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
• • 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
  • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants

Definitions

• cytokines and cytokine receptors play a vital role in the regulation of cell growth, cell differentiation, and a variety of specific cellular
• a number of medically useful proteins including erythropoietin, granulocyte- macrophage colony stimulating factor, human growth hormone, and various interleukins, are secreted proteins.
• receptors which bind a ligand and transduce an intracellular signal, leading to a variety of cellular responses.
• 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.,
• the present invention is based, at least in part, on the discovery of cDNA molecule? encoding TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO
• nucleic acids ofthe invention are collectively referred to as nucleic acids ofthe invention.
• nucleic acids and polypeptides ofthe present invention are useful as modulating
• the present invention provides isolated nucleic acid molecules encoding a polypeptide ofthe invention or a biologically active portion thereof.
• the present invention also provides nucleic acid molecules which are suitable as primers or hybridization probes for the detection of nucleic acids encoding a polypeptide ofthe invention.
• nucleic acid molecules which are at least 45% (or 55%, 65%,
• 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 any of SEQ ID NOs:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or the nucleotide sequence ofthe cDNA of a clone deposited with ATCC as any of Accession Numbers 98999, 202171, 98965, and 98966 (the "cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966"), 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 invention features nucleic acid molecules of at least 570, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, 2500, 2600, 2700, 2800 or 2835 nucleotides ofthe nucleotide sequence of SEQ ID NO:l, the nucleotide sequence ofthe TANGO 128 cDNA clone of ATCC Accession No. 98999, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 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 2230 nucleotides of nucleic acids 1 to 2233 of SEQ ID NO:l, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 15, 25, 50, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000 or 1030 nucleotides ofthe nucleotide sequence of SEQ ID NO:3, or a complement thereof.
• the invention features nucleic acid molecules of at least 250, 275, 300, 325, 350,
• nucleotide sequence of SEQ ID NO:53 the nucleotide sequence of a mouse TANGO 128 cDNA, or a complement thereof.
• the invention features nucleic acid molecules comprising at least 25 30, 35, 40, 45, 50, 55, 60, 65, 70 or 77 nucleotides of nucleic acids 1 to 78 of SEQ ID NO:53, or a complement thereof.
• the invention features nucleic acid molecules comprising at least 25 30, 35, 40, 45, 50, 55 or 60 nucleotides of nucleic acids 257 to 318 of SEQ ID NO:53, or a complement thereof.
• the invention features nucleic acid molecules comprising at least 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525 or 550 nucleotides ofthe nucleotide sequence of SEQ ID NO:55, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 30, 35, 40, 45, 50, 55 or 60 nucleotides of nucleic acids 46 to 107 of SEQ ID NO: 55, or a complement thereof.
• the invention features nucleic acid molecules of at least 425, 450, 475, 500, 525, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500 or 1540
• nucleotides ofthe nucleotide sequence of SEQ ID NO:4 the nucleotide sequence of a human TANGO 140-1 cDNA, the nucleotide sequence ofthe TANGO 140-1 cDNA clone of ATCC Accession No. 98999, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350 400, 450, 500 or 540 nucleotides of nucleic acids 1 to 545 of SEQ ID NO:4, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550 or 580 nucleotides of nucleic acids 980 to 1550 of SEQ ID NO:4, or a complement thereof.
• the invention features nucleic acid molecules of at least 425, 450, 475, 500, 525, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1650,
• nucleotide sequence of SEQ ID NO:6 the nucleotide sequence of a human TANGO 140-2 cDNA, the nucleotide sequence ofthe TANGO 140-2 cDNA clone of ATCC Accession No. 98999, or a complement
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350 400, 450, 500 or 540 nucleotides of nucleic acids 1 to 545 of SEQ ID NO:6, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1650, 1700, 1750, 1800,
• nucleic acids 980 to 3385 of SEQ ID NO:6, or a complement thereof are examples of nucleic acids 980 to 3385 of SEQ ID NO:6, or a complement thereof.
• the invention features nucleic acid molecules comprising at least 75, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or 615 nucleotides ofthe nucleotide sequence of SEQ ID NO:38 or 39, or a complement thereof.
• the invention features nucleic acid
• 30 molecules comprising at least 25, 75, 100, 150, 200, 250, 300, 350, 400, 450, 500 or 545 nucleotides of nucleic acids 1 to 545 of SEQ ID NO:38 or 39, or a complement thereof.
• the invention features nucleic acid molecules of at least 520, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2200, 2250 or 2270 nucleotides ofthe nucleotide sequence of SEQ ID NO:8,
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750 or 785 nucleotides of nucleic acids 1 to 789 of SEQ ID NO:8, or a complement thereof.
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450 or 500 nucleotides of nucleic acids 1164 to 1669 of SEQ ID NO:8,
• the invention also features nucleic acid molecules comprising at least 25, 50 or 80 nucleotides of nucleic acids 2190 to 2272 of SEQ ID NO:8, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 380, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300,
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550 or 575 nucleotides of nucleic acids 1 to 576 of SEQ ID NO:10, or a complement thereof.
• the invention features nucleic acid molecules of at least 515, 550, 600, 650, 700,
• nucleotide sequence of a mouse TANGO 197 cDNA or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 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, 1950, 2000, 2050, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500,
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300 or 320 nucleotides of nucleic acids 4094 to 4417 of SEQ ID NO:56, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least
• the invention features nucleic acid molecules of at least 545, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000,
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250 or 1270 nucleotides of nucleic acids 1 to 1273 of SEQ ID NO: 11, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250 or 1270 nucleotides of nucleic acids 1 to 1273 of SEQ ID NO: 11, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300 or 320 nucleotides of nucleic acids 4094 to 4417 of SEQ ID NO:l 1, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 240, 275, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600 or 1660 nucleotides of the
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850 or 900 nucleotides of nucleic acids 1 to 905 of SEQ ID NO:13, or a complement thereof.
• the invention features nucleic acid molecules of at least 785, 800, 850, 900, 950,
• nucleic acid molecules comprising at least 25, 50, 100, 150 or 190 nucleotides of nucleic acids 983 to 1180 of SEQ ID NO:59, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least
• nucleic acid molecules comprising at least 25, 50, 100, 150 or 180 nucleotides of nucleic acids 804 to 999 of SEQ ID NO:61, or a complement thereof.
• the invention features nucleic acid molecules of at least 530, 600, 650, 700, 750,
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300 or 360 nucleotides of nucleic acids 1 to 361 of SEQ ID NO: 14, or a complement thereof.
• nucleic acid molecules comprising at least 25, 40, 50 or 60 nucleotides of nucleic acids 759 to 822 of SEQ ID NO: 14, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 250, 275, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800 or 810 nucleotides ofthe nucleotide sequence of SEQ ID NO: 16, or a complement thereof.
• the invention also features nucleic acid molecules which include a fragment of at least 250, 275, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800 or 810 nucleotides ofthe nucleotide sequence of SEQ ID NO: 16, or a complement thereof.
• the invention also provides nucleic acid molecules which include a fragment of at least 250, 275, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800 or 810 nucleotides ofthe nucleotide sequence of SEQ ID NO: 16, or a complement thereof.
• the invention also features nucleic acid molecules which include a fragment of at least 250, 275
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250 or 300 nucleotides of nucleic acids 1 to 304 of SEQ ID NO: 16, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 40, 50 or 60 nucleotides of nucleic acids 701 to 764 of SEQ ID NO: 16, or a complement thereof.
• the invention features nucleic acid molecules of at least 530, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000,
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950 or 1000 nucleotides of nucleic acids 1 to 1018 of SEQ ID NO:62, or a complement thereof.
• the invention also features
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900 or 920 nucleotides of nucleic acids 1227 to 2154 of SEQ ID NO:62, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 25, 50, 100, 150, 200, 250, 275, 300, 350, 400, 450, 500, 550 or 575 nucleotides ofthe
• the invention features nucleic acid molecules of at least 570, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650 or 2680 nucleotides ofthe nucleotide sequence of SEQ ID NOs:17 or 65, the nucleotide sequence of
• the invention also features nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250 or 270 nucleotides of nucleic acids 1 to 272 of SEQ ID NO:17 or 65, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least
• the invention features nucleic acid molecules which include a fragment of at least 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100,
• nucleic acid molecules comprising at least 25, 40, 50, 100, 150 or 200 nucleotides of nucleic acids 1 to 204 of SEQ ID NO:19, or a complement thereof.
• nucleic acid molecules comprising at least 25, 40, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800,
• nucleic acid molecules which include a fragment of at least 570, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650 or 2680 nucleotides ofthe nucleotide sequence of SEQ ID NO:67, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 40, 50, 100, 150 or 200 nucleotides of nucleic acids 1 to 204 of SEQ ID NO:67, or a complement thereof.
• the invention also features nucleic acid molecules comprising at least 25, 40, 50, 100, 150, 200, 250, 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 or 1530 nucleotides of nucleic acids 507 to 2038 of SEQ ID NO:67, or a complement thereof.
• the invention features nucleic acid molecules of at least 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2150, 2200, 2250, 2300, 2350, 2400, 2450, 2500, 2550, 2600, 2650, 2700, 2750, 2800, 2850, 2900, 2950, 3000, 3050, 3100, 3150, 3200, 3250, 3300, 3350 or 3400 nucleotides ofthe nucleotide sequence of SEQ ID NOs:20 or 68, the nucleotide sequence of the TANGO 239 cDNA clone of ATCC Accession No.
• nucleic acid molecules comprising at least 25, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1100, 1200, 1300, 1400, 1500, 1600, 1700, 1800, 1900, 2000, 2100, 2150, 2200 or 2225 nucleotides of nucleic acids 1 to 2227 of SEQ ID NOs:20 or 68, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 25, 50, 100, 150, 200, 250, 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 or 1650 nucleotides ofthe nucleotide sequence of SEQ ID NO:22, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least
• nucleic acid molecules of at least 25, 50, 100, 150, 200, 250, 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, 1950, 2000 or 2050 nucleotides ofthe nucleotide sequence of SEQ ID NO:70, or a complement thereof.
• the invention features nucleic acid molecules of at least 25, 50, 100, 150, 200, 250,
• nucleotide sequence of SEQ ID NOs:20 or 68 the nucleotide sequence of a mouse TANGO 239 cDNA, or a complement thereof.
• the invention features nucleic acid molecules which include a fragment of at least 25, 50, 100, 150 or 160 nucleotides ofthe nucleotide sequence of SEQ ID NO: 73, or a complement thereof.
• 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 ofthe nucleotide sequence of any of SEQ ID Nos: 1, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or the
• 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 ofthe nucleotide sequence of any of SEQ ID Nos: 1, 3, 4, 6, 8, 10, 11, 13, 14,
• nucleic acid molecules encode polypeptides or proteins that exhibit at least one structural and/or functional feature of a polypeptide ofthe invention.
• 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%o, 75%, 85%, 95%, or 98%) identical to the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or the amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and
• 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 any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or the amino acid sequence
• the nucleic acid molecules have the nucleotide sequence 30 of any of SEQ ID NOs:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or the nucleotide sequence ofthe cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, or a complement thereof
• nucleic acid molecules which encode a fragment of a polypeptide having the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 35 21, 54, 57, 60, 63, 66, 69, 72, the fragment including at least 15 (20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390 or 400) contiguous amino acids of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or the polypeptide encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965,
• nucleic acid molecules which encode a fragment of a polypeptide having the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, the fragment including at least 15 (20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380,
• the invention includes nucleic acid molecules which encode a naturally occurring
• allelic variant of a polypeptide comprising the amino acid sequence of any of SEQ ID NO: 1
• nucleic acid molecule hybridizes under stringent conditions to a nucleic acid molecule having a nucleic acid sequence encoding any of SEQ 0 ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or a complement thereof.
• the invention includes nucleic acid molecules which encode a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, or a 5 complement thereof, wherein the nucleic acid molecule hybridizes under stringent conditions to a nucleic acid molecule having a nucleic acid sequence encoding any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, 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 ofthe invention.
• isolated polypeptides or proteins having an amino acid sequence that is at least about 65%>, preferably 75%>, 85%>, 95%>, or 98% identical to the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, or 72.
• polypeptides or proteins also exhibit at least one structural and/or functional feature of a polypeptide ofthe invention.
• isolated polypeptides or proteins which preferably are encoded by a nucleic acid molecule having a nucleotide sequence that is at least about 65%,
• polypeptides or proteins preferably also exhibit at least one structural and/or functional feature of a polypeptide ofthe invention, and isolated polypeptides or proteins which are encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization
• nucleic acid molecule having the sequence of any of SEQ ID NOs: 1 , 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71,
• polypeptides which are naturally occurring allelic 15 variants of a polypeptide that includes the amino acid sequence of any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes under stringent conditions to a nucleic acid molecule having the sequence of any of SEQ ID Nos:l, 3, 4, 6, 0 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or a complement thereof.
• polypeptides which are naturally occurring allelic variants of a polypeptide that includes the amino acid sequence of any of SEQ ID NOs:2, 5,
• nucleic acid molecules encode polypeptides or
• the invention also features nucleic acid molecules that hybridize under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence of any of SEQ ID NO: 1
• 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 comprising the nucleotide sequence of any of SEQ ID NOs:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, ofthe cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, or a complement thereof.
• the isolated nucleic acid molecules encode a o cytoplasmic, transmembrane, or extracellular 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 ofthe invention.
• Another aspect ofthe invention provides vectors, e.g., recombinant expression vectors, comprising a nucleic acid molecule ofthe invention.
• the 5 invention provides host cells containing such a vector, or engineered to contain a nuclei ec acid ofthe invention and/or to express a nucleic acid ofthe invention.
• the invention also provides methods for producing a polypeptide ofthe invention by culturing, in a suitable medium, a host cell ofthe invention such that the polypeptide ofthe invention is produced.
• Another aspect of this invention features isolated or recombinant proteins and 0 polypeptides ofthe invention. Preferred proteins and polypeptides possess at least one biological activity possessed by the corresponding naturally-occurring human polypeptide.
• An activity, a biological activity, and a functional activity of a polypeptide ofthe invention refers to an activity exerted by a protein or polypeptide ofthe invention on a responsive cell as determined in vivo, or in vitro, according to standard techniques.
• activities can be a 5 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 ofthe protein with a second protein.
• activities include, e.g., (1) the ability to form protein-protein interactions with proteins in the signaling pathway ofthe naturally- occurring polypeptide; (2) the ability to bind a ligand ofthe naturally-occurring 0 polypeptide; (3) the ability to bind to an intracellular target ofthe naturally-occurring polypeptide.
• activities include, e.g., (1) the ability to modulate cellular proliferation; (2) the ability to modulate cellular differentiation; (3) the ability to modulate chemotaxis and/or migration; and (4) the ability to modulate cell death.
• a polypeptide ofthe invention has an amino acid sequence 5 sufficiently identical to an identified domain of a polypeptide ofthe 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 65% identity, preferably 75% identity, more preferably 85%>, 95%>, or 98% identity are defined herein as sufficiently identical.
• the isolated polypeptide ofthe invention lacks both a transmembrane and a cytoplasmic domain. In another embodiment, the polypeptide lacks o both a transmembrane domain and a cytoplasmic domain and is soluble under physiological conditions.
• polypeptides ofthe 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 ofthe invention 5 such as monoclonal or polyclonal antibodies.
• polypeptides ofthe invention or biologically active portions thereof, or antibodies ofthe invention can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
• the present invention provides methods for detecting the presence 0 ofthe activity or expression of a polypeptide ofthe 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 ofthe invention comprising contacting a cell with an agent that modulates 5 (inhibits or stimulates) the activity or expression of a polypeptide ofthe invention such that activity or expression in the cell is modulated.
• the agent is an antibody that specifically binds to a polypeptide ofthe invention.
• the agent modulates expression of a polypeptide ofthe invention by modulating transcription, splicing, or translation of an mRNA encoding a 0 polypeptide ofthe 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 ofthe invention.
• the present invention also provides methods to treat a subject having a disorder characterized by abenant activity of a polypeptide ofthe invention or aberrant expression of 5 a nucleic acid ofthe invention by administering an agent which is a modulator of the activity of a polypeptide ofthe invention or a modulator ofthe expression of a nucleic acid ofthe invention to the subject.
• the modulator is a protein ofthe invention.
• the modulator is a nucleic acid ofthe 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) abenant modification or mutation of a gene encoding a polypeptide ofthe invention, (ii) mis-regulation of a gene encoding a polypeptide ofthe invention, and (iii) aberrant post- translational modification of a polypeptide ofthe invention wherein a wild-type form ofthe gene encodes a polypeptide having the activity ofthe polypeptide ofthe invention.
• the invention provides a method for identifying a compound that binds to or modulates the activity of a polypeptide ofthe invention.
• such methods entail measuring a biological activity ofthe polypeptide in the presence and absence of a test compound and identifying those compounds which alter the activity ofthe polypeptide.
• the invention also features methods for identifying a compound which modulates the expression of a polypeptide or nucleic acid ofthe invention by measuring the expression ofthe polypeptide or nucleic acid in the presence and absence ofthe compound.
• Figure 1 depicts the cDNA sequence of human TANGO 128 (SEQ ID NO:l) and predicted amino acid sequence of TANGO 128 (SEQ ID NO:2).
• the open reading frame of SEQ ID NO:l extends from nucleotide 288 to 1322 of SEQ ID NO:l (SEQ ID NO:3).
• Figure 2 depicts the cDNA sequence of human TANGO 140-1 (SEQ ID NO:4) and predicted amino acid sequence of TANGO 140-1 (SEQ ID NO: 5).
• the open reading frame of SEQ ID NO:4 extends from nucleotide 2 to 619 of SEQ ID NO:4 (SEQ ID NO:38).
• Figure 3 depicts the cDNA sequence of human TANGO 140-2 (SEQ ID NO:6) and predicted amino acid sequence of TANGO 140-2 (SEQ ID NO:7).
• the open reading frame of SEQ ID NO:6 extends from nucleotide 1 to 591 of SEQ ID NO:6 (SEQ ID NO:39).
• Figure 4 depicts the cDNA sequence of human TANGO 197 (SEQ ID NO: 8) and predicted amino acid sequence of TANGO 197 (SEQ ID NO:9).
• the open reading frame of SEQ ID NO:8 extends from nucleotide 213 to 1211 of SEQ ID NO:8 (SEQ ID NO: 10).
• Figure 5 depicts the cDNA sequence of human TANGO 212 (SEQ ID NO: 11) and predicted amino acid sequence of TANGO 212 (SEQ ID NO:12).
• the open reading frame of SEQ ID NO:l 1 extends from nucleotide 269 to 1927 of SEQ ID NO:l 1 (SEQ ID NO: 11).
• Figure 6 depicts the cDNA sequence of human TANGO 213 (SEQ ID NO: 14) and predicted amino acid sequence of TANGO 213 (SEQ ID NO:15).
• the open reading frame of SEQ ID NO:14 extends from nucleotide 58 to 870 of SEQ ID NO:14 (SEQ ID NO: 16).
• Figure 7 depicts the cDNA sequence of human TANGO 224, form 1 (SEQ ID NO: 16
• SEQ ID NO: 17 and predicted amino acid sequence of TANGO 224, form 1 (SEQ ID NO: 18).
