EP1141269A2 - Proteines secretees et leurs utilisations - Google Patents

Proteines secretees et leurs utilisations

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Publication number
EP1141269A2
EP1141269A2 EP99967735A EP99967735A EP1141269A2 EP 1141269 A2 EP1141269 A2 EP 1141269A2 EP 99967735 A EP99967735 A EP 99967735A EP 99967735 A EP99967735 A EP 99967735A EP 1141269 A2 EP1141269 A2 EP 1141269A2
Authority
EP
European Patent Office
Prior art keywords
atcc
amino acid
seq
polypeptide
accession number
Prior art date
Legal status (The legal status 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 status listed.)
Withdrawn
Application number
EP99967735A
Other languages
German (de)
English (en)
Other versions
EP1141269A4 (fr
Inventor
John D. Sharp
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Millennium Pharmaceuticals Inc
Original Assignee
Millennium Pharmaceuticals 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.)
Filing date
Publication date
Application filed by Millennium Pharmaceuticals Inc filed Critical Millennium Pharmaceuticals Inc
Publication of EP1141269A2 publication Critical patent/EP1141269A2/fr
Publication of EP1141269A4 publication Critical patent/EP1141269A4/fr
Withdrawn legal-status Critical Current

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Classifications

    • 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; CARE OF BIRDS, FISHES, INSECTS; 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)

Definitions

  • secreted proteins for example, cytokines
  • cytokines Many secreted proteins, for example, cytokines, play a vital role in the regulation of cell growth, cell differentiation, and a variety of specific cellular responses.
  • a number of medically useful proteins including erythropoietin, granulocyte-macrophage colony stimulating factor, human growth hormone, and various interleukins, are secreted proteins.
  • erythropoietin granulocyte-macrophage colony stimulating factor
  • human growth hormone and various interleukins
  • the identification and characterization of such a receptor enables one to identify both the ligands which bind to the receptor and the intracellular molecules and signal transduction pathways associated with the receptor, permitting one to identify or design modulators of receptor activity, e.g., receptor agonists or antagonists and modulators of signal transduction.
  • the present invention is based, at least in part, on the discovery of cDNA molecules encoding TANGO 221, TANGO 222, TANGO 176, and TANGO 232, all of which are predicted to be either wholly secreted or transmembrane proteins. These proteins, fragments, derivatives, and variants thereof are collectively referred to as “polypeptides of the invention” or “proteins of the invention.” Nucleic acid molecules encoding the polypeptides or proteins of the invention are collectively referred to as “nucleic acids of the invention.” The nucleic acids and polypeptides of the present invention are useful as modulating agents in regulating a variety of cellular processes.
  • this invention provides isolated nucleic acid molecules encoding a polypeptide of the invention or a biologically active portion thereof.
  • the present invention also provides nucleic acid molecules which are suitable for use as primers or hybridization probes for the detection of nucleic acids encoding a polypeptide of the invention.
  • the invention features nucleic acid molecules which are at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the nucleotide sequence of SEQ ID NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207044 (the "cDNA of ATCC 207044"), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207043 (the "cDNA of ATCC 207043"), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207042 (the "cDNA of ATCC 207042”), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207045 (the "cDNA of ATCC 207045”),
  • the invention features nucleic acid molecules which are at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the nucleotide sequence of SEQ LD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207044 (the "cDNA of ATCC 207044"), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207043 (the "cDNA of ATCC 207043"), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207042 (the "cDNA of ATCC 207042”), the nucleotide sequence of the cDNA insert of a clone deposited with ATCC as Accession Number 207045 (the "cDNA of ATCC 207045”)
  • nucleotide sequence of SEQ LD NO:l 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, the nucleotide sequence of the cDNA of ATCC 207044, the nucleotide sequence of the cDNA of ATCC 207043, the nucleotide sequence of the cDNA of ATCC 207042, the nucleotide sequence of the cDNA of ATCC 207045, or the nucleotide sequence of the cDNA of ATCC 207045, or a complement thereof.
  • the invention features nucleic acid molecules of at least 525, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1025, 1050, or 1070 nucleotides of the nucleotide sequence of SEQ LD NO:l, the nucleotide sequence of the human TANGO 221 cDNA clone of ATCC Accession No. 207044, or a complement thereof.
  • the invention also features nucleic acid molecules comprising at least 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, or 510 nucleotides of nucleic acids 1 to 515 of SEQ ID NO: 1 , or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 675, 700, or 710 nucleotides of the nucleotide sequence of SEQ LD NO:2, or a complement thereof.
  • the invention features nucleic acid molecules of at least 210, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, or
  • nucleic acid molecules comprising at least 15, 20, 25, 30, or 35 nucleotides of nucleic acids 1 to 40 of SEQ LD NO:6, or a complement thereof.
  • the invention features nucleic acid molecules comprising at least 210, 225, 250,
  • nucleotide sequence of SEQ LD NO: 7, or a complement thereof is a nucleotide sequence of SEQ LD NO: 7, or a complement thereof.
  • the invention features nucleic acid molecules of at least 680, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600,
  • nucleic acid molecules comprising at least 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, or 640 nucleotides of nucleic acids 1 to
  • the invention features nucleic acid molecules which include a fragment of at least 540, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, or 1425 nucleotides of the nucleotide sequence of SEQ ID NO:12, or a complement thereof.
  • the invention features nucleic acid molecules of at least 810, 850, 900, 950, 1000,
  • nucleotide sequence of SEQ ID NO:16 the nucleotide sequence of a mouse TANGO 176 cDNA, or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least 810, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1460, or 1470 nucleotides of the nucleotide sequence of SEQ LD NO: 17, or a complement thereof.
  • the invention features nucleic acid molecules of at least 285, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1925, or 1930 nucleotides of the nucleotide sequence of SEQ ID NO:21, the nucleotide sequence of the macaque TANGO 232 cDNA clone of ATCC Accession No. 207045 or a complement thereof.
  • the invention also features nucleic acid molecules comprising at least 25, 50, 75,
  • nucleic acids 505 to 1050 of SEQ ID NO:21 or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 675, 700, or 710 nucleotides of the nucleotide sequence of
  • the invention features nucleic acid molecules of at least 275, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, or 1450 nucleotides of the nucleotide sequence of SEQ ID NO:29, the nucleotide sequence of the human TANGO 232 form 1 cDNA clone of ATCC Accession
  • the invention also features nucleic acid molecules comprising at least 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, or 410 nucleotides of nucleic acids 1 to 415 of SEQ LD NO:29, or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least
  • nucleotide sequence of SEQ ED NO:30 25 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, or 360 nucleotides of the nucleotide sequence of SEQ ED NO:30, or a complement thereof.
  • the invention features nucleic acid molecules of at least 320, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 725, 750, 775, 800, 825, 850, 875, 900, 925, 950, 975, 1000, 1025, 1050, 1075, 1100, 1125, or 1130 nucleotides of the
  • nucleotide sequence of SEQ LD NO:36 the nucleotide sequence of a human TANGO 232 form 2 cDNA, or a complement thereof.
  • the invention also features nucleic acid molecules comprising at least 15, 20, 25, 30, 35, 40, 45, 50, or 55 nucleotides of nucleic acids 40 to 100 of SEQ ID NO:36, or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least 320, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 710, or 714 nucleotides of the nucleotide sequence of SEQ LD NO: 37, or a complement thereof.
  • the invention features nucleic acid molecules of at least 325, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, 2100, 2150, 2200, or 2215 nucleotides of the nucleotide sequence of SEQ LD NO:44, the nucleotide sequence of a mouse TANGO 232 cDNA, or a complement thereof.
  • the invention also features nucleic acid molecules comprising at least 25, 50, 75, 100, 125, 150,
  • nucleic acids 490 to 865 of SEQ LD NO:44 or a complement thereof.
  • the invention features nucleic acid molecules which include a fragment of at least 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 675, 700, or 710 nucleotides of the nucleotide sequence of
  • the invention features nucleic acid molecules which include a fragment of at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1200) nucleotides of the nucleotide sequence of SEQ ID NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the nucleotide sequence of the cDNA of ATCC 207044, the
  • the invention also features nucleic acid molecules which include a nucleotide
  • the invention also features nucleic acid molecules which include a nucleotide sequence encoding a protein having an amino acid sequence that is at least 45% (or 55%, 65%, 75%, 85%, 95%, or 98%) identical to the amino acid sequence of SEQ ID NO:3, 8,
  • polypeptides or proteins also exhibit at least one structural and/or functional feature of a polypeptide of the invention.
  • the nucleic acid molecules have the nucleotide sequence of SEQ ID NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the nucleotide sequence of the cDNA of ATCC 207044, the nucleotide sequence of the cDNA of ATCC 207043, the nucleotide sequence of the cDNA of ATCC 207042, the nucleotide sequence of the cDNA of ATCC 207045, or the nucleotide sequence of the cDNA of ATCC 207045.
  • nucleic acid molecules which encode a fragment of a polypeptide having the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, or a fragment including at least 15 (25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046.
  • nucleic acid molecules which encode a fragment of a polypeptide having the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, or a fragment including at least 15 (25, 30, 50, 100, 150, 300, or 400) contiguous amino acids of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the fragment exhibits at least one structural and/or functional feature of a polypeptide of the invention.
  • the invention includes nucleic acid molecules which encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule consisting of a nucleic acid sequence encoding SEQ ID NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of
  • the invention includes nucleic acid molecules which encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule consisting of a nucleic acid sequence encoding SEQ ID NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of
  • isolated polypeptides or proteins having an amino acid sequence that is at least about 60%, preferably 65%, 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046.
  • isolated polypeptides or proteins having an amino acid sequence that is at least about 60%, preferably 65%, 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31, 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the polypeptides or proteins also exhibit at least one structural and/or functional feature of a polypeptide of the invention.
  • isolated polypeptides or proteins which preferably are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 60%, preferably 65%, 75%, 85%, or 95% identical the nucleic acid sequence encoding SEQ ID NO:3, 8, 13, 18, 23, 31 , 38, or 46, wherein the polypeptides or proteins preferably also exhibit at least one structural and/or functional feature of a polypeptide of the invention, and isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence of SEQ LD NO:l, 2, 6, 1, 11, 12, 16, 17, 21,
  • the non-coding strand of the 10 cDNA of ATCC 207044 the non-coding strand of the cDNA of ATCC 207043, the non- coding strand of the cDNA of ATCC 207042, the non-coding strand of the cDNA of ATCC 207045, or the non-coding strand of the cDNA of ATCC 207046.
  • isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 60%, preferably 15 65%, 75%, 85%, or 95% identical the nucleic acid sequence encoding SEQ ID NO:3, 8, 13, 18, 23, 31 , 38, or 46, and isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ED NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, or complement thereof, the non- 20 coding strand of the cDNA of ATCC 207044, the non-coding strand of the cDNA of ATCC 207043, the non-coding strand of the cDNA of ATCC 207042, the non-coding strand of the cDNA of ATCC 207045, or the non-coding
  • amino acid sequence encoded by the cDNA of ATCC 207044 the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of
  • ATCC 207045 or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule having the sequence of SEQ ID NO: 1, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, or a complement thereof, under stringent conditions.
  • polypeptides which are naturally occurring allelic are also within the invention.
  • polypeptide that includes the amino acid sequence of SEQ LD NO:3, 8, 13, 18, 23, 31 , 38, or 46, the amino acid sequence encoded by the cDNA of ATCC 207044, the amino acid sequence encoded by the cDNA of ATCC 207043, the amino acid sequence encoded by the cDNA of ATCC 207042, the amino acid sequence encoded by the cDNA of ATCC 207045, or the amino acid sequence encoded by the cDNA of ATCC 207046, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule having the sequence of SEQ ED NO: 1, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, or a complement thereof, under stringent conditions, wherein such nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide of the invention.
  • the invention also features nucleic acid molecules that hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the cDNA of ATCC 207044, the cDNA of ATCC 207043, the cDNA of ATCC 207042, the cDNA of ATCC 207045, or the cDNA of ATCC 207046, or a complement thereof.
  • the nucleic acid molecules are at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides in length and hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:l, 2, 6, 1, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the cDNA of ATCC 207044, the cDNA of ATCC 207043, the cDNA of ATCC 207042, the cDNA of ATCC 207045, the cDNA of ATCC 207046, or a complement thereof.
  • the invention also features nucleic acid molecules that hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ ID O:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the cDNA of ATCC 207044, the cDNA of ATCC 207043, the cDNA of ATCC 207042, the cDNA of ATCC 207045, the cDNA of ATCC 207046, or a complement thereof.
  • the nucleic acid molecules are at least 300 (325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, or 1290) nucleotides in length and hybridize under stringent conditions to a nucleic acid molecule having the nucleotide sequence of SEQ LD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, 45, the cDNA of ATCC 207044, the cDNA of ATCC 207043, the cDNA of ATCC 207042, the cDNA of ATCC 207045, the cDNA of ATCC 207046, or a complement thereof, wherein such nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide of the invention.
  • the isolated nucleic acid molecules encode an extracellular, transmembrane, or cytoplasmic domain of a polypeptide of the invention.
  • the invention provides an isolated nucleic acid molecule which is antisense to the coding strand of a nucleic acid of the invention.
  • vectors e.g., recombinant expression vectors, comprising a nucleic acid molecule of the invention.
  • the invention provides host cells containing such a vector, or engineered to contain a nucleic acid molecule of the invention and/or to express a nucleic acid of the invention.
  • the invention also provides methods for producing a polypeptide of the invention by culturing, in a suitable medium, a host cell of the invention containing a recombinant expression vector such that a polypeptide is produced.
  • Another aspect of this invention features isolated or recombinant proteins and polypeptides of the invention.
  • Preferred proteins and polypeptides possess at least one biological activity possessed by the corresponding naturally-occurring human polypeptide.
  • An activity, a biological activity, or a functional activity of a polypeptide or nucleic acid of the invention refers to an activity exerted by a protein, polypeptide or nucleic acid molecule of the invention on a responsive cell as determined in vivo, or in vitro, according to standard techniques.
  • Such activities can be a direct activity, such as an association with or an enzymatic activity on a second protein or an indirect activity, such as a cellular signaling activity mediated by interaction of the protein with a second protein.
  • biological activities include, e.g., (1) the ability to form protein- protein interactions with proteins in the signaling pathway of the naturally-occurring polypeptide; (2) the ability to bind a ligand of the naturally-occurring polypeptide; and (3) the ability to interact with a TANGO 221 receptor.
  • Other activities include the ability to modulate function, survival, morphology, proliferation and or differentiation of cells of tissues in which it is expressed (e.g., cells of adipose tissue, breast tissue, and fetal liver and spleen tissues).
  • examples of biological activities of TANGO 221 include the ability to modulate synthesis, storage, and release of lipids, and to modulate the conversion of stored chemical energy into heat.
  • biological activities include, e.g., (1) the ability to form protein- protein interactions with proteins in the signaling pathway of the naturally-occurring polypeptide; (2) the ability to bind a ligand of the naturally-occurring polypeptide; and (3) the ability to interact with a TANGO 222 receptor.
  • Other activities include: (1) the ability to modulate function, survival, morphology, proliferation and/or differentiation of cells of tissues in which it is expressed (e.g., cells of adipose tissue).
  • TANGO 222 biological activities include the ability to modulate synthesis, storage, and release of lipids, and to modulate the conversion of stored chemical energy into heat.
  • biological activities include, e.g., (1) the ability to form protein- protein interactions with proteins in the signaling pathway of the naturally-occurring polypeptide; (2) the ability to bind a ligand of the naturally-occurring polypeptide; (3) the ability to interact with a TANGO 176 receptor; (4) the ability to act as a serine carboxypeptidase, e.g., act as a serine carboxypeptidase at an acidic lysosomal pH (e.g., between pH 2 and pH 6); (5) the ability to act as a deamidase, e.g., act as a deamidase at a neutral pH (e.g., between pH 7 and pH 7.5); and (6) the ability to perform a function of cathepsin A.
  • Other activities include the ability to modulate function, survival, morphology, proliferation and/or differentiation of cells of tissues in which it is expressed (e.g., cells of the pituitary gland).
  • biological activities include, e.g., (1) the ability to form protein- protein interactions with proteins in the signaling pathway of the naturally-occurring polypeptide; (2) the ability to bind a ligand of the naturally-occurring polypeptide; and (3) the ability to interact with a TANGO 232 receptor.
  • Other activities include the ability to modulate function, survival, morphology, proliferation and/or differentiation of cells of tissues in which it is expressed (e.g., cells of adipose tissue).
  • TANGO 232 biological activities include the ability to modulate synthesis, storage, and release of lipids, and to modulate the conversion of stored chemical energy into heat.
  • a polypeptide of the invention has an amino acid sequence sufficiently identical to an identified domain of a polypeptide of the invention.
  • the term "sufficiently identical" refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have a common structural domain and/or common functional activity.
  • amino acid or nucleotide sequences which contain a common structural domain having about 60% identity, preferably 65% identity, more preferably 75%, 85%, 95%, 98% or more identity are defined herein as sufficiently identical.
  • a TANGO 221 or TANGO 222 polypeptide of the invention includes a signal sequence.
  • a nucleic acid molecule of the invention encodes a TANGO 221 or TANGO 222 polypeptide which includes a signal sequence.
  • a TANGO 176 or TANGO 232 polypeptide of the invention includes one or more of the following domains: (1) a signal sequence; (2) an extracellular domain; (3) a transmembrane domain; and (4) a cytoplasmic domain.
  • a nucleic acid molecule of the invention encodes a TANGO 176 or TANGO 232 polypeptide with one or more of the following domains: (1) a signal sequence; (2) an extracellular domain; (3) a transmembrane domain; and (4) a cytoplasmic domain.
  • a TANGO 232 polypeptide of the invention includes a cysteine-rich domain.
  • polypeptides of the present invention can be operably linked to a heterologous amino acid sequence to form fusion proteins.
  • the invention further features antibodies that specifically bind a polypeptide of the invention such as monoclonal or polyclonal antibodies.
  • the polypeptides of the invention or biologically active portions thereof, or antibodies of the invention can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
  • the present invention provides methods for detecting the presence of the activity or expression of a polypeptide of the invention in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of activity such that the presence of activity is detected in the biological sample.
  • the invention provides methods for modulating activity of a polypeptide of the invention comprising contacting a cell with an agent that modulates (inhibits or stimulates) the activity or expression of a polypeptide of the invention such that activity or expression in the cell is modulated.
  • the agent is an antibody that specifically binds to a polypeptide of the invention.
  • the agent modulates expression of a polypeptide of the invention by modulating transcription, splicing, or translation of an mRNA encoding a polypeptide of the invention.
  • the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of an mRNA encoding a polypeptide of the invention.
  • the present invention also provides methods to treat a subject having a disorder characterized by aberrant activity of a polypeptide of the invention or aberrant expression of a nucleic acid of the invention by administering an agent which is a modulator of the activity of a polypeptide of the invention or a modulator of the expression of a nucleic acid of the invention to the subject.
  • the modulator is a protein of the invention.
  • the modulator is a nucleic acid of the invention.
  • the modulator is a peptide, peptidomimetic, or other small organic molecule.
