S. Patent Number 5,910,434 to Rigg discloses a method for obtaining retrovirus packaging ceU Mnes and is hereby inco ⁇ orated by reference. Propagation of retrovirus vectors, transduction of a population of ceUs (e.g., CD4 + T-ceUs), and the return of transduced ceUs to a patient are proceedmes well known to persons skiUed in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol.
  • an adeno virus-based gene therapy deMvery system is used to deMver sptm to cells which have one or more genetic abnormaMties with respect to the expression of sptm.
  • the construction and packaging of adenovirus-based vectors are weU known to those with ordinary skill in the art.
  • RepMcation defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M.E. et al. (1995) Transplantation 27:263-268).
  • PotentiaUy useful adenoviral vectors are described in U.S. Patent Number 5,707,618 to Armentano ("Adenovirus vectors for gene therapy"), hereby inco ⁇ orated by reference.
  • Adenovirus vectors for gene therapy For adenoviral vectors, see also Antinozzi, P.A. et al. (1999) Annu. Rev. Nutr. 19:511-544- and Verma, I.M. and Somia, N.
  • he ⁇ es-based, gene therapy deMvery system is used to deMver sptm to target ceUs which have one or more genetic abnormaMties with respect to the expression of sptm.
  • HSV he ⁇ es simplex virus
  • HSV he ⁇ es simplex virus
  • Patent Number 5,804,413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a ceU under the control of the appropriate promoter for pmposes including human gene therapy. Also taught by this patent are the constraction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. 1999 J. Virol. 73:519-532 and Xu, H. et al., (1994) Dev. Biol. 163:152-161, hereby inco ⁇ orated by reference.
  • an alphaviras (positive, single-stranded RNA virus) vector is used to 5 deMver sptm to target ceUs.
  • SFV SemMki Forest Viras
  • This subgenomic RNA repMcates to higher levels than the fuU-length genomic RNA, resulting in the ove ⁇ roduction of capsid 0 proteins relative to the viral proteins with enzymatic activity (e.g., protease and polymerase).
  • enzymatic activity e.g., protease and polymerase
  • sptm into the alphaviras genome in place of the capsid-coding region results in the production of a large number of sptm RNAs and the synthesis of high levels of SPTM in vector transduced ceUs.
  • alphaviras infection is typically associated with ceM lysis within a few days
  • the abihty to estabMsh a persistent infection in hamster normal kidney cells (BHK-21) with a variant of 5 Sindbis virus (SIN) indicates that the lytic repMcation of alphavirases can be altered to suit the needs of the gene therapy appMcation (Dryga, S.A. et al. (1997) Virology 228:74-83).
  • alphavirases wiU aU ow the introduction of sptm into a variety of ceU types.
  • the specific transduction of a subset of cells in a population may require the sorting of ceUs prior to transduction.
  • the methods of manipulating infectious cDNA clones of alphavirases, performing alphaviras cDNA and RNA o transfections, and performing alphaviras infections, are well known to those with ordinary skill in the art.
  • Anti-SPTM antibodies may be used to analyze protein expression levels.
  • Such antibodies 5 include, but are not Mmited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments.
  • polyclonal, monoclonal, chimeric, single chain, and Fab fragments For descriptions of and protocols of antibody technologies, see, e.g., Pound J.D. (1998) Immunochemical Protocols, Humana Press, Totowa, NX
  • amino acid sequence encoded by the sptm of the Sequence Listing may be analyzed by appropriate software (e.g., LASERGENE NAVIGATOR software, DNASTAR) to determine o regions of high immunogenicity.
  • appropriate software e.g., LASERGENE NAVIGATOR software, DNASTAR
  • the optimal sequences for immunization are selected from the C- terminus, the N-terminus, and those intervening, hydrophiMc regions of the polypeptide which are Mkely to be exposed to the external environment when the polypeptide is in its natural conformation. Analysis used to select appropriate epitopes is also described by Ausubel (1997, supra, Chapter 11.7). Peptides used for antibody induction do not need to have biological activity; however, they must be antigenic.
  • Peptides used to induce specific antibodies may have an amino acid sequence consisting of at least five amino acids, preferably at least 10 amino acids, and most preferably at least 15 amino acids.
  • a peptide which mimics an antigenic fragment of the natural polypeptide may be fused with another protein such as keyhole Mmpet hemocyanin (KLH; Sigma, St. Louis MO) for antibody production.
  • KLH keyhole Mmpet hemocyanin
  • a peptide encompassing an antigenic region may be expressed from an sptm, synthesized as described above, or purified from human cells.
  • mice, goats, and rabbits may be immunized by injection with a peptide.
  • various adjuvants may be used to increase immunological response.
  • peptides about 15 residues in length may be synthesized using an ABI 431 A peptide synthesizer (AppMed Biosystems) using fmoc-chemistry and coupled to KLH (Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinirnide ester (Ausubel, 1995, supra).
  • Rabbits are immunized with the peptide-KLH complex in complete Freund's adjuvant.
