WO2001083553A2 - Nouveaux recepteurs couples a la proteine g - Google Patents

Nouveaux recepteurs couples a la proteine g Download PDF

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Publication number
WO2001083553A2
WO2001083553A2 PCT/US2001/014050 US0114050W WO0183553A2 WO 2001083553 A2 WO2001083553 A2 WO 2001083553A2 US 0114050 W US0114050 W US 0114050W WO 0183553 A2 WO0183553 A2 WO 0183553A2
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Prior art keywords
seq
ngpcr
polypeptide
sequence
nucleic acid
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PCT/US2001/014050
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English (en)
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WO2001083553A3 (fr
Inventor
Luis A. Parodi
Peter Lind
Torsten Sejlitz
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Pharmacia & Upjohn Company
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Priority to EP01932827A priority Critical patent/EP1278844A2/fr
Priority to AU2001259322A priority patent/AU2001259322A1/en
Publication of WO2001083553A2 publication Critical patent/WO2001083553A2/fr
Publication of WO2001083553A3 publication Critical patent/WO2001083553A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2799/00—Uses of viruses
    • C12N2799/02—Uses of viruses as vector
    • C12N2799/021—Uses of viruses as vector for the expression of a heterologous nucleic acid

Definitions

  • the present invention relates generally to the fields of genetics and cellular and molecular biology. More particularly, the invention relates to novel G protein coupled receptors, to polynucleotides that encode such novel receptors, to reagents such as antibodies, probes, primers and kits comprising such antibodies, probes, primers related to the same, and to methods which use the novel G protein coupled receptors, polynucleotides or reagents.
  • GPCRs G protein-coupled receptors
  • transmembrane receptors are sometimes also referred to as seven transmembrane (7TM) receptors.
  • These seven transmembrane domains define three extracellular loops and three intracellular loops, in addition to the amino- and carboxy- terminal domains.
  • the extracellular portions of the receptor have a role in recognizing and binding one or more extracellular binding partners (e.g., ligands), whereas the intracellular portions have a role in recognizing and communicating with downstream molecules in the signal transduction cascade.
  • the G protein-coupled receptors bind a variety of ligands including calcium ions, hormones, chemokines, neuropeptides, neurotransmitters, nucleotides, lipids, odorants, and even photons, and are important in the normal (and sometimes the aberrant) function of many cell types.
  • ligands including calcium ions, hormones, chemokines, neuropeptides, neurotransmitters, nucleotides, lipids, odorants, and even photons.
  • G-protein heterotrimeric guanine-nucleotide-binding regulatory protein
  • the G protein in turn transmits a signal to an effector molecule within the cell, by either stimulating or inhibiting the activity of that effector molecule.
  • effector molecules include adenylate cyclase, phospholipases and ion channels.
  • Adenylate cyclase and phospholipases are enzymes that are involved in the production of the second messenger molecules cAMP, inositol triphosphate and diacyglycerol. It is through this sequence of events that an extracellular ligand stimuli exerts intracellular changes through a G protein-coupled receptor. Each such receptor has its own characteristic primary structure, expression pattern, ligand-binding profile, and intracellular effector system.
  • G protein-coupled receptors Because of the vital role of G protein-coupled receptors in the communication between cells and their environment, such receptors are attractive targets for therapeutic intervention, for example by activating or antagonizing such receptors.
  • receptors having a known ligand the identification of agonists or antagonists may be sought specifically to enhance or inhibit the action of the ligand.
  • Some G protein-coupled receptors have roles in disease pathogenesis (e.g., certain chemokine receptors that act as HIV co-receptors may have a role in AIDS pathogenesis), and are attractive targets for therapeutic intervention even in the absence of knowledge of the natural ligand of the receptor.
  • Other receptors are attractive targets for therapeutic intervention by virtue of their expression pattern in tissues or cell types that are themselves attractive targets for therapeutic intervention.
  • Examples of this latter category of receptors include receptors expressed in immune cells, which can be targeted to either inhibit autoimmune responses or to enhance immune responses to fight pathogens or cancer; and receptors expressed in the brain or other neural organs and tissues, which are likely targets in the treatment of mental disorder, depression, schizophrenia, bipolar disease, or other neurological disorders.
  • This latter category of receptor is also useful as a marker for identifying and/or purifying (e.g., via fluorescence-activated cell sorting) cellular subtypes that express the receptor.