• the open reading frame of SEQ ID NO: 17 extends from nucleotide 1 to 1440 of SEQ ID NO: 17
• Figure 8 depicts the cDNA sequence of human TANGO 239, form 1 (SEQ ID NO: 19).
• SEQ ID NO:20 and predicted amino acid sequence of TANGO 239, form 1(SEQ ID NO:21).
• the open reading frame of SEQ ID NO:20 extends from nucleotide 344 to 1990 of SEQ ID NO:21
• Figure 9 depicts a hydropathy plot of a human TANGO- 128. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 10 depicts a hydropathy plot of a human TANGO 140-1. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 11 depicts a hydropathy plot of a human TANGO 140-2. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 12 depicts a hydropathy plot of a human TANGO 197. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 13 depicts a hydropathy plot of a human TANGO 212. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 14 depicts a hydropathy plot of a human TANGO 213. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 15 depicts a hydropathy plot of a human TANGO 224. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 16 depicts a hydropathy plot of a human TANGO 239. Relatively hydrophobic residues are above the dashed horizontal line, and relatively hydrophilic residues 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.
• Figure 17 depicts the alignment of amino acids 269 to 337 of TANGO 128 (amino acids 269 to 337 of SEQ ID NO:2)(SEQ ID NO: X) and the platelet derived growth factor (PDGF) consensus sequence (SEQ ID NO:40).
• amino acids 269 to 337 of TANGO 128 amino acids 269 to 337 of SEQ ID NO:2
• SEQ ID NO: X amino acids 269 to 337 of SEQ ID NO:2
• PDGF platelet derived growth factor
• Figure 18 depicts the alignment of amino acids 48 to 160 of TANGO 128 (amino acids 48 to 160 of SEQ ID NO:2)(SEQ ID NO: X) and the CUB consensus sequence (SEQ ID NO:41). In these alignments, an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 19 depicts the alignment of amino acids 11 to 49 (SEQ ID NO: X) and amino acids 52 to 91 (SEQ ID NO: X) of TANGO 140-1 (SEQ ID NO:5) with the tumor necrosis factor receptor (TNF-R) consensus sequence (SEQ ID NO:42).
• TNF-R tumor necrosis factor receptor
• Figure 20 depicts the alignment of amino acids 25 to 63 (SEQ ID NO: X) and amino acids 66 to 105 (SEQ ID NO: X) of TANGO 140-2 (SEQ ID NO:7) with the tumor necrosis factor receptor (TNF-R) consensus sequence (SEQ ID NO:42). In these alignments, an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 21 depicts the alignment of amino acids 44 to 215 of TANGO 197 (amino acids 44 to 215 of SEQ ID NO:9)(SEQ ID NO: X) and the von Willebrand Factor (vWF) consensus sequence (SEQ ID NO:43). In these alignments, an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 22 depicts the alignment of amino acids 61 to 91 (SEQ ID NO: X), amino acids 98 to 132 (SEQ ID NO: X), amino acids 138 to 172 (SEQ ID NO: X), amino acids 178 to 217 (SEQ ID NO: X), and amino acids 223 to 258 (SEQ ID NO: X) of TANGO 212 (SEQ ID NO: 12) and the epidermal growth factor (EGF) consensus sequence (SEQ ID NO:44).
• EGF epidermal growth factor
• Figure 23 depicts the alignment of amino acids 400 to 546 of TANGO 212 (amino acids 400 to 546 of SEQ ID NO:12)(SEQ ID NO: X) and the MAM consensus sequence (SEQ ID NO:45). In these alignments, an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 24 depicts the alignment of amino acids 37 to 81 of TANGO 224, form 1 (amino acids 37 to 81 of SEQ ID NO:18)(SEQ ID NO: X) and the thrombospondin type-I (TSP-I) consensus sequence (SEQ ID NO:46).
• an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 25 depicts the alignment of amino acids 24 to 169 (SEQ ID NO: X), amino acids 170 to 329 (SEQ ID NO: X) and amino acids 340 to 498 (SEQ ID NO: X) of TANGO 239 (SEQ ID NO:21) and the MAM consensus sequence (SEQ ID NO:45).
• an uppercase letter between the two sequences indicates an exact match, and a (+) indicates a conservative amino acid substitution.
• Figure 26 depicts the cDNA sequence of mouse TANGO 128 (SEQ ID NO:53) and predicted amino acid sequence of mouse TANGO 128 (SEQ ID NO:54).
• the open reading frame of SEQ ID NO:53 comprises from nucleotides 211 to 750 of SEQ ID NO:53 (SEQ ID NO:55).
• Figure 27 depicts the cDNA sequence of mouse TANGO 197 (SEQ ID NO:56) and predicted amino acid sequence of mouse TANGO 197 (SEQ ID NO:57).
• the open reading frame of SEQ ID NO:56 extends from nucleotide 3 to 1145 of SEQ ID NO:56 (SEQ ID NO:58).
• Figure 28 depicts the cDNA sequence of mouse TANGO 212 (SEQ ID NO:59) and predicted amino acid sequence of mouse TANGO 212 (SEQ ID NO:60).
• the open reading frame of SEQ ID NO:60 extends from nucleotide 180 to 1179 of SEQ ID NO:60 (SEQ ID NO:61).
• Figure 29 depicts the cDNA sequence of mouse TANGO 213 (SEQ ID NO: 62) and predicted amino acid sequence of mouse TANGO 213 (SEQ ID NO:63).
• the open reading frame of SEQ ID NO:62 extends from nucleotide 41 to 616 of SEQ ID NO:62 (SEQ ID NO:64).
• Figure 30 depicts the cDNA sequence of human TANGO 224, form 2 (clone Afhsa25a8) (SEQ ID NO:65) and predicted amino acid sequence of human TANGO 224, form 2 (clone Athsa25a8)(SEQ ID NO:66).
• the open reading frame of SEQ ID NO:65 extends from nucleotide 67 to 2690 of SEQ ID NO:65 (SEQ ID NO:67).
• Figure 31 depicts the cDNA sequence of human TANGO 239, form 2 (clone Athxe3b8)(SEQ ID NO:68) and predicted amino acid sequence of human TANGO 239, form 2 (clone Athxe3b8)(SEQ ID NO:69).
• the open reading frame of SEQ ID NO:68 extends from nucleotide 344 to 2401 of SEQ ID NO:68 (SEQ ID NO:70).
• Figure 32 depicts the cDNA sequence of mouse TANGO 239 (SEQ ID NO:71) and predicted amino acid sequence of mouse TANGO 239 (SEQ ID NO:72).
• the open reading frame of SEQ ID NO:71 extends from nucleotide 209 to 370 of SEQ ID NO:71 (SEQ ID NO:73).
• Figure 33 depicts the cDNA sequence of rat TANGO 213 (SEQ ID NO:).
• the present invention is based on the discovery of cDNA molecules encoding TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239, all of which are either wholly secreted or transmembrane proteins.
• the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins having sequence identity to vascular endothehal growth factor (NEGF), referred to herein as TANGO 128 proteins.
• TANGO 128 proteins and nucleic acid molecules comprise a family of molecules having certain conserved structural and functional features.
• the term "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 comprises 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. Members of the same family may also have common structural domains.
• the VEGF family to which the TANGO 128 proteins ofthe invention bear sequence identity are a family of mitogens which contain a platelet-derived growth factor (PDGF) domain having conserved cysteine residues. These cysteine residues form intra- and inter-chain disulfide bonds which can affect the structural integrity ofthe protein.
• a PDGF-domain refers to an amino acid sequence of about 55 to 80, preferably about 60 to 75, 65 to 70, and more preferably about 69 amino acids in length.
• a PDGF domain of TANGO 128 extends, for example, from about amino acids 269 to 337 of SEQ ID NO:2. (SEQ ID NO:75).
• conserved amino acid motifs can be used to identify TANGO 128 family members (and/or PDGF family members) having a PDGF domain.
• the following signature pattern can be used to identify TANGO 128 family members: P - x - C -[LV] - x (3) - R -C- [GSTA] - G - x (0, 3) - C- C (SEQ ID NO:46).
• TANGO 128 has such a signature pattern at about amino acids 272 to 287 of SEQ ID NO:2 (SEQ ID NO:74).
• a PDGF domain further contains at least about 2 to 10, preferably, 3 to 9, 4 to 8, or 6 to 7 conserved cysteine residues.
• SEQ ID NO:40 that conesponds to a cysteine residue at amino acid 296 of TANGO 128 (SEQ ID NO:2); there is a sixth cysteine residue in the PDGF consensus sequence (SEQ ID NO:40) that corresponds to a cysteine residue at amino acid 335 of TANGO 128 (SEQ ID NO:2); and/or there is a seventh cysteine residue in the PDGF consensus sequence (SEQ ID NO:40) that corresponds to a cysteine residue at amino acid 337 of TANGO 128 (SEQ ID NO:2).
• the PDGF consensus sequence is also available from the HMMer version 2.0 software as Accession Number PF00341.
• the present invention also features TANGO 128 proteins having a CUB domain.
• the CUB domain is associated with various developmentally regulated proteins and as such is likely to be involved in developmental processes.
• a CUB domain refers to an amino acid sequence of about 90 to about 140, preferably about 100 to 125, 110 to 115, and more preferably about 113 amino acids in length.
• a CUB domain of TANGO 128 extends, for example, from about amino acids 48 to 160 of SEQ ID NO:2. (SEQ ID NO:77)
• SEQ ID NO:77 An alignment of TANGO 128 and the CUB consensus sequence is shown in Figure 18.
• conserved amino acid motifs can be used to identify TANGO 128 family members having a CUB domain.
• the following signature pattern can be used to identify TANGO 128 family members: GS - x (3, 11) -[ST] - [PLYA] - x (2) - P - x (2,3) - Y- x (6, 8) - [WY] - x (9, 11) - [LVIF] - x - [LIF] - x (7,10) - C (SEQ ID NO:47).
• TANGO 128 has such a signature pattern at about amino acids 56 to 104 of SEQ ID NO:2 (SEQ ID NO:76).
• a CUB domain further contains at 2 or more conserved cysteine residues which are likely to form disulfide bonds which affect the structural integrity ofthe protein.
• TANGO 128 proteins having a signal sequence.
• a signal sequence includes a peptide of at least about 15 or 20 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, tryptophan, or valine.
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 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 128 family member has the amino acid sequence of SEQ ID NO:2, and the signal sequence is located at amino acids 1 to 20, 1 to 21, 1 to 22, 1 to 23 or 1 to 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 to 22 of SEQ ID NO:2 results in a mature TANGO 128 protein corresponding to amino acids 23 to 345 of SEQ ID NO:2 (SEQ ID NO:29).
• the signal sequence is normally cleaved during processing ofthe mature protein.
• a TANGO 128 protein ofthe invention includes a PDGF domain and/or a CUB domain. In another embodiment, a TANGO 128 protein ofthe invention includes a PDGF domain, a CUB domain, a signal sequence, and is secreted.
• Various features of human and mouse TANGO 128 are summarized below.
• Human TANGO 128 includes a 2839 nucleotide cDNA ( Figure 1; SEQ ID NO:l).
• nucleotide sequence depicted in SEQ ID NO: 1 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((5' GTCGACCCACGCGTCCG 3' (SEQ ID NO:), and 5' GGGCGGCCGC 3' (SEQ ID NO:), respectively).
• nucleic acid molecules ofthe 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 288 to 1322 (SEQ ID NO:3) encodes a 345 amino acid secreted protein ( Figure 1 ; SEQ ID NO:2).
• human TANGO 128 includes a 22 amino acid signal peptide (amino acids 1 to amino acid 22 of SEQ ID NO:2)(SEQ ID NO:23) preceding the mature TANGO 128 protein (corresponding to amino acid 23 to amino acid 345 of SEQ ID NO:2)(SEQ ID NO:29).
• Human TANGO 128 includes a PDGF domain from about amino acids 269 to 337 of SEQ ID NO:2 (SEQ ID NO:75).
• Human TANGO 128 further includes a CUB domain (about amino acids 48 to 160 of SEQ ID NO:2)(SEQ ID NO:77).
• EpDH237 which encodes human TANGO 128 was deposited as part of EpDHMixl with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209) on November 20, 1998 which was assigned Accession Number 98999. This deposit will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience to those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
• Figure 9 depicts a hydropathy plot of human TANGO 128. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, the hydrophobic region at the beginning ofthe plot which corresponds to about amino acids 1 to 22 of SEQ ID NO:2 is the signal sequence of TANGO 128 (SEQ ID NO:23). The cysteine residues (cys) and potential N- glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• Northern analysis of human TANGO 128 mRNA expression revealed the presence of approximately a 3.8 kb transcript that is expressed in a wide range of tissues including heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, prostate, testis, ovary, small intestine, colon, and peripheral blood leukocytes. The highest levels of expression were seen in the pancreas, kidney and ovary. An additional TANGO 128 transcript of approximately 3 kb is seen in the ovary, prostate, pancreas, and kidney.
• the human gene for TANGO 128 was mapped on radiation hybrid panels to the long arm of chromosome 4, in the region q28-31. Flanking markers for this region are WI- 3936 and AFMCO27ZB9.
• the FGC fusenogen gene cluster
• GYP glycophorin cluster
• IL15 interlukin 15
• TDO2 tryptophab oxygenase
• MLR mineralcorticoid receptor
• TANGO 128 protein binds to endothehal cells with high affinity: In vitro studies of AP-T128 binding to bACE cells (novine adrenal cortical capillary endothehal cells) were performed with Phospha-Light chemiluminescent assay system (Tropix, Inc. Bedford, MA). bACE cells were plated into gelatinized 96- well plates (3000 cells/well) and allowed to grow to confiuency. The cells were then fixed with acetone. AP-hT128 was incubated with the cells for 1 hour. Specific binding was detected with a microplate luminometer according to the manufacturer's instruction.
• AP- T128 was capable of exhibiting binding to adrenal cortex, ovary (medulla), mucosal layer of colon, and bronchial epithelium of lung in the mouse.
• Recombinant TANGO 128 protein stimulates endothehal cell proliferation in vitro The ability of Al protein to stimulate the growth of endothehal cells was tested by bovine o adrenal capillary endothehal (bACE) cell proliferation assay. Briefly, cultured bovine capillary endothehal cells dispersed with 0.05%> trypsin/0.53 mM EDTA were plated onto gelatinized (Difco) 24- well culture plates (12,500 cell/well) in DMEM containing 10%> bovine calf serum (BCS) and incubated for 24 hours. The media was replaced with 0.5 ml DMEM containing 5%> bovine calf serum and either buffer only or buffer containing AP- 5 hT 128 were added.
• bovine o adrenal capillary endothehal (bACE) cell proliferation assay Briefly, cultured bovine capillary endothehal cells dispersed with 0.05%> trypsin/0.53 mM EDTA were plated onto gelatinized (
• TANGO 128 was shown to exhibit proliferative activity on endothehal cells in vitro. Preliminary studies show that AP- T128 has mitogenic activity on primary bovine adrenal cortical capillary endothehal cells (bACE cells). 0
• a mouse homolog of human TANGO 128 was identified.
• a cDNA encoding mouse TANGO 128 was identified by analyzing the sequences of clones present in a mouse osteoblast lipolysaccharide (LPS) stimulated cDNA library. This analysis led to the 5 identification of a clone, jtmoal l4h01, encoding full-length mouse TANGO 128.
• the murine TANGO 128 cDNA of this clone is 764 nucleotides long ( Figure 26; SEQ ID NO:53).
• nucleotide sequence depicted in SEQ ID NO:53 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGT CCG (SEQ ID NO:), and GGGCGGCCGC (SEQ ID NO:), respectively).
• nucleic acid molecules ofthe 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 comprises nucleotides 211 to 750 of SEQ ID NO:53 (SEQ ID NO:55), and encodes a 179 amino acid secreted protein ( Figure 26; SEQ ID NO:54).
• nucleotide at position 595 is a guanine (G) (SEQ ID NO: 78).
• amino acid at position 129 is glycine (G)(SEQ ID NO:79)
• nucleotide at position 595 is a cytosine (C) (SEQ ID NO: 80).
• the amino acid at position 129 is arginine (R)(SEQ ID NO:81)
• the nucleotide at position 595 is a thymidine (T) (SEQ ID NO:82).
• the amino acid at position 129 is a stop codon (Opal) and results in a polypeptide of 128 aa in length (SEQ ID NO:83).
• nucleotide sequence of mouse Tango 1208 is a thymidine (T) (SQ ID NO:84).
• amino acid at position 167 is valine (V)(SEQ ID NO:85)
• nucleotide at position 710 is a cytosine (C) (SEQ ID NO:86).
• amino acid at position 167 is alanine (A)(SEQ ID NO:87)
• nucleotide at position 710 is adenine (A)(SEQ ID NO:88).
• the amino acid at position 167 is glutamine (E)(SEQ ID NO:89).
• the nucleotide at position 710 is guanine (G)(SEQ ID NO:90).
• the amino acid at position 167 is glycine (G)(SEQ ID NO:91).
• nucleotide sequence of mouse Tango 12 the nucleotide at position 725 is a thymidine (T) (SQ ID NO:92).
• amino acid at position 172 is leucine (L)(SEQ ID NO:93)
• nucleotide at position 725 is a cytosine (C) (SEQ ID NO:94).
• amino acid at position 172 is serine (S)(SEQ ID NO:95)
• nucleotide at position 725 is a adenine (A) (SEQ ID NO:96).
• the amino acid at position 172 is a stop codon (Amber) and results in a polypeptide of 171 aa in length (SEQ ID NO:97).
• the nucleotide at position 725 is a guanine (G) (SEQ ID NO:98).
• the amino acid at position 172 is tryptophan (SEQ ID NO:99).
• In situ tissue screening was performed on mouse adult and embryonic tissue to analyze the expression of mouse TANGO 128 mRNA. Ofthe tissues tested, expression in the adult mouse was highest in the reproductive tract, testes and ovary.
• Embryonic expression was seen in a number of tissues. The highest expressing tissue was the capsule ofthe kidney which was seen at E14.5 and continues to PI.5. Adult kidney did not show this expression pattern. Other tissues with strong expression include the frontal cortex and developing cerebellum ofthe brain, various cartilage structures ofthe head including Meckel's cartilage and the spinal column. Numerous tissues with a smooth muscle component also showed expression including the small intestine and stomach as well as the diaphragm at early embryonic stages, E13.4 and E14.5. At E13.5, signal in the brain was seen in areas adjacent to the ventricles, which includes the roof of the midbrain and the roof of the neopallial cortex.
• the capsule ofthe adrenal gland had expression but to a lesser extent than that seen in the kidney.
• the developing musculature ofthe feet had strong expression as well.
• signal in the muscle and skin was decreased.
• Diaphragm expression was no longer apparent but the smooth muscle ofthe intestine was still seen.
• Strongest signal was seen in the skin and muscle ofthe snout and feet, capsule ofthe kidney, the frontal cortex, and the cerebellar promordium.
• Signal from lung had decreased and become ubiquitous.
• signal was most apparent in the frontal cortex and cerebellar primordium ofthe brain, the snout, Meckel's cartilage, submandibular gland, spinal column, and capsule ofthe kidney which had the strongest signal.
• Signal was also seen from the smooth muscle ofthe gut.
• the pattern was nearly identical to that seen at E17.5.