  • the present invention also provides diagnostic assays for identifying the presence or absence of a genetic lesion or mutation characterized by at least one of: (i) aberrant modification or mutation of a gene encoding a polypeptide of the invention, (ii) mis- regulation of a gene encoding a polypeptide of the invention, and (iii) aberrant post- translational modification of the invention wherein a wild-type form of the gene encodes a protein having the activity of the polypeptide of the invention.
  • the invention provides a method for identifying a compound that binds to or modulates the activity of a polypeptide of the invention.
  • such methods entail measuring a biological activity of the polypeptide in the presence and absence of a test compound and identifying those compounds which alter the activity of the polypeptide.
  • the invention also features methods for identifying a compound which modulates the expression of a polypeptide or nucleic acid of the invention by measuring the expression of the polypeptide or nucleic acid in the presence and absence of the compound.
  • Figure 1 depicts the cDNA sequence (SEQ ID NO:l) and the predicted amino acid sequence (SEQ ID NO:3) of human TANGO 221.
  • the open reading frame of SEQ ID NO:l extends from nucleotide 6 to nucleotide 716 of SEQ ID NO:l (SEQ ID NO:2).
  • Figure 2 depicts a hydropathy plot of human TANGO 221. Relatively hydrophobic regions are above the dashed horizontal line, and relatively hydrophilic regions are below the dashed horizontal line. The cysteine residues (cys) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence on the left from the mature protein on the right.
  • Figure 3 depicts the cDNA sequence (SEQ ID NO: 6) and the predicted amino acid sequence (SEQ ED NO:8) of human TANGO 222.
  • the open reading frame of SEQ ID NO:6 extends from nucleotide 33 to nucleotide 434 of SEQ ED NO:6 (SEQ ID NO:7).
  • Figure 4 depicts a hydropathy plot of human TANGO 222. Relatively hydrophobic regions are above the dashed horizontal line, and relatively hydrophilic regions are below the dashed horizontal line. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence on the left from the mature protein on the right.
  • Figures 5A-5B depict the cDNA sequence (SEQ ID NO:l 1) and the predicted amino acid sequence (SEQ ID NO: 13) of human TANGO 176.
  • SEQ ID NO:ll extends from nucleotide 101 to nucleotide 1528 of SEQ ID NO:ll (SEQ ID NO:12).
  • Figure 6 depicts a hydropathy plot of human TANGO 176. Relatively hydrophobic regions are above the dashed horizontal line, and relatively hydrophilic regions are below the dashed horizontal line. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence on the left from the mature protein on the right.
  • Figures 7A-7B depict the cDNA sequence (SEQ ID NO:21) and the predicted amino acid sequence (SEQ ED NO:23) of macaque TANGO 232.
  • the open reading frame of SEQ ED NO: 19 extends from nucleotide 96 to nucleotide 809 of SEQ ID NO: 19 (SEQ ID NO:22).
  • Figure 8 depicts a hydropathy plot of macaque TANGO 232. Relatively hydrophobic regions are above the dashed horizontal line, and relatively hydrophilic regions are below the dashed horizontal line. The cysteine residues (cys) and potential N- glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence on the left from the mature protein on the right.
  • Figure 9 depicts an alignment of a portion of the macaque TANGO 232 amino acid sequence (amino acids 1-132 of SEQ ID NO:23) with a translation of a rabbit nucleotide sequence (GenBank Accession Number C83084; SEQ DD NO:30) and a mouse nucleotide sequence (clone jtmoa31fl; SEQ DD NO:).
  • This alignment defines a cysteine-rich domain that is conserved among these three species.
  • the arrows point to the conserved cysteine residues at positions 49, 54, 61, 72, and 74 of SEQ DD NO.
  • An additional cysteine residue at position 106 is conserved in the macaque and rabbit sequences.
  • Figure 10 depicts the cDNA sequence (SEQ ID NO:29) and the predicted amino acid sequence (SEQ DD NO:31) of human TANGO 232, form 1.
  • the open reading frame of SEQ DD NO: 19 comprises nucleotide 1 to nucleotide 366 of SEQ DD NO:27 (SEQ DD NO:30).
  • Figures 11A-11C depict an alignment of a portion of the cDNA sequence of macaque (nucleotides 424-1937 of SEQ DD NO:21) and human (SEQ DD NO:29) TANGO 232, form 1 and shows that there is 83.4% identity between the two sequences.
  • Figure 12 depicts an alignment of the amino acid sequence of macaque (amino acids 93-238 of SEQ DD NO:21) and human (SEQ DD NO:29) TANGO 232 and shows that there is 94.9% identity between the two sequences.
  • Figure 13 depicts the cDNA sequence of mouse TANGO 176 (SEQ DD NO: 16) and predicted amino acid sequence of mouse TANGO 176 (SEQ DD NO:18).
  • the open reading frame of SEQ ED NO:31 extends from nucleotide 49 to 1524 of SEQ DD NO:31 (SEQ DD NO: 17).
  • Figure 14 depicts the cDNA sequence of human TANGO 232 (SEQ DD NO:36) and predicted amino acid sequence of human TANGO 232 (SEQ DD NO:38).
  • the open reading frame of SEQ DD NO:36 extends from nucleotide 110 to 823 of SEQ DD NO:36 (SEQ DD NO:37).
  • Figure 15 depicts the cDNA sequence of mouse TANGO 232 (SEQ DD NO:44) and predicted amino acid sequence of mouse TANGO 232 (SEQ DD NO:46).
  • the open reading frame of SEQ DD NO:44 extends from nucleotide 79 to 795 of SEQ DD NO:44 (SEQ DD NO:45).
  • the present invention is based, at least in part, on the discovery of cDNA molecules encoding TANGO 221, TANGO 222, TANGO 232, and TANGO 176, all of which are predicted to be either wholly secreted or transmembrane proteins.
  • proteins and nucleic acid molecules of the present invention comprise a family of molecules having certain conserved structural and functional features.
  • family is intended to mean two or more proteins or nucleic acid molecules having a common structural domain and having sufficient amino acid or nucleotide sequence identity as defined herein.
  • Family members can be from either the same or different species.
  • a family can comprise two or more proteins of human origin, or can comprise one or more proteins of human origin and one or more of non- human origin.
  • a TANGO 221, TANGO 222, TANGO 176, or TANGO 232 family member includes a signal sequence.
  • a "signal sequence” includes a peptide of at least about 15 amino acid residues in length which occurs at the N-terminus of secretory and membrane-bound proteins and which contains at least about 70% hydrophobic amino acid residues such as alanine, leucine, isoleucine, phenylalanine, proline, tyrosine, trypotophan, or valine.
  • a signal sequence contains at least about 15 to 25 amino acid residues, preferably about 17-22 amino acid residues, and has at least about 60- 80%, more preferably 65-75%, and more preferably at least about 70% hydrophobic residues.
  • a signal sequence serves to direct a protein containing such a sequence to a lipid bilayer.
  • a TANGO 221 family member has the amino acid sequence of SEQ DD NO:3, and the signal sequence is located at amino acids 1 to 15, 1 to 16, 1 to 17, 1 to 18, or 1-19.
  • the domains and the mature protein resulting from cleavage of such signal peptides are also included herein.
  • the cleavage of a signal sequence consisting of amino acids 1-17 of SEQ DD NO:3 results in a mature TANGO 221 protein corresponding to amino acids 18 to 237 of SEQ DD NO:3 (SEQ DD NO: 5).
  • the signal sequence is normally cleaved during processing of the mature protein.
  • a TANGO 222 family member has the amino acid sequence of SEQ DD NO:3, and the signal sequence is located at amino acids 1 to 17, 1 to 18, 1 to 19, 1 to 20, or 1-21.
  • the domains and the mature protein resulting from cleavage of such signal peptides are also included herein.
  • the cleavage of a signal sequence consisting of amino acids 1-19 of SEQ DD NO: 8 results in a mature TANGO 222 protein corresponding to amino acids 20 to 134 of SEQ DD NO:8 (SEQ DD NO: 10).
  • the signal sequence is normally cleaved during processing of the mature protein.
  • a TANGO 232 family member has the amino acid sequence of SEQ DD NO:21, and the signal sequence is located at amino acids 1 to 20, 1 to 21, 1 to 22, 1 to 23, or 1-24.
  • the domains and the mature protein resulting from cleavage of such signal peptides are also included herein.
  • the cleavage of a signal sequence consisting of amino acids 1-22 of SEQ ED NO:21 results in a mature TANGO 232 protein corresponding to amino acids 23 to 238 of SEQ DD NO:21 (SEQ DD NO: X).
  • the signal sequence is normally cleaved during processing of the mature protein.
  • a TANGO 232 family member also includes one or more of the following domains: (1) an extracellular domain; (2) a transmembrane domain; and (3) a cytoplasmic domain.
  • a TANGO 232 protein contains an extracellular domain of about amino acids 23-194 of SEQ DD NO:21 (SEQ ED NO:24).
  • a TANGO 232 protein contains a transmembrane domain of about amino acids 195-216 of SEQ DD NO:21 (SEQ DD NO:25).
  • a TANGO 232 protein contains a cytoplasmic domain of about amino acids 217-238 of SEQ DD NO:21 (SEQ DD NO:26).
  • TANGO 232 family members can also include a cysteine-rich domain.
  • a cysteine-rich domain includes at least about 30 to 70 amino acid residues, more preferably at least about 40 to 60 amino acid residues, and most preferably at least about 40 to 50 amino acid residues. Of these residues at least about five are cysteine residues.
  • the cysteine-rich domain can also include at least the following consensus sequence: C-D-Y-D- Xaa(l)-C-R-H-L-Q-V-Xaa(2)-C-Xaa(3)-E-L-Q-Xaa(l)-Xaa(4)-Xaa(5)-P-Xaa(4)-Xaa(4)-C- L-C-P-G-L-S-Xaa(6)-Xaa(7)-Xaa(7)-Q-Xaa(2)-P- Xaa(8)-Xaa(2)-P-R-Xaa(4)-G (SEQ DD NO:); wherein Xaa(l) is an amino acid with a basic side chain, e.g., R, H, or K; Xaa(2) is an amino acid with an uncharged polar side chain or a nonpolar side chain, e.g., S, P, or Q; Xaa(3) is an amino acid with a basic side chain or an uncharged polar side
  • the cysteine-rich domain of macaque TANGO 232 is located from amino acid residues 49 to 90 of SEQ DD NO:21 (SEQ DD NO:), and the cysteine residues are at positions 49, 54, 61, 72, and 74.
  • a TANGO 232 polypeptide is a human polypeptide which includes a cysteine-rich domain as described herein.
  • the human polypeptide is at least about 95%, 96%, 97%, or 98% identical to the macaque TANGO 232 amino acid sequence shown in SEQ ED NO:21.
  • human TANGO 221, human TANGO 222, human and mouse TANGO 176, and macaque, human and mouse TANGO 232 are summarized below.
  • a cDNA encoding TANGO 221 was identified by analyzing the sequences of clones present in a non-obese human subcutaneous adipose tissue cDNA library. This analysis led to the identification of a clone, Athfa28cl2, encoding full-length TANGO 221.
  • the cDNA of this clone is 1061 nucleotides long ( Figure 1; SEQ DD NO:l). It is noted that the nucleotide sequence depicted in SEQ ED NO: 1 contains a Not /adapter sequence on the 3' end (5' GGGCGGCCGC 3' (SEQ ED NO:), respectively).
  • nucleic acid molecules of the invention include not only those sequences with such an adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequence.
  • the nucleotide at position 128 is a guanine (G) (SQ DD NO:l).
  • the amino acid at position 41 is glutamate (E)(SEQ DD NO: 3)
  • the nucleotide at position 128 is a cytosine (C)(SEQ DD NO:52).
  • the amino acid at position is 41 aspartate (D)(SEQ DD NO:53)
  • the nucleotide at position 131 is adenine (A)(SEQ DD NO:l).
  • the amino acid at position 43 is glutamate (E)(SEQ DD NO:3).
  • the nucleotide at position 131 is cytosine (C)(SEQ DD NO:54).
  • the amino acid at position 42 is aspartate (D)(SEQ DD NO:55).
  • the nucleotide at position 134 is guanine (G)(SEQ DD NO:l).
  • the amino acid at position 43 is
  • the nucleotide at position 134 is cytosine (C)(SEQ DD NO:56).
  • the amino acid at position 43 is aspartate (D)(SEQ DD NO:57).
  • the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that TANGO 221 includes an 17 amino acid signal peptide
  • TANGO 221 is predicted to have a molecular weight of 24.7 kDa prior to cleavage of its signal peptide and a molecular weight of 22.8 kDa subsequent to cleavage of its signal peptide.
  • a casein kinase D phosphorylation site having the sequence SRLD is found from amino acids 208 to 211 of SEQ DD NO:3.
  • a protein kinase C phosphorylation site having the sequence TGR is found from amino acids 59 to 61.
  • a second protein kinase C phosphorylation site having the sequence SRR is found from amino acids 174 to 176.
  • a third protein kinase C phosphorylation site having the sequence SGR is found from amino
  • a fourth protein kinase C phosphorylation site having the sequence SSR is found from amino acids 207 to 209.
  • An N-myristoylation site having the sequence GQQPSQ is found from amino acids 28 to 33 (SEQ DD NO:).
  • a second N-myristoylation site having the sequence GTGRCS is found from amino acids 58 to 63 (SEQ DD NO:).
  • a third second N-myristoylation site having the sequence GASPCV is found from amino acids
  • a fourth N-myristoylation site having the sequence GAQRAE is found from amino acids 71 to 76 (SEQ DD NO:).
  • a fifth N-myristoylation site having the sequence GAGLTE is found from amino acids 91 to 96 (SEQ DD NO:).
  • a sixth N- myristoylation site having the sequence GGGAGQ is found from amino acids 101 to 106 (SEQ DD NO:).
  • a seventh N-myristoylation site having the sequence GLHQGG is found from amino acids 107 to 112 (SEQ ID NO:).
  • An eighth N-myristoylation site having the sequence GLASGR is found from amino acids 187 to 192 (SEQ DD NO:).
  • a ninth N- myristoylation site having the sequence GVGLGS is found from amino acids 223 to 228.
  • An amidation site having the sequence GGRR is found from amino acids 177 to 180 (SEQ DD NO:).
  • a clone EpT221 which encodes human TANGO 221 , was deposited with the
  • Figure 2 depicts a hydropathy plot of human TANGO 221. Relatively hydrophobic regions are above the horizontal line, and relatively hydrophilic regions are below the horizontal line. The cysteine residues (cys) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence (amino acids 1- 17 of SEQ DD NO:3 (SEQ DD NO:4) on the left from the mature protein (amino acids 18- 237 of SEQ DD NO:3 (SEQ DD NO:5) on the right.
  • TANGO 221 Nucleic Acids. Polypeptides. and Modulators Thereof Because TANGO 221 is expressed in cells of subcutaneous adipose tissue, breast tissue, and fetal liver and spleen tissue, TANGO 221 polypeptides, nucleic acids, and modulators thereof, can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the tissues in which it is expressed.
  • TANGO 221 nucleic acids, proteins and modulators thereof can be utilized to modulate adipocyte function and adipocyte-related processes and disorders such as, e.g., obesity, regulation of body temperature, lipid metabolism, carbohydrate metabolism, body weight regulation, obesity, anorexia nervosa, diabetes mellitus, unusual susceptibility or insensitivity to heat or cold, arteriosclerosis, atherosclerosis, and disorders involving abnormal vascularization, e.g., vascularization of solid tumors.
  • adipocyte function and adipocyte-related processes and disorders such as, e.g., obesity, regulation of body temperature, lipid metabolism, carbohydrate metabolism, body weight regulation, obesity, anorexia nervosa, diabetes mellitus, unusual susceptibility or insensitivity to heat or cold, arteriosclerosis, atherosclerosis, and disorders involving abnormal vascularization, e.g., vascularization of solid tumors.
  • such molecules can be used to treat disorders associated with abnormal fat metabolism,
  • TANGO 221 exhibits expression in the spleen
  • TANGO 221 nucleic acids, proteins, and modulators thereof can be used to modulate the proliferation, differentiation, and/or function of cells that form the spleen, e.g., cells of the splenic connective tissue, e.g., splenic smooth muscle cells and/or endothelial cells of the splenic blood vessels.
  • TANGO 221 nucleic acids, proteins, and modulators thereof can also be used to modulate the proliferation, differentiation, and/or function of cells that are processed, e.g., regenerated or phagocytized within the spleen, e.g., erythrocytes and/or B and T lymphocytes and macrophages.
  • TANGO 221 nucleic acids, proteins, and modulators thereof can be used to treat spleen, e.g., the fetal spleen, associated diseases and disorders.
  • splenic diseases and disorders include e.g., splenic lymphoma and/or splenomegaly, and/or phagocytotic disorders, e.g., those inhibiting macrophage engulfment of bacteria and viruses in the bloodstream.
  • splenic lymphoma and/or splenomegaly e.g., splenic lymphoma and/or splenomegaly
  • phagocytotic disorders e.g., those inhibiting macrophage engulfment of bacteria and viruses in the bloodstream.
  • TANGO 221 exhibits expression in the liver, TANGO
  • 221 polypeptides, nucleic acids, or modulators thereof can be used to treat hepatic (liver) disorders, such as jaundice, hepatic failure, hereditary hyperbiliruinemias (e.g., Gilbert's syndrome, Crigler-Naijar syndromes and Dubin- Johnson and Rotor's syndromes), hepatic circulatory disorders (e.g., hepatic vein thrombosis and portal vein obstruction and thrombosis) hepatitis (e.g., chronic active hepatitis, acute viral hepatitis, and toxic and drug-induced hepatitis) cirrhosis (e.g., alcoholic cirrhosis, biliary cirrhosis, and hemochromatosis), or malignant tumors (e.g., primary carcinoma, hepatoblastoma, and angiosarcoma).
  • hepatic (liver) disorders such as jaundice, hepatic failure, hereditary hyper
  • a cDNA encoding TANGO 222 was identified by analyzing the sequences of clones present in a non-obese human subcutaneous adipose tissue cDNA library. This analysis led to the identification of a clone, Athfa59d4, encoding full-length TANGO 222.
  • the cDNA of this clone is 745 nucleotides long ( Figure 3; SEQ ED NO:6).
  • the nucleotide at position 236 is a guanine (G)(SQ DD NO:6).
  • the amino acid at position 68 is glutamate (E)(SEQ DD NO: 8)
  • the nucleotide at position 236 is a cytosine (C)(SEQ DD NO:58).
  • the amino acid at position 68 is aspartate (D)(SEQ ED NO:59)
  • the nucleotide at position 305 is thymine (T)(SEQ DD NO:6).
  • the amino acid at position 91 is aspartate (D)(SEQ DD NO: 8).
  • the nucleotide at position 305 is cytosine (C)(SEQ DD NO:60).
  • the amino acid at position 91 is glutamate (E)(SEQ ED NO:61).
  • the nucleotide at position 362 is cytosine (C)(SEQ DD NO:6).
  • the amino acid at position 110 is aspartate (D)(SEQ DD NO: 8).
  • the nucleotide at position 362 is guanine (G)(SEQ DD NO:62).
  • the amino acid at position 110 is glutamate (E)(SEQ DD NO:63).