  • the resulting antisera are tested for antipeptide activity by binding the peptide to plastic, blocking with 1 % bovine seram albumin (BSA), reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG.
  • Antisera with antipeptide activity are tested for anti-SPTM activity using protocols weU known in the art, including ELISA, radioimmunoassay (RIA), and immunoblotting.
  • isolated and purified peptide may be used to immunize mice (about 100 ⁇ g of peptide) or rabbits (about 1 mg of peptide). Subsequently, the peptide is radioiodinated and used to screen the immunized animals' B-lymphocytes for production of antipeptide antibodies. Positive cells are then used to produce hybridomas using standard techniques. About 20 mg of peptide is sufficient for labeUng and screening several thousand clones. Hybridomas of interest are detected by screening with radioiodinated peptide to identify those fusions producing peptide-specific monoclonal antibody.
  • weUs of a multi-weU plate (FAST, Becton-Dickinson, Palo Alto, CA) are coated with affinity-purified, specific rabbit-anti-mouse (or suitable anti-species IgG) antibodies at 10 mg/ml.
  • the coated wells are blocked with 1 % BSA and washed and exposed to supernatants from hybridomas. After incubation, the weUs are exposed to radiolabeled peptide at 1 mg/ml.
  • Clones producing antibodies bind a quantity of labeled peptide that is detectable above background. Such clones are expanded and subjected to 2 cycles of cloning. Cloned hybridomas are injected into pristane-treated mice to produce ascites, and monoclonal antibody is purified from the ascitic fluid by affinity chromatography on protein A (Amersham Pharmacia Biotech). Several procedures for the production of monoclonal antibodies, including in vitro production, are described in Pound (supra). Monoclonal antibodies with antipeptide activity are tested for anti-SPTM activity using protocols weU known in the art, including EXISA, RIA, and immunoblotting.
  • Antibody fragments containing specific binding sites for an epitope may also be generated.
  • such fragments include, but are not Mmited to, the F(ab')2 fragments produced by pepsin digestion of the antibody molecule, and the Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments.
  • construction of Fab expression Mbraries in filamentous bacteriophage allows rapid and easy identification of monoclonal fragments with desired specificity (Pound, supra. Chaps. 45-47).
  • Antibodies generated against polypeptide encoded by sptm can be used to purify and characterize fuU-length SPTM protein and its activity, binding partners, etc.
  • Anti-SPTM antibodies may be used in assays to quantify the amount of SPTM found in a particular human ceU. Such assays include methods utiUzing the antibody and a label to detect expression level under normal or disease conditions.
  • the peptides and antibodies of the invention may be used with or without modification or labeled by joining them, either covalently or noncovalently, with a reporter molecule.
  • Protocols for detecting and measuring protein expression using either polyclonal or monoclonal antibodies are well known in the art. Examples include ELISA, RIA, and fluorescent activated cell sorting (FACS). Such immunoassays typicaUy involve the formation of complexes between the SPTM and its specific antibody and the measurement of such complexes. These and other assays are described in Pound (supra).
  • RNA was purchased from CLONTECH Laboratories, Inc. (Palo Alto CA) or isolated from various tissues. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixtme of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated with either isopropanol or sodium acetate and ethanol, or by other routine methods.
  • RNA was provided with RNA and constructed the corresponding cDNA Mbraries. Otherwise, cDNA was synthesized arid cDNA Mbraries were constructed with the UNIZAP vector system (Stratagene Cloning Systems, Inc. (Stratagene), La Jolla CA) or
  • SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, Chapters 5.1 through 6.6.) Reverse transcription was initiated using oMgo d(T) or random primers. Synthetic oMgoniicleotide adapters were Mgated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes. For most Mbraries, the cDNA was size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis.
  • cDNAs were Mgated into compatible restriction enzyme sites of the polyMnker of a suitable plasmid, e.g., PBLUESCREPT plasmid (Stratagene), PSPORT1 plasmid (Life Technologies), PCDNA2.1 plasmid (Invitrogen, Carlsbad CA), PBK-CMV plasmid (Stratagene), or pEMCY (Incyte Genomics, Palo Alto CA), or derivatives thereof.
  • Recombinant plasmids were transformed into competent E. coM ceUs including XLl-Blue, XLl-BlueMRF, or SOLR from Stratagene or DH5 ⁇ , DH10B, or ElectroMAX DH10B from Life Technologies. II. Isolation of cDNA Clones
  • Plasmids were recovered from host ceUs by in vivo excision using the UNIZAP vector system (Stratagene) or by ceU lysis. Plasmids were purified using at least one of the foUowing: the Magic or WIZARD Minipreps DNA purification system (Promega); the AGTC Miniprep purification kit (Edge BioSystems, Gaithersburg MD); and the QIAWELL 8, QIAWELL 8 Plus, and QIAWELL 8 Ultra plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit (QIAGEN). FoUowing precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophiUzation, at 4°C
  • plasmid DNA was ampMfied from host cell lysates using direct Mnk PCR in a high-throughput format.