• the pattern was very similar to that seen at E17.5 and 18.5 with strongest signal seen from Meckel's cartilage, basiocippital and basisphenoid bone, spinal column, developing cerebellum, and capsule ofthe kidney. By this stage of development, expression in most other tissues and organs had dropped to nearly background levels.
• Human and murine TANGO 128 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 77.8%> .
• the human and murine TANGO 128 full length cDNAs are 83.3% identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
• human and murine TANGO 128 are 81.3% identical.
• TANGO 128 proteins ofthe invention bear some similarity to the VEGF family of growth factors. Accordingly, TANGO 128 proteins likely function in a similar manner as members ofthe VEGF family. Thus, TANGO 128 modulators can be used to treat any VEGF-associated disorders and modulate normal VEGF functions.
• VEGF family members play a role in angiogenesis and endothehal cell growth.
• VEGF is an endothehal cell specific mitogen and has been shown to be a potent angiogenic factor. Fenara et al. (1992) Endocr. Rev. 13:18-32.
• VEGF family members can serve as regulators of normal and pathological angiogenesis. Olofsson et al. (1996) Proc. Natl. Acad. Sci. USA 93:2576-2581; Berse et al. (1992) Mol. Biol. Cell. 3:211-220; Shweiki et al. (1992) Nature 359:843-845.
• the TANGO 128 proteins ofthe invention likely play a role in angiogenesis. Accordingly, the TANGO 128 proteins, nucleic acids and/or modulators ofthe invention are useful angiogenic modulators.
• the TANGO 128 proteins, nucleic acids and/or modulators can be used in the treatment of wounds, e.g., modulate wound healing, and/or the regrowth of vasculature, e.g., the regrowth of vasculature into ischemic organs, e.g., such as in coronary bypass.
• TANGO 128 proteins, nucleic acids and/or modulators can be used to promote growth of cells in culture for cell based therapies.
• TANGO 128 polypeptides, nucleic acids and/or modulators thereof can be used to modulate angiogenesis in proliferative disorders such as cancer, (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endothelio sarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leimyosarcoma, rhabdotheliosarcoma, colon sarcoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma,
• TANGO 128 is expressed in the reproductive tract, particularly in the ovaries and testis, the TANGO 128 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 be used to treat or modulate disorders associated with the testis including, without limitation, the Klinefelter syndrome (both the classic and mosaic forms), XX male syndrome, variococele, germinal cell aplasia (the Sertoli cell-only syndrome), idiopathic azoospermia or severe oligospermia, crpytochidism, and immotile cilia syndrome, or testicular cancer (primary germ cell tumors ofthe testis).
• Klinefelter syndrome both the classic and mosaic forms
• XX male syndrome variococele
• germinal cell aplasia the Sertoli cell-only syndrome
• idiopathic azoospermia or severe oligospermia crpytochidism
• crpytochidism crpytochidism
• immotile cilia syndrome or testicular cancer (primary germ cell tumors ofthe testis).
• TANGO 128 polypeptides, nucleic acids, or modulators thereof can be used to treat testicular disorders, such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gonorchea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• testicular disorders such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gonorchea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• testicular disorders such as unilateral testi
• such molecules can be used to treat or modulate disorders associated with the ovaries, including, without limitation, ovarian tumors, McCune- Albright syndrome (polyostotic fibrous dysplasia).
• disorders associated with the ovaries including, without limitation, ovarian tumors, McCune- Albright syndrome (polyostotic fibrous dysplasia).
• the TANGO 128 polypeptides, nucleic acids and/or modulators can be used in the treatment of infertility.
• the TANGO 128 polypeptides, nucleic acids and/or modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the tissues ofthe reproductive tract other than the ovaries and testis.
• such molecules can be used to treat or modulate disorders associated with the female reproductive tract including, without limitation, uterine disorders, e.g., hyperplasia ofthe endometrium, uterine cancers (e.g., uterine leiomyomoma, uterine cellular leiomyoma, leiomyosarcoma ofthe uterus, malignant mixed mullerian Tumor of uterus, uterine Sarcoma), and dysfunctional uterine bleeding (DUB).
• uterine disorders e.g., hyperplasia ofthe endometrium
• uterine cancers e.g., uterine leiomyomoma, uterine cellular leiomyoma, leiomyosarcoma ofthe
• TANGO 140 In another aspect, the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins refened to herein as TANGO 140 proteins. Described herein are TANGO 140-1 (SEQ ID NO:4), and TANGO 140-2 (SEQ ID NO:6) nucleic acid molecules and the corresponding polypeptides which the nucleic acid molecules encode (SEQ ID NO:5 and SEQ ID NO:7, respectively).
• the TANGO 140 proteins and nucleic acid molecules comprise a family of molecules having certain conserved structural and functional features.
• the term "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. For example, a family can comprises 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. Members of the same family may also have common structural domains.
• the tumor necrosis factor receptor (TNF-R) family to which the TANGO 140 proteins ofthe invention bear sequence similarity are a family of cell surface proteins which function as receptors for cytokines and which contain conserved patterns of cysteine residues.
• conserved cysteine residues refer to cysteine residues which are maintained within TANGO 140 family members (and/or TNF-R family members). This cysteine pattern is referred to herein as a tumor necrosis factor receptor (TNF-R) domain.
• TNF-R tumor necrosis factor receptor
• TANGO 140 proteins having at least one to four TNF-R domains, preferably two TNF-R domains.
• a TNF-R domain refers to an amino acid sequence of about 25 to 50, preferably about 30 to 45, 30 to 40, and more preferably about 35 to 39 or 40 amino acids in length.
• a TNF-R domain of TANGO 140-1 extends, for example, from about amino acid 11 to amino acid 49 (SEQ ID NO: 100) and/or from about amino acid 52 to amino acid 91 of SEQ ID NO:5 (SEQ ID NO:101); a TNF-R domain of TANGO 140-2 extends, for example, from about amino acid 25 to amino acid 63 (SEQ ID NO: 102) and/or from about amino acid 66 to amino acid 105 of SEQ ID NO:7 (SEQ ID NO: 103).
• conserveed amino acid motifs refened to herein as "consensus patterns" or "signature patterns", can be used to identify TANGO 140 family members (and/or TNF-R family members) having a TNF-R domain.
• the following signature pattern can be used to identify TANGO 140 family members: C - x (4, 6) - [FYH] - x (5, 10) - C -x (0, 2) - C - x (2, 3) - C - x (7, 11) - C - x (4, 6) - [DNEQSKP] - x (2) - C (SEQ ID NO:48).
• the signature patterns or consensus patterns described herein are described according to Prosite Signature designation.
• amino acids are indicated according to their universal single letter designation; "x” designates any amino acid; x(n) designates “n” number of amino acids, e.g., x (2) designates any two amino acids, e.g., x (4, 6) designates any four to six amino acids; and, amino acids in brackets indicates any one ofthe amino acids within the brackets, e.g., [FYH] indicates any of one of either F (phenylalanine), Y (tyrosine) or H (histidine).
• This consensus sequence can also be obtained as Prosite Accession Number PDOC00561.
• TANGO 140-1 has such a signature pattern at about amino acids 11 to 49 (SEQ ID NO: 100) and at about amino acids 52 to 91 of SEQ ID NO:5 (SEQ ID NO:101).
• TANGO 140-2 has such a signature pattern at about amino acids 25 to 63 (SEQ ID NO: 102) and at amino acids 66 to 105 of SEQ ID NO:7 (SEQ ID NO: 103).
• a TNF-R domain further contains at least about 2 to 10, preferably, 3 to 8, or 4 to 6 conserved cysteine residues.
• conserved cysteine residues can be found at amino acids 52, 66, 69, 72, 83 and/or 91 ofthe second TNF-R domain of TANGO 140-1 (SEQ ID NO:5).
• conserved cysteine residues can be found at amino acids 25, 37, 40, 43, 53 and/or 63 ofthe first TNF- R domain of TANGO 140-2 (SEQ ID NO:7); and at amino acids 66, 80, 83, 86, 97 and/or 105 of TANGO-140-2 (SEQ ID NO:7).
• the TNF-R consensus sequence is available from the HMMer version 2.0 software as Accession Number PF00020.
• Software for HMM- . based profiles is available from http://www.csc.ucsc.edu/research/compbio/sam.html and from http://genome.wustl.edu/eddy/hmmer.html.
• the present invention also includes TANGO 140 proteins having a transmembrane domain.
• a transmembrane domain refers to an amino acid sequence having at least about 25 to about 40 amino acid residues in length and which contains at least about
• a transmembrane domain contains at least about 30-35 amino acid residues, preferably about
• transmembrane domain includes from about amino acids 147 to 170 of TANGO 140-1 (SEQ ID NO: 1
• a TANGO 140 protein includes at least one TNF-R domain, preferably two, three or four TNF-R domains and is secreted.
• a TANGO 140 protein ofthe invention includes at least one TNF-R domain, preferably two, three or four TNF-R domains, a transmembrane domain and is a membrane bound protein.
• Human TANGO 140-1 includes a 1550 nucleotide cDNA ( Figure 2; SEQ ID NO:4). It is noted that the nucleotide sequence depicted in SEQ ID NO:4 contains a Not I adapter sequence on the 3' end (5' GGGCGGCCGC 3')(SEQ ID NO:). Thus, it is to be understood that the nucleic acid molecules ofthe 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 TANGO 140-1 comprises nucleotides 2 to 619 of SEQ ID NO:4 (SEQ ID NO:38), and encodes a 206 amino acid putative membrane protein ( Figure 2; SEQ ID NO:5).
• human TANGO 140-1 includes an extracellular domain (about amino acids 1 to 146 of SEQ ID NO:5)(SEQ ID NO:35), a transmembrane (TM) domain (amino acids 147 to 170 of SEQ ID NO:5)(SEQ ID NO:36); and a cytoplasmic domain (amino acids 171 to 206 of SEQ ID NO:5)(SEQ ID NO:37).
• a human TANGO 140-1 protein contains an extracellular domain at amino acid residues 1 to 146 of SEQ ID NO:5 ( SEQ ID NO:), a transmembrane domain at amino acid residues 147 to 170 of SEQ ID NO:5 (SEQ ID NO:), and a cytoplasmic domain at amino acid residues 171 to 206 of SEQ ID NO:5 (SEQ ID NO:).
• the extracellular region of human TANGO 140-1 includes TNF-R domains from about amino acids 11 to 49 of SEQ ID NO:5 (SEQ ID NO: 100) and from about amino acids 52-91 of SEQ ID NO:5 (SEQ ID NO:101).
• EpDH137 which encodes human TANGO 140-1 was deposited as part of
• EpDHMixl with the American Type Culture Collection, 10801 University Boulevard,
• Figure 10 depicts a hydropathy plot of human TANGO 140-1. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, amino acids 147 to 170 of SEQ
• SEQ ID NO:5 (SEQ ID NO:36) conespond to a transmembrane domain of TANGO 140-1.
• the cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• TANGO 140-2 An additional clone having significant homology to human TANGO 140-1 was identified.
• the clone was sequenced and is likely to be a splice variant of TANGO 140-1. This variant is refened to herein as TANGO 140-2.
• the human TANGO 140-2 includes a 3385 nucleotide cDNA ( Figure 3; SEQ ID NO:6). It is noted that the nucleotide sequence depicted in SEQ ID NO:6 contains a Not I adapter sequence on the 3' end (5' GGGCGG CCGC 3' (SEQ ID NO:)).
• nucleic acid molecules ofthe 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 TANGO 140-2 comprises nucleotides 2 to 619 of SEQ ID NO:6 (SEQ ID NO:38), and encodes a 198 amino acid putative secreted protein (Figure 3; SEQ ID NO:7).
• Human TANGO 140-2 also includes TNF-R domains from about amino acids 25 to 63 of SEQ ID NO:7 (SEQ ID NO: 102), and from about amino acids 66 to 105 of SEQ ID NO:7 (SEQ ID NO:103).
• EpDH185 which encodes human TANGO 140-2 was deposited as part of EpDHMixl with the American Type Culture Collection (10801 University Boulevard,
• FIG. 11 depicts a hydropathy plot of TANGO 140-2. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, TANGO 140-2 does not have a transmembrane domain. The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• TANGO 140 Nucleic Acids, Polypeptides, and Modulators Thereof
• the TANGO 140 proteins ofthe invention comprise a family of proteins having sequence similarity to members ofthe TNF-R superfamily.
• the TANGO 140 proteins ofthe invention are members ofthe TNF-R superfamily. Accordingly, TANGO 140 proteins likely function in a similar manner as members ofthe TNF-R family and TANGO 140 modulators can be used to treat any TNF-R/NGF-R- associated disorders.
• TNF-R tumor necrosis factor receptor
• TANGO 140 molecules ofthe invention can modulate neuronal differentiation and survival.
• NGF nerve growth factor
• TANGO 140 polypeptides, nucleic acids and/or modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the nervous system.
• Such molecules may be used in the treatment of neural disorders, including, without limitation, epilepsy, muscular dystrophy, and neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease).
• TGF- and TGF- ⁇ bind to TGF-RI and TGF-RII, leading to a diverse range of effects including inflammation and tumor cell death.
• a soluble protein e.g., a cytokine, or membrane-bound protein
• TANGO 140 polypeptides, nucleic acids and/or modulators thereof can be used to treat TANGO 140 associated disorders which can include TNF-related disorders (e.g., acute myocarditis, myocardial infarction, congestive heart failure, T cell disorders (e.g., dermatitis, fibrosis)), immunological differentiative and apoptotic disorders (e.g., hyper-pro liferative syndromes such as systemic lupus ery hematosus (lupus)), and disorders related to angiogenesis (e.g., tumor formation and/or metastasis, cancer).
• TNF-related disorders e.g., acute myocarditis, myocardial infarction, congestive heart failure
• T cell disorders e.g., dermatitis, fibrosis
• immunological differentiative and apoptotic disorders e.g., hyper-pro liferative syndromes such as systemic lupus ery hematos
• cancers include benign tumors, neoplasms or tumors (such as carcinomas, sarcomas, adenomas or myeloid lymphoma tumors, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondro sarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leimyosarcoma, rhabdotheliosarcoma, colon sarcoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadeno
• acute lymphocytic leukemia acute myelocytic leukemia (myelolastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia), or polycythemia vera, or lymphomas (Hodgkin's disease and non-Hodgkin's diseases), multiple myelomas and Waldenstr ⁇ m's macroglobulinemia.
• acute myelocytic leukemia myelolastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia
• chronic leukemias chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia
• polycythemia vera or lymphomas (Hodgkin's disease and non-Hodgkin's
• TANGO 140 is expressed in a stimulated mesangial library
• the TANGO 140 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.
• Mesangial cells are known to play an important role in maintaining structure and function ofthe glomerulus and in the patho genesis of glomerular diseases.
• the local production of chemokines by mesangial cells has been linked to inflammatory processes within the glomerulus.
• high glucose directly increases oxidative stress in glomerular mesangial cells, a target cell of diabetic nephropathy.
• TANGO 140 polypeptides, nucleic acids and/or modulators thereof can be used to modulate the function, morphology, proliferation and/or differentiation of cells in the kidney. Such molecules can also be used to treat disorders associated with abnormal or abenant metabolism or function of cells in the kidney.
• kidney 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 eryfhematosus, 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 hypo
• glomerular diseases e.g., acute and chronic glomerulonephritis
• the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins refened to herein as TANGO 197 proteins.
• the TANGO 197 proteins and nucleic acid molecules comprise a family of molecules having certain conserved structural and functional features.
• the term "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. Members ofthe same family may also have common structural domains.
• a vWF domain refers to an amino acid sequence of about 150 to 200, preferably about 160 to 190, 170 to 180, and more preferably about 172 to 175 amino acids in length.
• a vWF domain of TANGO 197 extends, for example, from about amino acids 44 to 215 of SEQ ID NO:9 (SEQ ID NO: 105).
• conserved amino acid motifs can be used to identify TANGO 197 family members having a vWF domain.
• the following signature pattern can be used to identify TANGO 197 family members: D - x (2) - F -[ILN] - x - D - x - S - x (2, 3) - [ILN]- x (10, 12) - F (SEQ ID NO:
• the signature patterns or consensus patterns described herein are described according to the following designation: all amino acids are indicated according to their universal single letter designation; "x” designates any amino acid; x(n) designates “n” number of amino acids, e.g., x (2) designates any two amino acids, e.g., x (2, 3) designates any of two to three amino acids; and, amino acids in brackets indicates any one ofthe amino acids
• TANGO 197 has such a signature pattern at about amino acids 44 to 65 of SEQ ID NO:9 (SEQ ID NO: 104).
• TANGO 197 proteins having a signal sequence.
• a “signal sequence” includes a peptide of at least
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 amino acid residues, and has at least
• a signal sequence serves to direct a protein containing such a sequence to a lipid bilayer.
• a TANGO 197 family member has the amino acid sequence of SEQ ID NO:9, and the signal sequence is located at amino acids 1 to 25, 1 to
• a TANGO 197 protein contains a signal sequence of about amino acids 1 to 27 of SEQ ID NO:2 ((SEQ ID NO:24) which results in an extracellular domain consisting of amino acids 28 to 301 of SEQ ID NO:2 (SEQ ID NO:), and a mature
• TANGO 197 protein conesponding to amino acids 28 to 333 of SEQ ID NO:2 (SEQ ID NO:).
• the signal sequence is normally cleaved during processing ofthe mature protein.
• Various features of human and mouse TANGO 197 are summarized below.
• Human TANGO 197 includes a 2272 nucleotide cDNA ( Figure 4; SEQ ID NO:8). It is noted that the nucleotide sequence depicted in SEQ ID NO: 8 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCT (SEQ ID NO:), and GGGCGGCCGC (SEQ ID NO:), respectively).
• nucleic acid molecules ofthe invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
• the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 197 includes a 27 amino acid signal peptide (amino acids 1 to about amino acid 27 of SEQ ID NO:9)(SEQ ID NO:24) preceding the mature TANGO 197 protein (conesponding to about amino acid 28 to amino acid 333 of SEQ ID NO:9)(SEQ ID NO:30).
• Human TANGO 197 includes a vWF domain from about amino acids 44 to 215 of SEQ ID NO:9.
• EpDH213 which encodes human TANGO 197 was deposited as part of EpDHMixl with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209) on November 20, 1998 which was assigned Accession Number 98999. This deposit will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience to those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
• Figure 12 depicts a hydropathy plot of human TANGO 197. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, the hydrophobic region at the beginning ofthe plot which corresponds to about amino acids 1 to 27 of SEQ ID NO:9 (SEQ ID NO:24) is the signal sequence of TANGO 197. The cysteine residues (cys) and potential N- glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• cysteine residues cys
• Ngly potential N- glycosylation sites
• human TANGO 197 protein is a transmembrane protein that contains an extracellular domain at amino acid residues 28-301 of SEQ ID NO:9 (SEQ ID NO:), a transmembrane domain at amino acid residues 302 to 319 of SEQ ID NO:9 (SEQ ID NO:), and a cytoplasmic domain at amino acid residues 320 -333 of SEQ ID NO:9 (SEQ ID NO:).
• a human TANGO 197 protein contains an extracellular domain at amino acid residues 320 to 333 of SEQ ID NO:9 ( SEQ ID NO:), a transmembrane domain at amino acid residues 302 to 319 of SEQ ID NO:9 (SEQ ID NO:), and a cytoplasmic domain at amino acid residues 1 to 301 of SEQ ID NO:9 (SEQ ID NO:).