  • TANGO 222 includes a 19 amino acid signal peptide (amino acid 1 to about amino acid 19 of SEQ DD NO:8 (SEQ ID NO:9) preceding the mature TANGO 222 protein (corresponding to about amino acid 20 to amino acid 134 of SEQ DD NO: 8 (SEQ DD NO: 10).
  • TANGO 222 is predicted to have a molecular weight of 15.1 kDa prior to cleavage of its signal peptide and a molecular weight of 13.1 kDa subsequent to cleavage of its signal peptide.
  • N-glycosylation site having the sequence NVTM is found from amino acids 27 to 30 of SEQ ED NO:8.
  • a cGMP-dependent protein kinase phosphorylation site having the sequence KKRS is found from amino acids 121 to 124.
  • a protein kinase C phosphorylation site having the sequence SCK is found from amino acids 33 to 35.
  • a second protein kinase C phosphorylation site having the sequence TLR is found from amino acids 56 to 58.
  • a microbdies C-terminal targeting signal having the sequence SRL is found from amino acids 132 to 134.
  • EpT222 which encodes human TANGO 222
  • ASTYRENAGE 222 was deposited with the American Type Culture Collection (10801 University Boulevard, Manassas, VA 20110-2209) on January 7, 1999 and assigned Accession Number 207043. This deposit will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience for those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
  • Figure 4 depicts a hydropathy plot of human TANGO 222. Relatively hydrophobic regions are above the horizontal line, and relatively hydrophilic regions are below the horizontal line. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence (amino acids 1-19 of SEQ ED NO:8; SEQ ED NO:9) on the left from the mature protein (amino acids 20-134 of SEQ ED NO:8; SEQ DD NO:10) on the right.
  • TANGO 222 is expressed in subcutaneous adipose tissue
  • TANGO 222 polypeptides, nucleic acids, and modulators of TANGO 222 expression or activity can be used to modulate adipocyte function, e.g., fat metabolism.
  • TANGO 222 polypeptides, nucleic acids, and modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the tissues in which it is expressed.
  • TANGO 222 nucleic acids, proteins and modulators thereof can be utilized to modulate adipocyte function and adipocyte-related processes and disorders such as, e.g., obesity, regulation of body temperature, lipid metabolism, carbohydrate metabolism, body weight regulation, obesity, anorexia nervosa, diabetes mellitus, unusual susceptibility or insensitivity to heat or cold, arteriosclerosis, atherosclerosis, and disorders involving abnormal vascularization, e.g., vascularization of solid tumors. Additionally, such molecules can be used to treat disorders associated with abnormal fat metabolism, e.g., cachexia.
  • such molecules can be used to treat disorders associated with abnormal proliferation of these tissues, e.g., cancer, e.g., breast cancer or liver cancer.
  • cancer e.g., breast cancer or liver cancer.
  • Such molecules can be used to treat disorders associated with abnormal fat metabolism, e.g., obesity, arteriosclerosis, or cachexia.
  • cDNA encoding human TANGO 176 was identified by analyzing the sequences of clones present in a human pituitary cDNA library. This analysis led to the identification of a clone, Athbb28g6, encoding full-length human TANGO 176.
  • the cDNA of this clone is 1697 nucleotides long ( Figures 5A-5B; SEQ DD NO:l 1). It is noted that the nucleotide sequence depicted in SEQ ED NO: 11 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCT (SEQ DD NO:), and
  • nucleic acid molecules of the invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
  • the nucleotide at position 250 is an adenine (A) (SQ ED NO:l 1).
  • the amino acid at position 50 is glutamate (E)(SEQ ED NO: 13)
  • the nucleotide at position 250 is a cytosine (C)(SEQ DD NO:64).
  • the amino acid at position 50 is aspartate (D)(SEQ ED NO:65)
  • the nucleotide at position 277 is adenine (A)(SEQ DD NO:l 1).
  • the amino acid at position 50 is aspartate (D)(SEQ ED NO:65)
  • the nucleotide at position 277 is adenine (A)(SEQ DD NO:l 1).
  • the amino acid at position 50 is aspartate (D)(SEQ ED NO:65)
  • the nucleotide at position 277 is adenine (A)(SEQ DD NO:l 1).
  • the amino acid at position 50 is aspartate (D)(SEQ ED NO:65)
  • the nucleotide at position 277 is adenine (A)(SEQ DD NO:l 1).
  • 10 position 59 is glutamate (E)(SEQ ED NO: 13).
  • the nucleotide at position 277 is cytosine (C)(SEQ ED NO:66).
  • the amino acid at position 59 is aspartate (D)(SEQ DD NO:67).
  • the nucleotide at position 400 is adenine (A)(SEQ DD NO:l 1). In this embodiment, the amino acid at position
  • the nucleotide at position 400 is cytosine (C)(SEQ DD NO:68).
  • the amino acid at position 100 is aspartate (D)(SEQ DD NO:69).
  • the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 176 includes a 22 amino acid signal
  • Human TANGO 176 is predicted to have a molecular weight of approximately 71 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 68 kDa subsequent to cleavage of its signal peptide.
  • N-glycosylation site having the sequence NKTY is found from amino acids 81 to
  • a second N-glycosylation site having the sequence NMTL is found from amino acids 132 to 135.
  • a third N-glycosylation site having the sequence NVTG is found from amino acids 307 to 310.
  • a fourth N-glycosylation site having the sequence NQTF is found from amino acids 346 to 349.
  • TLR is found from amino acids 134 to 136.
  • a second protein kinase C phosphorylation site having the sequence SNK is found from amino acids 366 to 368.
  • a third protein kinase C phosphorylation site having the sequence TER is found from amino acids 396 to 398.
  • a casein kinase II phosphorylation site having the sequence TLRD is found from amino acids 134 to 137.
  • sequence SFTD is found from amino acids 160 to 163.
  • a third casein kinase D phosphorylation site having the sequence SDPE is found from amino acids 240 to 243.
  • a fourth casein kinase LI phosphorylation site having the sequence TEPE is found from amino acids 321 to 324.
  • a fifth casein kinase II phosphorylation site having the sequence SLPE is found from amino acids 334 to 337.
  • a sixth casein kinase D phosphorylation site having the sequence TFND is found from amino acids 348 to 351.
  • a seventh casein kinase H phosphorylation site having the sequence TE ⁇ is found from amino acids 353 to 356.
  • An eighth casein kinase D phosphorylation site having the sequence SDSE is found from amino acids 424 to 427.
  • a tyrosine kinase phosphorylation site having the sequence KSDSEVAGY is found from amino acids 423 to 431 (SEQ DD NO:).
  • a 10 site having the sequence GLFRSL is found from amino acids 22 to 27 (SEQ DD NO:).
  • a second N-myristoylation site having the sequence GGPGGS is found from amino acids 110 to 115 (SEQ ED NO:).
  • a third N-myristoylation site having the sequence GTGFSF is found from amino acids 156 to 161 (SEQ DD NO:).
  • a fourth N-myristoylation site having the sequence GIAIGD is found from amino acids 232 to 237 (SEQ ED NO:).
  • VTGESYAG 15 site, e.g., from a serine carboxypeptidase, having the sequence VTGESYAG is found from amino acids 200 to 207 (SEQ DD NO:).
  • Human TANGO 176 has a high proportion of charged amino acids in the predicted extracellular (20%, not including histidines) and cytoplasmic (29%) domains. Human TANGO 176 is predicted to have a molecular weight of 54.2 kDa prior to cleavage of its signal peptide and a molecular weight of 51.9 kDa subsequent to cleavage of its signal peptide.
  • Secretion assays indicate that the polypeptide encoded by human TANGO 176 is secreted.
  • the secretion assays were performed essentially as follows: 8xl0 5 293T cells were plated per well in a 6-well plate and the cells were incubated in growth medium (DMEM, 10% fetal bovine serum, penicillin/ strepomycin) at 37°C, 5% CO 2 overnight. 293T cells were transfected with 2 ⁇ g of full-length TANGO 176 inserted in the pMET7
  • 35 ⁇ Ci Trans- 35 S (ICN Cat. # 51006) was added to each well and the cells were incubated at 37°C, 5% CO 2 for the appropriate time period.
  • a 150 ⁇ l aliquot of conditioned medium was obtained and 150 ⁇ l of 2X SDS sample buffer was added to the aliquot.
  • the sample was heat-inactivated and loaded on a 4-20% SDS-PAGE gel. The gel was fixed and the presence of secreted protein was detected by autoradiography.
  • a clone, EpT176 which encodes human TANGO 176, was deposited as with the
  • Figure 6 depicts a hydropathy plot of human TANGO 176. Relatively hydrophobic regions are above the horizontal line, and relatively hydrophilic regions are below the horizontal line. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence (amino acids 1-22 of SEQ DD NO: 13; SEQ DD NO: 14) on the left from the mature protein (amino acids 23-476 of SEQ DD NO: 13; SEQ ED NO: 15) on the right.
  • a human TANGO 176 polypeptide differs from known molecules (e.g., the serine carboxypeptidase of WO 98/44128) at the sequence KAE found from amino acids 413 to 415 of SEQ DD NO: 13.
  • the sequence is KAE.
  • the sequence is AEK.
  • Human TANGO 176 exhibited the most homology with mosquito vitellogenic carboxypetidase.
  • Northern analysis of human TANGO 176 mRNA revealed expression in a wide range of tissues including heart, spleen, kidney, placenta, and peripheral blood leukocytes. Human TANGO 176 mRNA expression was not detected in the brain, skeletal muscle, colon, thymus, liver, small intestine, and lung.
  • Mouse TANGO 176 A cDNA encoding mouse TANGO 176 was identified by analyzing the sequences of clones present in a mouse alveolar macrophage cell line cDNA library. This analysis led to the identification of a clone, jtmca099e05 encoding full-length mouse TANGO 176.
  • the murine TANGO 176 cDNA of this clone is 1904 nucleotides long ( Figure 13; SEQ DD NO: 16).
  • nucleotide sequence depicted in SEQ DD NO: 16 contains Sail and Not /adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACG CGTCCT (SEQ DD NO:), and GGGCGGCCGC (SEQ DD NO:), respectively).
  • the nucleic acid molecules of the invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
  • the nucleotide at position 81 is an guanine (G) (SQ ED NO: 16).
  • the amino acid at position 11 is glutamate (E)(SEQ DD NO: 18)
  • the nucleotide at position 81 is a cytosine (C)(SEQ DD NO:70).
  • the amino acid at position 11 is aspartate (D)(SEQ DD NO:71)
  • the nucleotide at position 96 is adenine (A)(SEQ DD NO: 16).
  • the amino acid at position 16 is glutamate (E)(SEQ DD NO: 18).
  • the nucleotide at position 96 is cytosine (C)(SEQ DD NO:72).
  • the amino acid at position 16 is aspartate (D)(SEQ DD NO:73).
  • the nucleotide at position 102 is guanine (G)(SEQ ID NO: 16). In this embodiment, the amino acid at position 18 is glutamate (E)(SEQ DD NO: 18). In another embodiment of a nucleotide sequence of mouse TANGO 176, the nucleotide at position 102 is cytosine (C)(SEQ DD NO:74). In this embodiment, the amino acid at position 18 is aspartate (D)(SEQ ED NO:75).
  • mouse TANGO 176 includes a 41 amino acid signal peptide (amino acid 1 to about amino acid 41 of SEQ DD NO:18)(SEQ DD NO:19) preceding the mature mouse TANGO 176 protein (corresponding to about amino acid 42 to amino acid 492 of SEQ DD NO:18)(SEQ DD NO:20).
  • Mouse TANGO 176 is predicted to have a molecular weight of approximately 74 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 68 kDa subsequent to cleavage of its signal peptide.
  • In situ tissue screening was performed on mouse adult and embryonic tissue to analyze for the expression of mouse TANGO 176 mRNA. Expression was observed at moderate to high levels in a number of adult tissues. Expression was generally ubiquitous in positive tissues. Expression during embryogenesis was ubiquitous as well and consistently higher in the liver. A sense control probe was used and had minimal or no signal. Ubiquitous signals were detected in the liver, kidney, adrenal gland, and lymph nodes. A moderate, ubiquitous signal was detected in the submandibular gland. A moderate signal in the mucosal epithelium of the stomach. A signal was observed in the mucosal epithelium and the villi of the small intestine, cortex of the thymus, mucosal epithelium of the colon.
  • a strong signal was observed in the follicles of the spleen.
  • a moderate, ubiquitous signal was observed in the bladder.
  • a moderate signal outlining the seminiferous tubules of the testes was observed.
  • a strong signal was observed in the ovaries.
  • a strong, ubiquitous signal was observed in the placenta. No expression was observed in the following tissues: brain, eye and harderian gland, white fat, brown fat, heart, pancreas, and skeletal muscle.
  • Human and murine TANGO 176 sequences exhibit considerable similarity at the protein, nucleic acid, and open reading frame levels.
  • An alignment (made using the ALIGN software ⁇ Myers and Miller (1989) CABIOS, ver. 2.0 ⁇ ; BLOSUM 62 scoring matrix; gap penalties -12/-4), reveals a protein identity of 29.8% .
  • the human and murine TANGO 176 full length cDNAs are 52.9% identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
  • human and murine TANGO 176 are 52.9% identical.
  • the TANGO 176 protein molecules of the invention comprise a family of proteins with homology to lysosomal protective protein cathepsin A (PPCA), an important enzyme with serine carboxypeptidase activity at lysosomal pH and deamidase/esterase activity at neutral pH.
  • PPCA lysosomal protective protein cathepsin A
  • PPCA is thought to be involved in the activation and stabilization of lysosomal b-galactosidase and neuraminidase and can be active extracellularly.
  • PPCA is also thought to affect vaso- and neuroactive peptide activity when released, for example, from cells (e.g., blood cells, such as platelets or white blood cells, macrophages, endothelial cells and fibroblasts), in response to stimulation.
  • cells e.g., blood cells, such as platelets or white blood cells, macrophages, endothelial cells and fibroblasts
  • PPCA may also have chemotactic activity on neutrophils or monocytes when part of a protein complex formed from PPCA, an alternatively spliced b-galactosidase and neuraminidase.
  • TANGO 176 (and members of the TANGO 176 family) likely function in a manner similar to that of PPCA.
  • TANGO 176 nucleic acids, polypeptides, and modulators thereof can be used to treat PPCA-associated disorders.
  • PPCA deficiency is associated with lysosomal accumulation of sialyloligosaccharides, e.g., galactosialidosis (Goldberg Syndrome). PPCA deficiency may also be associated with a defect in neutrophil or monocyte chemotaxis.
  • sialyloligosaccharides e.g., galactosialidosis (Goldberg Syndrome).
  • PPCA deficiency may also be associated with a defect in neutrophil or monocyte chemotaxis.
  • TANGO 176 polypeptides, nucleic acids, and modulators thereof can be used to treat lysosomal disorders, e.g., sialyloligosaccharide accumulation (e.g., PPCA deficiency or galactosialidosis) and disorders associated with impaired neutrophil or monocyte chemotaxis (e.g., recurrent or chronic bacterial infections).
  • lysosomal disorders e.g., sialyloligosaccharide accumulation (e.g., PPCA deficiency or galactosialidosis) and disorders associated with impaired neutrophil or monocyte chemotaxis (e.g., recurrent or chronic bacterial infections).
  • TANGO 176 is expressed in pituitary tissue.
  • the pituitary secretes such hormones as thyroid stimulating hormone (TSH), follicle stimulating hormone (FSH), adrenocotropic hormone (ACTH), and others. It controls the activity of many other endocrine glands (thyroid, ovaries, adrenal, etc.).
  • Pituitary related disorders include, among others, acromegaly, Cushing's syndrome, craniopharyngiomas, Empty Sella syndrome, hypogonadism, hypopituitarism, and hypophysitis, in addition to disorders of the endocrine glands the pituitary controls.
  • TANGO 176 polypeptides, nucleic acids, or modulators thereof can be used to treat disorders of the adrenal cortex, such as hypoadrenalism (e.g., primary chronic or acute adrenocortical insufficiency, and secondary adrenocortical insufficiency), hyperadrenalism (Cushing's syndrome, primary hyperaldosteronism, adrenal virihsm, and adrenal hyperplasia), or neoplasia (e.g., adrenal adenoma and cortical carcinoma).
  • hypoadrenalism e.g., primary chronic or acute adrenocortical insufficiency, and secondary adrenocortical insufficiency
  • hyperadrenalism Cushing's syndrome, primary hyperaldosteronism, adrenal virihsm, and adrenal hyperplasia
  • neoplasia e.g., adrenal adenoma and cortical carcinoma
  • TANGO 176 polypeptides, nucleic acids, or modulators thereof can be used to treat disorders of the adrenal medulla, such as neoplasms (e.g., pheochromocytomas, neuroblastomas, and ganglioneuromas).
  • neoplasms e.g., pheochromocytomas, neuroblastomas, and ganglioneuromas.
  • TANGO 176 polypeptides, nucleic acids, or modulators thereof can be used to treat disorders of the thyroid gland, such as hyperthyroidism (e.g., diffuse toxic hyperplasia, toxic multinodular goiter, toxic adenoma, and acute or subacute thyroiditis), hypothyroidism (e.g., cretinism and myxedema), thyroiditis (e.g., Hashimoto's thyroiditis, subacute granulomatous thyroiditis, subacute lymphocytic thyroiditis, Riedel's thryroiditis), Graves' disease, goiter (e.g., simple diffuse goiter and multinodular goiter), or tumors (e.g., adenoma, papillary carcinoma, follicular carcinoma, medullary carcinoma, undifferentiated malignant carcinoma, Hodgkin's disease, and non-Hodgkin's lymphoma).
  • hyperthyroidism e.
  • TANGO 176 polypeptides, nucleic acids, and modulators thereof can also be used to modulate pituitary function, and thus, to treat disorders associated with abnormal pituitary function.
  • disorders include pituitary dwarfism, hyperthyroidism associated with inappropriate thyrotropin secretion, acromegaly, and pituitary growth hormone secreting tumors.
  • TANGO 176 is expressed in the follicles of the spleen, liver, kidney, adrenal gland, lymph node, submandibular gland, mucosal epithelium of the stomach, mucosal epithelium and the villi of the small intestine, cortex of the thymus, and mucosal epithelium of the colon, the TANGO 176 polypeptides, nucleic acids and/or modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the tissues in which it is expressed.
  • TANGO 176 is expressed in the kidney, the TANGO 176 polypeptides, nucleic acids and/or modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the tissues in which it is expressed. Such molecules can also be used to treat disorders associated with abnormal or aberrant metabolism or function of cells in the tissues in which it is expressed.
  • Such molecules can be used to treat or modulate renal (kidney) disorders, such as glomerular diseases (e.g., acute and chronic glomerulonephritis, rapidly progressive glomerulonephritis, nephrotic syndrome, focal proliferative glomerulonephritis, glomerular lesions associated with systemic disease, such as systemic lupus erythematosus, Goodpasture's syndrome, multiple myeloma, diabetes, neoplasia, sickle cell disease, and chronic inflammatory diseases), tubular diseases (e.g., acute tubular necrosis and acute renal failure, polycystic renal diseasemedullary sponge kidney, medullary cystic disease, nephrogenic diabetes, and renal tubular acidosis), tubulointerstitial diseases (e.g., pyelonephritis, drug and toxin induced tubulointerstitial nephritis, hypercalcemic nephropathy, and hypokale
  • TANGO 176 exhibits expression in the spleen
  • TANGO 176 nucleic acids, proteins, and modulators thereof can be used to modulate the proliferation, differentiation, and/or function of cells that form the spleen, e.g., cells of the splenic connective tissue, e.g., splenic smooth muscle cells and/or endothelial cells of the splenic blood vessels.