  • Host ceU lysis and thermal cycMng steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of ampMfied plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Inc. (Molecular Probes), Eugene OR) and a FLUOROSKAN II fluorescence scanner (Labsystems Oy, Helsinki, Finland).
  • cDNA sequencing reactions were processed using standard methods or high-thiOughput instrumentation such as the ABI CATALYST 800 thermal cycler (AppMed Biosystems) or the PTC- 200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific Co ⁇ ., Sunnyvale CA) or the MICROLAB 2200 Mquid transfer system (Hamilton).
  • cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or suppMed in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (AppMed Biosystems).
  • Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing system (AppMed Biosystems) in conjunction with standard ABI protocols and base calMng software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, Chapter 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example VDX
  • Component sequences from chromatograms were subject to PHRED analysis and assigned a quaMty score.
  • the sequences having at least a required quaMty score were subject to various pre- processing editing pathways to eMminate, e.g., low quaMty 3' ends, vector and Mnker sequences, polyA tails, Alu repeats, mitochondrial and ribosomal sequences, bacterial contamination sequences, and sequences smaller than 50 base pairs.
  • low-information sequences and repetitive elements e.g., dinucleotide repeats, Alu repeats, etc.
  • sequences were then subject to assembly procedures in which the sequences were assigned to gene bins (bins). Each sequence could only belong to one bin. Sequences in each gene bin were assembled to produce consensus sequences (templates). Subsequent new sequences were added to existing bins using BLASTn (v.1.4 WashU) and CROSSMATCH. Candidate pairs were identified as all BLAST hits having a quaMty score greater than or equal to 150. AMgnments of at least 82% local identity were accepted into the bin. The component sequences from each bin were assembled using a version of PHRAP. Bins with several overlapping component sequences were assembled using DEEP PHRAP.
  • each assembled template was determined based on the number and orientation of its component sequences. Template sequences as disclosed in the sequence Msting correspond to sense strand sequences (the "forward" reading frames), to the best determination. The complementary (antisense) strands are inherently disclosed herein.
  • the component sequences which were used to assemble each template consensus sequence are Msted in Table 3 along with their positions along the template nucleotide sequences.
  • Bins were compared against each other and those having local similarity of at least 82% were combined and reassembled. Reassembled bins having templates of insufficient overlap (less than 95% local identity) were re-spMt. Assembled templates were also subject to analysis by STITCHER/EXON MAPPER algorithms which analyze the probabiMties of the presence of spMce variants, alternatively spMced exons, spMce junctions, differential expression of alternative spMced genes across tissue types or disease states, etc. These resulting bins were subject to several rounds of the above assembly procedures .
  • bins were clone joined based upon clone information. If the 5' sequence of one clone was present in one bin and the 3' sequence from the same clone was present in a different bin, it was Mkely that the two bins actuaUy belonged together in a single bin. The resulting combined bins underwent assembly procedures to regenerate the consensus sequences.
  • the template sequences were further analyzed by translating each template in all three forward reading frames and searching each translation against the Pfam database of hidden Markov - model-based protein famiUes and domains using the HMMER software package (available to the pubMc from Washington University School of Medicine, St. Louis MO). (See also World Wide Web site http://pfam.wustl.edu/ for detailed descriptions of Pfam protein domains and famiMes.) Additionally, the template sequences were translated in all three forward reading frames, and each translation was searched against hidden Markov models for signal peptides using the HMMER software-package.
  • Template sequences are further analyzed using the bioinformatics tools Usted in Table 6, or using sequence analysis software known in the art such as MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Template sequences may be further queried against pubMc databases such as the GenBank rodent, mammaMan, vertebrate, prokaryote, and eukaryote databases.
  • polypeptide sequences were translated to derive the corresponding longest open reading 5 frame as presented by the polypeptide sequences as reported in Table 1.
  • a polypeptide of the invention may begin at any of the methionine residues within the full length translated polypeptide.
  • Polypeptide sequences were subsequently analyzed by querying against the GenBank protein database (GENPEPT, (GenBank version 124)). FuU length polynucleotide sequences are also analyzed using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco o CA) and LASERGENE software (DNASTAR).
  • Polynucleotide and polypeptide sequence aMgnments are generated using default parameters specified by the CLUSTAL algorithm as inco ⁇ orated into the MEGALIGN multisequence ahgnment program (DNASTAR), which also calculates the percent identity between aUgned sequences.
  • Table 5 shows sequences with homology to the polypeptides of the invention as identified by 5 BLAST analysis against the GenBank protein (GENPEPT) database.
  • Column 1 shows the polypeptide sequence identification number (SEQ DD NO:) for the polypeptide segments of the invention.
  • Column 2 shows the reading frame used in the translation of the polynucleotide sequences * encoding the polypeptide segments.
  • Column 3 shows the length of the translated polypeptide ; segments.