• Northern analysis of human TANGO 197 mRNA expression revealed expression in a wide variety of tissues such as brain, skeletal muscle, colon, thymus, spleen, kidney, liver, and the small intestine. The highest levels of expression were seen in tissues such as the heart, placenta and lung. There was no expression ofthe transcript in peripheral blood leukocytes.
• a mouse homolog of human TANGO 197 was identified.
• a cDNA encoding mouse TANGO 197 was identified by analyzing the sequences of clones present in a mouse testis (Sertoli TM4 cells) cDNA library. This analysis led to the identification of a clone, jtmzb062c08, encoding full-length mouse TANGO 197.
• the murine TANGO 197 cDNA of this clone is 4417 nucleotides long ( Figure 27; SEQ ID NO:56). It is noted that the nucleotide sequence depicted in SEQ ID NO:56 contains a Not I adapter sequence on the 3' end (5' GGGCGGCCGC 3' (SEQ ID NO:)).
• nucleic acid molecules ofthe 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 comprises nucleotides 3-1145 of SEQ ID NO:56 (SEQ ID NO:58), encodes a 381 amino acid transmembrane protein (Figure 27; SEQ ID NO:57).
• mouse TANGO 197 protein is a transmembrane protein that contains an extracellular domain at amino acid residues 161 to 381 of SEQ ID NO:57 (SEQ ID NO:), a transmembrane domain at amino acid residues 139 to 160 of SEQ ID NO:57 (SEQ ID NO:), and a cytoplasmic domain at amino acid residues 1 to 138 of SEQ ID NO:57 (SEQ ID NO:).
• a mouse TANGO 197 protein contains an extracellular domain at amino acid residues 1 to 139 of SEQ ID NO:57 ( SEQ ID NO:), a transmembrane domain at amino acid residuesl39 to 160 of SEQ ID NO:57 (SEQ ID NO:), and a cytoplasmic domain at amino acid residues 161 to 381 of SEQ ID NO:57 (SEQ ID NO:).
• the library array procedure entailed preparing a PCR mixture by adding to the standards reagents (Taq Polymerase, dNTPs, and PCR buffer) a vector primer, a primer internal to the gene of interest, and an aliquot of a library in which expression was to be tested.
• This procedure was performed with many libraries at a time in a 96 well PCR tray, with 80 or more wells containing libraries and a control well in which the above primers were combined with the clone of interest itself.
• the control well served as an indicator ofthe fragment size to be expected in the library wells, in the event the clone of interest was expressed within.
• Amplification was performed in a PCR machine, employing standard PCR conditions for denaturing, annealing, and elongation, and the resultant mixture was mixed with an appropriate loading dye and run on an ethidium bromide-stained agarose gel. The gel was later viewed with UN light after the D ⁇ A loaded within its lanes had time to migrate into the gels. Lanes in which a band corresponding with the control band was visible indicated the libraries in which the clone of interest was expressed.
• Results ofthe library array procedure revealed strong expression in the choroid plexus, 12.5 day whole mouse embryo, LPS-stimulated osteoblast tissue, hyphae stimulated long term bone marrow cells. Weak expression was detected in TM4 (Sertoli cells), from testis, esophagus, LPS-stimulated osteoblast tissue.
• Human and murine TANGO 197 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 88.0 %> .
• the human and murine TANGO 197 full length cDNAs are 52.8% identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
• human and murine TANGO 197 are 51.6% identical.
• TANGO 197 exhibits expression in the lung
• TANGO 197 polypeptides, nucleic acids, or modulators thereof can be used to treat pulmonary (lung) disorders, such as atelectasis, pulmonary congestion or edema, chronic obstructive airway disease (e.g., emphysema, chronic bronchitis, bronchial asthma, and bronchiectasis), diffuse interstitial diseases (e.g., sarcoidosis, pneumoconiosis, hypersensitivity pneumonitis, Goodpasture's syndrome, idiopathic pulmonary hemosiderosis, pulmonary alveolar proteinosis, desquamative interstitial pneumonitis, chronic interstitial pneumonia, fibrosing alveolitis, hamman-rich syndrome, pulmonary eosinophilia, diffuse interstitial fibrosis, Wegener's granulomatosis, lymphomatoid granulomatosis, and lipid pneumonia), or
• TANGO 197 polypeptides, nucleic acids, or modulators thereof can be used to treat testicular disorders, such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gononhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• testicular disorders such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gononhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• the TANGO 197 polypeptides, nucleic acids and/or modulators thereof can be used to modulate, for example and without limitation, Klinefelter syndrome (both the classic and mosaic forms), XX male syndrome, variococele, germinal cell aplasia (the Sertoli cell-only syndrome), idiopathic azoospermia or severe oligospermia, crpytochidism, and immotile cilia syndrome, or testicular cancer (primary germ cell tumors ofthe testis).
• Klinefelter syndrome both the classic and mosaic forms
• XX male syndrome variococele
• germinal cell aplasia the Sertoli cell-only syndrome
• idiopathic azoospermia or severe oligospermia crpytochidism
• crpytochidism crpytochidism
• immotile cilia syndrome or testicular cancer (primary germ cell tumors ofthe testis).
• TANGO 197 polypeptides, nucleic acids, or modulators thereof can be used to treat testicular disorders, such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gonorrhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• testicular disorders such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gonorrhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• Proteins ofthe type A module superfamily which incorporate a vWF domain participate in multiple ECM and cell/ECM interactions.
• proteins having a vWF domain have been found to play a role in cellular adhesion, migration, homing, pattern formation and/or signal transduction after interaction with several different ligands (Colombatti et al. (1993) Matrix 13:297-306).
• TANGO 197 proteins ofthe invention likely play a role in various extracellular matrix interactions, e.g., matrix binding, and/or cellular adhesion.
• a TANGO 197 activity is at least one or more ofthe following activities: 1) regulation of extracellular matrix structuring; 2) modulation of cellular adhesion, either in vitro or in vivo; 3) regulation of cell trafficking and/or migration.
• the TANGO 197 proteins, nucleic acid molecules and/or modulators can be used to modulate cellular interactions such as cell-cell and/or cell-matrix interactions and thus, to treat disorders associated with abnormal cellular interactions.
• TANGO 197 polypeptides, nucleic acids and/or modulators thereof can also be used to modulate cell adhesion in prohferative disorders, such as cancer.
• types of cancers include benign tumors, neoplasms or tumors (such as carcinomas, sarcomas, adenomas or myeloid lymphoma tumors, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondro sarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leimyosarcoma, rhabdotheliosarcoma, colon sarcoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal
• acute lymphocytic leukemia acute myelocytic leukemia (myelolastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia), or polycythemia vera, or lymphomas (Hodgkin's disease and non-Hodgkin's diseases), multiple myelomas and Waldenstr ⁇ m's macroglobulinemia.
• TANGO 212 acute myelocytic leukemia
• acute myelocytic leukemia myelolastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia
• chronic leukemias chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia
• polycythemia vera or lymphomas (
• the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins refened to herein as TANGO 212 proteins.
• the TANGO 212 proteins and nucleic acid molecules comprise a family of molecules having certain conserved structural and functional features.
• the term "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 comprises 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. Members of the same family may also have common structural domains.
• the EGF family to which the TANGO 212 proteins ofthe invention bear sequence similarity are a family of mitogens which contain a conserved pattern of cysteine residues.
• conserved cysteine residues refer to cysteine residues which are maintained within TANGO 212 family members (and or EGF family members). This cysteine pattern is refened to herein as an epidermal growth factor (EGF) domain. These cysteine residues form disulfide bonds which can affect the structural integrity ofthe protein.
• EGF epidermal growth factor
• an EGF- domain refers to an amino acid sequence of about 25 to 50, preferably about 30 to 45, 30 to 40, and more preferably about 31, 35, 36 to 40 amino acids in length.
• conserved amino acid motifs can be used to identify TANGO 212 family members (and/or EGF family members) having an EGF domain.
• the following signature pattern referred to herein as a EGF-like conscensus sequence can be used to identify TANGO 212 family members: C - x - C - x (5, 11) - G - x (2, 3) - C (SEQ ID NO:50).
• TANGO 212 has such a signature pattern at about amino acids 80 to 91 (SEQ ID NO:106), amino acids 156 to 172 (SEQ ID NO:107), amino acids 200 to 217 (SEQ ID NO: 108) and/or amino acids 245 to 258 of SEQ ID NO:12 (SEQ ID NO:109).
• An EGF domain of TANGO 212 extends, for example, from about amino acids 61 to 91 of SEQ ID NO:12 (SEQ ID NO:110), from about amino acids 98 to 132 of SEQ ID NO:12 (SEQ ID NO:l l l), from about amino acids 138 to 172 of SEQ ID NO:12 (SEQ ID NO:112), from about amino acids 178 to 217 of SEQ ID NO:12 (SEQ ID NO:l 13), and/or from about amino acids 223 to 258 of SEQ ID NO: 12 (SEQ ID NO:l 14).
• An EGF domain further contains at least about 2 to 10, preferably, 3 to 9, 4 to 8, or 6 to 7 conserved cysteine residues.
• cysteine residue in the EGF-like consensus sequence that corresponds to a cysteine residue at amino acid 61 ofthe first EGF domain of TANGO 212 (SEQ ID NO: 12); there is a second cysteine residue in the EGF-like consensus sequence that conesponds to a cysteine residue at amino acid 69 ofthe first EGF domain of TANGO 212 (SEQ ID NO:12); there is a third cysteine residue in the EGF-like consensus sequence that conesponds to a cysteine residue at amino acid 74 ofthe first EGF domain of TANGO 212 (SEQ ID NO:12); there is a fourth cysteine residue in the EGF-like consensus sequence that conesponds to a cysteine residue at amino acid 80 ofthe first EGF domain of TANGO 212 (SEQ ID NO:12); there is a fifth cysteine residue in the EGF-like consensus sequence that conesponds to a cysteine residue at amino acid 82
• conserved cysteine residues can be found at amino acids 98, 105, 109, 118, 120 and/or 132 ofthe second EGF domain of TANGO 212 (SEQ ID NO:12); at amino acids 138, 143, 147, 156, 158 and/or 172 ofthe third EGF domain of TANGO 212 (SEQ ID NO:12); at amino acids 178, 185, 191, 200, 202 and/or 217 ofthe fourth EGF domain of TANGO 212 (SEQ ID NO:12); and at amino acids 223, 230, 236, 245, 247 and/or 258 ofthe fifth EGF domain of TANGO 212 (SEQ ID NO: 12).
• the EGF-like consensus sequence is available from the HMMer version 2.0 software as Accession Number PF00008.
• Software for HMM-based profiles is available from http://www.csc.ucsc.edu/research/compbio/sam.html and from http://genome.wustl.edu eddy/nmmer.html.
• the present invention also features TANGO 212 proteins having a MAM domain.
• the MAM domain is associated with various adhesive proteins and as such is likely to have adhesive function. Within MAM domains are conserved cysteine residues which play a role in the adhesion of a MAM domain to other proteins.
• a MAM domain refers to an amino acid sequence of about 120 to about 170, preferably about 130 to 160, 140 to 150, and more preferably about 145 to 147 amino acids in length. conserveed amino acid motifs, refened to herein as "consensus patterns" or
• signature patterns can be used to identify TANGO 212 family members having a MAM domain.
• the following signature pattern can be used to identify TANGO 212 family members: G - x - [LIVMFY] (2) - x (3) - [STA] - x (10, 11) - [LV] - x (4,6) - [LIVMF] - x (6, 7) - C - [LIVM] - x (3) - [LIVMFY] - x (3, 4) - [GSC] (SEQ ID NO:51).
• TANGO 212 has such a signature pattern at about amino acids 431 to 472 of SEQ ID NO:12 (SEQ ID NO:115).
• a MAM domain further contains at least about 2 to 6, preferably, 3 to 5, more preferably 4 conserved cysteine residues.
• conserved cysteine residues can be found. For example, as shown in Figure 23, there is a first cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 402 of TANGO 212 (SEQ ID NO: 12); there is a second cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 409 of TANGO 212 (SEQ ID NO: 12); there is a third cysteine residue in the MAM consensus sequence that corresponds to a cysteine residue at amino acid 463 of TANGO 212 (SEQ ID NO:12); and/or there is a fourth cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 544 of TANGO 212 (SEQ ID NO:12).
• the MAM consensus sequence is available from the HMMer version 2.0 software as Accession Number PF00629.
• Software for HMM-based profiles is available from http://www.csc.ucsc.edu/research/compbio/sam.html and from http ://genome.wustl.edu/eddy/hmmer.html.
• TANGO 212 proteins having a signal sequence.
• a signal sequence includes a peptide of at least about 15 or 20 amino acid residues in length which occurs at the N-terminus of secretory and membrane-bound proteins and which contains at least about 75 %> hydrophobic amino acid residues such as alanine, leucine, isoleucine, phenylalanine, proline, tyrosine, tryptophan, or valine.
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 amino acid residues, and has at least about 65-85%o, more preferably 70-80%>, and more preferably at least about 75%> hydrophobic residues.
• a signal sequence serves to direct a protein containing such a sequence to a lipid bilayer.
• a TANGO 212 family member has the amino acid sequence of SEQ ID NO:12, and the signal sequence is located at amino acids 1 to 16, 1 to 17, 1 to 18, 1 to 19, or 1 to 20.
• 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 to 18 of SEQ ID NO:12 results in a mature TANGO 212 protein conesponding to amino acids 19 to 553 of SEQ ID NO:12 (SEQ ID NO:31).
• the signal sequence is normally cleaved during processing ofthe mature protein.
• a TANGO 212 protein ofthe invention includes at least one EGF domain, preferably two, three, four, or five EGF domains and a MAM domain. In another embodiment, a TANGO 212 protein ofthe invention includes at least one EGF domain, preferably two, three, four, or five EGF domains, a MAM domain, a signal sequence, and is secreted.
• a cDNA encoding human TANGO 212 was identified by screening a human fetal lung library. A clone, comprising TANGO 212, was selected for complete sequencing based on its ability to direct the secretion of a protein of approximately 30 kDa in 35 -S labeled supernatants of 293T cells.
• TANGO 212 includes a 2435 nucleotide cDNA ( Figure 5; SEQ ID NO:l 1). It is noted that the nucleotide sequence depicted in SEQ ID NO: 11 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCG (SEQ ID NO:), and GGGCGGCCGC (SEQ ID NO:), respectively). Thus, it is to be understood that the nucleic acid molecules ofthe 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 269 to 1927 (SEQ ID NO: 13), encodes a 553 amino acid secreted protein ( Figure 5; SEQ ID NO: 12).
• human TANGO 212 includes an 18 amino acid signal peptide (amino acids 1 to about amino acid 18 of SEQ ID NO: 12) (SEQ ID NO:25) preceding the mature TANGO 212 protein (conesponding to about amino acid 19 to amino acid 553 of SEQ ID NO:12)(SEQ ID NO:31).
• Human TANGO 212 is predicted to have a molecular weight of approximately 61 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 59 kDa subsequent to cleavage of its signal peptide.
• gel analysis of 35 -S labeled supernatants of 293T cells transfected with TANGO 212 expression plasmid identified a band at approximately 30 kDa. Thus, further processing of human TANGO 212 is likely to occur.
• SPOT SignalP Optimized Tool
• Human TANGO 212 includes five EGF domains from about amino acids 61 to 91 (SEQ ID NO: 110), amino acids 98 to 132 (SEQ ID NO:l l l), amino acids 138 to 172 (SEQ ID NO:l 12), amino acids 178 to 217 (SEQ ID NO:l 13), and amino acids 223 to 258 of SEQ ID NO:12 (SEQ ID NO: 114).
• Human TANGO 212 further includes a MAM domain (about amino acids 400 to 546 of SEQ ID NO:12)(SEQ ID NO:l 16).
• EpDH202 which encodes human TANGO 212 was deposited with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209) on September 10, 1998 and assigned Accession Number 202171. This deposit will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience to those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
• Figure 13 depicts a hydropathy plot of human TANGO 212. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, the hydrophobic region at the beginning ofthe plot which corresponds to about amino acids 1 to 18 of SEQ ID NO: 12 is the signal sequence of TANGO 212 (SEQ ID NO:25), cleavage of which yields the mature protein of lengtht 19-553 (SEQ ID NO:31). The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• Northern analysis of human TANGO 212 mRNA expression revealed that is expressed at a very high level in placenta, strong levels in fetal lung and kidney, and at a low level in adult lung. No expression was seen in adult heart, liver, brain, skeletal muscle, kidney, pancreas, spleen, thymus, prostate, testis, ovary, small intestine, colon, peripheral blood leukocytes, or fetal brain and liver.
• a mouse homolog of human TANGO 212 was identified.
• a cDNA encoding mouse TANGO 212 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, jtmoal03g01, encoding mouse TANGO 212.
• the murine TANGO 212 cDNA of this clone is 1180 nucleotides long ( Figure 28; SEQ ID NO:59).
• the open reading frame of this cDNA comprises nucleotides 180 to 1179 of SEQ ID NO:59 (SEQ ID NO:61), and encodes a polypeptide comprising the 334 amino acid secreted sequence depicted in Figure 28 (SEQ ID NO:60).
• In situ tissue screening was performed on mouse adult and embryonic tissue to analyze for the expression of mouse TANGO 212 mRNA. Ofthe adult tissues tested, only the renal medulla (kidney and medullary collecting tubules) was positive. Expression was observed primarily in the embryo. Signal was observed at El 3.5 in the lung, skin (especially the upper lip), diaphragm, and muscle ofthe abdominal cavity and skin. This pattern remained through El 8.5 with increasing lung expression. Muscle expression was still apparent at El 8.5 but decreased to near background levels by postnatal day 1.5 with residual expression in the upper lip.
• Human and murine TANGO 212 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 77.2%> .
• the human and murine TANGO 212 full length cDNAs are 80.5%> identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
• human and murine TANGO 212 are 83.3% identical.
• the TANGO 212 proteins ofthe invention comprise a family of proteins having the hallmarks of a secreted protein ofthe EGF family. Accordingly, TANGO 212 proteins likely function in a similar manner as members ofthe EGF family. Thus, TANGO 212 modulators can be used to treat EGF-associated disorders.
• the TANGO 212 proteins likely play a role in tissue regeneration and/or wound healing.
• EGF EGF
• TGF- ⁇ TGF- ⁇
• these proteins influence a number of cellular processes involved in soft tissue repair leading to their categorization as wound hormones in wound healing.
• the affects of these proteins include cellular proliferation and chemotaxis.
• the TANGO 212 proteins ofthe invention likely affect various cells associated with wound healing. Effects that the TANGO 212 proteins have on various cells include proliferation and chemotaxis.
• the TANGO 212 proteins, nucleic acids and/or modulators ofthe invention are useful in the treatment of wounds and/or the modulation of prohferative disorders, e.g., cancer.
• TANGO 212 is expressed in the kidney, the TANGO 212 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 abenant 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 prohferative glomerulonephritis, glomerular lesions associated with systemic disease, such as systemic lupus eryfhematosus, 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 hypokal
• TANGO 213 In another aspect, the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins having sequence similarity to progesterone binding protein, refened to herein as TANGO 213 proteins.