  • TANGO 176 nucleic acids, proteins, and modulators thereof can also be used to modulate the proliferation, differentiation, and/or function of cells that are processed, e.g., regenerated or phagocytized within the spleen, e.g., erythrocytes and/or B and T lymphocytes and macrophages.
  • TANGO 176 nucleic acids, proteins, and modulators thereof can be used to treat spleen, e.g., the fetal spleen, associated diseases and disorders.
  • splenic diseases and disorders include e.g., splenic lymphoma and/or splenomegaly, and/or phagocytotic disorders, e.g., those inhibiting macrophage engulfinent of bacteria and viruses in the bloodstream.
  • TANGO 176 polypeptides, nucleic acids, or modulators thereof can be used to treat hepatic (liver) disorders, such as jaundice, hepatic failure, hereditary hyperbiliruinemias (e.g., Gilbert's syndrome, Crigler-Naijar syndromes and Dubin- Johnson and Rotor's syndromes), hepatic circulatory disorders (e.g., hepatic vein thrombosis and portal vein obstruction and thrombosis) hepatitis (e.g., chronic active hepatitis, acute viral hepatitis, and toxic and drug-induced hepatitis) cirrhosis (e.g., alcoholic cirrhosis, biliary cirrhosis, and hemochromatosis), or malignant tumors (e.g., primary carcinoma, hepatoblastoma, and angiosarcoma).
  • hepatic (liver) disorders such as jaundice, hepatic failure, her
  • TANGO 176 exhibits expression in the small intestine
  • TANGO 176 polypeptides, nucleic acids, or modulators thereof can be used to treat intestinal disorders, such as ischemic bowel disease, infective enterocolitis, Crohn's disease, benign tumors, malignant tumors (e.g., argentaffinomas, lymphomas, adenocarcinomas, and sarcomas), malabsorption syndromes (e.g., celiac disease, tropical sprue, Whipple's disease, and abetalipoproteinemia), obstructive lesions, hernias, intestinal adhesions, intussusception, or volvulus.
  • intestinal disorders such as ischemic bowel disease, infective enterocolitis, Crohn's disease, benign tumors, malignant tumors (e.g., argentaffinomas, lymphomas, adenocarcinomas, and sarcomas), malabsorption syndromes (e.g
  • a cDNA encoding macaque TANGO 232 was identified by analyzing the sequences of clones present in a macaque adipose tissue cDNA library.
  • nucleic acid molecules of the invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
  • nucleotide at position 182 is an adenine (A) (SEQ DD NO:21).
  • amino acid at position 29 is glutamate (E)(SEQ DD NO:23)
  • nucleotide at position 182 is a cytosine (C)(SEQ DD NO:76).
  • the amino acid at position 29 is aspartate (D)(SEQ DD NO:77)
  • the nucleotide at position 185 is adenine (A)(SEQ DD NO:21).
  • the amino acid at position 30 is glutamate (E)(SEQ DD NO:23).
  • the nucleotide at position 185 is cytosine (C)(SEQ DD NO:78).
  • the amino acid at position 30 is aspartate (D)(SEQ ED NO:79).
  • the nucleotide at position 188 is guanine (G)(SEQ ED NO:21). In this embodiment, the amino acid at position 31 is glutamate (E)(SEQ DD NO:23). In another embodiment of a nucleotide sequence of macaque TANGO 232, the nucleotide at position 188 is cytosine (C)(SEQ DD NO: 80). In this embodiment, the amino acid at position 31 is aspartate (D)(SEQ DD NO:81).
  • the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that macaque TANGO 232 includes an 22 amino acid signal peptide (amino acid 1 to about amino acid 22 of SEQ DD NO:23; SEQ DD NO:24) preceding the mature macaque TANGO 232 protein (corresponding to about amino acid 23 to amino acid 238 of SEQ ED NO:23; SEQ DD NO:25).
  • Macaque TANGO 232 has a high proportion of charged amino acids in the predicted extracellular (22%, not including histidines) and cytoplasmic (27%) domains. Macaque TANGO 232 is predicted to have a molecular weight of 25.4 kDa prior to cleavage of its signal peptide and a molecular weight of 23.0 kDa subsequent to cleavage of its signal peptide.
  • EpT232m which encodes macaque TANGO 232, was deposited with the
  • Figure 8 depicts a hydropathy plot of macaque TANGO 232. Relatively hydrophobic regions are above the horizontal line, and relatively hydrophilic regions are below the horizontal line. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace. The dashed vertical line separates the signal sequence (amino acids 1-22 of SEQ DD NO:23; SEQ DD NO:24) on the left from the mature protein (amino acids 23-238 of SEQ DD NO:23; SEQ DD NO:25) on the right.
  • macaque TANGO 232 is predicted to be a transmembrane protein having a 172 amino acid extracellular domain (amino acids 23-194 of SEQ DD
  • a macaque TANGO 232 protein contains an extracellular domain at amino acid residues 217 to 238 of SEQ DD NO:21 ( SEQ DD NO:), a transmembrane domain at amino acid residues 195 to 216 of SEQ DD NO:21 (SEQ DD NO:), and a cytoplasmic domain at amino acid residues 1 to 194 of SEQ DD NO:21 (SEQ DD NO:).
  • N-glycosylation site having the sequence NATN is found from amino acids 132 to 135 of SEQ ED ⁇ O:21.
  • a protein kinase C phosphorylation site having the sequence TNR is found from amino acids 134 to 136.
  • An ⁇ -myristoylation site having the sequence GSEAAQ is found from amino acids 121 to 126 (SEQ DD NO:).
  • a second N-myristoylation site having the sequence GLKPGG is found from amino acids 142 to 147 (SEQ ED NO:).
  • a third N-myristoylation site having the sequence GLEGAD is found from amino acids 171 to 176 (SEQ DD NO:).
  • a fourth N-myristoylation site having the sequence GVGTAL is found from amino acids 201 to 206 (SEQ DD NO:).
  • Figure 9 depicts an alignment of a portion of the macaque TANGO 232 amino acid sequence (amino acids 1-132 of SEQ ED NO:23) with a translation of a rabbit nucleotide sequence (GenBank Accession Number C83084; SEQ ED NO:) and a mouse nucleotide sequence (clone jtmoa31fl; SEQ DD NO:).
  • This alignment defines a cysteine-rich domain that is conserved and which is described in detail herein.
  • the arrows indicate the conserved cysteine residues at positions 49, 54, 61, 72, and 74.
  • An additional cysteine residue at position 106 is conserved in the macaque and rabbit sequences.
  • Human TANGO 232 A clone, Athke96c4, encoding human TANGO 232 was identified. The cDNA of this clone is 1459 nucleotides long ( Figure 10; SEQ DD NO:29). It is noted that the nucleotide sequence depicted in SEQ ED NO: 27 contains a Not I adapter sequence on the 3' end (5' GGGCGGCCGC 3' (SEQ DD NO:), respectively). Thus, it is to be understood that the nucleic acid molecules of the invention include not only those sequences with such an adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequence. In one embodiment, human TANGO 232 is referred to as human TANGO 232, form 1.
  • the open reading frame of this human TANGO 232, form 1 cDNA comprises nucleotides 1 to 366 of SEQ ED NO:27 (SEQ DD NO:30), and encodes a polypeptide comprising the 122 amino acid sequence shown in Figure 10 (SEQ ID NO:31).
  • Secretion assays indicate that the polypeptide encoded by human TANGO 232 is not secreted and thus, likely a transmembrane protein. The secretion assays were performed as described above for human TANGO 176.
  • the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 232 form 1 does not appear to include a signal peptide. Accordingly, the mature human TANGO 232 form 1 protein corresponds to about amino acid 1 to about amino acid 294 of SEQ DD NO:31; SEQ DD NO:32).
  • human TANGO 232 form 1 protein is a transmembrane protein that contains an extracellular domain at amino acid residues 1 to 78 of SEQ DD NO:31 (SEQ ED NO:33), a transmembrane domain at amino acid residues 79 to 100 of SEQ ED NO:31 (SEQ DD NO:34), and a cytoplasmic domain at amino acid residues 101 to 122 of SEQ DD NO:31 (SEQ DD NO:35).
  • a human TANGO 232 form 1 protein contains an extracellular domain at amino acid residues 101 to 122 of SEQ DD NO:31 ( SEQ DD NO:), a transmembrane domain at amino acid residues 79 to 100 of SEQ DD NO:31 (SEQ DD NO:), and a cytoplasmic domain at amino acid residues 1 to 78 of SEQ DD NO:31 (SEQ DD NO:).
  • EpT232h which encodes human TANGO 232
  • the American Type Culture Collection (10801 University Boulevard, Manassas, NA 20110-2209) on January 7, 1999 and assigned Accession Number 207046. This deposit will be maintained under the terms of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience for those of skill in the art and is not an admission that a deposit is required under 35 U.S. C. ⁇ 112.
  • Figures 11 A-l IC depicts an alignment of a portion of the cDNA sequence of macaque TANGO 232 (nucleotides 424 to 1937 of SEQ DD NO:21) and nucleotides 1 to 1459 of human TANGO 232 clone Athke96c4 (SEQ DD NO:29).
  • FASTA Pearson, W.R., and Lipman, D.J. (1988) Proc. Natl Acad. Sci. USA 85:2444-2448
  • version 2.0u53 July 1996) indicates that there is 83.4% identity between the two sequences.
  • Figure 12 depicts an alignment of a portion of the amino acid sequence of macaque TANGO 232 (amino acids 93 to 238 of SEQ DD NO:23)(SEQ DD NO:) and human TANGO 232 clone Athke96c4 (SEQ DD NO:31)(SEQ DD NO:).
  • FASTA Pearson, W.R., and Lipman, D.J. (1988) Proc. Natl Acad. Sci. USA 85:2444-2448) version 2.0u53 (July 1996) indicates that there is 94.9% identity between the two sequences.
  • Another cDNA clone, Arhoc 109b 10, encoding full length human TANGO 232 was identified.
  • the cDNA of this clone is 1136 nucleotides long ( Figure 14; SEQ DD NO:36). It is noted that the nucleotide sequence depicted in SEQ ED NO: contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCT (SEQ DD NO:), and GGGCGGCCGC (SEQ DD NO:), respectively). Thus, it is to be understood that the nucleic acid molecules of the invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences. In one embodiment, human TANGO 232 is referred to as human TANGO 232, form 2.
  • nucleotide sequence of human TANGO 232 form 2 is an adenine (A)(SEQ ED NO:36).
  • amino acid at position 30 is glutamate (E)(SEQ DD NO:38)
  • nucleotide at position 196 is a cytosine (C)(SEQ DD NO:82).
  • the amino acid at position 30 is aspartate (D)(SEQ DD NO: 83)
  • the nucleotide at position 199 is adenine (A)(SEQ DD NO:36).
  • the amino acid at position 31 is glutamate (E)(SEQ DD NO:3).
  • the nucleotide at position 199 is cytosine (C)(SEQ ED NO:84).
  • the amino acid at position 31 is aspartate (D)(SEQ ED NO:85).
  • nucleotide sequence of human TANGO 232 in another embodiment of a nucleotide sequence of human TANGO 232 form 2, the nucleotide at position 202 is guanine (G)(SEQ DD NO:36). In this embodiment, the amino acid at position 32 is glutamate (E)(SEQ DD NO:38). In another embodiment of a nucleotide sequence of human TANGO 232 form 2, the nucleotide at position 202 is cytosine (C)(SEQ DD NO:86). In this embodiment, the amino acid at position 32 is aspartate (D)(SEQ DD NO:87).
  • the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 232 form 2 includes a 22 amino acid signal peptide (amino acid 1 to about amino acid 22 of SEQ ED NO:38; SEQ DD NO:39) preceding the mature human TANGO 232 form 2 protein (corresponding to about amino acid 23 to amino acid 238 of SEQ DD NO:38; SEQ DD NO:40).
  • human TANGO 232 form 2 protein is a transmembrane protein that contains an extracellular domain at amino acid residues 23 to 194 of SEQ DD NO:38 (SEQ DD NO:41), a transmembrane domain at amino acid residues 195 to 216 of SEQ ED NO:38 (SEQ DD NO:42), and a cytoplasmic domain at amino acid residues 217 to 238 of SEQ DD NO:38 (SEQ DD NO:43).
  • a human TANGO 232 form 2 protein contains an extracellular domain at amino acid residues 217 to 238 of SEQ DD NO:38 ( SEQ DD NO:), a transmembrane domain at amino acid residues 195 to 216 of SEQ DD NO:38 (SEQ ED NO:), and a cytoplasmic domain at amino acid residues 1 to 194 of SEQ DD NO:38 (SEQ DD NO:).
  • the human gene for TANGO 232 was mapped on radiation hybrid panels to the long arm of chromosome 11, in the region ql3. Flanking markers for this region are Dl IS 1965 and WI-1409.
  • the ARRB1 (arrestin, beta), GIF (gastric intrinsic factor), ACTN3 (actinin, alpha 3) genes also map to this region of the human chromosome.
  • the HBM high bone mass
  • OPTB1 osteoporosis, auto.rec
  • OPPG osteoporosis, pseudoglioma syndrome
  • BBS1 Bardet-Biedl syndrome
  • HND Hardtnup disorder
  • MKS2 Meckel syndrome 2
  • the oc (osteosclerotic), dc (dancer), nmd (meuromuscular degeneration), ocd (osteochondrodystrophy) loci also map to this region of the mouse chromosome.
  • the pcx (pyruvate decarboxylase), chk (choline kinase), gain (galanin) genes also map to this region of the mouse chromosome.
  • a cDNA encoding mouse TANGO 232 was identified by analyzing the sequences of clones present in a mouse osteoblast, LPS stimulated cDNA library. This analysis led to the identification of a clone, jtmoa31 fl , encoding full-length mouse TANGO 232.
  • the murine TANGO 232 cDNA of this clone is 2221 nucleotides long ( Figure 15; SEQ ED NO:44). It is noted that the nucleotide sequence depicted in SEQ DD NO: contains a Sal I adapter sequence on the 5' end ((GTCGACCCACGCGTCCT (SEQ DD NO:)).
  • nucleic acid molecules of the invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
  • the open reading frame of this cDNA nucleotides 79 to 795 of SEQ DD NO:44 (SEQ ED NO:45), encodes the 239 amino acid transmembrane protein depicted in Figure 15 ( SEQ ED NO:46).
  • the nucleotide at position 171 is an adenine (A) (SEQ DD NO:44).
  • the amino acid at position 31 is glutamate (E)(SEQ ED NO:46)
  • the nucleotide at position 171 is a cytosine (C)(SEQ ED NO:88).
  • the amino acid at position 31 is aspartate (D)(SEQ DD NO:89)
  • the nucleotide at position 177 is adenine (A)(SEQ DD NO:44).
  • the amino acid at position 33 is glutamate (E)(SEQ DD NO:46).
  • the nucleotide at position 177 is cytosine (C)(SEQ DD NO:90). In this embodiment, the amino acid at position 33 is aspartate (D)(SEQ DD NO:91). In another embodiment of a nucleotide sequence of mouse TANGO 232, the nucleotide at position 180 is guanine (G)(SEQ DD NO:44). In this embodiment, the amino acid at position 34 is glutamate (E)(SEQ ED NO:46). In another embodiment of a nucleotide sequence of mouse TANGO 232, the nucleotide at position 180 is cytosine (C)(SEQ DD NO:92). In this embodiment, the amino acid at position 34 is aspartate (D)(SEQ DD NO:93).
  • mouse TANGO 232 includes a 19 amino acid signal peptide (amino acid 1 to about amino acid 19 of SEQ DD NO:46; SEQ ED NO:47) preceding the mature mouse TANGO 232 protein (corresponding to about amino acid 20 to amino acid 239 of SEQ DD NO:46; SEQ DD NO:48).
  • mouse TANGO 232 protein is a transmembrane protein that contains an extracellular domain at amino acid residues 20 to 192 of SEQ DD NO:46 (SEQ DD NO:49), a transmembrane domain at amino acid residues 193 to 216 of SEQ ED NO:46 (SEQ ED NO:50), and a cytoplasmic domain at amino acid residues 217 to 239 of SEQ DD NO:46 (SEQ DD NO:51).
  • a mouse TANGO 232 protein contains an extracellular domain at amino acid residues 217 to 239 of SEQ DD NO:46 ( SEQ DD NO:), a transmembrane domain at amino acid residues 193 to 216 of SEQ DD NO:46 (SEQ DD NO:), and a cytoplasmic domain at amino acid residues 1 to 192 of SEQ DD NO:46 (SEQ DD NO:).
  • In situ tissue screening was performed on mouse adult and embryonic tissue to analyze for the expression of mouse TANGO 232 mRNA. In summary, the embryonic signal pattern was suggestive of expression by developing muscle. Expression was observed in a layer just under the skin beginning at El 4.5.
  • This signal may be from the peritoneum.
  • a weak, multifocal signal which is predominately in the muscle portion of the bladder tissue.
  • a signal is observed in the labyrinth zone of the placenta. No expression was observed in the following tissues: Brain, spinal cord, eye and harderian gland, submandibular gland, white fat, brown fat, stomach, heart, lung, liver, kidney, adrenal gland, colon, small intestine, thymus, lymph node, spleen, pancreas, testes, and the ovaries.
  • the signal pattern was very similar to that observed at E16.5 with most of the thin muscle layers being positive thus outlining many major structures.
  • the small intestine was outlined indicating some smooth muscle expression.
  • PI.5 a signal in the region of the gut, heart, and head appears to have decreased.
  • a moderate signal was still observed just under the skin.
  • Human and murine TANGO 232 sequences exhibit considerable similarity at the protein, nucleic acid, and open reading frame levels.
  • An alignment (made using the ALIGN software ⁇ Myers and Miller (1989) CABIOS, ver. 2.0 ⁇ ; BLOSUM 62 scoring matrix; gap penalties -12/-4), reveals a protein identity of 68.8 % .
  • the human and murine TANGO 232 full length cDNAs are 69.1% identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
  • human and murine TANGO 232 are 72.6% identical.
  • TANGO 232 is expressed in subcutaneous adipose tissue
  • TANGO 232 polypeptides, nucleic acids, and modulators of TANGO 232 expression or activity can be useful for modulation of adipocyte function, e.g., fat metabolism.
  • Such molecules can also be used to treat disorders associated with abnormal fat metabolism, e.g., obesity, arteriosclerosis, or cachexia.
  • TANGO 232 nucleic acids, proteins, and modulators thereof can be used to modulate the proliferation, differentiation, and/or function of cells that form bone matrix, e.g., osteoblasts and osteoclasts, and can be used to modulate the formation of bone matrix.
  • TANGO 232 nucleic acids, proteins, and modulators thereof can be used to treat cartilage and bone associated diseases and disorders, and can play a role in bone growth, formation, and remodeling.