  • Columns 4 and 5 show the start and stop nucleotide positions of the polynucleotide o sequences encoding the polypeptide segments.
  • Column 6 shows the GenBank identification number
  • GenBank homolog (GI Number) of the nearest GenBank homolog.
  • Column 7 shows the probabiMty score for the match between each polypeptide and its GenBank homolog.
  • Column 8 shows the annotation of the GenBank homolog.
  • Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound.
  • BXAST a sequence of nucleotide sequences
  • This analysis is much faster than multiple membrane-based hybridizations.
  • the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar.
  • the basis of the search is the product score, which is defined as:
  • the product score takes into account both the degree of similarity between two sequences and the length of the sequence match.
  • the product score is a normaMzed value between 0 and 100, and is calculated as foUows: the BLAST score is multipMed by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences).
  • the BLAST score is l o calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and -4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate the product score.
  • the product score represents a balance between fractional overlap and quaMty in a BLAST aMgnment. For example, a product score of 100 is produced only for 100% identity over the
  • a product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other.
  • a product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.
  • polynucleotide sequences encoding SPTM are analyzed with respect to the
  • Each cDNA sequence is derived from a cDNA Mbrary constructed from a human tissue.
  • Each human tissue is classified into one of the foUowing organ tissue categories: cardiovascular system; connective tissue; digestive system; embryonic stractures; endocrine system; exocrine glands; genitaUa, female; genitaMa, male;
  • each human tissue is classified into one of the following disease/condition
  • a tissue distribution profile is determined for each template by compiMng the cDNA Mbrary tissue classifications of its component cDNA sequences.
  • Each component sequence is derived from a cDNA Mbrary constructed from a human tissue.
  • Each human tissue is classified into one of the following categories: cardiovascular system; connective tissue; digestive system; embryonic 0 structures; endocrine system; exocrine glands; genitaMa, female; genitaMa, male; germ cells; hemic and immune system; Mver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract.
  • Template sequences, component sequences, and cDNA Mbrary/tissue information are found in the LIFESEQ GOLD database (Incyte Genomics, Palo Alto CA). 5 Table 4 shows the tissue distribution profile for the templates of the invention. For each template, the three most frequently observed tissue categories are shown in column 2, along with the percentage of component sequences belonging to each category. Only tissue categories with percentage values of >10% are shown. A tissue distribution of "widely distributed" in column 2 indicates percentage values of ⁇ 10% in aU tissue categories. 0
  • Transcript images are generated as described in Seilhamer et al., "Comparative Gene Transcript Analysis," U.S. Patent Number 5,840,484, inco ⁇ orated herein by reference.
  • OMgonucleotide primers designed using an sptm of the Sequence Listing are used to extend the nucleic acid sequence.
  • One primer is synthesized to initiate 5' extension of the template, and the other primer, to initiate 3' extension of the template.
  • the initial primers may be designed using OLIGO 4.06 software (National Biosciences, Inc. (National Biosciences), Plymouth MN), or another o appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68°C to about 72°C Any stretch of nucleotides which would result in hahpin structures and primer-primer dimerizations are avoided.
  • Selected human cDNA Mbraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.
  • the concentration of DNA in each well is determined by dispensing 100 ⁇ l PICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolved in IX Tris-EDTA (TE) and 0.5 ⁇ l of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Inco ⁇ orated (Corning), Corning NY), allowing the DNA to bind to the reagent.
  • the plate is scanned in a FLUOROSKAN D (Labsystems Oy) to measure the fluorescence of the sample and to quantify the concentration of DNA.
  • a 5 ⁇ l to 10 ⁇ l aUquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions are successful in extending the sequence.
  • the extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera viras endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to reUgation into pUC 18 vector (Amersham Pharmacia Biotech).
  • CviJI cholera viras endonuclease Molecular Biology Research, Madison WI
  • sonicated or sheared prior to reUgation into pUC 18 vector
  • the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with AGAR ACE (Promega).
  • Extended clones are reMgated using T4 Mgase (New England Biolabs, Inc., Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fiU-in restriction site overhangs, and transfected into competent E. coM ceUs. Transformed ceUs are selected on antibiotic-containing media, individual colonies are picked and cultured overnight at 37 °C in 384-weU plates in LB/2x carbenicillin Mquid media.
  • the ceUs are lysed, and DNA is ampMfied by PCR using Taq DNA polymerase (Amersham Pharmacia Biotech) and Pfu DNA polymerase (Stratagene) with the foUowing parameters: Step 1 :
  • Step 7 storage at 4°C DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reampMfied using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1 :2, v/v), and sequenced using DYENAMIC energy transfer sequencing primers and the DYENAMIC DIRECT kit (Amersham Pharmacia Biotech) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (AppMed Biosystems). In Mke manner, the sptm is used to obtain regulatory sequences (promoters, introns, and enhancers) using the procedure above, oMgonucleotides designed for such extension, and an appropriate genomic Mbrary.