  • CNS central nervous system
  • the present invention relates to an isolated nucleic acid molecule that comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence homologous to sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO:136, or a fragment thereof.
  • the nucleic acid molecule comprises a sequence that encodes a polypeptide comprising a sequence selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, or a fragment thereof.
  • the nucleic acid molecule comprises a sequence homologous to a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67, or a fragment thereof.
  • the nucleic acid molecule comprises a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID
  • the present invention provides vectors which comprise the nucleic acid molecule of the invention.
  • the vector is an expression vector.
  • the present invention provides host cells which comprise the vectors of the invention.
  • the host cells comprise expression vectors.
  • the present invention provides an isolated nucleic acid molecule comprising a nucleotide sequence complementary to at least a portion of a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, said portion comprising at least 10 nucleotides.
  • the present invention provides a method of producing a polypeptide comprising a sequence selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, or a homolog or fragment thereof. The method comprising the steps of introducing a recombinant expression vector that includes a nucleotide sequence that encodes the polypeptide into a compatible host cell, growing the host cell under conditions for expression of the polypeptide and recovering the polypeptide.
  • the present invention provides an isolated antibody which binds to an epitope on a polypeptide comprising a sequence selected from the group consisting of SEQ ID NO: 68 to
  • SEQ ID NO: 136 or a homolog or fragment thereof.
  • the present invention provides an method of inducing an immune response in a mammal against a polypeptide comprising a sequence selected from the group consisting of SEQ ID NO: 1
  • the method comprises administering to a mammal an amount of the polypeptide sufficient to induce said immune response.
  • the present invention provides a method for identifying a compound which binds nGPCR-x.
  • the method comprises the steps of contacting nGPCR-x with a compound and determining whether the compound binds nGPCR-x.
  • the present invention provides a method for identifying a compound which binds a nucleic acid molecule encoding nGPCR-x.
  • the method comprises the steps of contacting said nucleic acid molecule encoding nGPCR-x with a compound and determining whether said compound binds said nucleic acid molecule.
  • the present invention provides a method for identifying a compound which modulates the activity of nGPCR-x.
  • the method comprises the steps of contacting nGPCR-x with a compound and determining whether nGPCR-x activity has been modulated.
  • the present invention provides a method of identifying an animal homolog of nGPCR-x.
  • the method comprises the steps screening a nucleic acid database of the animal with a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, or a portion thereof and determining whether a portion of said library or database is homologous to said sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, or portion thereof.
  • the present invention provides a method of identifying an animal homolog of nGPCR-x.
  • the methods comprises the steps screening a nucleic acid library of the animal with a nucleic acid molecule having a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67, or a portion thereof and determining whether a portion of said library or database is homologous to said sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67, or a portion thereof.
  • Another aspect of the present invention relates to methods of screening a human subject to diagnose a disorder affecting the brain or genetic predisposition therefor.
  • the methods comprise the steps of assaying nucleic acid of a human subject to determine a presence or an absence of a mutation altering an amino acid sequence, expression, or biological activity of at least one nGPCR that is expressed in the brain.
  • a diagnosis of the disorder or predisposition is made from the presence or absence of the mutation.
  • the presence of a mutation altering the amino acid sequence, expression, or biological activity of the nGPCR in the nucleic acid correlates with an increased risk of developing the disorder.
  • kits for screening a human subject to diagnose mental disorder or a genetic predisposition therefor include an oligonucleotide useful as a probe for identifying polymo ⁇ hisms in a human nGPCR-x.
  • the oligonucleotide comprises 6-50 nucleotides in a sequence that is identical or complementary to a sequence of a wild type human nGPCR-x gene sequence or nGPCR-x coding sequence, except for one sequence difference selected from the group consisting of a nucleotide addition, a nucleotide deletion, or nucleotide substitution.
  • the kit also includes a media packaged with the oligonucleotide.
  • the media contains information for identifying polymo ⁇ hisms that correlate with mental disorder or a genetic predisposition therefor, the polymo ⁇ hisms being identifiable using the oligonucleotide as a probe.
  • the present invention further relates to methods of identifying nGPCR allelic variants that correlates with mental disorders.