  • cartilage and bone associated diseases and disorders include e.g., bone cancer, achondroplasia, myeloma, fibrous dysplasia, scoliosis, osteoarthritis, osteosarcoma, and osteoporosis.
  • TANGO 232 exhibits weak homology to the F3 domain of Ephrin receptor and G- CSF receptor.
  • G-CSF is the major growth factor involved in the production of neutrophilic granulocytes.
  • G-CSF exerts its function via the activation of a membrane receptor that belongs to the super-family of hematopoietin receptors, also referred to as class I cytokine receptors.
  • TANGO 232 polypeptides, nucleic acids, and modulators of TANGO 232 expression or activity can be useful for modulation of the function of the G-CSF receptor in normal granulopoiesis.
  • TANGO 232 polypeptides, nucleic acids, and modulators of TANGO 232 expression or activity can be useful for modulation of G-CSF-induced STAT3 activation during basal granulopoiesis (low G-CSF) and "emergency" granulopoiesis (high G-CSF).
  • TANGO 232 polypeptides, nucleic acids, and modulators of TANGO 232 expression or activity can be useful for the modulation of diseases characterized by disturbed myeloid maturation such as severe congenital neutropenia and acute myeloblastic leukemia.
  • the TANGO 232 proteins, nucleic acids and/or modulators can be used for the treatment of a disorder characterized by aberrant TANGO 232 expression and/or an aberrant TANGO 232 activity, such as maturation signaling.
  • Tables 1 and 2 below provide summaries of TANGO 221, TANGO 222, TANGO 176, and TANGO 232 sequence information.
  • TABLE 1 Summary of Sequence Information of Human TANGO 221 , Human TANGO 222, Human TANGO 176, Mouse TANGO 176, Macaque TANGO 232, Human TANGO 232, and Mouse TANGO 232.
  • nucleic acid molecules that encode a polypeptide of the invention or a biologically active portion thereof, as well as nucleic acid molecules sufficient for use as hybridization probes to identify nucleic acid molecules encoding a polypeptide of the invention and fragments of such nucleic acid molecules suitable for use as PCR primers for the amplification or mutation of nucleic acid molecules.
  • nucleic acid molecule is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule can be single- stranded or double-stranded, but preferably is double-stranded DNA.
  • an “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule.
  • an “isolated” nucleic acid molecule is free of sequences (preferably protein encoding sequences) which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • the isolated nucleic acid molecule can contain less than about 5 kB, 4 kB, 3 kB, 2 kB, 1 kB, 0.5 kB or 0.1 kB of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
  • an "isolated" nucleic acid molecule such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • a nucleic acid molecule of the present invention e.g., a nucleic acid molecule having the nucleotide sequence of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, or a complement thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or a portion of the nucleic acid sequences of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45 as a hybridization probe, nucleic acid molecules of the invention can be isolated using standard hybridization and cloning techniques (e.g., as described in
  • a nucleic acid molecule of the invention can be amplified using cDNA, mRNA or genomic DNA as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • the nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • oligonucleotides corresponding to all or a portion of a nucleic acid molecule of the invention can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of the nucleotide sequence of
  • a nucleic acid molecule which is complementary to a given nucleotide sequence is one which is sufficiently complementary to the given nucleotide sequence that it can hybridize to the given nucleotide sequence thereby forming a stable duplex.
  • a nucleic acid molecule of the invention can comprise only a portion of a nucleic acid sequence encoding a full length polypeptide of the invention for example, a fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of a polypeptide of the invention.
  • the nucleotide sequence determined from the cloning one gene allows for the generation of probes and primers designed for use in identifying and/or cloning homologues in other cell types, e.g., from other tissues, as well as homologues from other mammals.
  • the probe/primer typically comprises substantially purified oligonucleotide.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12, preferably about 25, more preferably about 50, 75, 100, 125, 150, 175, 200, 250, 300, 350 or 400 consecutive nucleotides of the sense or anti-sense sequence of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, or of a naturally occurring mutant of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45.
  • Probes based on the sequence of a nucleic acid molecule of the invention can be used to detect transcripts or genomic sequences encoding the same protein molecule encoded by a selected nucleic acid molecule.
  • the probe comprises a label group attached thereto, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Such probes can be used as part of a diagnostic test kit for identifying cells or tissues which mis-express the protein, such as by measuring levels of a nucleic acid molecule encoding the protein in a sample of cells from a subject, e.g., detecting mRNA levels or determining whether a gene encoding the protein has been mutated or deleted.
  • a nucleic acid fragment encoding a "biologically active portion" of a polypeptide of the invention can be prepared by isolating a portion of any of SEQ DD NO:3, 8, 13, 18, 23, 31, 38, or 46, expressing the encoded portion of the polypeptide protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the polypeptide.
  • the invention further encompasses nucleic acid molecules that differ from the nucleotide sequence of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, due to degeneracy of the genetic code and thus encode the same protein as that encoded by the nucleotide sequence of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45.
  • DNA sequence polymorphisms that lead to changes in the amino acid sequence may exist within a population (e.g., the human population). Such genetic polymorphisms may exist among individuals within a population due to natural allelic variation.
  • An allele is one of a group of genes which occur alternatively at a given genetic locus.
  • TANGO 232 has been mapped to chromosome 11, between flanking markers Dl IS 1965 and WI- 1409, and therefore, TANGO 232 family members can include nucleotide sequence polymorphisms (e.g., nucleotide sequences that vary from SEQ DD NO: 39) that map to this chromosome 11 region (i.e., between markers Dl IS 1965 and WI-1409).
  • nucleotide sequence polymorphisms e.g., nucleotide sequences that vary from SEQ DD NO: 39
  • the phrase "allelic variant” refers to a nucleotide sequence which occurs at a given locus or to a n polypeptide encoded by the nucleotide sequence.
  • the terms "gene” and “recombinant gene” refer to nucleic acid molecules comprising an open reading frame encoding a polypeptide of the invention.
  • Such natural allelic variations can typically result in 1-5% variance in the nucleotide sequence of a given gene.
  • Alternative alleles can be identified by sequencing the gene of interest in a number of different individuals. This can be readily carried out by using hybridization probes to identify the same genetic locus in a variety of individuals. Any and all such nucleotide variations and resulting amino acid polymorphisms or variations that are the result of natural allelic variation and that do not alter the functional activity are intended to be within the scope of the invention.
  • nucleic acid molecules encoding proteins of the invention from other 0 species which have a nucleotide sequence which differs from that of the human protein described herein are intended to be within the scope of the invention.
  • Nucleic acid molecules corresponding to natural allelic variants and homologues of a cDNA of the invention can be isolated based on their identity to the human nucleic acid molecule disclosed herein using the human cDNAs, or a portion thereof, as a hybridization probe 5 according to standard hybridization techniques under stringent hybridization conditions.
  • a cDNA encoding a soluble form of a membrane-bound protein of the invention isolated based on its hybridization to a nucleic acid molecule encoding all or part of the membrane-bound form.
  • a cDNA encoding a membrane-bound form can be isolated based on its hybridization to a nucleic acid molecule encoding all or part of the soluble form.
  • an isolated nucleic acid molecule of the invention is at least 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, 650, 675, 700, 775, 800, 825, 850, 900, 950, 1000, 1,100, 1,150, 1200, 1250, or 1290) nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence, preferably the coding sequence, of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, or a complement thereof.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 60% (65%, 70%, preferably 75%) identical to each other typically remain hybridized to each other.
  • stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50-65°C.
  • an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ED NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, or a complement thereof, corresponds to a naturally-occurring nucleic acid molecule.
  • a "naturally- occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ ED NO:52, 54, and 56, which in particular hybridize to the human TANGO 221 sequences listed above (SEQ DD NOs:l and 2).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ DD NO:58, 60, and 62, which in particular hybridize to the human TANGO 222 sequences listed above (SEQ DD NOs:6 and 7).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ ED NO:64, 66, and 68, which in particular hybridize to the human TANGO 176 sequences listed above (SEQ LD NOs:l 1 and 12).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ DD NO:70, 72, and 74, which in particular hybridize to the mouse TANGO 176 sequences listed above (SEQ DD NOs:16 and 17).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ DD NOs:76, 78, and 80, which in particular hybridize to the macaque TANGO 232 sequences listed above (SEQ DD NOs:21 and 22).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ ED NO: 82, 84, and 86, which in particular hybridize to the human TANGO 232 sequences listed above (SEQ ED NOs:36 and 38).
  • Representative species that hybridize under such conditions to one or more of the sequences above include, but are not limited to, SEQ DD NO:88, 90, and 92, which in particular hybridize to the human TANGO 221 sequences listed above (SEQ DD NOs:44 and 45).
  • allelic variants of a nucleic acid molecule of the invention sequence that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation thereby leading to changes in the amino acid sequence of the encoded protein, without altering the biological activity of the protein. For example, one can make nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues.
  • a "non-essential” amino acid residue is a residue that can be altered from the wild-type sequence without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity.
  • amino acid residues that are not conserved or only semi-conserved among homologues of various species may be non-essential for activity and thus would be likely targets for alteration.
  • amino acid residues that are conserved among the homologues of various species e.g., murine and human
  • amino acid residues that are conserved among the homologues of various species may be essential for activity and thus would not be likely targets for alteration.
  • representative species of the amino acid residues that are not conserved or only semi-conserved among homologues of various species may be non-essential for activity and thus would be likely targets for alteration.
  • amino acid residues that are conserved among the homologues of various species e.g., murine and human
  • TANGO 221 presented for illustrative purposes only and not byway of limitation include but are not limited to, SEQ DD NOs:53, 55, and 55.
  • representative species of the TANGO 222 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ ED NOs:59, 61, and 63.
  • representative species of the human TANGO 176 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ ED NOs:65, 67, 69, and 55.
  • representative species of the mouse TANGO 176 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ DD NOs:71, 73, and 75.
  • representative species of the human TANGO 232 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ ED Nos:83, 85, and 87.
  • representative species of the mouse TANGO 232 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ DD NOs:89, 91, and 93.
  • nucleic acid molecules encoding a polypeptide of the invention that contain changes in amino acid residues that are not essential for activity. Such polypeptides differ in amino acid sequence from SEQ DD NO:3, 8, 13, 21, or 29, yet retain biological activity.
  • the isolated nucleic acid molecule includes a nucleotide sequence encoding a protein that includes an amino acid sequence that is at least about 45% identical, 65%, 75%, 85%, 95%, or 98% identical to the amino acid sequence of SEQ ED NO: 3, 8, 13, 21, or 29.
  • An isolated nucleic acid molecule encoding a variant protein can be created by introducing one or more nucleotide substitutions, additions or deletions into the nucleotide sequence of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45,
  • variant proteins retain or exhibit at least one structural or biological activity of the polypeptides of the invention.
  • Mutations can be introduced by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis.
  • conservative amino acid substitutions are made at one or more predicted non-
  • a "conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan,
  • mutations can be introduced randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for biological activity to identify mutants that retain activity.
  • the encoded protein can be expressed recombinantly and the activity of the protein can be determined.
  • a mutant polypeptide that is a variant of a polypeptide of the invention can be assayed for: (1) the ability to form proteimprotein interactions with 35 proteins in a signaling pathway of the polypeptide of the invention; (2) the ability to bind a ligand of the polypeptide of the invention; or (3) the ability to bind to an intracellular target protein of the polypeptide of the invention.
  • the mutant polypeptide can be assayed for the ability to modulate cellular proliferation, cellular migration or chemotaxis, or cellular differentiation.
  • the present invention encompasses antisense nucleic acid molecules, i.e., molecules which are complementary to a sense nucleic acid encoding a polypeptide of the invention, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid.
  • the antisense nucleic acid can be complementary to an entire coding strand, or to only a portion thereof, e.g., all or part of the protein coding
  • An antisense nucleic acid molecule can be antisense to all or part of a non-coding region of the coding strand of a nucleotide sequence encoding a polypeptide of the invention.
  • the non-coding regions (“5' and 3' untranslated regions") are the 5' and 3' sequences which flank the coding region and are not translated into amino acids. 15
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40,
  • An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • _ n can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5- fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4- acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5-carboxymethylaminomethyl-2- thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2- methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7- methylguanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D- mannosylqueosine, 5'-
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
  • the antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a selected polypeptide of the invention to thereby inhibit expression, e.g., by inhibiting transcription and/or translation.
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site.
  • antisense nucleic acid molecules can be modified to target selected cells and then administered systemically.
  • antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens.
  • the antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol D or pol DI promoter are preferred.
  • An antisense nucleic acid molecule of the invention can be an a-anomeric nucleic acid molecule.
  • An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual beta-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids Res. 15:6625-6641).
  • the antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region.
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585- 591)
  • a ribozyme having specificity for a nucleic acid molecule encoding a polypeptide of the invention can be designed based upon the nucleotide sequence of a cDNA disclosed herein.
  • a derivative of a Tetrahymena L-19 INS R ⁇ A can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a Cech et al. U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742.
  • an mRNA encoding a polypeptide of the invention can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel and Szostak (1993) Science 261:1411-1418.
  • the invention also encompasses nucleic acid molecules which form triple helical structures.
  • expression of a polypeptide of the invention can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the gene encoding the polypeptide (e.g., the promoter and/or enhancer) to form triple helical structures that prevent transcription of the gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the gene encoding the polypeptide e.g., the promoter and/or enhancer
  • the nucleic acid molecules of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule.
  • the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al. (1996) Bioorganic & Medicinal Chemistry 4(1): 5-23).
  • peptide nucleic acids refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained.
  • the neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength.
  • the synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al. (1996), supra; Perry-O'Keefe et al. (1996) Proc. Natl. Acad. Sci. USA 93: 14670-675.
  • PNAs can be used in therapeutic and diagnostic applications.
  • PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g., inducing transcription or translation arrest or inhibiting replication.
  • PNAs can also be used, e.g., in the analysis of single base pair mutations in a gene by, e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., SI nucleases (Hyrup (1996), supra; or as probes or primers for DNA sequence and hybridization (Hyrup (1996), supra; Perry-O'Keefe et al. (1996) Proc. Natl. Acad. Sci.
  • PNAs can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art.
  • PNA-DNA chimeras can be generated which may combine the advantageous properties of PNA and DNA.
  • Such chimeras allow DNA recognition enzymes, e.g., RNAse H and DNA polymerases, to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity.
  • PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996), supra).
  • the synthesis of PNA-DNA chimeras can be performed as described in Hyrup (1996), supra, and Finn et al. (1996) Nucleic Acids Res. 24(17):3357-63.
  • a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs.
  • chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser et al. (1975)
  • the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA
  • oligonucleotides can be modified with hybridization-triggered cleavage agents (see, e.g., Krol et al. (1988) Bio/Techniques 6:958-976) or intercalating agents (see, e.g., Zon (1988) Pharm. Res. 5:539-549).
  • the oligonucleotide may be conjugated to another molecule, e.g., a peptide, hybridization triggered cross-linking agent, transport agent, hybridization-triggered cleavage agent, etc.
  • One aspect of the invention pertains to isolated proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise antibodies directed against a polypeptide of the invention.
  • the native polypeptide can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques.
  • polypeptides of the invention are produced by recombinant DNA techniques.
  • a polypeptide of the invention can be synthesized chemically using standard peptide synthesis techniques.
  • an “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the protein is derived, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • protein that is substantially free of cellular material includes preparations of protein having less than about 30%, 20%, 10%, or 5% (by dry weight) of heterologous protein (also referred to herein as a "contaminating protein").
  • the protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • culture medium represents less than about 20%, 10%, or 5% of the volume of the protein preparation.
  • the protein is produced by chemical synthesis, it is preferably substantially free of chemical precursors or other chemicals, i.e., it is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.
  • preparations of the protein have less than about 30%, 20%, 10%, 5% (by dry weight) of chemical precursors or compounds other than the polypeptide of interest.
  • Biologically active portions of a polypeptide of the invention include polypeptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence of the protein (e.g., the amino acid sequence shown in any of SEQ DD NO:3, 8, 13, 18, 23, 31, 38, or 46), which include fewer amino acids than the full length protein, and exhibit at least one activity of the corresponding full-length protein.
  • biologically active portions comprise a domain or motif with at least one activity of the corresponding protein.
  • a biologically active portion of a protein of the invention can be a polypeptide _ n which is, for example, 10, 25, 50, 100 or more amino acids in length.
  • other biologically active portions, in which other regions of the protein are deleted can be prepared by recombinant techniques and evaluated for one or more of the functional activities of the native form of a polypeptide of the invention.
  • Preferred polypeptides have the amino acid sequence of SEQ DD NO:3, 8, 13, 18, 23, 35 31, 38, or 46.
  • Other useful proteins are substantially identical (e.g., at least about 45%, preferably 55%, 65%, 75%, 85%, 95%, or 99%) to any of SEQ ED NO:3, 8, 13, 18, 23, 31, 38, or 46 and retain the functional activity of the protein of the corresponding naturally- occurring protein yet differ in amino acid sequence due to natural allelic variation or mutagenesis.
  • the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino or nucleic acid sequence).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position.
  • the determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • a preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and
  • Gapped BLAST can be utilized as described in Altschul et al. (1997)
  • PSI-Blast can be used to perform an iterated search which detects distant relationships between molecules (Id.).
  • the percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, only exact matches are counted.
  • a "chimeric protein” or “fusion protein” comprises all or part (preferably biologically active) of a polypeptide of the invention operably linked to a heterologous polypeptide (i.e., a polypeptide other than the same polypeptide of the invention).
  • a heterologous polypeptide i.e., a polypeptide other than the same polypeptide of the invention.
  • the term "operably linked” is intended to indicate that the polypeptide of the invention and the heterologous polypeptide are fused in-frame to each other.
  • the heterologous polypeptide can be fused to the N-terminus or C-terminus of the polypeptide of the invention.
  • One useful fusion protein is a GST fusion protein in which the polypeptide of the invention is fused to the C-terminus of GST sequences. Such fusion proteins can facilitate the purification of a recombinant polypeptide of the invention.
  • the fusion protein contains a heterologous signal sequence at its N-terminus.
  • the native signal sequence of a polypeptide of the invention can be removed and replaced with a signal sequence from another protein.
  • the gp67 secretory sequence of the baculovirus envelope protein can be used as a heterologous signal sequence (Current Protocols in Molecular Biology, Ausubel et al, eds., John Wiley & Sons, 1992).
  • Other examples of eukaryotic heterologous signal sequences include the secretory sequences of melittin and human placental alkaline phosphatase (Stratagene; La Jolla, California).
  • useful prokaryotic heterologous signal sequences include the phoA secretory signal (Sambrook et al., supra) and the protein A secretory signal (Pharmacia Biotech; Piscataway, New Jersey).
  • the fusion protein is an immunoglobulin fusion protein in which all or part of a polypeptide of the invention is fused to sequences derived from a member of the immunoglobulin protein family.
  • the immunoglobulin fusion proteins of the invention can be inco ⁇ orated into pharmaceutical compositions and administered to a subject to inhibit an interaction between a ligand (soluble or membrane-bound) and a protein on the surface of a cell (receptor), to thereby suppress signal transduction in vivo.