  • PICOGREEN reagent Molecular Probes
  • Hybridization probes derived from the sptm of the Sequence Listing are employed for screening cDNAs, mRNAs, or genomic DNA.
  • the labeMng of probe nucleotides between 100 and 1000 nucleotides in length is specificaUy described, but essentially the same procedure may be used with larger cDNA fragments.
  • Probe sequences are labeled at room temperature for 30 minutes using a T4 polynucleotide kinase, ⁇ 32 P-ATP, and 0.5X One-Phor-AU Plus (Amersham Pharmacia Biotech) buffer and purified using a ProbeQuant G-50 Microcolumn (Amersham Pharmacia Biotech).
  • the probe mixture is diluted to 10 7 dpm/ ⁇ g/ml hybridization buffer and used in a typical membrane-based hybridization analysis.
  • the DNA is digested with a restriction endonuclease such as Eco RV and is electrophoresed through a 0.7% agarose gel.
  • the DNA fragments are transferred from the agarose to nylon membrane (NYTRAN Plus, Schleicher & SchueU, Inc., Keene NH) using procedures specified by the manufacturer of the membrane.
  • Prehybridization is carried out for three or more horns at 68 °C, and hybridization is carried out overnight at 68 °C
  • blots are sequentially washed at room temperature under increasingly stringent conditions, up to O.lx saMne sodium citrate (SSC) and 0.5% sodium dodecyl sulfate. After the blots are placed in a PHOSPHORIMAGER cassette (Molecular Dynamics) or are exposed to autoradiography film, hybridization patterns of standard and experimental lanes are compared. Essentiahy the same procedure is employed when screening RNA.
  • SSC O.lx saMn
  • Inclusion of a mapped sequence in a cluster wiU result in the assignment of aU sequences of that cluster, including its particular SEQ D NO:, to that map location.
  • the genetic map locations of SEQ BD NOX-184 are described as ranges, or intervals, of human chromosomes.
  • the map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p-arm.
  • centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers.
  • cM is roughly equivalent to 1 megabase (Mb) of DNA in humans, although this can vary widely due to hot and cold spots of recombination.
  • Mb megabase
  • the cM distances are based on genetic markers mapped by Genethon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters.
  • RNA is isolated from tissue samples using the guanidinium thiocyanate method and polyA + RNA is purified using the oMgo (dT) cellulose method.
  • Each polyA + RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pg/ ⁇ l oMgo-dT primer (21mer), IX first strand buffer, 0.03 units/ ⁇ l RNase inhibitor, 500 ⁇ M dATP, 500 ⁇ M dGTP, 500 ⁇ M dTTP, 40 ⁇ M dCTP, 40 ⁇ M dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Pharmacia Biotech).
  • the reverse transcription reaction is performed in a 25 ml volume containing 200 ng polyA + RNA with GEMBRIGHT kits (Incyte).
  • Specific control polyA + RNAs are synthesized by in vino transcription from non-coding yeast genomic DNA (W. Lei, unpubMshed).
  • the control mRNAs at 0.002 ng, 0.02 ng, 0.2 ng, and 2 ng are diluted into reverse transcription reaction at ratios of 1 :100,000, 1 :10,000, 1 :1000, 1 :100 (w/w) to sample mRNA respectively.
  • control mRNAs are diluted into reverse transcription reaction at ratios of 1:3, 3:1, 1:10, 10:1, 1:25, 25:1 (w/w) to sample mRNA differential expression patterns. After incubation at 37° C for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labehng) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Probes are purified using two successive CHROMA SPIN 30 gel filtration spin columns (CLONTECH Laboratories, Inc.
  • reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300 ml of 100% ethanol.
  • the probe is then dried to completion using a SpeedVAC (Savant Instruments Inc., HolbrookNY) and resuspended in 14 ⁇ l 5X SSC/0.2% SDS.
  • Sequences of the present invention are used to generate array elements.
  • Each array element 5 is ampMfied from bacterial ceUs containing vectors with cloned cDNA inserts.
  • PCR ampMfication uses primers complementary to the vector sequences flanking the cDNA insert.
  • Array elements are ampMfied in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 ⁇ g.
  • AmpMfied array elements are then purified using SEPHACRYL-400 (Amersham Pharmacia Biotech). Purified array elements are immobiMzed on polymer-coated glass sMdes.
  • Glass microscope 0 sMdes (Corning) are cleaned by ultrasound in 0.1% SDS and acetone, with extensive distiUed water washes between and after treatments.
  • Glass sMdes are etched in 4% hydrofluoric acid (VWR Scientific Products Co ⁇ oration (VWR), West Chester, PA), washed extensively in distilled water, and coated with 0.05% aminopropyl silane (Sigma) in 95% ethanol.
  • Coated sMdes are cured in a 110°C oven. 5 Array elements are appMed to the coated glass substrate using a procedure described in US
  • Patent No. 5,807,522 inco ⁇ orated herein by reference.