  • the methods comprise the steps of providing biological samples that comprise nucleic acid from a human patient diagnosed with a mental disorder, or from the patient's genetic progenitors or progeny, and detecting in the nucleic acid the presence of one or more mutations in an nGPCR that is expressed in the brain.
  • the nucleic acid includes sequences corresponding to the gene or genes encoding nGPCR.
  • the one or more mutations detected indicate an allelic variant that correlates with a mental disorder.
  • the present invention further relates to purified polynucleotides comprising nucleotide sequences encoding alleles of nGPCR-x from a human with mental disorder.
  • the polynucleotide hybridizes to the complement of nGPCR-x under the following hybridization conditions: (a) hybridization for 16 hours at 42C in a hybridization solution comprising 50% formamide, 1% SDS, 1 M NaCI, 10% dextran sulfate and (b) washing 2 times for 30 minutes at 60C in a wash solution comprising O.lx SSC and 1% SDS.
  • the present invention also provides methods for identifying a modulator of biological activity of nGPCR-x comprising the steps of contacting a cell that expresses nGPCR-x in the presence and in the absence of a putative modulator compound and measuring nGPCR-x biological activity in the cell. The decreased or increased nGPCR-x biological activity in the presence versus absence of the putative modulator is indicative of a modulator of biological activity.
  • the present invention further provides methods to identify compounds useful for the treatment of mental disorders. The methods comprise the steps of contacting a composition comprising nGPCR-x with a compound suspected of binding nGPCR-x. The binding between nGPCR-x and the compound suspected of binding nGPCR-x is detected.
  • Compounds identified as binding nGPCR-x are candidate compounds useful for the treatment of mental disorder.
  • Compounds identified as binding nGPCR-x, or other nGPCRs can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate their activity.
  • the present invention further provides methods for identifying a compound useful as a modulator of binding between nGPCR-x and a binding partner of nGPCR-x.
  • the methods comprise the steps of contacting the binding partner and a composition comprising nGPCR-x in the presence and in the absence of a putative modulator compound and detecting binding between the binding partner and nGPCR-x. Decreased or increased binding between the binding partner and nGPCR-x in the presence of the putative modulator, as compared to binding in the absence of the putative modulator is indicative a modulator compound useful for the treatment of a related disease or disorder.
  • nGPCR- x Compounds identified as modulating binding between nGPCR- x, or other nGPCRs and an nGPCR-x binding partner can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate their activity as modulators.
  • Another aspect of the present invention relates to methods of purifying a G protein from a sample containing a G protein.
  • the methods comprise the steps of contacting the sample with an nGPCR for a time sufficient to allow the G protein to form a complex with the nGPCR, isolating the complex from remaining components of the sample, maintaining the complex under conditions which result in dissociation of the G protein from the nGPCR, and isolating said G protein from the nGPCR.
  • Synchronization refers to polynucleotides produced by purely chemical, as opposed to enzymatic, methods. “Wholly” synthesized D ⁇ A sequences are therefore produced entirely by chemical means, and “partially” synthesized D ⁇ As embrace those wherein only portions of the resulting D ⁇ A were produced by chemical means.
  • region is meant a physically contiguous portion of the primary structure of a biomolecule.
  • a region is defined by a contiguous portion of the amino acid sequence of that protein.
  • domain is herein defined as referring to a structural part of a biomolecule that contributes to a known or suspected function of the biomolecule. Domains may be coextensive with regions or portions thereof; domains may also inco ⁇ orate a portion of a biomolecule that is distinct from a particular region, in addition to all or part of that region.
  • GPCR protein domains include, but are not limited to, the extracellular (i.e., ⁇ - terminal), transmembrane and cytoplasmic (i.e., C-terminal) domains, which are co-extensive with like-named regions of GPCRs; each of the seven transmembrane segments of a GPCR; and each of the loop segments (both extracellular and intracellular loops) connecting adjacent transmembrane segments.
  • the term "activity” refers to a variety of measurable indicia suggesting or revealing binding, either direct or indirect; affecting a response, i.e.
  • a measurable affect in response to some exposure or stimulus including, for example, the affinity of a compound for directly binding a polypeptide or polynucleotide of the invention, or, for example, measurement of amounts of upstream or downstream proteins or other similar functions after some stimulus or event.
  • gpcr refers to a gene, cDNA, RNA or nucleic acid sequence
  • GPCR refers to a protein, polypeptide, peptide, oligopeptide, or amino acid sequence.