  • the immunoglobulin fusion protein can be used to affect the bioavailability of a cognate ligand of a polypeptide of the invention. Inhibition of ligand/receptor interaction may be useful therapeutically, both for treating proliferative and differentiative disorders and for modulating (e.g., promoting or inhibiting) cell survival.
  • the immunoglobulin fusion proteins of the invention can be used as immunogens to produce antibodies directed against a polypeptide of the invention in a subject, to purify ligands and in screening assays to identify molecules which inhibit the interaction of receptors with ligands.
  • Chimeric and fusion proteins of the invention can be produced by standard recombinant DNA techniques.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
  • PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, e.g., Ausubel et al., supra).
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • a nucleic acid encoding a polypeptide of the invention can be cloned into such an expression vector such that the fusion moiety is linked in- frame to the polypeptide of the invention.
  • a signal sequence of a polypeptide of the invention can be used to facilitate secretion and isolation of the secreted protein or other proteins of interest.
  • Signal sequences are typically characterized by a core of hydrophobic
  • ⁇ amino acids which are generally cleaved from the mature protein during secretion in one or more cleavage events.
  • Such signal peptides contain processing sites that allow cleavage of the signal sequence from the mature proteins as they pass through the secretory pathway.
  • the invention pertains to the described polypeptides having a signal sequence, as well as to the signal sequence itself and to the polypeptide in the absence of the signal sequence (i.e., the cleavage products).
  • a nucleic acid sequence encoding a signal sequence of the invention can be operably linked in an expression vector to a protein of interest, such as a protein which is ordinarily not secreted or is otherwise difficult to isolate.
  • the signal sequence directs secretion of the protein, such as from a eukaryotic host into which the expression vector is transformed, and the signal sequence is subsequently or n concurrently cleaved.
  • the protein can then be readily purified from the extracellular medium by art recognized methods.
  • the signal sequence can be linked to the protein of interest using a sequence which facilitates purification, such as with a GST domain.
  • the signal sequences of the present invention can be used to 5 identify regulatory sequences, e.g., promoters, enhancers, repressors. Since signal sequences are the most amino-terminal sequences of a peptide, it is expected that the nucleic acids which flank the signal sequence on its amino-terminal side will be regulatory sequences which affect transcription. Thus, a nucleotide sequence which encodes all or a portion of a signal sequence can be used as a probe to identify and isolate signal sequences and their flanking regions, and these flanking regions can be studied to identify regulatory elements therein.
  • regulatory sequences e.g., promoters, enhancers, repressors.
  • the present invention also pertains to variants of the polypeptides of the invention.
  • variants have an altered amino acid sequence which can function as either agonists (mimetics) or as antagonists.
  • Variants can be generated by mutagenesis, e.g., discrete point mutation or truncation.
  • An agonist can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of the protein.
  • An antagonist of a protein can inhibit one or more of the activities of the naturally occurring form of the protein by, for example, competitively binding to a downstream or upstream member of a cellular signaling cascade which includes the protein of interest.
  • specific biological effects can be elicited by treatment with a variant of limited function. Treatment of a subject with a variant having a subset of the biological activities of the naturally occurring form of the protein can have fewer side effects in a subject relative to treatment with the naturally occurring form of the protein.
  • Variants of a protein of the invention which function as either agonists (mimetics) or as antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of the protein of the invention for agonist or antagonist activity.
  • a variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library.
  • a variegated library of variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential protein sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display).
  • methods which can be used to produce libraries of potential variants of the polypeptides of the invention from a degenerate oligonucleotide sequence. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang (1983) Tetrahedron 39:3; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477).
  • libraries of fragments of the coding sequence of a polypeptide of the invention can be used to generate a variegated population of polypeptides for screening and subsequent selection of variants.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of the coding sequence of interest with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with SI nuclease, and ligating the resulting fragment library into an expression vector.
  • an expression library can be derived which encodes N-terminal and internal fragments of various sizes of the protein of interest.
  • An isolated polypeptide of the invention, or a fragment thereof, can be used as an immunogen to generate antibodies using standard techniques for polyclonal and monoclonal antibody preparation.
  • the full-length polypeptide or protein can be used or, alternatively, the invention provides antigenic peptide fragments for use as immunogens.
  • the antigenic peptide of a protein of the invention comprises at least 8 (preferably 10, 15, 20, or 30) amino acid residues of the amino acid sequence of SEQ ED NO:3, 8, 13, 18, 23, 31, 38, or
  • Preferred epitopes encompassed by the antigenic peptide are regions that are located on the surface of the protein, e.g., hydrophilic regions.
  • Figures 2, 4, 6, and 8 are hydropathy plots of the proteins of the invention. These plots or similar analyses can be used to identify hydrophilic regions.
  • An immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal).
  • a suitable subject e.g., rabbit, goat, mouse or other mammal.
  • An appropriate immunogenic preparation can contain, for example, recombinantly expressed or chemically synthesized polypeptide.
  • the preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent.
  • antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds an antigen, such as a polypeptide of the invention, e.g., an epitope of a polypeptide of the invention.
  • a molecule which specifically binds to a given polypeptide of the invention is a molecule which binds the polypeptide, but does not substantially bind other molecules in a sample, e.g., a biological sample, which naturally contains the polypeptide.
  • immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin.
  • the invention provides polyclonal and monoclonal antibodies.
  • the term "monoclonal antibody” or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope.
  • Polyclonal antibodies can be prepared as described above by immunizing a suitable subject with a polypeptide of the invention as an immunogen.
  • 9 ⁇ antibody compositions are ones that have been selected for antibodies directed against a polypeptide or polypeptides of the invention.
  • Particularly preferred polyclonal antibody preparations are ones that contain only antibodies directed against a polypeptide or polypeptides of the invention.
  • Particularly preferred immunogen compositions are those that contain no other human proteins such as, for example, immunogen compositions made
  • the antibody titer in the immunized subject can be monitored over time by standard 30 techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized polypeptide.
  • ELISA enzyme linked immunosorbent assay
  • the antibody molecules can be isolated from the mammal (e.g., from the blood) and further purified by well-known techniques, such as protein A chromatography to obtain the IgG fraction.
  • antibodies specific for a protein or polypeptide of the invention can be selected for (e.g. , partially purified) or 35 purified by, e.g., affinity chromatography.
  • a recombinantly expressed and purified (or partially purified) protein of the invention is produced as described herein, and covalently or non-covalently coupled to a solid support such as, for example, a chromatography column.
  • the column can then be used to affinity purify antibodies specific for the proteins of the invention from a sample containing antibodies directed against a large number of different epitopes, thereby generating a substantially purified antibody composition, i.e., one that is substantially free of contaminating antibodies.
  • a substantially purified antibody composition is meant, in this context, that the antibody sample contains at most only 30% (by dry weight) of contaminating antibodies directed against epitopes other than those on the desired protein or polypeptide of the invention, and preferably at most 20%, yet more preferably at most 10%, and most preferably at most 5% 0 (by dry weight) of the sample is contaminating antibodies.
  • a purified antibody composition means that at least 99% of the antibodies in the composition are directed against the desired protein or polypeptide of the invention.
  • antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497, the human B cell hybridoma technique (Kozbor et al. (1983) Immunol. Today 4:72), the EBN-hybridoma technique (Cole et al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques.
  • the technology for producing hybridomas is well known (see generally 0
  • Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind the polypeptide of interest, e.g., using a standard ELISA assay.
  • a monoclonal antibody directed against a polypeptide of the invention can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with the polypeptide of interest.
  • Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Display Kit, Catalog No. 240612).
  • examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, U.S. Patent No. 5,223,409; PCT Publication No. WO 92/18619; PCT Publication No. WO 91/17271; PCT Publication No. WO 92/20791; PCT Publication No. WO
  • recombinant antibodies such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
  • a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region. (See, e.g., Cabilly et al., U.S. Patent No. 4,816,567; and Boss et al., U.S. Patent No.
  • Humanized antibodies are antibody molecules from non-human species having one or more complementarily determining regions (CDRs) from the non-human species and a framework region from a human immunoglobulin molecule.
  • CDRs complementarily determining regions
  • Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in PCT Publication No. WO 87/02671; European Patent Application 184,187; European Patent Application 171,496; European Patent Application 173,494; PCT Publication No. WO 86/01533; U.S. Patent No. 4,816,567; European Patent Application 125,023; Better et al. (1988) Science
  • Fully human antibodies are particularly desirable for therapeutic treatment of human patients.
  • Such antibodies can be produced, for example, using transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chains genes, but which can express human heavy and light chain genes.
  • the transgenic mice are immunized in the normal fashion with a selected antigen, e.g., all or a portion of a polypeptide of the invention.
  • Monoclonal antibodies directed against the antigen can be obtained using conventional hybridoma technology.
  • the human immunoglobulin transgenes harbored by the transgenic mice rearrange during B cell differentiation, and subsequently undergo class switching and somatic mutation. Thus, using such a technique, it is possible to produce therapeutically useful IgG, IgA and IgE antibodies.
  • Completely human antibodies which recognize a selected epitope can be generated using a technique referred to as "guided selection.”
  • a selected non-human monoclonal antibody e.g., a mouse antibody, is used to guide the selection of a completely human antibody recognizing the same epitope.
  • An antibody directed against a polypeptide of the invention can be used to isolate the polypeptide by standard techniques, such as affinity chromatography or immunoprecipitation. Moreover, such an antibody can be used to detect the protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the polypeptide.
  • the antibodies can also be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance.
  • detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • bioluminescent materials include luciferase, luciferin, and aequorin, and
  • suitable radioactive material include 125 ⁇ 131 ⁇ 35 ⁇ or 3JJ.
  • an antibody can be conjugated to a therapeutic moiety such as a cytotoxin, a therapeutic agent or a radioactive metal ion.
  • a cytotoxin or cytotoxic agent includes any agent that is detrimental to cells. Examples include taxol, cytochalasin B, gramicidin D, ethidium bromide, emetine, mitomycin, etoposide, tenoposide, vincristine, vinblastine, colchicin, doxorubicin, daunorubicin, dihydroxy anthracin dione, mitoxantrone, mithramycin, actinomycin D, 1-dehydrotestosterone, glucocorticoids, procaine, tetracaine, lidocaine, propranolol, and puromycin and analogs or homologs thereof.
  • Therapeutic agents include, but are not limited to, antimetabolites (e.g., methotrexate, 6-mercaptopurine, 6- thioguanine, cytarabine, 5-fluorouracil decarbazine), alkylating agents (e.g., mechlorethamine, thioepa chlorambucil, melphalan, carmustine (BSNU) and lomustine (CCNU), cyclothosphamide, busulfan, dibromomannitol, streptozotocin, mitomycin C, and cis-dichlorodiamine platinum (D) (DDP) cisplatin), anthracyclines (e.g., daunorubicin (formerly daunomycin) and doxorubicin), antibiotics (e.g. , dactinomycin (formerly actinomycin), bleomycin, mithramycin, and anthramycin (AMC)), and anti-mitotic agents (e.g
  • the drug moiety is not to be construed as limited to classical chemical therapeutic agents.
  • the drug moiety may be a protein or polypeptide possessing a desired biological activity.
  • proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, .alpha. - interferon, .beta.
  • -interferon nerve growth factor, platelet derived growth factor, tissue plasminogen activator; or, biological response modifiers such as, for example, lymphokines, interleukin- 1 ("E -1"), interleukin-2 ("IL-2”), interleukin-6 (“IL-6”), granulocyte macrophase colony stimulating factor (“GM-CSF”), granulocyte colony stimulating factor
  • E -1 interleukin- 1
  • IL-2 interleukin-2
  • IL-6 interleukin-6
  • GM-CSF granulocyte macrophase colony stimulating factor
  • GM-CSF granulocyte colony stimulating factor
  • G-CSF G-CSF
  • Monoclonal Antibodies '84 Biological And Clinical Applications, Pinchera et al. (eds.), pp.
  • an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in U.S. Patent No. 4,676,980.
  • the invention provides substantially purified antibodies or fragment thereof, and non-human antibodies or fragments thereof, which antibodies or fragments specifically bind to a polypeptide comprising an amino acid sequence selected from the group consisting of: the amino acid sequence of any one of SEQ DD NO:3, 8, 13,
  • the percent identity is determined using the ALIGN program of the GCG software package with a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4; and an amino acid sequence which is encoded by a nucleic acid molecule which hybridizes to the nucleic acid molecule consisting of any one of SEQ ED NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45, or the cDNA of a clone deposited
  • the substantially purified antibodies of the invention, or fragments thereof can be human, non-human, chimeric and/or humanized antibodies.
  • the invention provides non-human antibodies or fragments thereof, which antibodies or fragments specifically bind to a polypeptide comprising an amino acid sequence selected from the group consisting of: the amino acid sequence of any one of SEQ DD NO:3, 8, 13, 18, 23, 31, 38, or 46, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC Accession No. 207044, 207043, 207042,
  • nucleic acid molecule which hybridizes to the nucleic acid molecule consisting of any one of SEQ DD NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45 , or the cDNA of a clone deposited as any of ATCC Accession No. 207044, 207043, 207042, 207045, and 207046, respectively, or a complement thereof, under conditions of
  • non-human antibodies can be goat, mouse, sheep, horse, chicken, rabbit, or rat antibodies.
  • non-human antibodies of the invention can be chimeric and/or humanized antibodies.
  • the non-human antibodies of the invention can be polyclonal antibodies or monoclonal antibodies.
  • the invention provides monoclonal antibodies or fragments thereof, which antibodies or fragments specifically bind to a polypeptide comprising an amino acid sequence selected from the group consisting of: the amino acid sequence of any one of SEQ DD NO:3, 8, 13, 18, 23, 31, 38, or 46, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC Accession No.
  • the substantially purified antibodies or fragments thereof, the non-human antibodies or fragments thereof, and/or the monoclonal antibodies or fragments thereof, of the invention specifically bind to an extracellular domain of the amino acid sequence of SEQ DD NOs:25, 32, 40, and 48.
  • the extracellular domain to which the antibody, or fragment thereof, binds comprises from about amino acids 23 to 194 of SEQ DD NO:25 (SEQ DD NO:26), from about amino acid residues 1 to 78 of SEQ DD NO: 32 (SEQ DD NO: 33), from about amino acids 23 to 194 of SEQ DD NO:40 (SEQ DD NO:41) and from about amino acids 20 to 192 of SEQ DD NO:48 (SEQ DD NO:49).
  • any of the antibodies of the invention can be conjugated to a therapeutic moiety or to a detectable substance.
  • detectable substances that can be conjugated to the antibodies of the invention are an enzyme, a prosthetic group, a fluorescent material, a luminescent material, a bioluminescent material, and a radioactive material.
  • the invention also provides a kit containing an antibody of the invention conjugated to a detectable substance, and instructions for use.
  • Still another aspect of the invention is a pharmaceutical composition comprising an antibody of the invention and a pharmaceutically acceptable carrier.
  • the pharmaceutical composition contains an antibody of the invention, a therapeutic moiety, and a pharmaceutically acceptable carrier.
  • Still another aspect of the invention is a method of making an antibody that specifically recognizes TANGO 221, TANGO 222, TANGO 176, and TANGO 232, the method comprising immunizing a mammal with a polypeptide.
  • the polypeptide used as an immungen comprises an amino acid sequence selected from the group consisting of: the amino acid sequence of any one of SEQ DD NO:3, 8, 13, 18, 23, 31, 38, or 46, or an amino ⁇ acid sequence encoded by the cDNA of a clone deposited as any of ATCC Accession No.
  • a sample is collected from the mammal that contains an antibody that specifically recognizes GPVI.
  • the polypeptide is recombinantly produced using a non-human host cell.
  • the antibodies can be further purified Q from the sample using techniques well known to those of skill in the art.
  • the method can further comprise producing a monoclonal antibody-producing cell from the cells of the mammal.
  • antibodies are collected from the antibody-producing cell.
  • vectors preferably expression vectors, containing a nucleic acid encoding a polypeptide of the invention (or a portion thereof).
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • expression vectors are capable of directing the expression of genes to which they are operably linked.
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids (vectors).
  • the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
  • the recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell.
  • the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operably linked to the nucleic acid sequence to be expressed.
  • "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription translation system or in a host cell when the vector is introduced into the host cell).
  • regulatory sequence is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cell and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, etc.
  • the expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein.
  • the recombinant expression vectors of the invention can be designed for expression of a polypeptide of the invention in prokaryotic (e.g., E. coli) or eukaryotic cells (e.g., insect cells (using baculovirus expression vectors), yeast cells or mammalian cells). Suitable host cells are discussed further in Goeddel, supra.
  • the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase.
  • Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein.
  • Such fusion vectors typically serve three pu ⁇ oses: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification.
  • a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein.
  • enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Ine; Smith and Johnson (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.
  • GST glutathione S-transferase
  • suitable inducible non-fusion E. coli expression vectors include pTrc
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid t ⁇ -lac fusion promoter.
  • Target gene expression from the pET l id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident ⁇ prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.
  • One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128).
  • Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al. (1992) Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • the expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S. cerivisae include pYepSecl (Baldari et al. (1987) EMBOJ. 6:229-234), pMFa (Kurian and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al. (1987) Gene 54:113-123), pYES2 (Invitrogen Co ⁇ oration, San Diego, CA), and pPicZ (Invitrogen Co ⁇ , San Diego, CA).
  • the expression vector is a baculovirus expression vector.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al. ( 1983) Mol Cell Biol. 3 :2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
  • a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector.
  • mammalian expression vectors include pCDM8 (Seed (1987) Nature 329:840) and pMT2PC (Kaufman et al. (1987) EMBOJ. 6:187-195).
  • the expression vector's control functions are often provided by viral regulatory elements.
  • commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook et al., supra.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235- 275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J.
  • promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the ⁇ -fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
  • the invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operably linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to the mRNA encoding a polypeptide of the invention.
  • Regulatory sequences operably linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA.
  • the antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced.
  • a high efficiency regulatory region the activity of which can be determined by the cell type into which the vector is introduced.
  • host cell and "recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • a host cell can be any prokaryotic (e.g., E. coli) or eukaryotic cell (e.g., insect cells, yeast or mammalian cells).
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid into a host cell, including calcium phosphate or calcium chloride co- precipitation, DEAE-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (supra), and other laboratory manuals.
  • a gene that encodes a selectable marker (e.g., for resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
  • selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate.
  • Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have inco ⁇ orated the selectable marker gene will survive, while the other cells die).
  • an endogenous nucleic acid within a cell, cell line or microorganism may be modified by inserting a DNA regulatory element heterologous to the endogenous gene of interest into the genome of a cell, stable cell line or cloned microorganism such that the inserted regulatory element is operatively linked with the endogenous gene (e.g., TANGO 221, TANGO 222 , TANGO 176, and TANGO 232) and controls, modulates or activates the endogenous gene.
  • a DNA regulatory element heterologous to the endogenous gene of interest into the genome of a cell, stable cell line or cloned microorganism such that the inserted regulatory element is operatively linked with the endogenous gene (e.g., TANGO 221, TANGO 222 , TANGO 176, and TANGO 232) and controls, modulates or activates the endogenous gene.