  • 1 ⁇ l of the array element DNA is loaded into the open capillary printing element by a high-speed robotic apparatus.
  • the apparatus then deposits about 5 nl of array element sample per sMde.
  • Microarrays are UV-crossMnked using a STRATALINKER UV-crossMnker (Stratagene). 0 Microarrays are washed at room temperature once in 0.2% SDS and three times in distiUed water. Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate buffered saMne (PBS) (Tropix, Inc., Bedford, MA) for 30 minutes at 60° C followed by washes in 0.2% SDS and distiUed water as before.
  • PBS phosphate buffered saMne
  • Hybridization reactions contain 9 ⁇ l of probe mixture consisting of 0.2 ⁇ g each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer.
  • the probe mixture is heated to 65° C for 5 minutes and is ahquoted onto the microarray surface and covered with an 1.8 cm 2 coversMp.
  • the arrays are transferred to a wate ⁇ roof chamber having a cavity just sMghtly larger o than a microscope sMde.
  • the chamber is kept at 100% humidity intemaUy by the addition of 140 ⁇ l of 5x SSC in a corner of the chamber.
  • the chamber containing the arrays is incubated for about 6.5 horns at 60° C.
  • the arrays are washed for 10 min at 45° C in a first wash buffer (IX SSC, 0.1 % SDS), three times for 10 minutes each at 45° C in a second wash buffer (0.1X SSC), and dried. Detect
  • Reporter-labeled hybridization complexes are detected with a microscope equipped with an Innova 70 mixed gas 10 W laser (Coherent, Inc., Santa Clara CA) capable of generating spectral Mnes at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5.
  • the excitation laser Mght is focused on the array using a 20X microscope objective (Nikon, Inc., Melville NY).
  • the sMde containing the array is placed on a computer-controUed X-Y stage on the microscope and raster- scanned past the objective.
  • the 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.
  • a mixed gas multiMne laser excites the two fluorophores sequentially. Emitted Mght is spMt, based on wavelength, into two photomultipMer tube detectors (PMT R1477,
  • a specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1 : 100,000.
  • the caUbration is done by labeMng samples of the caMbrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.
  • the output of the photomultipMer tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc., Norwood, MA) instaUed in an IBM-compatible PC computer.
  • the digitized data are displayed as an image where the signal intensity is mapped using a Mnear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal).
  • the data is also analyzed quantitatively. Where two. different fluorophores are excited and measmed simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.
  • a grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid.
  • the fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal.
  • the software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte).
  • Sequences complementary to the sptm are used to detect, decrease, or inhibit expression of the naturaUy occmring nucleotide.
  • the use of oMgonucleotides comprising from about 15 to 30 base pairs is typical in the art. However, smaller or larger sequence fragments can also be used.
  • Appropriate oMgonucleotides are designed from the sptm using OLIGO 4.06 software (National Biosciences) or other appropriate programs and are synthesized using methods standard in the art or ordered from a commercial suppMer.
  • a complementary oMgonucleotide is designed from the most unique 5' sequence and used to prevent transcription factor binding to the promoter sequence.
  • To inhibit translation, a complementary oMgonucleotide is designed to prevent ribosomal binding and processing of the transcript.
  • SPTM Expression and purification of SPTM is accompMshed using bacterial or virus-based expression systems.
  • cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription.
  • promoters include, but are not Mmited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element.
  • Recombinant vectors are transformed into suitable bacterial hosts, e.g.,
  • SPTM BL21 (DE3). Antibiotic resistant bacteria express SPTM upon induction with isopropyl beta-D- thiogalactopyranoside (D?TG). Expression of SPTM in eukaryotic ceUs is achieved by infecting insect or mammaMan ceU Mnes with recombinant Autographica caMfornica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding SPTM by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription.
  • AcMNPV Autographica caMfornica nuclear polyhedrosis virus
  • baculo viras Recombinant baculo viras is used to infect Spodoptera fragiperda (Sf9) insect ceUs in most cases, or human hepatocytes, in some cases. Infection of the latter requires additional genetic modifications to baculovirus. (See e.g., Engelhard, supra; and Sandig, supra.)
  • SPTM is synthesized as a fusion protein with, e.g., glutathione S- transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crade ceU lysates.
  • GST a 26-kilodalton enzyme from Schistosoma iaponicum. enables the purification of fusion proteins on immobiUzed glutathione under conditions that maintain protein activity and antigenicity (Amersham Pharmacia Biotech).
  • the GST moiety can be proteolyticaUy cleaved from SPTM at specificaUy engineered sites.
  • FLAG an 8-amino acid peptide
  • 6-His a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, Chapters 10 and 16). Purified SPTM obtained by these methods can be used directly in the following activity assay.
  • An assay for SPTM activity measures the expression of SPTM on the cell surface.
  • cDNA encoding SPTM is subcloned into an appropriate mammaMan expression vector suitable for high levels of cDNA expression.