  • nGPCR-x refers to any of the nGPCRs taught herein, while specific reference to a nGPCR (for example nGPCR- 2653) refers only to that specific nGPCR.
  • antibody is meant to refer to complete, intact antibodies, and Fab, Fab', F(ab)2, and other fragments thereof.
  • Complete, intact antibodies include monoclonal antibodies such as murine monoclonal antibodies, chimeric antibodies and humanized antibodies.
  • binding means the physical or chemical interaction between two proteins or compounds or associated proteins or compounds or combinations thereof. Binding includes ionic, non-ionic, Hydrogen bonds, Van der Waals, hydrophobic interactions, etc.
  • the physical interaction, the binding can be either direct or indirect, indirect being through or due to the effects of another protein or compound. Direct binding refers to interactions that do not take place through or due to the effect of another protein or compound but instead are without other substantial chemical intermediates. Binding may be detected in many different manners. As a non-limiting example, the physical binding interaction between a nGPCR-x of the invention and a compound can be detected using a labeled compound.
  • functional evidence of binding can be detected using, for example, a cell transfected with and expressing a nGPCR-x of the invention. Binding of the transfected cell to a ligand of the nGPCR that was transfected into the cell provides functional evidence of binding. Other methods of detecting binding are well-known to those of skill in the art.
  • the term "compound” means any identifiable chemical or molecule, including, but not limited to, small molecule, peptide, protein, sugar, nucleotide, or nucleic acid, and such compound can be natural or synthetic.
  • the term “complementary” refers to Watson-Crick basepairing between nucleotide units of a nucleic acid molecule.
  • the term “contacting” means bringing together, either directly or indirectly, a compound into physical proximity to a polypeptide or polynucleotide of the invention.
  • the polypeptide or polynucleotide can be in any number of buffers, salts, solutions etc. Contacting includes, for example, placing the compound into a beaker, microtiter plate, cell culture flask, or a microarray, such as a gene chip, or the like, which contains the nucleic acid molecule, or polypeptide encoding the nGPCR or fragment thereof.
  • homologous nucleotide sequence refers to sequences characterized by a homology, at the nucleotide level or amino acid level, of at least the specified percentage.
  • Homologous nucleotide sequences include those sequences coding for isoforms of proteins. Such isoforms can be expressed in different tissues of the same organism as a result of, for example, alternative splicing of RNA. Alternatively, isoforms can be encoded by different genes.
  • Homologous nucleotide sequences include nucleotide sequences encoding for a protein of a species other than humans, including, but not limited to, mammals.
  • Homologous nucleotide sequences also include, but are not limited to, naturally occurring allelic variations and mutations of the nucleotide sequences set forth herein.
  • a homologous nucleotide sequence does not, however, include the nucleotide sequence encoding other known GPCRs.
  • Homologous amino acid sequences include those amino acid sequences which contain conservative amino acid substitutions and which polypeptides have the same binding and/or activity.
  • a homologous amino acid sequence does not, however, include the amino acid sequence encoding other known GPCRs.
  • Percent homology can be determined by, for example, the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison WI), using the default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489, which is inco ⁇ orated herein by reference in its entirety).
  • isolated nucleic acid molecule refers to a nucleic acid molecule (DNA or RNA) that has been removed from its native environment.
  • isolated nucleic acid molecules include, but are not limited to, recombinant DNA molecules contained in a vector, recombinant DNA molecules maintained in a heterologous host cell, partially or substantially purified nucleic acid molecules, and synthetic DNA or RNA molecules.
  • modulates or “modifies” means an increase or decrease in the amount, quality, or effect of a particular activity or protein.
  • oligonucleotide refers to a series of linked nucleotide residues which has a sufficient number of bases to be used in a polymerase chain reaction (PCR). This short sequence is based on (or designed from) a genomic or cDNA sequence and is used to amplify, confirm, or reveal the presence of an identical, similar or complementary DNA or RNA in a particular cell or tissue. Oligonucleotides comprise portions of a DNA sequence having at least about 10 nucleotides and as many as about 50 nucleotides, preferably about 15 to 30 nucleotides. They are chemically synthesized and may be used as probes.