  • endogenous TANGO 221, TANGO 222 , TANGO 176, and TANGO 232 which are normally "transcriptionally silent", i.e., TANGO 221, TANGO 222 , TANGO 176, and TANGO 232 genes which are normally not expressed, or are expressed only at very low levels in a cell line or microorganism, may be activated by inserting a regulatory element which is capable of promoting the expression of a normally expressed gene product in that cell line or microorganism.
  • transcriptionally silent, endogenous TANGO 221, TANGO 222 , TANGO 176, and TANGO 232 genes may be activated by insertion of a promiscuous regulatory element that works across cell types.
  • a heterologous regulatory element may be inserted into a stable cell line or cloned microorganism, such that it is operatively linked with and activates expression of endogenous TANGO 221, TANGO 222 , TANGO 176, and TANGO 232 genes, using techniques, such as targeted homologous recombination, which are well known to those of skill in the art, and described e.g., in Chappel, U.S. Patent No. 5,272,071; PCT publication No. WO 91/06667, published May 16, 1991.
  • a host cell of the invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce a polypeptide of the invention. Accordingly, the invention further provides methods for producing a polypeptide of the invention using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding a polypeptide of the invention has been introduced) in a suitable medium such that the polypeptide is produced. In another embodiment, the method further comprises isolating the polypeptide from the medium or the host cell.
  • the host cells of the invention can also be used to produce nonhuman transgenic animals.
  • a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which a sequences encoding a polypeptide of the invention have been introduced.
  • Such host cells can then be used to create non-human transgenic animals in which exogenous sequences encoding a polypeptide of the invention have been introduced into their genome or homologous recombinant animals in which endogenous encoding a polypeptide of the invention sequences have been altered.
  • Such animals are useful for studying the function and/or activity of the polypeptide and for identifying and/or evaluating modulators of polypeptide activity.
  • a "transgenic animal” is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.
  • Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, etc.
  • a transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal.
  • an "homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
  • a transgenic animal of the invention can be created by introducing nucleic acid encoding a polypeptide of the invention (or a homologue thereof) into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal.
  • Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene.
  • a tissue-specific regulatory sequence(s) can be operably linked to the transgene to direct expression of the polypeptide of the invention to particular cells.
  • transgenic founder animal can be identified based upon the presence of the transgene in its genome and/or expression of mRNA encoding the transgene in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying the transgene can further be bred to other transgenic animals carrying other transgenes.
  • a vector which contains at least a portion of a gene encoding a polypeptide of the invention into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the gene.
  • the vector is designed such that, upon homologous recombination, the endogenous gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector).
  • the vector can be designed such that, upon homologous recombination, the endogenous gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous protein).
  • the altered portion of the gene is flanked at its 5' and 3' ends by additional nucleic acid of the gene to allow for homologous recombination to occur between the exogenous gene carried by the vector and an endogenous gene in an embryonic stem cell.
  • the additional flanking nucleic acid sequences are of sufficient length for successful homologous recombination with the endogenous gene.
  • flanking DNA both at the 5' and 3' ends
  • flanking DNA both at the 5' and 3' ends
  • the vector is introduced into an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced gene has homologously recombined with the endogenous gene are selected (see, e.g., Li et al. (1992) Cell 69:915).
  • the selected cells are then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see, e.g., Bradley in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, ed. (IRL, Oxford, 1987) pp. 113-152).
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term.
  • Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene.
  • transgenic non-human animals can be produced which contain selected systems which allow for regulated expression of the transgene.
  • a system is the cre/loxP recombinase system of bacteriophage PI.
  • cre/loxP recombinase system of bacteriophage PI.
  • FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251 :1351-1355.
  • mice containing transgenes encoding both the Cre recombinase and a selected protein are required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut et al. (1997) Nature 385:810-813 and PCT Publication NOS. WO 97/07668 and WO 97/07669.
  • nucleic acid molecules also referred to herein as antibodies
  • compositions suitable for administration can be inco ⁇ orated into pharmaceutical compositions suitable for administration.
  • compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and abso ⁇ tion delaying agents, and the like, compatible with pharmaceutical administration.
  • the invention includes methods for preparing pharmaceutical compositions for modulating the expression or activity of a polypeptide or nucleic acid of the invention. Such methods comprise formulating a pharmaceutically acceptable carrier with an agent which modulates expression or activity of a polypeptide or nucleic acid of the invention. Such compositions can further include additional active agents. Thus, the invention further includes methods for preparing a pharmaceutical composition by formulating a pharmaceutically acceptable carrier with an agent which modulates expression or activity of a polypeptide or nucleic acid of the invention and one or more addtional active compounds.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g., intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELO (BASF; Parsippany, NJ) or phosphate buffered saline (PBS).
  • the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, sodium chloride in the composition.
  • Prolonged abso ⁇ tion of the injectable compositions can be brought about by including in the composition an agent which delays abso ⁇ tion, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by inco ⁇ orating the active compound (e.g., a polypeptide or antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by inco ⁇ orating the active compound into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the pu ⁇ ose of oral therapeutic administration, the active compound can be inco ⁇ orated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed.
  • compositions can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art.
  • the materials can also be obtained commercially from Alza Co ⁇ oration and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811. 15
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to
  • the preferred dosage is 0.1 mg/kg to 100 mg/kg of body weight
  • lipidation can be used to stabilize antibodies and to enhance uptake and tissue penetration (e.g., into the brain).
  • a method for lipidation of antibodies is described by Cruikshank et al. ((1997) J. Acquired Immune Deficiency Syndromes and Human Retrovirology 14:193).
  • the nucleic acid molecules of the invention can be inserted into vectors and used as 35 gene therapy vectors.
  • Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (U.S. Patent 5,328,470) or by stereotactic injection (see, e.g., Chen et al. (1994) Proc. Natl Acad. Sci. USA 91:3054-3057).
  • the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
  • the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
  • compositions can be included in a container, pack, or dispenser together with instructions for administration.
  • the nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: a) screening assays; b) detection assays (e.g., chromosomal mapping, tissue typing, forensic biology); c) predictive medicine (e.g., diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenomics); and d) methods of treatment (e.g., therapeutic and prophylactic).
  • the TANGO 221, TANGO 222, TANGO 176, and TANGO 232 polypeptides of the invention can to used to modulate cellular function, survival, mo ⁇ hology, proliferation, and/or differentiation of the cells in which they are expressed.
  • the isolated nucleic acid molecules of the invention can be used to express proteins (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect mRNA (e.g., in a biological sample) or a genetic lesion, and to modulate activity of a polypeptide of the invention.
  • the polypeptides of the invention can be used to screen drugs or compounds which modulate activity or expression of a polypeptide of the invention as well as to treat disorders characterized by insufficient or excessive production of a protein of the invention or production of a form of a protein of the invention which has decreased or aberrant activity compared to the wild type protein.
  • the antibodies of the invention can be used to detect and isolate a protein of the and modulate activity of a protein of the invention.
  • This invention further pertains to novel agents identified by the above-described screening assays and uses thereof for treatments as described herein.
  • the invention provides a method (also referred to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to polypeptide of the invention or have a stimulatory or inhibitory effect on, for example, expression or activity of a polypeptide of the invention.
  • modulators i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to polypeptide of the invention or have a stimulatory or inhibitory effect on, for example, expression or activity of a polypeptide of the invention.
  • the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of the membrane-bound form of a polypeptide of the invention or biologically active portion thereof.
  • the test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the "one-bead one-compound” library method; and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non- peptide oligomer or small molecule libraries of compounds (Lam (1997) Anticancer Drug Des. 12:145).
  • an assay is a cell-based assay in which a cell which expresses a membrane-bound form of a polypeptide of the invention, or a biologically active portion thereof, on the cell surface is contacted with a test compound and the ability of the test compound to bind to the polypeptide determined.
  • the cell for example, can be a yeast cell or a cell of mammalian origin. Determining the ability of the test compound to bind to the polypeptide can be accomplished, for example, by coupling the test compound with a radioisotope or enzymatic label such that binding of the test compound to the polypeptide or biologically active portion thereof can be determined by detecting the labeled compound in a complex.
  • test compounds can be labeled with 125 1, 35 S, 14 C, or 3 H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting.
  • test compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.
  • the assay comprises contacting a cell which expresses a membrane- bound form of a polypeptide of the invention, or a biologically active portion thereof, on the cell surface with a known compound which binds the polypeptide to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the polypeptide, wherein determining the ability of the test compound to interact with the polypeptide comprises determining the ability of the test compound to preferentially bind to the polypeptide or a biologically active portion thereof as compared to the known compound.
  • an assay is a cell-based assay comprising contacting a cell expressing a membrane-bound form of a polypeptide of the invention, or a biologically active portion thereof, on the cell surface with a test compound and determining the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the polypeptide or biologically active portion thereof. Determining the ability of the test compound to modulate the activity of the polypeptide or a biologically active portion thereof can be accomplished, for example, by determining the ability of the polypeptide protein to bind to or interact with a target molecule.
  • a target molecule is a molecule with which a selected polypeptide (e.g., a polypeptide of the invention binds or interacts with in nature, for example, a molecule on the surface of a cell which expresses the selected protein, a molecule on the surface of a second cell, a molecule in the extracellular milieu, a molecule associated with the internal surface of a cell membrane or a cytoplasmic molecule.
  • a target molecule can be a polypeptide of the invention or some other polypeptide or protein.
  • a target molecule can be a component of a signal transduction pathway which facilitates transduction of an extracellular signal (e.g., a signal generated by binding of a compound to a polypeptide of the invention) through the cell membrane and into the cell or a second intercellular protein which has catalytic activity or a protein which facilitates the association of downstream signaling molecules with a polypeptide of the invention. Determining the ability of a polypeptide of the invention to bind to or interact with a target molecule can be accomplished by determining the activity of the target molecule.
  • an extracellular signal e.g., a signal generated by binding of a compound to a polypeptide of the invention
  • the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (e.g., intracellular Ca 2+ , diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity of the target on an appropriate substrate, detecting the induction of a reporter gene (e.g., a regulatory element that is responsive to a polypeptide of the invention operably linked to a nucleic acid encoding a detectable marker, e.g. luciferase), or detecting a cellular response, for example, cellular differentiation, or cell proliferation.
  • a reporter gene e.g., a regulatory element that is responsive to a polypeptide of the invention operably linked to a nucleic acid encoding a detectable marker, e.g. luciferase
  • detecting a cellular response for example, cellular differentiation, or cell proliferation.
  • an assay of the present invention is a cell-free assay comprising contacting a polypeptide of the invention or biologically active portion thereof with a test compound and determining the ability of the test compound to bind to the polypeptide or biologically active portion thereof. Binding of the test compound to the polypeptide can be determined either directly or indirectly as described above.
  • the assay includes contacting the polypeptide of the invention or biologically active portion thereof with a known compound which binds the polypeptide to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the polypeptide, wherein determining the ability of the test compound to interact with the polypeptide comprises determining the ability of the test compound to preferentially bind to the polypeptide or biologically active portion thereof as compared to the known compound.
  • an assay is a cell- free assay comprising contacting a polypeptide of the invention or biologically active portion thereof with a test compound and determining the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the polypeptide or biologically active portion thereof. Determining the ability of the test compound to modulate the activity of the polypeptide can be accomplished, for example, by determining the ability of the polypeptide to bind to a target molecule by one of the methods described above for determining direct binding. In an alternative embodiment, determining the ability of the test compound to modulate the activity of the polypeptide can be accomplished by determining the ability of the polypeptide of the invention to further modulate the target molecule.
  • the catalytic/enzymatic activity of the target molecule on an appropriate substrate can be determined as previously described.
  • the cell-free assay comprises contacting a polypeptide of the invention or biologically active portion thereof with a known compound which binds the polypeptide to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the polypeptide, wherein determining the ability of the test compound to interact with the polypeptide comprises determining the ability of the polypeptide to preferentially bind to or modulate the activity of a target molecule.
  • the cell-free assays of the present invention are amenable to use of both a soluble form or the membrane-bound form of a polypeptide of the invention.
  • solubilizing agents include non-ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-octylmaltoside, octanoyl-N- methylglucamide, decanoyl-N-methylglucamide, Triton X-100, Triton X-114, Thesit, Isotridecypoly(ethylene glycol ether)n, 3-[(3-cholamidopropyl)dimethylamminio]-l-propane sulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylamminio]-2 -hydroxy- 1 -propane sulfonate (CHAPSO), or N-dodecyl-N,N-dimethyl-3-ammonio-l -propane sulfonate.
  • non-ionic detergents such as n-octylglucoside
  • _ n it may be desirable to immobilize either the polypeptide of the invention or its target molecule to facilitate separation of complex ed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay.
  • Binding of a test compound to the polypeptide, or interaction of the polypeptide with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable , say for containing the reactants. Examples of such vessels include microtitre plates, test tubes, and micro-centrifuge tubes.
  • a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
  • glutathione-S-transferase fusion proteins or glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical; St. Louis, MO) or glutathione - _ derivatized microtitre plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or A polypeptide of the invention, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtitre plate wells are washed to remove any unbound components and complex formation is measured either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of binding or activity of the polypeptide of the invention can be determined using standard techniques.
  • polypeptide of the invention or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
  • Biotinylated polypeptide of the invention or target molecules can be prepared from biotin- NHS (N-hydroxy-succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals; Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • antibodies reactive with the polypeptide of the invention or target molecules but which do not interfere with binding of the polypeptide of the invention to its target molecule can be derivatized to the wells of the plate, and unbound target or polypeptide of the invention trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the polypeptide of the invention or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the polypeptide of the invention or target molecule.
  • modulators of expression of a polypeptide of the invention are identified in a method in which a cell is contacted with a candidate compound and the expression of the selected mRNA or protein (i.e., the mRNA or protein corresponding to a polypeptide or nucleic acid of the invention) in the cell is determined.
  • the level of expression of the selected mRNA or protein in the presence of the candidate compound is compared to the level of expression of the selected mRNA or protein in the absence of the candidate compound.
  • the candidate compound can then be identified as a modulator of expression of the polypeptide of the invention based on this comparison.
  • the candidate compound when expression of the selected mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of the selected mRNA or protein expression.
  • the candidate compound when expression of the selected mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of the selected mRNA or protein expression.
  • the level of the selected mRNA or protein expression in the cells can be determined by methods described herein.
  • a polypeptide of the inventions can be used as
  • binding proteins in a two-hybrid assay or three hybrid assay (see, e.g., U.S. Patent No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem. 268:12046-12054; Bartel et al. (1993) Bio/Techniques 14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and PCT Publication No. WO 94/10300), to identify other proteins, which bind to or interact with the polypeptide of the invention and modulate activity of the polypeptide of the invention. Such binding proteins are also likely to be involved in the propagation of signals by the polypeptide of the inventions as, for example, upstream or downstream elements of a signaling pathway involving the polypeptide of the invention.
  • This invention further pertains to novel agents identified by the above-described screening assays and uses thereof for treatments as described herein.
  • cDNA sequences identified herein can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.
  • sequence (or a portion of the sequence) of a gene has been isolated, this sequence can be used to map the location of the gene on a chromosome. Accordingly, nucleic acid molecules described herein or fragments thereof, can be used to map the location of the corresponding genes on a chromosome. The mapping of the sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease.
  • genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the sequence of a gene of the invention.
  • Computer analysis of the sequence of a gene of the invention can be used to rapidly select primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process.
  • These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the gene sequences will yield an amplified fragment.
  • D'Eustachio et al. see D'Eustachio et al. ((1983) Science 220:919-924).
  • PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the nucleic acid sequences of the invention to design oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map a gene to its chromosome include in situ hybridization (described in Fan et al. (1990) Proc. Natl.
  • FISH Fluorescence in situ hybridization
  • Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping pu ⁇ oses. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.
  • differences in the D ⁇ A sequences between individuals affected and unaffected with a disease associated with a gene of the invention can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that D ⁇ A sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymo ⁇ hisms.
  • the human gene for TANGO 232 was mapped on radiation hybrid panels to the long arm of chromosome 11, in the region ql3. Flanking markers for this region are Dl 1S1965 and WI-1409.
  • the ARRB1 (arrestin, beta), GIF (gastric intrinsic factor), ACTN3 (actinin, alpha 3) genes also map to this region of the human chromosome.
  • the oc (osteosclerotic), dc (dancer), nmd (meuromuscular degeneration), ocd (osteochondrodystrophy) loci also map to this region of the mouse chromosome.
  • the pcx (pyruvate decarboxylase), chk (choline kinase), gain (galanin) genes also map to this region of the mouse chromosome.
  • the nucleic acid sequences of the present invention can also be used to identify individuals from minute biological samples.
  • the United States military for example, is considering the use of restriction fragment length polymo ⁇ hism (RFLP) for identification of its personnel.
  • RFLP restriction fragment length polymo ⁇ hism
  • an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification.
  • This method does not suffer from the current limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult.
  • the sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).
  • sequences of the present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome.
  • the nucleic acid sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
  • Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences.
  • the sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue.
  • the nucleic acid sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases.
  • Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification pu ⁇ oses.
  • the noncoding sequences of SEQ ED NO:l, 2, 6, 7, 11, 12, 16, 17, 21, 22, 29, 30, 29, 30, 36, 37, 44, or 45 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers which each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ED NO:2, 7, 12, 17, 22, 30, 37, or 45 , are used, a more appropriate number of primers for positive individual identification would be 500-2,000.
  • a panel of reagents from the nucleic acid sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual.
  • positive identification of the individual, living or dead can be made from extremely small tissue samples.
  • DNA-based identification techniques can also be used in forensic biology. Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a pe ⁇ etrator of a crime.
  • PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample.
  • sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual).
  • an "identification marker” i.e. another DNA sequence that is unique to a particular individual.
  • actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments.
  • Sequences targeted to noncoding regions are particularly appropriate for this use as greater numbers of polymo ⁇ hisms occur in the noncoding regions, making it easier to differentiate individuals using this technique.
  • polynucleotide reagents include the nucleic acid sequences of the invention or portions thereof, e.g., fragments derived from noncoding regions having a length of at least 20 or 30 bases.
  • nucleic acid sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such probes can be used to identify tissue by species and/or by organ type.
  • polynucleotide reagents e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such probes can be used to identify tissue by species and/or by organ type.
  • the present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, pharmacogenomics, and monitoring clinical trails are used for prognostic (predictive) pu ⁇ oses to thereby treat an individual prophylactically.
  • diagnostic assays for determining expression of a polypeptide or nucleic acid of the invention and/or activity of a polypeptide of the invention, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant expression or activity of a polypeptide of the invention.
  • a biological sample e.g., blood, serum, cells, tissue
  • the invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with aberrant expression or activity of a polypeptide of the invention. For example, mutations in a gene of the invention can be assayed in a biological sample. Such assays can be used for prognostic or predictive pu ⁇ ose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with aberrant expression or activity of a polypeptide of the invention.
  • Another aspect of the invention provides methods for expression of a nucleic acid or polypeptide of the invention or activity of a polypeptide of the invention in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (referred to herein as "pharmacogenomics").
  • Pharmacogenomics allows for the selection of agents (e.g., drugs) for therapeutic or prophylactic treatment of an individual based on the genotype of the individual (e.g., the genotype of the individual examined to determine the ability of the individual to respond to a particular agent).