• the TANGO 213 proteins and nucleic acid molecules 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 comprises 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. Members of the same family may also have common structural domains.
• TANGO 213 proteins having a signal sequence.
• a signal sequence includes a peptide of at least about 15 or 20 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, tryptophan, or valine.
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 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 213 family member has the amino acid sequence of SEQ ID NO: 15, and the signal sequence is located at amino acids 1 to 20, 1 to 22, 1 to 22, or 1 to 23.
• 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 to 22 of SEQ ID NO:15 results in a mature TANGO 213 protein conesponding to amino acids 23 to 371 of SEQ ID NO:12 (SEQ ID NO:32).
• the signal sequence is normally cleaved during processing ofthe mature protein..
• TANGO 213 proteins ofthe invention are likely to function similarly to steroid binding-proteins.
• Steroid binding protein activities include the ability to form protein-protein interactions with steroid hormones in signaling pathways and/or the ability to modulate intracellular ion levels, e.g., sodium and/or calcium levels.
• TANGO 213 proteins, nucleic acids and/or modulators can be used to treat steroid binding protein-associated disorders.
• Human TANGO 213 includes a 1496 nucleotide cDNA ( Figure 6; SEQ ID NO: 14). It is noted that the nucleotide sequence depicted in SEQ ID NO: 14 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTGCG (SEQ ID NO:), and GGGCGGCCGC (SEQ ID NO:), respectively). Thus, it is to be understood that the nucleic acid molecules ofthe invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
• human TANGO 213 includes a 22 amino acid signal peptide (amino acids 1 to about amino acid 22 of SEQ ID NO:15)(SEQ ID NO:26) preceding the mature TANGO 213 protein (conesponding to about amino acid 23 to amino acid 271 of SEQ ID NO:15)(SEQ ID NO:32).
• Human TANGO 213 is predicted to have a molecular weight of approximately 29.5 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 27.5 kDa subsequent to cleavage of its signal peptide.
• EpDH156 which encodes human TANGO 213 was deposited with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209) on October 30, 1998 and assigned Accession Number 98965. This deposit will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience to those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
• Figure 14 depicts a hydropathy plot of human TANGO 213. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, the hydrophobic region at the beginning ofthe plot which conesponds to about amino acids 1 to 22 of SEQ ID NO: 15 is the signal sequence of TANGO 213 (SEQ ID NO:26). The cysteine residues (cys) and potential N- glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• Northern analysis of human TANGO 213 mRNA expression revealed expression at a very high level in testis and kidney.
• the human gene for TANGO 213 was mapped on radiation hybrid panels to the long arm of chromosome 17, in the region pi 3.3. Flanking markers for this region are WI- 5436 and WI-6584.
• the MDCR (Miller-Dieker syndrome), PEDF (pigment epithelium derived factor), and PFNl(profillin 1) genes also map to this region ofthe human chromosome. This region is syntenic to mouse chromosome 11, locus 46(g).
• the ti (tipsy) loci also maps to this region ofthe mouse chromosome.
• the pfhl (profilin 1), htt (5- hydroxytryptamine (serotonin) transporter), acrb (acetylcholine receptor beta) genes also map to this region ofthe mouse chromosome.
• Mouse and Rat TANGO 213 A mouse homolog of human TANGO 213 was identified. A cDNA encoding mouse
• TANGO 213 was identified by analyzing the sequences of clones present in a mouse testis cDNA library. This analysis led to the identification of a clone, jtmz213a01, encoding mouse TANGO 213.
• the murine TANGO 213 cDNA of this clone is 2154 nucleotides long ( Figure 29; SEQ ID NO:62). It is noted that the nucleotide sequence depicted in SEQ ID NO:62 contains a Not I adapter sequence on the 3' end (5' GGGCGGCCGC 3')(SEQ ID NO:), respectively).
• nucleic acid molecules ofthe 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 comprises nucleotides 41 to 616 of SEQ ID NO:62 (SEQ ID NO:64) and encodes a protein comprising the 192 amino acid sequence protein depicted in Figure 29 (SEQ ID NO:63).
• a rat homolog of human TANGO 213 was identified.
• a cDNA encoding rat TANGO 213 was identified by analyzing the sequences of clones present in a rat testis cDNA library. This analysis led to the identification of a clone encoding rat TANGO 213.
• the rat TANGO 213 cDNA of this clone is 455 nucleotides long ( Figure 33; SEQ ID NO:) .
• In situ tissue screening was performed on mouse adult and embryonic tissue to analyze for the expression of mouse TANGO 213 mRNA. The strongest expression was observed in the seminiferous tubules ofthe testes. Moderate or weak expression is observed in several other adult tissues including the liver, kidney, and placenta.
• a weak, ubiquitous signal was observed in brain, heart, liver, kidney, adrenal gland, and the spleen. A signal was observed in the ovaries. A ubiquitous signal was seen in the labyrinth zone and slightly higher signal in the zone of giant cells. No signal was detected in the following tissues: spinal cord, eye and harderian gland, submandibular gland, white fat, brown fat, stomach, lung, colon, small intestine, thymus, lymph node, pancreas, skeletal muscle, and bladder. Embryonic expression is negligible. A weak signal was observed in the developing liver and CNS. The signal in the CNS was near background levels. Specifically, at E13.5, a weak, ubiquitous signal observed in the liver.
• Human and murine TANGO 213 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 64.6%> .
• the human and murine TANGO 213 full length cDNAs are 68.8%> identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
• human and murine TANGO 213 are 77.1% identical.
• TANGO 213 activity refers to an activity exerted by a TANGO 213 protein or nucleic acid molecule on a TANGO 213 responsive cell in vivo or in vitro.
• TANGO 213 activities include at least one or more ofthe following activities: 1) interaction of a TANGO 213 protein with a TANGO 213-target molecule; 2) activation of a TANGO 213 target molecule; 3) modulation of cellular proliferation; 4) modulation of cellular differentiation; or 5) modulation of a signaling pathway.
• the TANGO 213 proteins, nucleic acids and/or modulators can be used for the treatment of a disorder characterized by abenant TANGO 213 expression and/or an aberrant TANGO 213 activity, such as prohferative and/or differentiative disorders.
• TANGO 213 is expressed in the kidney
• the TANGO 213 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 abenant metabolism or function of cells in the tissues in which it is expressed.
• kidney diseases e.g., acute and chronic glomerulonephritis, rapidly progressive glomerulonephritis, nephrotic syndrome, focal prohferative 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 disease, medullary 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 hypokalemic
• the TANGO 213 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 be used to treat or modulate disorders associated with the testis including, without limitation, the Klinefelter syndrome (both the classic and mosaic forms), XX male syndrome, variococele, germinal cell aplasia (the Sertoli cell-only syndrome), idiopathic azoospermia or severe oligospermia, crpytochidism, and immotile cilia syndrome, or testicular cancer (primary germ cell tumors ofthe testis).
• TANGO 213 polypeptides, nucleic acids, or modulators thereof can be used to treat testicular disorders, such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gononhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• testicular disorders such as unilateral testicular enlargment (e.g., nontuberculous, granulomatous orchitis), inflammatory diseases resulting in testicular dysfunction (e.g., gononhea and mumps), and tumors (e.g., germ cell tumors, interstitial cell tumors, androblastoma, testicular lymphoma and adenomatoid tumors).
• the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins refened to herein as TANGO 224 proteins.
• the TANGO 224 proteins and nucleic acid molecules 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 comprises 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. Members of the same family may also have common structural domains.
• the TANGO 224 proteins ofthe invention include a thrombospondin type I (TSP-I) domain.
• TSP-I domain is involved in the binding to both soluble and matrix macromolecules (e.g., sulfated glycoconjugates).
• a thrombospondin type I (TSP-I) domain refers to an amino acid sequence of about 30 to about 60, preferably about 35 to 55, 40 to 50, and more preferably about 45 amino acids in length.
• TANGO 224 has such a signature pattern at about amino acids 42 to 81 of SEQ ID NO: 18 (SEQ ID NO:117).
• conserved amino acid motifs can be used to identify TANGO 224 family members having a TSP-I domain.
• the following signature pattern can be used to identify TANGO 224 family members: W - S - x - C - [SD] - x (2) - C - x (2) - G - x (3, 5) - R - x (7, 15) - C - x (9, 11) - C - x (4, 5) - C (SEQ ID NO:52).
• a TSP-I domain of TANGO 224 extends, for example, from about amino acids 37 to 81 of SEQ ID NO: 18 (SEQ ID NO: 118).
• a TSP-I domain further contains at least about 4 to 9, preferably, 5 to 8, more preferably 6 conserved cysteine residues.
• cysteine residue in the TSP-I consensus sequence that corresponds to a cysteine residue at amino acid 45 of TANGO 224 (SEQ ID NO: 18); there is a second cysteine residue in the TSP-I consensus sequence that corresponds to a cysteine residue at amino acid 49 of TANGO 224 (SEQ ID NO: 18); there is a third cysteine residue in the TSP-I consensus sequence that corresponds to a cysteine residue at amino acid 60 of TANGO 224 (SEQ ID NO: 18); there is a fourth cysteine residue in the TSP-I consensus sequence that corresponds to a cysteine residue at amino acid 66 of TANGO 224 (SEQ ID NO: 18); there is a fifth cysteine residue in the TSP-I consensus sequence that corresponds to a cysteine residue at amino acid 76 of TANGO 224 (SEQ ID NO: 18); and/or there is a sixth cysteine residue in the TSP-I consensus sequence
• TSP-I consensus sequence is available from the HMMer version 2.0 software as Accession Number PF00090.
• Software for HMM-based profiles is available from http://www.csc.ucsc.edu/research/ compbio/sam.html and from http://genome.wustl.edu/eddy/hmmer.html.
• the TANGO 224 proteins ofthe invention include a Furin-like cysteine rich domain (Accession number :PF00757).
• the consensus sequence for the Furin-like cysteine rich domain is: C-Xaa(3)-C-Xaa-G-G-Xaa(n)-C-Xaa(5)-D-G, wherein C is cysteine, Xaa is any amino acid, G is glycine, n is about 5 to 15, preferably 6 to 14, more preferably about 7 to 12, and D is aspartic acid.
• a Furin-like cysteine rich domain refers to an amino acid sequence of about 80 to 160, preferably of about 100 to 150, and more preferably about 110 to 130, amino acids in length.
• Human TANGO 224, form 2 has such a signature pattern at about amino acids 707-829 of SEQ ID NO:66 (SEQ ID NO:).
• TANGO 224 proteins having a signal sequence.
• a signal sequence includes a peptide of at least about 15 or 20 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, tryptophan, or valine.
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 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 224 family member has the amino acid sequence of SEQ ID NO: 18, and the signal sequence is located at amino acids 1 to 26, 1 to 27, 1 to 28, 1 to 29 or 1 to 30.
• 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 to 28 of SEQ ID NO: 18 results in a mature TANGO 224 protein corresponding to amino acids 29 to 458 of SEQ ID NO: 18 (SEQ ID NO:33).
• the signal sequence is normally cleaved during processing of the mature protein.
• a cDNA encoding human TANGO 224 was identified by screening a human fetal spleen library. A clone comprising human TANGO 224 was selected for complete sequencing. In one embodiment, TANGO 224 is refened to as TANGO 224, form 1. Human TANGO 224, form 1 comprises a 2689 nucleotide cDNA ( Figure 7; SEQ ID NO: 17). The open reading frame of this TANGO 224, form 1 cDNA clone comprises nucleotides 1 to 1440 (SEQ ID NO:19), and encodes a secreted protein comprising the 480 amino acid sequence depicted in Figure 7 (SEQ ID NO: 18).
• TANGO 224 clone includes a 2691 nucleotide cDNA ( Figure 30; SEQ ID NO:65), and encodes a human TANGO 224 and is refened to as human TANGO 224, form 2.
• the open reading frame of human TANGO 224, form 2 cDNA clone comprises nucleotides 67 to 2690 (SEQ ID NO:67), and encodes a secreted protein comprising the 874 amino acid sequence depicted in Figure 30 (SEQ ID NO:66).
• the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 224 form 1 includes an 28 amino acid signal peptide (amino acids 1 to about amino acid 28 of SEQ ID NO: 18) (SEQ ID NO:27) preceding the mature TANGO 224 protein (conesponding to about amino acid 29 to amino acid 458 of SEQ ID NO:18)(SEQ ID NO:33).
• Human TANGO 224 is predicted to have a molecular weight of approximately 50 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 47 kDa subsequent to cleavage of its signal peptide.
• the signal peptide prediction program SIGNALP (Nielsen et al. (1997) Protein Engineering 10:1-6) predicted that human TANGO 224 form 1 includes an 28 amino acid signal peptide (amino acids 1 to about amino acid 28 of SEQ ID NO: 18) (SEQ ID
• Human TANGO 224 form 2 includes an 28 amino acid signal peptide (amino acids 1 to about amino acid 28 of SEQ ID NO:18)(SEQ ID NO:27) preceding the mature TANGO 224, form 2 protein (conesponding to about amino acid 29 to amino acid 874 of SEQ ID NO: 18)(SEQ ID NO:).
• Human TANGO 224 is predicted to have a molecular weight of approximately 131 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 127 kDa subsequent to cleavage of its signal peptide.
• Human TANGO 224, form 1 includes a TSP-I domain from about amino acids 37 to 81 of SEQ ID NO: 18 (SEQ ID NO: 118).
• Human TANGO 224, form 2 includes a TSP-I domain from about amino acids 37 to
• Human TANGO 224, form 2 has a Furin-like cysteine rich domain from amino acids 707 to 829 of SEQ ID NO:66 (SEQ ID NO:).
• the hydrophobic region at the beginning ofthe plot which corresponds to about amino acids 1 to 28 of SEQ ID NO: 18 is the signal sequence of TANGO 224 (SEQ ID NO:27).
• the cysteine residues (cys) and potential N- glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• HMC-1 control mast cell line
• fetal dorsal spinal cord human colon to liver metastasis
• erythroblasts from CD34+ Blood human spinal cord (ION 3)
• HUVEC TGF-B h. umbilical endothelia
• hUVEC h.
• umbilical endothelia human spinal cord (ION 3), brain K563 (red blood cell line), uterus, Hep-G2 (human insulinoma), human normal colon, human colon to liver metastasis, skin, HUVEC controls (umbilical endothehal cells), human colon (inflammatory bowel disease), melanoma (G361 cell line), adult bone arrow CD34+ cells, HPK, human lung, mammary gland, normal breast epithelium, colon to liver metastasis (CHT128), normal breast, bone marrow (CD34+), WI38 (H.
• TANGO 224 Nucleic Acids. Polypeptides. and Modulators Thereof
• the TSP-I domain of TANGO 224 is involved in matrix interactions.
• the TANGO 224 proteins ofthe invention likely play a role in various matrix interactions, e.g., matrix binding.
• a TANGO 224 activity is at least one or more ofthe following activities: 1) regulation of extracellular matrix structuring; 2) modulation of cellular adhesion, either in vitro or in vivo; 3) regulation of cell trafficking and/or migration.
• the TANGO 224 proteins, nucleic acid molecules and/or modulators can be used to modulate cellular interactions such as cell-cell and/or cell-matrix interactions and thus, to treat disorders associated with abnormal cellular interactions.
• TANGO 224 was originally found in a fetal spleen library, TANGO 228 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 ofthe splenic connective tissue, e.g., splenic smooth muscle cells and/or endothehal cells ofthe splenic blood vessels.
• cells that form the spleen e.g., cells ofthe splenic connective tissue, e.g., splenic smooth muscle cells and/or endothehal cells ofthe splenic blood vessels.
• TANGO 224 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 224 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.
• the present invention is based on the discovery of cDNA molecules which encode a novel family of proteins refened to herein as TANGO 239 proteins.
• the TANGO 239 proteins and nucleic acid molecules comprise a family of molecules having certain conserved structural and functional features.
• the term "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 comprises 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. Members of the same family may also have common structural domains.
• the present invention features TANGO 239 proteins having at least one, preferably two or three, MAM domain(s).
• the MAM domain is associated with various adhesive proteins and as such is likely to have adhesive function.
• Within MAM domains are conserved cysteine residues which play a role in the adhesion of a MAM domain to other proteins.
• a MAM domain refers to an amino acid sequence of about 130 to about 170, preferably about 140 to 165, and more preferably about 145, 146 to 159 or 160 amino acids in length.
• signature patterns can be used to identify TANGO 239 family members having a MAM domain.
• the following signature pattern can be used to identify TANGO 239 family members: G - x - [LIVMFY] (2) - x (3) - [STA] - x (10, 11) - [LV] - x (4,6) - [LIVMF] - x (6, 7) - C - [LIVM] - x (3) - [LIVMFY] - x (3, 4) - [GSC] (SEQ ID NO:51).
• signature patterns or consensus patterns described herein are described according to the following designations: all amino acids are indicated according to their universal single letter designation; "x” designates any amino acid; x(n) designates “n” number of amino acids, e.g., x (2) designates any two amino acids, e.g., x (6, 7) designates any six to seven amino acids; and, amino acids in brackets indicates any one ofthe amino acids within the brackets, e.g., [STA] indicates any of one of either S (serine), T (threonine) or A (alanine).
• TANGO 239 has such a signature pattern at about amino acids 50 to 90 (SEQ ID NO:l 19), amino acids 215 to 256 (SEQ ID NO: 120) and/or amino acids 380 to 420 of SEQ ID NO:21 (SEQ ID NO:121).
• a MAM domain further contains at least about 2 to 6, preferably, 3 to 5, more preferably 4 conserved cysteine residues.
• conserved cysteine residues can be found. For example, as shown in Figure 25, there is a first cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 26 ofthe first MAM domain of TANGO 239 (SEQ ID NO:21); there is a second cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 33 of TANGO 239 (SEQ ID NO:21); there is a third cysteine residue in the MAM consensus sequence that corresponds to a cysteine residue at amino acid 80 of TANGO 239 (SEQ ID NO:21); and/or there is a fourth cysteine residue in the MAM consensus sequence that conesponds to a cysteine residue at amino acid 167 of TANGO 239 (SEQ ID NO:
• conserved cysteine residues can be found at amino acids 170, 178, 246 and/or 327 ofthe second MAM domain of TANGO 239 (SEQ ID NO:21); and at amino acids 342, 349, 411 and/or 496 ofthe third MAM domain of TANGO 239 (SEQ ID NO:21).
• the MAM consensus sequence is available from the HMMer version 2.0 software as Accession Number PF00629.
• Software for HMM-based profiles is available from http://www.csc.ucsc.edu/rese.arch/compbio /sam.html and from http://genome.wustl.edu/eddy/hmmer.html.
• a MAM domain of TANGO 239 extends, for example, from about amino acids 26 to 169 of SEQ ID NO:21 (SEQ ID NO: 122), from about amino acids 170 to 329 of SEQ ID NO:21 (SEQ ID NO:123), from about amino acids 342 to 498 of SEQ ID NO:21 (SEQ ID NO:124), and/or from about amino acids 509 to 666 of SEQ ID NO:21 (SEQ ID NO:).
• TANGO 239 proteins having a signal sequence.
• a signal sequence includes a peptide of at least about 15 or 20 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, tryptophan, or valine.