  • the resulting construct is transfected into a nonhuman cell Mne such as N1H3T3.
  • Cell surface proteins are labeled with biotin using methods known in the art.
  • Immunoprecipitations are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques. The ratio of labeled immunoprecipitant to unlabeled immunoprecipitant is proportional to the amount of SPTM expressed on the ceU surface.
  • an assay for SPTM activity measures the amount of SPTM in secretory, membrane-bound organeUes. Transfected ceUs as described above are harvested and lysed. The lysate is fractionated using methods known to those of skill in the art, for example, sucrose gradient ultracentrifugation.
  • Such methods aUow the isolation of subceUular components such as the Golgi apparatas, ER, smaU membrane-bound vesicles, and other secretory organelles.
  • Immunoprecipitations from fractionated and total cell lysates are performed using SPTM-specific antibodies, and immunoprecipitated samples are analyzed using SDS-PAGE and immunoblotting techniques.
  • concentration of SPTM in secretory organeUes relative to SPTM in total ceU lysate is proportional to the amount of SPTM in transit through the secretory pathway.
  • SPTM function is assessed by expressing sptm at physiologicaUy elevated levels in mammaMan cell culture systems.
  • cDNA is subcloned into a mammaMan expression vector containing a strong promoter that drives high levels of cDNA expression.
  • Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen Co ⁇ oration, Carlsbad CA), both of which contain the cytomegalovirus promoter.
  • 5-10 ⁇ g of recombinant vector are transiently transfected into a human ceU Mne, preferably of endotheMal or hematopoietic origin, using either Mposome formulations or electroporation.
  • 1-2 ⁇ g of an additional plasmid containing sequences encoding a marker protein are co-transfected.
  • marker protein provides a means to distinguish transfected ceUs from nontransfected ceUs and is a reUable predictor of cDNA expression from the recombinant vector.
  • Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; CLONTECH), CD64, or a CD64-GFP fusion protein. How cytometry (FCM), an automated laser optics-based technique, is used to identify transfected ceUs expressing GFP or CD64-GFP and to evaluate the apoptotic state of the ceUs and other ceUular properties.
  • FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as . measured by staining of DNA with propidium iodide; changes in ceU size and granularity as measured by forward Mght scatter and 90 degree side Mght scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intraceUular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods, in flow cytometry are discussed in Orrherod, M. G. (1994) Flow Cytometry, Oxford, New York NY.
  • CD64 and CD64-GFP are expressed on the surface of transfected ceUs and bind to conserved regions of human immunoglobuMn G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Inc., Lake
  • mRNA can be purified from the cells using methods weU known by those of skill in the art. Expression of mRNA encoding SPTM and other genes of interest can be analyzed by northern analysis or microarray techniques.
  • the SPTM amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding peptide is synthesized and used to raise antibodies by means known to those of skiU in the art.
  • LASERGENE software DNASTAR
  • Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophiUc regions are weU described in 5 the art. (See, e.g., Ausubel, 1995, supra, Chapter 11.)
  • peptides 15 residues in length are synthesized using an ABI 431 A peptide synthesizer (AppMed Biosystems) using fmoc-cbemistry and coupled to KLH (Sigma) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity.
  • MBS N-maleimidobenzoyl-N-hydroxysuccinimide ester
  • Rabbits are immunized with the peptide-KLH complex in complete Freund's o adjuvant.
  • Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated goat anti-rabbit IgG.
  • Antisera with antipeptide activity are tested for anti-SPTM activity using protocols well known in the art, including EXISA, RIA, and immunoblotting.
  • Naturally occmring or recombinant SPTM is substantiaUy purified by immunoaffinity chromatography using antibodies specific for SPTM.
  • An immunoaffinity column is constructed by covalently coupMng anti-SPTM antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia Biotech). After the coupMng, the resin is o blocked and washed according to the manufacturer's instructions.
  • Media containing SPTM are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of SPTM (e.g., high ionic strength buffers in the presence of detergent).
  • the column is eluted under conditions that disrupt antibody/SPTM binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as 5 urea or thiocyanate ion), and SPTM is coUected.
  • SPTM or biologicahy active fragments thereof, are labeled with 125 I Bolton-Hunter reagent.
  • Bolton-Hunter reagent See, e.g., Bolton, A.E. and W.M. Hunter (1973) Biochem. J. 133:529-539.
  • Candidate molecules o previously arrayed in the weUs of a multi-weU plate are incubated with the labeled SPTM, washed, and any weUs with labeled SPTM complex are assayed. Data obtained using different concentrations of SPTM are used to calculate values for the number, affinity, and association of SPTM with the candidate molecules.
  • molecules interacting with SPTM are analyzed using the yeast two-hybrid system as described in Fields, S. and O. Song (1989) Nature 340:245-246, or using commerciaUy available kits based on the two-hybrid system, such as the MATCHMAKER system (CLONTECH).