  • Yet another aspect of the invention pertains to monitoring the influence of agents
  • An exemplary method for detecting the presence or absence of a polypeptide or nucleic acid of the invention in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting a polypeptide or nucleic acid (e.g., mRNA, genomic DNA) of the
  • a preferred agent for detecting mRNA or genomic DNA encoding a polypeptide of the invention is a labeled nucleic acid probe capable of hybridizing to mRNA or genomic DNA encoding a polypeptide of the invention.
  • the nucleic acid probe can be, for example, a full-length cDNA, such as the nucleic acid of SEQ DD NO: 1, 2, 6, 7,
  • oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to a mRNA or genomic DNA encoding a polypeptide of the invention.
  • Other suitable probes for use in the diagnostic assays of the invention are described herein.
  • a preferred agent for detecting a polypeptide of the invention is an antibody capable
  • Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab') 2 ) can be used.
  • labeled with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as
  • indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
  • indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.
  • biological sample is intended to include tissues, cells and biological fluids isolated from a subject, as well as 0 tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo.
  • in vitro techniques for detection of mRNA include Northern hybridizations and in situ hybridizations.
  • In vitro techniques for detection of a polypeptide of the invention include enzyme linked immunosorbent assays (ELISAs),
  • In vitro techniques for detection of genomic DNA include Southern hybridizations.
  • in vivo techniques for detection of a polypeptide of the invention include introducing into a subject a labeled antibody directed against the polypeptide.
  • the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
  • the biological sample contains protein molecules from the test subject.
  • the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject.
  • a preferred biological sample is a peripheral blood leukocyte sample isolated by conventional means from a subject.
  • the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting a polypeptide of the invention or mRNA or genomic DNA encoding a polypeptide of the invention, such that the presence of the polypeptide or mRNA or genomic DNA encoding the polypeptide is detected in the biological sample, and comparing the presence of the polypeptide or mRNA or genomic DNA encoding the polypeptide in the control sample with the presence of the polypeptide or mRNA or genomic DNA encoding the polypeptide in the test sample.
  • kits for detecting the presence of a polypeptide or nucleic acid of the invention in a biological sample can be used to determine if a subject is suffering from or is at increased risk of developing a disorder associated with aberrant expression of a polypeptide of the invention (e.g., a proliferative disorder, e.g., psoriasis or cancer).
  • a disorder associated with aberrant expression of a polypeptide of the invention e.g., a proliferative disorder, e.g., psoriasis or cancer.
  • the kit can comprise a labeled compound or agent capable of detecting the polypeptide or mRNA encoding the polypeptide in a biological sample and means for determining the amount of the polypeptide or mRNA in the sample (e.g., an antibody which binds the polypeptide or an oligonucleotide probe which binds to DNA or mRNA encoding the polypeptide).
  • Kits can also include instructions for observing that the tested subject is suffering from or is at risk of developing a disorder associated with aberrant expression of the polypeptide if the amount of the polypeptide or mRNA encoding the polypeptide is above or below a normal level.
  • the kit can comprise, for example: (1) a first antibody (e.g., attached to a solid support) which binds to a polypeptide of the invention; and, optionally,
  • the kit can comprise, for example: (1) an oligonucleotide, e.g., a detectably labeled oligonucleotide, which hybridizes to a nucleic acid sequence encoding a polypeptide of the invention or (2) a pair of primers useful for amplifying a nucleic acid molecule encoding a polypeptide of the invention.
  • the kit can also comprise, e.g., a buffering agent, a preservative, or a protein stabilizing agent.
  • the kit can also comprise components necessary for detecting the detectable agent (e.g., an enzyme or a substrate).
  • the kit can also contain a control sample or a series of control samples which can be assayed and compared to the test sample contained.
  • Each component of the kit is usually enclosed within an individual container and all of the various containers are within a single package along with instructions for observing whether the tested subject is suffering from or is at risk of developing a disorder associated with aberrant expression of the polypeptide.
  • the methods described herein can furthermore be utilized as diagnostic or prognostic assays to identify subjects having or at risk of developing a disease or disorder associated with aberrant expression or activity of a polypeptide of the invention.
  • the assays described herein such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with aberrant expression or activity of a polypeptide of the invention.
  • the prognostic assays can be utilized to identify a subject having or at risk for developing such a disease or disorder.
  • test sample refers to a biological sample obtained from a subject of interest.
  • a test sample can be a biological fluid (e.g., serum), cell sample, or tissue.
  • the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant expression or activity of a polypeptide of the invention.
  • an agent e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • agents e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • agents e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • such methods can be used to determine whether a subject can be effectively treated with a specific agent or class of agents (e.g., agents of a type which decrease activity of the
  • the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant expression or activity of a polypeptide of the invention in which a test sample is obtained and the polypeptide or nucleic acid encoding the polypeptide is detected (e.g., wherein the presence of the polypeptide or nucleic acid is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant expression or activity of the polypeptide).
  • the methods of the invention can also be used to detect genetic lesions or mutations in a gene of the invention, thereby determining if a subject with the lesioned gene is at risk for a disorder characterized aberrant expression or activity of a polypeptide of the invention.
  • the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic lesion or mutation characterized by at least one of an alteration affecting the integrity of a gene encoding the polypeptide of the invention, or the mis-expression of the gene encoding the polypeptide of the invention.
  • such genetic lesions or mutations can be detected by ascertaining the existence of at least one of: 1) a deletion of one or more nucleotides from the gene; 2) an addition of one or more nucleotides to the gene; 3) a substitution of one or more nucleotides of the gene; 4) a chromosomal rearrangement of the gene; 5) an alteration in the level of a messenger RNA transcript of the gene; 6) an aberrant modification of the gene, such as of the methylation pattern of the genomic DNA; 7) the presence of a non- wild type splicing pattern of a messenger RNA transcript of the gene; 8) a non- wild type level of a the protein encoded by the gene; 9) an allelic loss of the gene; and 10) an inappropriate post-translational modification of the protein encoded by the gene.
  • assay techniques known in the art which can be used for detecting lesions in a gene.
  • detection of the lesion involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91 :360-364), the latter of which can be particularly useful for detecting point mutations in a gene (see, e.g., Abravaya et al.
  • PCR polymerase chain reaction
  • LCR ligation chain reaction
  • This method can include the steps of collecting a sample of cells from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to the selected gene under conditions such that hybridization and amplification of the gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
  • nucleic acid e.g., genomic, mRNA or both
  • Alternative amplification methods include: self sustained sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh, et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q- Beta Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
  • mutations in a selected gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns.
  • sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA.
  • sequence specific ribozymes see, e.g., U.S. Patent No. 5,498,531 can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
  • genetic mutations can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin et al. (1996) Human Mutation 7:244-255; Kozal et al. (1996) Nature Medicine 2:753-759).
  • genetic mutations can be identified in two-dimensional arrays containing light-generated DNA probes as described in Cronin et al., supra. Briefly, a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations.
  • This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected.
  • Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
  • any of a variety of sequencing reactions known in the art can be used to directly sequence the selected gene and detect mutations by comparing the sequence of the sample nucleic acids with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxim and Gilbert ((1977) Proc. Natl Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463).
  • any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Bio/Techniques 19:448), including sequencing by mass spectrometry (see, e.g., PCT Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993) Appl. Biochem. Biotechnol. 38:147-159).
  • RNA/RNA or RNA/DNA heteroduplexes Other methods for detecting mutations in a selected gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science 230:1242).
  • the technique of "mismatch cleavage" entails providing heteroduplexes formed by hybridizing (labeled) RNA or DNA containing the wild-type sequence with potentially mutant RNA or DNA obtained from a tissue sample.
  • the double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands.
  • RNA/DNA duplexes can be treated with RNase to digest mismatched regions, and DNA/DNA hybrids can be treated with S 1 nuclease to digest mismatched regions.
  • either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, e.g., Cotton et al. (1988) Proc. Natl. Acad. Sci. USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217:286-295.
  • the control DNA or RNA can be labeled for detection.
  • the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in cDNAs obtained from samples of cells.
  • DNA mismatch repair enzymes
  • the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662).
  • a probe based on a selected sequence is hybridized to a cDNA or other DNA product from a test cell(s).
  • the duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, e.g., U.S. Patent No. 5,459,039.
  • alterations in electrophoretic mobility will be used to identify mutations in genes.
  • single strand conformation polymo ⁇ hism may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al. (1989) Proc. Natl. Acad. Sci. USA 86:2766; see also Cotton (1993) Mutat. Res. 285:125-144; Hayashi (1992) Genet. Anal. Tech. Appl. 9:73-79). Single-stranded DNA fragments of sample and control nucleic acids will be denatured and allowed to renature.
  • the secondary structure of single-stranded nucleic acids varies according to sequence, and the resulting alteration in electrophoretic mobility enables the detection of even a single base change.
  • the DNA fragments may be labeled or detected with labeled probes.
  • the sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence.
  • the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
  • the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495).
  • DGGE denaturing gradient gel electrophoresis
  • DNA will be modified to insure that it does not completely denature, for example by adding a ⁇ GC clamp of approximately 40 bp of high-melting GC- rich DNA by PCR.
  • a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys. Chem. 265:12753).
  • oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki et al. (1989) Proc. Natl. Acad. Sci. USA 86:6230).
  • allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
  • allele specific amplification technology which depends on selective PCR amplification may be used in conjunction with the instant invention.
  • Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res.
  • amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl Acad. Sci. USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
  • the methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a gene encoding a polypeptide of the invention.
  • any cell type or tissue, preferably peripheral blood leukocytes, in which the polypeptide of the invention is expressed maybe utilized in the prognostic assays described herein.
  • Agents, or modulators which have a stimulatory or inhibitory effect on activity or expression of a polypeptide of the invention as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) disorders associated with aberrant activity of the polypeptide.
  • the pharmacogenomics i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug
  • Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug.
  • the pharmacogenomics of the individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration of the individual's genotype. Such pharmacogenomics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of a polypeptide of the invention, expression of a nucleic acid of the invention, or mutation content of a gene of the invention in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual.
  • Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons.
  • G6PD glucose-6-phosphate dehydrogenase deficiency
  • the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action.
  • drug metabolizing enzymes e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19
  • NAT 2 N-acetyltransferase 2
  • CYP2D6 and CYP2C19 cytochrome P450 enzymes
  • the gene coding for CYP2D6 is highly polymo ⁇ hic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, a PM will show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite mo ⁇ hine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra-rapid metabolism has been identified to be due to CYP2D6 gene amplification.
  • the activity of a polypeptide of the invention, expression of a nucleic acid encoding the polypeptide, or mutation content of a gene encoding the polypeptide in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment of the individual.
  • pharmacogenetic studies can be used to apply genotyping of polymo ⁇ hic alleles encoding drug-metabolizing enzymes to the identification of an individual's drug responsiveness phenotype. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with a modulator of activity or expression of the polypeptide, such as a modulator identified by one of the exemplary screening assays described herein.
  • a polypeptide of the invention e.g., the ability to modulate aberrant cell proliferation chemotaxis, and/or differentiation
  • agents e.g., drugs, compounds
  • the effectiveness of an agent, as determined by a screening assay as described herein, to increase gene expression, protein levels or protein activity can be monitored in clinical trials of subjects exhibiting decreased gene expression, protein levels, or protein activity.
  • the effectiveness of an agent, as determined by a screening assay, to decrease gene expression, protein levels or protein activity can be monitored in clinical trials of subjects exhibiting increased gene expression, protein levels, or protein activity.
  • expression or activity of a polypeptide of the invention and preferably, that of other polypeptide that have been implicated in for example, a cellular proliferation disorder can be used as a marker of the immune responsiveness of a particular cell.
  • genes including those of the invention, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates activity or expression of a polypeptide of the invention (e.g., as identified in a screening assay described herein) can be identified.
  • an agent e.g., compound, drug or small molecule
  • a polypeptide of the invention e.g., as identified in a screening assay described herein
  • cells can be isolated and RNA prepared and analyzed for the levels of expression of a gene of the invention and other genes implicated in the disorder.
  • the levels of gene expression can be quantified by Northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of a gene of the invention or other genes.
  • the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment of the individual with the agent.
  • the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) comprising the steps of (i) obtaining a pre-administration sample from a subject prior to administration of the agent; (ii) detecting the level of the polypeptide or nucleic acid of the invention in the preadministration sample; (iii) obtaining one or more post- administration samples from the subject; (iv) detecting the level the of the polypeptide or nucleic acid of the invention in the post- administration samples; (v) comparing the level of the polypeptide or nucleic acid of the invention in the pre-administration sample with the level of the polypeptide or nucleic acid of the invention in the post-administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.
  • an agent e.g., an agonist, antagonist,
  • increased administration of the agent may be desirable to increase the expression or activity of the polypeptide to higher levels than detected, i.e., to increase the effectiveness of the agent.
  • decreased administration of the agent may be desirable to decrease expression or activity of the polypeptide to lower levels than detected, i.e., to decrease the effectiveness of the agent.
  • the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant expression or activity of a polypeptide of the invention.
  • disorders characterized by abberant expression or activity of the polypeptides of the invention include metabolic disorders.
  • the polypeptides of the invention can be used to modulate cellular function, survival, mo ⁇ hology, proliferation and/or differentiation (e.g., to treat tumors).
  • the invention provides a method for preventing in a subject, a disease or condition associated with an aberrant expression or activity of a polypeptide of the invention, by administering to the subject an agent which modulates expression or at least one activity of the polypeptide.
  • Subjects at risk for a disease which is caused or contributed to by aberrant expression or activity of a polypeptide of the invention can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.
  • Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the abereancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
  • an agonist or antagonist agent can be used for treating the subject.
  • the modulatory method of the invention involves contacting a cell with an agent that modulates one or more of the activities of the polypeptide.
  • An agent that modulates activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring cognate ligand of the polypeptide, a peptide, a peptidomimetic, or other small molecule.
  • the agent stimulates one or more of the biological activities of the polypeptide.
  • stimulatory agents include the active polypeptide of the invention and a nucleic acid molecule encoding the polypeptide of the invention that has been introduced into the cell.
  • the agent inhibits one or more of the biological activities of the polypeptide of the invention.
  • inhibitory agents include antisense nucleic acid molecules and antibodies.
  • the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., upregulates or downregulates) expression or activity.
  • an agent e.g., an agent identified by a screening assay described herein
  • the method involves administering a polypeptide of the invention or a nucleic acid molecule of the invention as therapy to compensate for reduced or aberrant expression or activity of the polypeptide.
  • Stimulation of activity is desirable in situations in which activity or expression is abnormally low or downregulated and/or in which increased activity is likely to have a beneficial effect. Conversely, inhibition of activity is desirable in situations in which activity or expression is abnormally high or upregulated and/or in which decreased activity is likely to have a beneficial effect.

Abstract

Cette invention a trait à des molécules d'acide nucléique isolées, désignées sous le nom de TANGO 221, TANGO 176, et TANGO 232 codant des protéines entièrement sécrétées ou associées à des membranes. Elle porte, de surcroît, sur des molécules d'acide nucléique antisens, sur des vecteurs d'expression contenant les molécules d'acide nucléique de l'invention, des cellules hôtes dans lesquelles les vecteurs d'expression ont été introduits et des animaux transgéniques chez qui une molécule d'acide nucléique de l'invention a été introduite ou disloquée. Elle concerne, en outre, des polypeptides isolés, des polypeptides de fusion, des peptides antigéniques et des anticorps. Il est encore question, dans cette invention, de méthodes diagnostiques, de criblage et de méthodes thérapeutiques utilisant des compositions de l'invention.
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Non-Patent Citations (12)

* Cited by examiner, † Cited by third party
Title
DATABASE EM_EST [Online] 11 September 1997 (1997-09-11) STRAUSBERG R.: "nk18g01.s1 NCI_CGAP_Co11 Homo sapiens cDNA clone IMAGE:1013904 3', mRNA sequence." retrieved from EBI Database accession no. AA565877 XP002215352 *
DATABASE EM_EST [Online] 15 July 1997 (1997-07-15) STRAUSBERG R.: "ni07h03.s1 NCI_CGAP_Br2 Homo sapiens cDNA clone IMAGE:967349 3', mRNA sequence." retrieved from EBI Database accession no. HS1309771 XP002215348 *
DATABASE EM_EST [Online] 17 August 1998 (1998-08-17) STRAUSBERG R.: "ow81b11.s1 Soares_fetal_liver_spleen_1NFLS_S1 Homo sapiens cDNA clone IMAGE:1653213 3', mRNA sequence." retrieved from EBI Database accession no. AI081694 XP002215350 *
DATABASE EM_EST [Online] 19 August 1998 (1998-08-19) STRAUSBERG R.: "qa98a02.x1 Soares_fetal_heart_NbHH19W Homo sapiens cDNA clone IMAGE:1694762 3', mRNA sequence." retrieved from EBI Database accession no. AI093175 XP002215349 *
DATABASE EM_EST [Online] 31 October 1997 (1997-10-31) STRAUSBERG R.: "np61c07.s1 NCI_CGAP_Br2 Homo sapiens cDNA clone IMAGE:1130796 3', mRNA sequence" retrieved from EBI Database accession no. AA631857 XP002215346 *
DATABASE EM_EST [Online] 4 December 1997 (1997-12-04) HILLIER L. ET AL: "zi14e06.s1 Soares fetal liver spleen 1NFLS S1 Homo sapiens cDNA clone 430786 3'." retrieved from EBI Database accession no. AA677989 XP002215347 *
DATABASE EM_EST [Online] 5 November 1998 (1998-11-05) STRAUSBERG R.: "qk27b03.x1 NCI_CGAP_Kid3 Homo sapiens cDNA clone IMAGE:1870157 3', mRNA sequence." retrieved from EBI Database accession no. AI245798 XP002215351 *
DATABASE GSN [Online] 26 June 2001 (2001-06-26) OTA T ET AL: "Human cDNA sequence SEQ ID NO:17096" retrieved from EBI Database accession no. AAH17594 XP002215353 & EP 1 074 617 A (HELIX RES INST.) 7 February 2001 (2001-02-07) *
DATABASE GSN [Online] 26 June 2001 (2001-06-26) OTA T ET AL: "Human cDNA sequence SEQ ID NO:18186." retrieved from EBI Database accession no. AAH18241 XP002215354 & EP 1 074 617 A (HELIX RES INST.) 7 February 2001 (2001-02-07) *
DATABASE GSN [Online] 8 February 2001 (2001-02-08) SHIMKETS RA, LEACH M: "Human ORFX ORF1337 polynucleotide sequence SEQ ID NO:2673." retrieved from EBI Database accession no. AAC75782 XP002215355 & WO 00 58473 A (CURAGEN CORP.) 5 October 2000 (2000-10-05) *
MAEDA K ET AL: "Analysis of an expression profile of genes in the human adipose tissue" GENE: AN INTERNATIONAL JOURNAL ON GENES AND GENOMES, ELSEVIER SCIENCE PUBLISHERS, BARKING, GB, vol. 190, no. 2, 1997, pages 227-235, XP004116085 ISSN: 0378-1119 *
See also references of WO0039150A2 *

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