• a signal sequence contains at least about 15 to 40 amino acid residues, preferably about 15-30 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 239 family member has the amino acid sequence of SEQ ID NO:21, and the signal sequence is located at amino acids 1 to 16, 1 to 17, 1 to 18, 1 to 19, and 1 to 20.
• 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 to 18 of SEQ ID NO:21 results in a mature TANGO 239 protein corresponding to amino acids 19 to 686 of SEQ ID NO:2 (SEQ ID NO:).
• the signal sequence is normally cleaved during processing ofthe mature protein.
• a cDNA encoding human TANGO 239 was identified by screening an IL-l ⁇ stimulated astrocyte library.
• a clone, comprising human TANGO 239, was selected for complete sequencing based on its ability to direct the secretion of a protein of approximately 60 kDa in 35 -S labeled supernatants of 293T cells.
• TANGO 239 includes a 3413 nucleotide cDNA ( Figure 8; SEQ ID NO:20). In one embodiment, TANGO 239 is refened to as TANGO 239, form 1.
• the open reading frame of this TANGO 239, form 1 cDNA comprises nucleotides 344 to 1990 (SEQ ID NO:22), and encodes a secreted protein comprising the 550 amino acid depicted in Figure 8 (SEQ ID NO:22).
• nucleotide sequence depicted in SEQ ID NO:20 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTC
• nucleic acid molecules ofthe invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
• human TANGO 239, form 1 includes an 18 amino acid signal peptide (amino acids 1 to about amino acid 18 of SEQ ID NO:21)(SEQ ID NO:28) preceding the mature TANGO 239, form 1 protein (conesponding to about amino acid 19 to amino acid 550 of SEQ ID NO:21)(SEQ ID NO:34).
• Human TANGO 239, form 1 is predicted to have a molecular weight of approximately 61.5 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 59.5 kDa subsequent to cleavage of its signal peptide.
• Human TANGO 239, form 1 includes three MAM domains from about amino acids
• Figure 16 depicts a hydropathy plot of human TANGO 239, form 1. Relatively hydrophobic residues are above the horizontal line, and relatively hydrophilic residues are below the horizontal line. As shown in the hydropathy plot, the hydrophobic region at the beginning ofthe plot which corresponds to about amino acids 1 to 18 of SEQ ID NO:21 is the signal sequence of TANGO 239, form 1 (SEQ ID NO:28). The cysteine residues (cys) and potential N-glycosylation sites (Ngly) are indicated by short vertical lines just below the hydropathy trace.
• EpDH233 which encodes human TANGO 239 form 1 was deposited as part of EpDHMixl with the American Type Culture Collection (ATCC, 10801 University Boulevard, Manassas, VA 20110-2209) on November 20, 1998 which was assigned Accession Number 98999. This deposit will be maintained under the terms ofthe Budapest Treaty on the International Recognition ofthe Deposit of Microorganisms for the Purposes of Patent Procedure. This deposit was made merely as a convenience to those of skill in the art and is not an admission that a deposit is required under 35 U.S.C. ⁇ 112.
• a cDNA encoding full length human TANGO 239 was identified by screening an IL-l ⁇ stimulated astrocyte library.
• a clone comprising human TANGO 239 was selected for complete sequencing based on its ability to direct the secretion of a protein of approximately 102.9 kDa in 35 -S labeled supernatants of 293T cells.
• Human TANGO 239 includes a 3413 nucleotide cDNA ( Figure 31; SEQ ID NO:68). In one embodiment, human TANGO 239 is referred to as TANGO 239, form 2.
• the open reading frame of this TANGO 239, form 2 cDNA comprises nucleotides 344 to 2395 (SEQ ID NO:70), and encodes a secreted protein comprising the 686 amino acid depicted in Figure 31 (SEQ ID NO:69).
• nucleotide sequence depicted in SEQ ID NO:70 contains Sal I adaptor sequences and adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCC (SEQ ID NO:), and GGGGGG (SEQ ID NO:), respectively).
• nucleic acid molecules ofthe invention include not only those sequences with such adaptor sequences but also the nucleic acid sequences described herein lacking the adaptor sequences.
• human TANGO 239, form 2 includes an 18 amino acid signal peptide (amino acids 1 to about amino acid 18 of SEQ ID NO:)(SEQ ID NO: 125) preceding the mature TANGO 239, form 2 protein (conesponding to about amino acid 19 to amino acid 686 of SEQ ID NO:126)(SEQ ID NO: 126).
• Human TANGO 239, form 2 is predicted to have a molecular weight of approximately 102.9 kDa prior to cleavage of its signal peptide and a molecular weight of approximately 100 kDa subsequent to cleavage of its signal peptide.
• Human TANGO 239, form 2 includes four MAM domains from about amino acids 26 to 169 of SEQ ID NO:126. (SEQ ID NO: 122), amino acids 170 to 329 of SEQ ID NO: 126 (SEQ ID NO: 123), amino acids 340 to 496 of SEQ ID NO: 126 (SEQ ID NO: 124), and amino acids 509 to 666 of SEQ ID NO: 126. (SEQ ID NO:).
• Northern analysis of human TANGO 239 mRNA expression using TANGO 239, form 2 nucleotide sequence as a probe revealed that TANGO 239 mRNA was highly expressed in skeletal muscle, placenta, and peripheral blood leukocytes. Expression was moderate in colon, thymus, kidney. Weak expression was observed in the liver, small intestine, and lung. No expression was detected in the brain, heart and spleen.
• Mouse TANGO 239 was identified by analyzing the sequences of clones present in a mouse inflammation model cDNA library. This analysis led to the identification of a clone, jymua038a02, encoding full-length mouse TANGO 239.
• the murine TANGO 239 cDNA of this clone is 1029 nucleotides long ( Figure 32; SEQ ID NO:71). It is noted that the nucleotide sequence depicted in SEQ ID NO:71 contains Sal I and Not I adapter sequences on the 5' and 3' ends, respectively ((GTCGACCCACGCGTCCG (SEQ ID NO:), and GGGCGGCCGC (SEQ ID NO:), respectively).
• nucleic acid molecules ofthe 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 209 to 370 of SEQ ID NO:71 (SEQ ID NO:73), encodes a 54 amino acid secreted protein ( Figure 32; SEQ ID NO:72).
• In situ tissue screening was performed on mouse adult and embryonic tissue to analyze for the expression of mouse TANGO 239 mRNA. In summary, expression in the adult mouse appeared to be restricted to bone structures. The in-situ screen only detected expression in developing bones of embryos starting at E14.5.
• brain included a sense control
• spinal cord eye and harderian gland
• submandibular gland white fat, brown fat, stomach
• heart included a sense control
• lung included a sense control
• liver included a sense control
• kidney included a sense control
• adrenal gland colon, small intestine, thymus, lymph node, spleen, pancreas (included a sense control), skeletal muscle, bladder, testes, ovaries, placenta (included a sense control).
• embryonic expression the following results were obtained: At E13.5, no signal was observed.
• a weak signal was observed outlining the vertebrae, incisors, and femur (included a sense control).
• most developing bone structures appeared to be outlined including the skull, Meckel's cartilage, scapula, vertebrae, primordium of basisphenoid bone, and femur (included a sense control).
• most developing bone structures had a weak signal in a pattern which outline the bone structures (included a sense control).
• PI.5 a weak signal was associated with many developing bone structures.
• Human and murine TANGO 239 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 79.6% .
• the human and murine TANGO 239 full length cDNAs are 58.8% identical, as assessed using the same software and parameters as indicated (without the BLOSUM 62 scoring matrix).
• human and murine TANGO 239 are 77.2% identical.
• human TANGO 239 proteins ofthe invention likely play a role in cellular adhesion and therefore, human TANGO 239 proteins, nucleic acid molecules and/or modulators can be used to modulate cellular adhesion.
• human TANGO 239 was originally identified in an astrocyte library, human TANGO 239 nucleic acids, proteins, and modulators thereof can be used to modulate the proliferation, activation, development, differentiation, and/or function of glial cells e.g., astrocytes.
• Human TANGO 239 nucleic acids, proteins and modulators thereof can be used to treat glial cell-related disorders, e.g. , astrocytoma and glioblastoma
• TANGO 239 exhibits expression in the lung
• TANGO 239 polypeptides, nucleic acids, or modulators thereof can be used to treat pulmonary (lung) disorders, such as atelectasis, pulmonary congestion or edema, chronic obstructive airway disease (e.g., emphysema, chronic bronchitis, bronchial asthma, and bronchiectasis), diffuse interstitial diseases (e.g., sarcoidosis, pneumoconiosis, hypersensitivity pneumonitis, Goodpasture's syndrome, idiopathic pulmonary hemosiderosis, pulmonary alveolar proteinosis, desquamative interstitial pneumonitis, chronic interstitial pneumonia, fibrosing alveolitis, hamman-rich syndrome, pulmonary eosinophilia, diffuse interstitial fibrosis, Wegener's granulomatosis, lymphomatoid granulomatosis, and lipid pneumonia), or
• TANGO 239 exhibits expression in the small intestine
• TANGO 239 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
• TANGO 239 exhibits expression in the spleen
• 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 ofthe splenic connective tissue, e.g., splenic smooth muscle cells and/or endothehal cells ofthe splenic blood vessels.
• TANGO 239 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 239 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.
• TANGO 239 exhibits expression in the heart
• nucleic acids, proteins, and modulators thereof can be used to treat heart disorders, e.g., ischemic heart disease, atherosclerosis, hypertension, angina pectoris, Hypertrophic Cardiomyopathy, and congenital heart disease.
• TANGO 239 exhibits expression in bone structures
• nucleic acids, proteins, and modulators thereof can be used to modulate the proliferation, differentiation, and/or function of bone and cartilage cells, e.g., chondrocytes and osteoblasts, and to treat bone and/or cartilage associated diseases or disorders.
• bone and/or cartilage diseases and disorders include bone and/or cartilage injury due to for example, trauma (e.g., bone breakage, cartilage tearing), degeneration (e.g., osteoporosis), degeneration of joints, e.g., arthritis, e.g., osteoarthritis, and bone wearing.
• TANGO 239 activities include at least one or more ofthe following activities: 1) modulation of cellular adhesion, either in vitro or in vivo; 2) regulation of cell trafficking and/or migration; 3) modulation of cellular proliferation; 4) modulation of inflammation; and/or 5) modulation of a signaling pathway.
• TANGO 239 proteins, nucleic acids and/or modulators can be used to treat a disorder characterized by abenant TANGO 239 expression and/or an aberrant TANGO 239 activity.
• Tables 1 and 2 below provide summaries of sequence information for the human TANGO molecules described herein.
• Tables 3 and 4 below provide summaries of sequence information for the mouse
• TANGO molecules described herein.
• nucleic acid molecules that encode a polypeptide ofthe 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 ofthe 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 ofthe 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 ofthe 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 ofthe nucleic acid) in the genomic DNA ofthe 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 ofthe present invention e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or a complement thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein.
• nucleic acid molecules of the invention can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook et al., eds., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).
• a nucleic acid molecule ofthe 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 ofthe invention can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
• an isolated nucleic acid molecule ofthe invention comprises a nucleic acid molecule which is a complement ofthe nucleotide sequence of SEQ ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or a portion thereof.
• 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 ofthe invention can comprise only a portion of a nucleic acid sequence encoding a full length polypeptide ofthe invention for example, a o fragment which can be used as a probe or primer or a fragment encoding a biologically active portion of a polypeptide ofthe 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 5 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 ofthe sense or anti-sense sequence of SEQ ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or of a 0 naturally occurring mutant of SEQ ID NO: 1, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20 or 22.
• Probes based on the sequence of a nucleic acid molecule ofthe 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. 5
• 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 0 the invention can be prepared by isolating a portion of any of SEQ ID NOs:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, expressing the encoded portion ofthe polypeptide protein (e.g., by recombinant expression in vitro) and assessing the activity ofthe encoded portion ofthe polypeptide.
• the invention further encompasses nucleic acid molecules that differ from the 5 nucleotide sequence of SEQ ID NO:l, 3, 4, 6, 8, 10, 1 1, 13, 14, 16, 17, 19, 20, 22, 38, 3,9, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, due to degeneracy ofthe genetic code and thus encode the same protein as that encoded by the nucleotide sequence of SEQ ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73.
• 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 128 has been mapped to chromosome 4, between flanking markers WI-3936 and AFMCO27ZB9, and therefore, TANGO 128 family members can include nucleotide sequence polymorphisms (e.g., nucleotide sequences that vary from SEQ ID NO:X) that map to this chromosome 4 region (i.e., between markers WI-3936 and AFMCO27ZB9).
• nucleotide sequence polymorphisms e.g., nucleotide sequences that vary from SEQ ID NO:X
• TANGO 213 has been mapped to chromosome 17, in the region pl3.3, between flanking markers WT-5436 and WI-6584, and therefore, TANGO 213 family members can include nucleotide sequence polymorphisms (e.g., nucleotide sequences that vary from SEQ ID NO:X) that map to this chromosome 17 region (i.e., between markers WI-5436 and WI-6584).
• allelic variant refers to a nucleotide sequence which occurs at a given locus or to a 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 ofthe 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 ofthe invention.
• nucleic acid molecules encoding proteins ofthe invention from other species which have a nucleotide sequence which differs from that ofthe human protein described herein are intended to be within the scope ofthe invention.
• Nucleic acid molecules corresponding to natural allelic variants and homologues of a cDNA ofthe 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 according to standard hybridization techniques under stringent hybridization conditions, For example, a cDNA encoding a soluble form of a membrane-bound protein ofthe invention isolated based on its hybridization to a nucleic acid molecule encoding all or part ofthe membrane-bound form. Likewise, a cDNA encoding a membrane-bound form can be isolated based on its hybridization to a nucleic acid molecule encoding all or part ofthe soluble form.
• an isolated nucleic acid molecule ofthe invention is at least 100 (125, 150, 175, 200, 225, 250, 275, 300 325, 350, 375, 400, 425, 450, 500, 550, 600, 650, 700, 800, 900, 1000, 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 ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20,
• 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
• a prefened, 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.
• SSC 6X sodium chloride/sodium citrate
• an isolated nucleic acid molecule ofthe invention that hybridizes under stringent conditions to the sequence of SEQ 0 ID ⁇ O:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or complement thereof, conesponds 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
• sequences above include, but are not limited to, SEQ ID Nos:78, 80, 82, 84, 86, 88, 90, 92, 94, 96, and 98, which in particular hybridize to the TANGO 128 sequences listed above (SEQ ID NO: 1).
• allelic variants of a nucleic acid molecule ofthe invention sequence that may exist in the population, the skilled artisan will further
• a "non-essential" amino acid residue is a residue that can be altered from the wild-type sequence without altering the biological
• 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
• representative species ofthe mouse TANGO 128 presented for illustrative purposes only and not by way of limitation include but are not limited to, SEQ ID Nos 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, and 98.
• nucleic acid molecules encoding a polypeptide ofthe invention that contain changes in amino acid residues that are not essential for activity. Such polypeptides differ in amino acid sequence from SEQ ID NO:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, 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 ID NO:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72.
• 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 ID NO:l, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein.
• Such variant proteins retain or exhibit at least one structural or biological activity ofthe polyeptides 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-essential amino acid residues.
• 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.
• 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
• aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine
• mutant polypeptide that is a variant of a polypeptide of the invention can be assayed for: (1) the ability to form proteimprotein interactions with proteins in a signaling pathway ofthe polypeptide ofthe invention; (2) the ability to bind a ligand ofthe polypeptide ofthe invention; or (3) the ability to bind to an intracellular target
• 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 ofthe invention,
• 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 ofthe protein coding region (or open reading frame).
• An antisense nucleic acid molecule can be antisense to all
• non-coding regions are the 5' and 3' sequences which flank the coding region and are not translated into amino acids.
• An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40,
• An antisense nucleic acid ofthe 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
• an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability ofthe molecules or to increase the
• 25 physical stability ofthe 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-
• 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
• 5 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 ofthe 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 ofthe invention to thereby inhibit
• 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 ofthe double helix.
• An example of a route of administration of antisense nucleic acid molecules ofthe invention includes direct injection
• 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
• the antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations ofthe antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.
• An antisense nucleic acid molecule ofthe invention can be an ⁇ -anomeric nucleic
• An ⁇ -anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -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.
• 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-
• a ribozyme having specificity for a nucleic acid molecule encoding a polypeptide ofthe invention can be designed based upon the nucleotide sequence of a cDNA disclosed herein.
• a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence ofthe 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 ofthe 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 o structures.
• expression of a polypeptide ofthe invention can be inhibited by targeting nucleotide sequences complementary to the regulatory region ofthe gene encoding the polypeptide (e.g., the promoter and/or enhancer) to form triple helical structures that prevent transcription ofthe gene in target cells.
• nucleotide sequences complementary to the regulatory region ofthe gene encoding the polypeptide e.g., the promoter and/or enhancer
• the nucleic acid molecules ofthe invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility ofthe molecule.
• the deoxyribose phosphate backbone ofthe nucleic acids can be modified to generate peptide nucleic acids 0 (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 5 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 0 expression by, e.g., inducing transcription or translation anest 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., Sl nucleases (Hyrup (1996), supra; or as probes or primers for DNA sequence and hybridization (Hyrup (1996), supra; Perry-O'Keefe et al. (1996) Proc. 5 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.
• 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 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No. WO 88/09810) or the blood-brain barrier (see, e.g., PCT Publication No. W0 89/10134).
• peptides e.g., for targeting host cell receptors in vivo
• agents facilitating transport across the cell membrane see, e.g., Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl.
• 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 ofthe 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 ofthe invention.
• the native polypeptide can be isolated from cells or tissue sources by an appropriate purification , scheme using standard protein purification techniques.
• polypeptides ofthe invention are produced by recombinant DNA techniques.
• a polypeptide ofthe 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 ofthe cells from which it is isolated or recombinantly produced.
• protein o 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 refened 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%> ofthe volume ofthe 5 protein preparation.
• culture medium represents less than about 20%, 10%>, or 5%> ofthe volume ofthe 5 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 ofthe protein. Accordingly such preparations ofthe protein have less than about 30%, 20%>, 10%>, 5% (by dry weight) of chemical precursors or compounds other than the polypeptide of interest.
• Bioly active portions of a polypeptide of the invention include polypeptides comprising amino acid sequences sufficiently identical to or derived from the amino acid sequence ofthe protein (e.g., the amino acid sequence shown in any of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72), which include fewer amino acids than the full length protein, and exhibit at least one activity of the conesponding full-length protein.
• biologically active portions comprise a domain or motif with at least one activity ofthe conesponding protein.
• a biologically active portion of a protein ofthe invention can be a polypeptide which is, for example, 10, 25, 50, 100 or more amino acids in length.
• other biologically active portions, in which other regions ofthe protein are deleted can be prepared by recombinant techniques and evaluated for one or more ofthe 0 functional activities ofthe native form of a polypeptide ofthe invention.
• Prefened polypeptides have the amino acid sequence of SEQ ID NO:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72
• Other useful proteins are substantially identical (e.g., at least about 45%, preferably 55%, 65%, 75%, 85%, 95%, or 99%) to any of SEQ ID NO:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72 and retain the functional activity ofthe 5 protein ofthe 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 conesponding 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 Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264-2268, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877.
• Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul, et al. (1990) J. Mol. Biol. 215:403-410.
• Gapped BLAST can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402.