  • SPTM may also be used in the PATHCALLING process (CuraGen Corp., New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine aU interactions between the proteins encoded by two large Mbraries of genes (Nandabalan, K. et al. (2000) U.S. Patent No. 6,057,101).
  • LG:980494.1:2000SEP08 304 357 forward 1 TM Nin 5 LG:980494.1:2000SEP08 1267 1335 forward 1 TM Nin 5 LG:980494.1:2000SEP08 1339 1410 forward 1 TM Nin 5 LG:980494.1:2000SEP08 1453 1524 forward 1 TM Nin 5 LG:980494.1:2000SEP08 ' 1564 1611 forward 1 TM Nin 5 LG:980494.1 :2000SEP08 563 628 forward 2 TM Nout 5 LG:980494.1:2000SEP08 1364 1450 forward 2 TM Nout 5 LG:980494.1 :2000SEP08 15 101 forward 3 TM Nin 5 LG:980494.1 :2000SEP08 855 941 forward 3 TM Nin 5 LG:980494.1:2000SEP08 1251 1337 forward 3 TM Nin 5 LG:980494.1:2000SEP08 1374 1424 forward 3 TM Nin

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Abstract

Cette invention a trait à des polynucléotides sécréteurs purifiés (sptm) et aux polypeptides (SPTM) codés par ceux-ci. Elle concerne également l'utilisation de sptm, ou de compléments, ou d'oligonucléotides, ou de fragments de ces derniers dans des épreuves diagnostiques. L'invention concerne en outre des vecteurs et des cellules hôtes contenant des sptm aux fins de l'expression de SPTM. L'invention concerne aussi l'utilisation de SPTM isolées et purifiées pour induire des anticorps et pour examiner des bibliothèques de composés et l'utilisation d'anticorps anti-SPTM dans des épreuves diagnostiques. L'invention concerne enfin des jeux ordonnés de microéchantillons contenant des sptm et des procédés d'utilisation.
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GB2372504A (en) * 2000-11-15 2002-08-28 Glaxo Group Ltd Cysteine protease polypeptide
WO2003072723A2 (fr) * 2002-02-22 2003-09-04 Incyte Corporation Molecules de signalisation intracellulaire
WO2004078980A1 (fr) * 2003-03-05 2004-09-16 National Institute Of Advanced Industrial Science And Technology Acide nucleique et procede d'evaluation de cancerisation au moyen de cet acide nucleique
US6863892B2 (en) 2000-08-22 2005-03-08 Agensys, Inc. Nucleic acid and corresponding protein named 158P1D7 useful in the treatment and detection of bladder and other cancers
US7358353B2 (en) 2000-08-22 2008-04-15 Agensys, Inc. Nucleic acid and corresponding protein named 158P1D7 useful in the treatment and detection of bladder and other cancers
US7476506B2 (en) 2002-06-03 2009-01-13 Novartis Vaccines And Diagnostics, Inc. Use of NRG4, or inhibitors thereof, in the treatment of colon and pancreatic cancers
US8968742B2 (en) 2012-08-23 2015-03-03 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
CN110850088A (zh) * 2019-12-06 2020-02-28 四川大学华西医院 Gtf2ird2自身抗体检测试剂在制备肺癌筛查试剂盒中的用途
WO2024076801A3 (fr) * 2022-08-09 2024-05-30 Wisconsin Alumni Research Foundation Nouveaux auto-anticorps et procédé pour détecter la maladie de sjögren

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GB2372504A (en) * 2000-11-15 2002-08-28 Glaxo Group Ltd Cysteine protease polypeptide
WO2003072723A2 (fr) * 2002-02-22 2003-09-04 Incyte Corporation Molecules de signalisation intracellulaire
WO2003072723A3 (fr) * 2002-02-22 2005-02-10 Incyte Corp Molecules de signalisation intracellulaire
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WO2004078980A1 (fr) * 2003-03-05 2004-09-16 National Institute Of Advanced Industrial Science And Technology Acide nucleique et procede d'evaluation de cancerisation au moyen de cet acide nucleique
US9926376B2 (en) 2012-08-23 2018-03-27 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
US8968742B2 (en) 2012-08-23 2015-03-03 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
US10669348B2 (en) 2012-08-23 2020-06-02 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
USRE47103E1 (en) 2012-08-23 2018-10-30 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
US11634503B2 (en) 2012-08-23 2023-04-25 Agensys, Inc. Antibody drug conjugates (ADC) that bind to 158P1D7 proteins
CN110850088A (zh) * 2019-12-06 2020-02-28 四川大学华西医院 Gtf2ird2自身抗体检测试剂在制备肺癌筛查试剂盒中的用途
CN110850088B (zh) * 2019-12-06 2021-08-20 四川大学华西医院 Gtf2ird2自身抗体检测试剂在制备肺癌筛查试剂盒中的用途
WO2024076801A3 (fr) * 2022-08-09 2024-05-30 Wisconsin Alumni Research Foundation Nouveaux auto-anticorps et procédé pour détecter la maladie de sjögren

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