• PSI-Blast can be used to perform an iterated search which detects distant relationships between molecules. Id.
• BLAST Gapped BLAST
• PSI-Blast programs the default parameters ofthe respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.
• Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, (1988) CABIOS 4:11-17. Such an algorithm is inco ⁇ orated into the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package.
• ALIGN program version 2.0
• 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.
• the invention also provides chimeric or fusion proteins.
• a "chimeric protein” or “fusion protein” comprises all or part (preferably biologically active) of a polypeptide ofthe invention operably linked to a heterologous polypeptide (i.e., a polypeptide other than the same polypeptide ofthe invention).
• a heterologous polypeptide i.e., a polypeptide other than the same polypeptide ofthe invention.
• the term "operably linked” is intended to indicate that the polypeptide ofthe 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 ofthe polypeptide ofthe invention.
• One useful fusion protein is a GST fusion protein in which the polypeptide ofthe invention is fused to the C-terminus of GST sequences. Such fusion proteins can facilitate o 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 ofthe invention can be removed and replaced with a signal sequence from another protein.
• the gp67 secretory sequence ofthe baculovirus envelope protein can be used as a heterologous 5 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 0 signal (Pharmacia Biotech; Piscataway, New Jersey).
• the fusion protein is an immunoglobulin fusion protein in which all or part of a polypeptide ofthe invention is fused to sequences derived from a member ofthe immunoglobulin protein family.
• the immunoglobulin fusion proteins ofthe invention can be incorporated into pharmaceutical compositions and administered to a 5 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 ofthe invention.
• Inhibition of ligand/receptor interaction may be useful therapeutically, both for treating prohferative and differentiative disorders and for 0 modulating (e.g. promoting or inhibiting) cell survival.
• the immunoglobulin fusion proteins ofthe invention can be used as immunogens to produce antibodies directed against a polypeptide ofthe 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 ofthe invention can be produced by standard 5 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 ofthe invention can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the polypeptide ofthe invention.
• a signal sequence of a polypeptide ofthe invention can be used to facilitate secretion and isolation ofthe 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 ofthe 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 ofthe signal sequence (i.e., the cleavage products).
• a nucleic acid sequence encoding a signal sequence ofthe 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 ofthe protein, such as from a eukaryotic host into which the expression vector is transformed, and the signal sequence is subsequently or concunently 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 ofthe present invention can be used to 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 ofthe polypeptides ofthe 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, ofthe biological activities ofthe naturally occurring form ofthe protein.
• An antagonist of a protein can inhibit one or more of the activities ofthe naturally occurring form ofthe 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 ofthe biological activities ofthe naturally occurring form ofthe protein can have fewer side effects in a subject relative to treatment with the naturally occurring form ofthe protein.
• Variants of a protein ofthe invention which function as either agonists (mimetics) or as antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, ofthe protein ofthe 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 ofthe polypeptides ofthe 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.
• libraries of fragments ofthe coding sequence of a polypeptide ofthe 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 ofthe 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 Sl 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 ofthe protein of interest.
• REM Recursive ensemble mutagenesis
• An isolated polypeptide ofthe 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 ofthe invention comprises at least 8 (preferably 10, 15, 20, or 30) amino acid residues ofthe amino acid sequence of SEQ ID NO:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, and encompasses an epitope ofthe protein such that an antibody raised against the peptide forms a specific immune complex with the protein.
• Prefened epitopes encompassed by the antigenic peptide are regions that are located on the surface ofthe protein, e.g., hydrophilic regions.
• Figures 8-14 are hydrophobicity plots ofthe proteins ofthe 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 ofthe invention, e.g., an epitope of a polypeptide ofthe invention.
• a molecule which specifically binds to a given polypeptide ofthe 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.
• Polyclonal antibodies can be prepared as described above by immunizing a suitable subject with a polypeptide ofthe invention as an immunogen.
• Preferred polyclonal antibody compositions are ones that have been selected for antibodies directed against a polypeptide or polypeptides ofthe invention.
• Particularly prefened polyclonal antibody preparations are ones that contain only antibodies directed against a polypeptide or polypeptides ofthe invention.
• Particularly prefened immunogen compositions are those that contain no other human proteins such as, for example, immunogen compositions made using a non-human host cell for recombinant expression of a polypeptide ofthe invention. In such a manner, the only human epitope or epitopes recognized by the resulting antibody compositions raised against this immunogen will be present as part of a polypeptide or polypeptides ofthe invention.
• the antibody titer in the immunized subject can be monitored over time by standard 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 ofthe invention can be selected for (e.g., partially purified) or purified by, e.g., affinity chromatography.
• a recombinantly expressed and purified (or partially purified) protein ofthe 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 ofthe 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 ofthe invention, and preferably at most 20%>, yet more preferably at most 10%, and most preferably at most 5%> (by dry weight) ofthe sample is contaminating antibodies.
• a purified antibody composition means that at least 99%o ofthe antibodies in the composition are directed against the desired protein or polypeptide ofthe 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 EBV-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 Current Protocols in Immunology (1994) Coligan et al.
• Hybridoma cells producing a monoclonal antibody ofthe 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 ofthe 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.
• 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 ofthe 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.
• 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 ofthe invention.
• Monoclonal antibodies directed against the antigen can be obtained using conventional hybridoma technology.
• the human immunoglobulin transgenes harbored by the transgenic mice reanange during B cell differentiation, and subsequently undergo class switching and somatic mutation.
• 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
• An antibody directed against a polypeptide ofthe invention e.g., monoclonal antibody
• such an antibody can be used to detect the protein (e.g.
• 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. Examples of 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;
• examples of bioluminescent materials include luciferase, luciferin, and aequorin, .and examples of suitable radioactive material include 125j ; 131 ; 35g 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 (II) (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 conjugates ofthe invention can be used for modifying a given biological response, 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.
• IL-1 interleukin-1
• IL-2 interleukin-2
• IL-6 interleukin-6
• GM-CSF granulocyte macrophase colony stimulating factor
• G-CSF granulocyte colony stimulating factor
• Monoclonal Antibodies '84 Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); "Analysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapy", in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp. 303-16 (Academic Press 1985), and Thorpe et al., "The Preparation And Cytotoxic Properties Of Antibody-Toxin Conjugates", Immunol. Rev., 62:119-58 (1982).
• 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 ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, respectively; a fragment of at least 15 amino acid residues ofthe amino acid sequence of any one of SEQ ID NOs: 2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, an amino acid sequence which is at least 95%> identical to the amino acid sequence of any one of SEQ ID NOs: 2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, wherein the percent identity is determined using the amino acid sequence of any one
• 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 ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, respectively; a fragment of at least 15 amino acid residues ofthe amino acid sequence of any one of SEQ ID NOs: 2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69,
• nucleic acid molecule consisting of any one of SEQ ID NOs: 1, 3, 4, 6, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 38, 39, 53, 55, 56, 58, 59, 61, 62, 64, 65, 67, 68, 70, 71, 73, or the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, or a complement thereof, under conditions of hybridization of 6X SSC at 45 °C and washing in 0.2 X SSC, 0.1%) SDS at 65 °C.
• Such non-human antibodies can be goat, mouse, sheep, horse, chicken,
• the non-human antibodies ofthe invention can be chimeric and/or humanized antibodies.
• the non-human antibodies ofthe 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
• 25 amino acid sequence selected from the group consisting of: the amino acid sequence of any one of SEQ ID NOs:2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69, 72, or an amino acid sequence encoded by the cDNA of a clone deposited as any of ATCC 98999, 202171, 98965, and 98966, respectively; a fragment of at least 15 amino acid residues ofthe amino acid sequence of any one of SEQ ID NOs: 2, 5, 7, 9, 12, 15, 18, 21, 54, 57, 60, 63, 66, 69,
• the monoclonal antibodies can be human, humanized, chimeric and/or non-human antibodies.
• the substantially purified antibodies or fragments thereof specifically bind to a signal peptide, a secreted sequence, an extracellular domain, a transmembrane or a cytoplasmic domain cytoplasmic membrane of a polypeptide ofthe invention.
• the substantially purified antibodies or fragments thereof, the non-human antibodies or fragments thereof, and/or the monoclonal antibodies or fragments thereof, ofthe invention specifically bind to a secreted sequence or an extracellular domain ofthe amino acid sequence of SEQ ID NOs:2, 5, 9, 12, 15, 18, 66, 21, 126.
• the secreted sequence or extracellular domain to which the antibody, or fragment thereof, binds comprises from about amino acids 23-345 of SEQ ID NO:2 (SEQ ID NO:), from amino acids 1-146 of SEQ ID NO:5 (SEQ ID NO:35), from about amino acids 28-301 of SEQ ID NO:9 (SEQ ID NO:), from about amino acids 19-553 of SEQ ID NO:12 (SEQ ID NO:), from about amino acids 23-271 of SEQ ID NO:15 (SEQ ID NO:), from about amino acids 29-458 of SEQ ID NO: 18 (SEQ ID NO:), from about amino acids 29-874 of SEQ ID NO:9 (SEQ ID NO:) and amino acid residues 1 to 146 of SEQ ID NO:35.
• any ofthe antibodies ofthe invention can be conjugated to a therapeutic moiety or to a detectable substance.
• detectable substances that can be conjugated to the antibodies ofthe 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 ofthe invention conjugated to a detectable substance, and instructions for use.
• Still another aspect ofthe invention is a pharmaceutical composition comprising an antibody ofthe invention and a pharmaceutically acceptable carrier.
• the pharmaceutical composition contains an antibody ofthe invention, a therapeutic moiety, and a pharmaceutically acceptable carrier.
• Still another aspect ofthe invention is a method of making an antibody that specifically recognizes TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239, 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 ID
• 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 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 ofthe mammal.
• antibodies are collected from the antibody-producing cell.
• vectors preferably expression vectors, containing a nucleic acid encoding a polypeptide ofthe 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 is another type of 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 ofthe invention comprise a nucleic acid ofthe invention in a form suitable for expression ofthe nucleic acid in a host cell.
• the recombinant expression vectors include one or more regulatory sequences, selected on the basis ofthe 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 ofthe 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 ofthe 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 ofthe expression vector can depend on such factors as the choice ofthe host cell to be transformed, the level of expression of protein desired, etc.
• the expression vectors ofthe 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 ofthe invention can be designed for expression of a polypeptide ofthe 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 ofthe recombinant protein.
• Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility ofthe recombinant protein; and 3) to aid in the purification ofthe recombinant protein by acting as a ligand in affinity purification.
• a proteolytic cleavage site is introduced at the junction ofthe fusion moiety and the recombinant protein to enable separation ofthe recombinant protein from the fusion moiety subsequent to purification ofthe fusion protein.
• enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
• Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; 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
• maltose E binding protein or protein A, respectively, to the target recombinant protein.
• Suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al., (1988) Gene 69:301-315) and pET l id (Studier et al., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60-89).
• Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-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 e prophage harboring a T7 gnl gene under the transcriptional control ofthe 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 ofthe 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 ofthe 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) EMBO J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al. (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, CA), and pPicZ (Invitrogen Corp, 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 ofthe 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) EMBO J. 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
• 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 :26S-211), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-
• T cell receptors Winoto and Baltimore (1989) EMBO J. 8:729-733
• immunoglobulins Bonerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748
• neuron-specific promoters e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477
• pancreas- specific promoters Edlund et al. (1985) Science 230:912-916)
• the invention further provides a recombinant expression vector comprising a DNA molecule ofthe invention cloned into the expression vector in an antisense orientation.
• the DNA molecule is operably linked to a regulatory sequence in a manner which allows for expression (by transcription ofthe DNA molecule) of an RNA molecule which is antisense to the mRNA encoding a polypeptide ofthe invention.
• Regulatory sequences 5 operably linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression ofthe 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
• 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 o foreign nucleic acid into a host cell, including calcium phosphate or calcium chloride co- precipitation, D ⁇ A ⁇ -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 0 methotrexate.
• Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
• an endogenous e.g., TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and 5 TANGO 239 nucleic acid within a cell, cell line or microorganism
• 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 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239) 0 and controls, modulates or activates the endogenous gene.
• endogenous TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239 which are normally "transcriptionally silent", i.e., TANGO 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239 genes which are normally not expressed, or are expressed only at very low levels in a cell line or 5 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 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239 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 128, TANGO 140, TANGO 197, TANGO 212, TANGO 213, TANGO 224, and TANGO 239 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 ofthe invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce a polypeptide ofthe invention. Accordingly, the invention further provides methods for producing a polypeptide ofthe invention using the host cells ofthe invention. In one embodiment, the method comprises culturing the host cell of invention (into which a recombinant expression vector encoding a polypeptide ofthe 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 ofthe invention can also be used to produce nonhuman transgenic animals.
• a host cell ofthe invention is a fertilized oocyte or an embryonic stem cell into which a sequences encoding a polypeptide ofthe invention have been introduced.
• Such host cells can then be used to create non-human transgenic animals in which exogenous sequences encoding a polypeptide ofthe invention have been introduced into their genome or homologous recombinant animals in which endogenous encoding a polypeptide ofthe invention sequences have been altered.
• Such animals are useful for studying the function and/or activity ofthe 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 ofthe cells ofthe 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 ofthe mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues ofthe 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 ofthe animal, e.g., an embryonic cell ofthe animal, prior to development ofthe animal.
• a transgenic animal ofthe invention can be created by introducing nucleic acid encoding a polypeptide ofthe 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 ofthe transgene.
• a tissue-specific regulatory sequence(s) can be operably linked to the transgene to direct expression ofthe polypeptide ofthe invention to particular cells.
• transgenic founder animal can be identified based upon the presence ofthe transgene in its genome and/or expression of mRNA encoding the transgene in tissues or cells ofthe animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene.
• transgenic animals carrying the transgene can further be bred to other transgenic animals carrying other transgenes.
• a vector is prepared which contains at least a portion of a gene encoding a polypeptide ofthe 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 ofthe endogenous protein).
• the altered portion ofthe gene is flanked at its 5' and 3' ends by additional nucleic acid ofthe 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 ofthe animal contain the homologously recombined DNA by germline transmission ofthe transgene.
• transgenic non-human animals can be produced which contain selected systems which allow for regulated expression ofthe transgene.
• a system is the cre/loxP recombinase system of bacteriophage PI.
• cre/loxP recombinase system of bacteriophage PI.
• a recombinase system is the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355.
• a cre/loxP recombinase system is used to regulate expression ofthe transgene
• animals 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 ofthe 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.
• compositions suitable for administration can be incorporated into pharmaceutical compositions suitable for administration.
• Such 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 absorption delaying agents, and the like, compatible with pharmaceutical administration.
• the use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
• the invention includes methods for preparing pharmaceutical compositions for modulating the expression or activity of a polypeptide or nucleic acid ofthe invention. Such methods comprise formulating a pharmaceutically acceptable carrier with an agent which modulates expression or activity of a polypeptide or nucleic acid ofthe 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 ofthe invention and one or more addtional active compounds.
• a pharmaceutical composition ofthe 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.
• a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycer
• 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 EL (BASF; Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists.
• 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 ofthe required particle size in the case of dispersion and by the use of surfactants.
• Prevention ofthe 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 absorption ofthe injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
• Sterile injectable solutions can be prepared by incorporating 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 incorporating the active compound into 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 ofthe 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 purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules. Oral compositions can also be prepared using a fluid canier 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 ofthe composition.
• the tablets, pills, capsules, troches and the like can contain any ofthe 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 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
• the compounds are delivered in the form of an aerosol spray from a pressurized container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
• 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 Corporation 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.
• 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 produce the desired therapeutic effect in association with the required pharmaceutical carrier.
• the specification for the dosage unit forms ofthe invention are dictated by and directly dependent on the unique characteristics ofthe active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
• the prefened dosage is 0.1 mg/kg to 100 mg/kg of body weight (generally 10 mg/kg to 20 mg/kg). If the antibody is to act in the brain, a dosage of 50 mg/kg to 100 mg/kg is usually appropriate. Generally, partially human antibodies and fully human antibodies have a longer half-life within the human body than other antibodies. Accordingly, lower dosages and less frequent administration is often possible. Modifications such as 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 ofthe invention can be inserted into vectors and used as 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 ofthe 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.
• the pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
• nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more ofthe 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).
• polypeptides ofthe invention can to used to (i) modulate cellular proliferation; (ii) modulate cell migration and chemotaxis; (iii) modulate cellular differentiation; and/or (iv) modulate angiogenesis.
• the isolated nucleic acid molecules ofthe 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 ofthe invention.
• the polypeptides ofthe invention can be used to screen drugs or compounds which modulate activity or expression of a polypeptide ofthe invention as well as to treat disorders characterized by insufficient or excessive production of a protein ofthe 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 ofthe invention can be used to detect and isolate a protein ofthe and modulate activity of a protein ofthe 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 refened 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 ofthe invention or have a stimulatory or inhibitory effect on, for example, expression or activity of a polypeptide ofthe invention.
• modulators i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to polypeptide ofthe invention or have a stimulatory or inhibitory effect on, for example, expression or activity of a polypeptide ofthe 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 ofthe invention or biologically active portion thereof.
• the test compounds of the present invention can be obtained using any ofthe 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, nonpeptide 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 ofthe invention, or a biologically active portion thereof, on the cell surface is contacted with a test compound and the ability ofthe 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 ofthe 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 ofthe 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, 5 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 ofthe 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 ofthe test compound to interact with the polypeptide, wherein determining the ability ofthe test compound to interact with the polypeptide comprises determining the ability ofthe 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 ofthe invention, or a biologically active portion thereof, on the cell surface with a test compound and determining the ability ofthe test compound to modulate (e.g., stimulate or inhibit) the activity ofthe polypeptide or biologically active portion thereof. Determining the ability ofthe test compound to modulate the activity ofthe polypeptide or a biologically active portion thereof can be accomplished, for example, by determining the ability ofthe 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 ofthe 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 ofthe 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 ofthe 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 ofthe 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 ofthe invention
• the activity ofthe target molecule can be determined by detecting induction of a cellular second messenger ofthe target (e.g., intracellular Ca 2+ , diacylglycerol, IP3, etc.), detecting catalytic/enzymatic activity ofthe 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 ofthe present invention is a cell-free assay comprising contacting a polypeptide ofthe invention or biologically active portion thereof with a test compound and determining the ability ofthe test compound to bind to the polypeptide or biologically active portion thereof. Binding ofthe test compound to the polypeptide can be determined either directly or indirectly as described above.
• the assay includes contacting the polypeptide ofthe 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 ofthe test compound to interact with the polypeptide, wherein determining the ability ofthe test compound to interact with the polypeptide comprises determining the ability ofthe 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 ofthe invention or biologically active portion thereof with a test compound and determining the ability ofthe test compound to modulate (e.g., stimulate or inhibit) the activity ofthe polypeptide or biologically active portion thereof. Determining the ability of the test compound to modulate the activity ofthe polypeptide can be accomplished, for example, by determining the ability ofthe polypeptide to bind to a target molecule by one ofthe methods described above for determining direct binding. In an alternative embodiment, determining the ability ofthe test compound to modulate the activity ofthe polypeptide can be accomplished by determining the ability ofthe polypeptide ofthe invention to further modulate the target molecule. For example, the catalytic/enzymatic activity ofthe 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 ofthe test compound to interact with the polypeptide, wherein determining the ability ofthe test compound to interact with the polypeptide comprises , determining the ability ofthe polypeptide to preferentially bind to or modulate the activity of a target molecule.
• the cell-free assays ofthe present invention are amenable to use of both a soluble form or the membrane-bound form of a polypeptide ofthe invention.
• non-ionic detergents such as n-octylglucoside, n-do
• binding of a test compound to the polypeptide, or interaction ofthe polypeptide with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable 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 ofthe 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 ofthe 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 ofthe polypeptide ofthe invention can be determined using standard techniques.
• polypeptide ofthe invention or its target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
• Biotinylated polypeptide ofthe 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 ofthe invention or target molecules but which do not interfere with binding ofthe polypeptide of the invention to its target molecule can be derivatized to the wells ofthe plate, and unbound target or polypeptidede ofthe invention trapped in the wells by antibody conjugation.
• Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the polypeptide ofthe invention or target molecule, as well as enzyme- linked assays o which rely on detecting an enzymatic activity associated with the polypeptide ofthe invention or target molecule.
• modulators of expression of a polypeptide ofthe invention are identified in a method in which a cell is contacted with a candidate compound and the expression ofthe selected mRNA or protein (i.e., the mRNA or protein conesponding to a 5 polypeptide or nucleic acid ofthe invention) in the cell is determined.
• the level of expression of the selected mRNA or protein in the presence ofthe candidate compound is compared to the level of expression ofthe selected mRNA or protein in the absence ofthe candidate compound.
• the candidate compound can then be identified as a modulator of expression ofthe polypeptide ofthe invention based on this comparison.
• the candidate compound when expression ofthe selected mRNA or protein is greater (statistically significantly greater) in the presence ofthe candidate compound than in its absence, the candidate compound is identified as a stimulator ofthe selected mRNA or protein expression.
• the 5 candidate compound when expression ofthe selected mRNA or protein is less (statistically significantly less) in the presence ofthe candidate compound than in its absence, the 5 candidate compound is identified as an inhibitor ofthe selected mRNA or protein expression.
• the level ofthe selected mRNA or protein expression in the cells can be determined by methods described herein.
• a polypeptide ofthe inventions can be used as "bait proteins" in a two-hybrid assay or three hybrid assay (see, e.g., U.S. Patent No. 0 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem.
• binding proteins are also likely to be involved in the 5 propagation of signals by the polypeptide ofthe inventions as, for example, upstream or , downstream elements of a signaling pathway involving the polypeptide ofthe 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 ofthe sequence) of a gene has been isolated, this sequence can be used to map the location ofthe gene on a chromosome. Accordingly, nucleic acid molecules described herein or fragments thereof, can be used to map the location ofthe conesponding genes on a chromosome. The mapping ofthe sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease. Briefly, genes can be mapped to chromosomes by preparing PCR primers
• 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 ofthe 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. Acad. Sci. USA 87:6223-27), pre-screening with labeled flow-sorted chromosomes, and pre- selection by hybridization to chromosome specific cDNA libraries.
• Fluorescence in situ hybridization of a DNA sequence to a metaphase chromosomal spread can further be used to provide a precise chromosomal location in one step.
• 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 ofthe genes actually are prefened for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping. Once a sequence has been mapped to a precise chromosomal location, the physical position ofthe sequence on the chromosome can be conelated with genetic map data. (Such data are found, for example, in V.
• differences in the DNA sequences between individuals affected and unaffected with a disease associated with a gene ofthe invention can be determined. If a mutation is observed in some or all ofthe affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent ofthe 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 DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.
• the human gene for TANGO 128 was mapped on radiation hybrid panels to the long arm of chromosome 4, in the region q28-31. Flanking markers for this region are WI-3936 and AFMCO27ZB9.
• the FGC fusenogen gene cluster
• GYP glycophorin cluster
• IL15 interlukin 15
• TDO2 tryptophab oxygenase
• MLR mineralcorticoid receptor
• the Q (quinky), pdw (proportional dwarf), and lyll (lymphoblastomic leukemia) loci also map to this region ofthe mouse chromosome.
• 1115 interlukin 15
• mlr mineralcorticoid receptor
• ucp uncoupling protein
• clgn calmegin
• the MDCR Miller-Dieker syndrome
• PEDF pigment epithelium derived factor
• PFNl(profillin 1) genes also map to this region of the human chromosome. This region is syntenic to mouse chromosome 11, locus 46(g).
• the ti (tipsy) loci also maps to this region ofthe mouse chromosome.
• the pfnl (profilin 1), htt (5-hydroxytryptamine (serotonin) transporter), acrb (acetylcholine receptor beta) genes also map to this region ofthe mouse chromosome.
• the nucleic acid sequences ofthe 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 polymorphism (RFLP) for identification of its personnel.
• RFLP restriction fragment length polymorphism
• 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 ofthe present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).
• sequences ofthe 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 ofthe 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 ofthe present invention can be used to obtain such identification sequences from individuals and from tissue.
• the nucleic acid sequences ofthe invention uniquely represent portions ofthe 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 ofthe sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification purposes.
• the noncoding sequences of SEQ ID NO:l, 4, 6, 8, 11, 14, 17, 20, ' 53, 56, 59, 62, 65, or 68 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 ID NO:3, 10, 13, 16, 19, 22, 38, 3955, 58, 61, 64, 67, 70, or 73, 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 ofthe 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 perpetrator 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 ofthe origin ofthe biological sample.
• sequences ofthe 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 polymorphisms occur in the noncoding regions, making it easier to differentiate individuals using this technique.
• polynucleotide reagents include the nucleic acid sequences ofthe invention or portions thereof, e.g., fragments derived from noncoding regions having a length of at least 20 or 30 bases.
• the 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. ' C. Predictive Medicine
• 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) purposes 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 ofthe 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 abenant 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 ofthe invention. For example, mutations in a gene ofthe invention can be assayed in a biological sample. Such assays can be used for prognostic or predictive purpose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with abenant expression or activity of a polypeptide ofthe invention.
• Another aspect ofthe invention provides methods for expression of a nucleic acid or polypeptide ofthe invention or activity of a polypeptide ofthe invention in an individual to thereby select appropriate therapeutic or prophylactic agents for that individual (refened 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 ofthe individual (e.g., the genotype ofthe individual examined to determine the ability ofthe individual to respond to a particular agent).
• Yet another aspect ofthe invention pertains to monitoring the influence of agents (e.g., drugs or other compounds) on the expression or activity of a polypeptide of the invention in clinical trials.
• agents e.g., drugs or other compounds
• An exemplary method for detecting the presence or absence of a polypeptide or nucleic acid ofthe 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) ofthe invention such that the presence of a polypeptide or nucleic acid ofthe invention is detected in the biological sample.
• a preferred agent for detecting mRNA or genomic DNA encoding a polypeptide ofthe invention is a labeled nucleic acid probe capable of hybridizing to mRNA or genomic DNA encoding a polypeptide ofthe invention.
• the nucleic acid probe can be, for example, a full-length cDNA, such as the nucleic acid of SEQ ID NO:l, 8, 11, 14, 17 or 20, or a portion thereof, such as an 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 ofthe invention.
• a full-length cDNA such as the nucleic acid of SEQ ID NO:l, 8, 11, 14, 17 or 20, or a portion thereof, such as an 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 ofthe invention.
• Other suitable probes for use in the diagnostic assays ofthe invention are described herein.
• a prefened agent for detecting a polypeptide ofthe invention is an antibody capable of binding to a polypeptide ofthe invention, preferably an antibody with a detectable label.
• 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.
• the term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling ofthe probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling ofthe probe or antibody by reactivity with another reagent that is directly labeled.
• Examples of 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 tissues, cells and fluids present within a subject. That is, the detection method ofthe 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 ofthe invention include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence.
• In vitro techniques for detection of genomic DNA include Southern hybridizations.
• in vivo techniques for detection of a polypeptide ofthe 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 ofthe invention or mRNA or genomic DNA encoding a polypeptide ofthe invention, such that the presence ofthe polypeptide or mRNA or genomic DNA encoding the polypeptide is detected in the biological sample, and comparing the presence ofthe polypeptide or mRNA or genomic DNA encoding the polypeptide in the control sample with the presence ofthe polypeptide or mRNA or genomic DNA encoding the polypeptide in the test sample.
• the invention also encompasses kits for detecting the presence of a polypeptide or nucleic acid ofthe invention in a biological sample (a test sample).
• kits can be used to determine if a subject is suffering from or is at increased risk of developing a disorder associated with abenant expression of a polypeptide ofthe invention (e.g., a prohferative disorder, e.g., psoriasis or cancer).
• a polypeptide ofthe invention e.g., a prohferative 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 ofthe 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 may also include instructions for observing that the tested subject is suffering from or is at risk of developing a disorder associated with aberrant expression ofthe polypeptide if the amount ofthe polypeptide or mRNA encoding the polypeptide is above or below a normal level.
• the kit may comprise, for example: (1) a first antibody (e.g., attached to a solid support) which binds to a polypeptide ofthe invention; and, optionally, (2) a second, different antibody which binds to either the polypeptide or the first antibody and is conjugated to a detectable agent.
• a first antibody e.g., attached to a solid support
• a second, different antibody which binds to either the polypeptide or the first antibody and is conjugated to a detectable agent.
• the kit may comprise, for example: (1) an oligonucleotide, e.g., a detectably labeled oligonucleotide, which hybridizes to a nucleic acid sequence encoding a polypeptide ofthe invention or (2) a pair of primers useful for amplifying a nucleic acid molecule encoding a polypeptide ofthe invention.
• the kit may also comprise, e.g., a buffering agent, a preservative, or a protein stabilizing agent.
• the kit may also comprise components necessary for detecting the detectable agent (e.g., an enzyme or a substrate).
• the kit may also contain a control sample or a series of control samples which can be assayed and compared to the test sample contained.
• Each component ofthe kit is usually enclosed within an individual container and all ofthe 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.
• Prognostic Assays 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 abenant expression or activity of a polypeptide ofthe 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 abenant expression or activity of a polypeptide ofthe invention, e.g., a prohferative disorder, e.g., psoriasis or cancer, or an angiogenic disorder.
• the prognostic assays can be utilized to identify a subject having or at risk for developing such a disease or disorder.
• the present invention provides a method in which a test sample is obtained from a subject and a polypeptide or nucleic acid (e.g., mRNA, genomic DNA) ofthe invention is detected, wherein the presence ofthe polypeptide or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant expression or activity ofthe polypeptide.
• a 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 abenant 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 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 ofthe invention in which a test sample is obtained and the polypeptide or nucleic acid encoding the polypeptide is detected (e.g., wherein the presence ofthe 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 ofthe polypeptide).
• the methods ofthe invention can also be used to detect genetic lesions or mutations in a gene ofthe invention, thereby determining if a subject with the lesioned gene is at risk for a disorder characterized abenant expression or activity of a polypeptide ofthe 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 ofthe invention, or the mis-expression ofthe gene encoding the polypeptide ofthe 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 ofthe gene; 4) a chromosomal rearrangement ofthe gene; 5) an alteration in the level of a messenger RNA transcript ofthe gene; 6) an abenant modification ofthe gene, such as ofthe methylation pattern ofthe genomic DNA; 7) the presence of a non- wild type splicing pattern of a messenger RNA transcript ofthe gene; 8) a non-wild type level of a the protein encoded by
• detection ofthe lesion involves the use of a probe/primer in
• 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 ofthe 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 ofthe gene (if present) occurs, and detecting the presence or absence of an amplification product, or 0 detecting the size ofthe 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 ofthe techniques used for detecting mutations described herein.
• nucleic acid e.g., genomic, mRNA or both
• Alternative amplification methods include: self sustained sequence replication
• 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 enzymes.
• 35 - 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 o 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 anay that allows the characterization of specific mutations by using smaller, specialized probe anays complementary to all variants or mutations detected.
• Each mutation array is composed of 5 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 ofthe sample nucleic acids with the conesponding wild-type (control) 0 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). It is also contemplated that 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 5 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 0 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 ofthe duplex such as which will exist due to basepair mismatches between the control and sample strands.
• RNA/DNA duplexes can be 5 treated with RNase to digest mismatched regions, and DNA/DNA hybrids can be treated with Sl 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 ofthe 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 proteins that recognize mismatched base pairs in double-stranded DNA
• 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 e.g., a wild-type 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.
• alterations in electrophoretic mobility will be used to identify mutations in genes.
• SSCP single strand conformation polymorphism
• 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 ofthe 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).
• Such allele specific o 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.
• Oligonucleotides 5 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. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent or reduce polymerase extension (Prossner (1993) Tibtech 11 :238).
• 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 ofthe 5' sequence making it possible to detect the presence of a known mutation at a 5 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 0 encoding a polypeptide ofthe invention.
• any cell type or tissue, preferably peripheral blood leukocytes, in which the polypeptide ofthe invention is expressed may be utilized in the prognostic assays described herein.
• Pharmacogenomics 5 Agents, or modulators which have a stimulatory or inhibitory effect on activity or expression of a polypeptide ofthe invention as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) disorders associated with abenant activity ofthe polypeptide.
• the pharmacogenomics i.e., the study ofthe 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 ofthe pharmacologically active drug.
• the pharmacogenomics ofthe individual permits the selection of effective agents (e.g., drugs) for prophylactic or therapeutic treatments based on a consideration ofthe individual's genotype. Such pharmacogenomics can further be used to determine appropriate dosages and therapeutic regimens. Accordingly, the activity of a polypeptide ofthe invention, expression of a nucleic acid ofthe invention, or mutation content of a gene ofthe invention in an individual can be determined to thereby select appropriate agent(s) for therapeutic or prophylactic treatment ofthe individual.
• Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, e.g., Linder (1997) Clin. Chem. 43(2):254-266.
• two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body are refened to as "altered drug action.” Genetic conditions transmitted as single factors altering the way the body acts on drugs are refened to as "altered drug metabolism”. These pharmacogenetic conditions can occur either as rare defects or as polymorphisms.
• glucose-6-phosphate dehydrogenase deficiency is a common inherited enzymopathy in which the main clinical complication is haemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and consumption of fava beans.
• oxidant drugs anti-malarials, sulfonamides, analgesics, nitrofurans
• the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action.
• the activity of a polypeptide ofthe 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 ofthe individual.
• pharmacogenetic studies can be used to apply genotyping of polymorphic 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 ofthe polypeptide, such as a modulator identified by one ofthe exemplary screening assays described herein.
• Monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of a polypeptide ofthe invention can be applied not only in basic drug screening, but also in clinical trials.
• 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 ofthe invention and preferably, that of other polypeptide that have been implicated in for example, a cellular proliferation disorder can be used as a marker ofthe immune responsiveness of a particular cell.
• genes including those ofthe 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 ofthe 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 ofthe 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 ofthe 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 ofthe invention or other genes.
• the gene expression pattern can serve as a marker, indicative ofthe physiological response ofthe cells to the agent. Accordingly, this response state may be determined before, and at various points during, treatment ofthe 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 ofthe agent; (ii) detecting the level ofthe polypeptide or nucleic acid ofthe invention in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level the ofthe polypeptide or nucleic acid ofthe invention in the post-administration samples; (v) comparing the level ofthe polypeptide or nucleic acid ofthe invention in the pre-administration sample with the level ofthe polypeptide or nucleic acid ofthe invention in the post-administration sample or samples; and (vi) altering the administration ofthe agent to the subject accordingly.
• an agent e.g., an agonist, antagonist,
• increased administration ofthe agent may be desirable to increase the expression or activity ofthe polypeptide to higher levels than detected, i.e., to increase the effectiveness ofthe agent.
• decreased administration ofthe agent may be desirable to decrease expression or activity ofthe polypeptide to lower levels than detected, i.e., to decrease the effectiveness ofthe 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 abenant expression or activity of a polypeptide ofthe invention.
• disorders characterized by abberant expression or activity ofthe polypeptides ofthe invention include prohferative disorders such as psoriasis and cancer.
• the polypeptides ofthe invention can be used to promote hair growth, promote wound healing, as well as other uses described herein.
• the invention provides a method for preventing in a subject, a disease or condition associated with an abenant expression or activity of a polypeptide ofthe invention, by administering to the subject an agent which modulates expression or at least one activity ofthe polypeptide.
• Subjects at risk for a disease which is caused or contributed to by aberrant expression or activity of a polypeptide ofthe 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 ofthe abenancy, 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.
• an antagonist of an ELVIS protein may be used to treat a prohferative disorder, e.g., psoriasis, associated with abberant ELVIS expression or activity.
• the appropriate agent can be determined based on screening assays described herein.
• the modulatory method ofthe invention involves contacting a cell with an agent that modulates one or more ofthe activities ofthe 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 ofthe polypeptide, a peptide, a peptidomimetic, or other small molecule.
• the agent stimulates one or more ofthe biological activities ofthe polypeptide. Examples of such stimulatory agents include the active polypeptide ofthe invention and a nucleic acid molecule encoding the polypeptide ofthe invention that has been introduced into the cell.
• the agent inhibits one or more ofthe biological activities ofthe polypeptide ofthe invention.
• inhibitory agents include antisense nucleic acid molecules and antibodies.
• These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g, by administering the agent to a subject).
• the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by abenant expression or activity of a polypeptide ofthe invention.
• 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.
• the method involves administering a polypeptide ofthe invention or a nucleic acid molecule ofthe invention as therapy to compensate for reduced or aberrant expression or activity ofthe 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, e.g., in wound healing.
• 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, e.g., in treatment of a prohferative disorder such as psoriasis.
• TANGO 140-2, TANGO 197 and TANGO 239 were deposited with the American Type Culture Collection (Manassas, VA) as composite deposits.
• Clones encoding TANGO 128, TANGO 140-1, TANGO 140-2, TANGO 197 and TANGO 239 were deposited on November 20, 1998 with the American Type Culture Collection under Accession Number ATCC 98999, (also referred to herein as mix EpDHMixl) from which each clone comprising a particular cDNA clone is obtainable.
• This deposit is a mixture of five strains, each carrying one recombinant plasmid harboring a particular cDNA clone.
• a strain harboring a particular cDNA clone To distinguish the strains and isolate a strain harboring a particular cDNA clone, one can first streak out an aliquot ofthe mixture to single colonies on nutrient medium (e.g., LB plates) supplemented with lOO ⁇ g/ml ampicillin, grow single colonies, and then extract the plasmid DNA using a standard minipreparation procedure. Next, one can digest a sample ofthe DNA minipreparation with a combination ofthe restriction enzymes Sal I and Not I and resolve the resultant products on a 0.8% agarose gel using standard DNA electrophoresis conditions. The digest will liberate fragments as follows: TANGO 128 (EpDH237) 2.8 kb and 4.3 kb
• TANGO 140-1 (EpDH137) 1.6 kb and 3.0 kb TANGO 140-2 (EpDH185) 3.4 kb and 4.3 kb TANGO 197 (EpDH213) 2.3 kb and 3.0 kb TANGO 239 (EpDH233) 3.0 kb and 3.4 kb
• EpDH137 1.6 kb and 3.0 kb TANGO 140-2
• EpDH185 3.4 kb and 4.3 kb
• TANGO 197 (EpDH213) 2.3 kb and 3.0 kb TANGO 239 (EpDH233) 3.0 kb and 3.4 kb
• EpDH233 3.0 kb and 3.4 kb

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