  • probe refers to nucleic acid sequences of variable length, preferably between at least about 10 and as many as about 6,000 nucleotides, depending on use. They are used in the detection of identical, similar, or complementary nucleic acid sequences. Longer length probes are usually obtained from a natural or recombinant source, are highly specific and much slower to hybridize than oligomers. They may be single- or double-stranded and carefully designed to have specificity in PCR, hybridization membrane-based, or ELISA- like technologies. The term “preventing” refers to decreasing the probability that an organism contracts or develops an abnormal condition.
  • treating refers to having a therapeutic effect and at least partially alleviating or abrogating an abnormal condition in the organism.
  • a therapeutic effect refers to the inhibition or activation factors causing or contributing to the abnormal condition.
  • a therapeutic effect relieves to some extent one or more of the symptoms of the abnormal condition.
  • a therapeutic effect can refer to one or more of the following: (a) an increase in the proliferation, growth, and/or differentiation of cells; (b) inhibition (i.e., slowing or stopping) of cell death; (c) inhibition of degeneration; (d) relieving to some extent one or more of the symptoms associated with the abnormal condition; and (e) enhancing the function of the affected population of cells.
  • Compounds demonstrating efficacy against abnormal conditions can be identified as described herein.
  • abnormal condition refers to a function in the cells or tissues of an organism that deviates from their normal functions in that organism.
  • An abnormal condition can relate to cell proliferation, cell differentiation, cell signaling, or cell survival.
  • An abnormal condition may also include obesity, diabetic complications such as retinal degeneration, and irregularities in glucose uptake and metabolism, and fatty acid uptake and metabolism.
  • Abnormal cell proliferative conditions include cancers such as fibrotic and mesangial disorders, abnormal angiogenesis and vasculogenesis, wound healing, psoriasis, diabetes mellitus, and inflammation.
  • Abnormal differentiation conditions include, but are not limited to, neurodegenerative disorders, slow wound healing rates, and slow tissue grafting healing rates.
  • Abnormal cell signaling conditions include, but are not limited to, psychiatric disorders involving excess neurotransmitter activity.
  • Abnormal cell survival conditions may also relate to conditions in which programmed cell death (apoptosis) pathways are activated or abrogated.
  • apoptosis programmed cell death
  • a number of protein kinases are associated with the apoptosis pathways. Aberrations in the function ofany one of the protein kinases could lead to cell immortality or premature cell death.
  • the term "administering” relates to a method of inco ⁇ orating a compound into cells or tissues of an organism.
  • the abnormal condition can be prevented or treated when the cells or tissues of the organism exist within the organism or outside of the organism. Cells existing outside the organism can be maintained or grown in cell culture dishes. For cells harbored within the organism, many techniques exist in the art to administer compounds, including (but not limited to) oral, parenteral, dermal, injection, and aerosol applications. For cells outside of the organism, multiple techniques exist in the art to administer the compounds, including (but not limited to) cell microinjection techniques, transformation techniques and carrier techniques.
  • the abnormal condition can also be prevented or treated by administering a compound to a group of cells having an aberration in a signal transduction pathway to an organism.
  • the effect of administering a compound on organism function can then be monitored.
  • the organism is preferably a mouse, rat, rabbit, guinea pig or goat, more preferably a monkey or ape, and most preferably a human.
  • amplification it is meant increased numbers of DNA or RNA in a cell compared with normal cells.
  • Amplification as it refers to RNA can be the detectable presence of RNA in cells, since in some normal cells there is no basal expression of RNA. In other normal cells, a basal level of expression exists, therefore in these cases amplification is the detection of at least 1 to 2-fold, and preferably more, compared to the basal level.
  • stringent hybridization conditions refers to conditions under which a probe, primer, or oligonucleotide will hybridize to its target sequence, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. Generally, stringent conditions are selected to be about 5C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH. The T m is the temperature (under defined ionic strength, pH and nucleic acid concentration) at which 50% of the probes complementary to the target sequence hybridize to the target sequence at equilibrium.
  • T m thermal melting point
  • stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30C for short probes, primers or oligonucleotides (e.g. 10 to 50 nucleotides) and at least about 60C for longer probes, primers or oligonucleotides.
  • Stringent conditions may also be achieved with the addition of destabilizing agents, such as formamide.
  • amino acid sequences are presented in the amino to carboxy direction, from left to right.
  • the amino and carboxy groups are not presented in the sequence.
  • the nucleotide sequences are presented by single strand only, in the 5' to 3' direction, from left to right.
  • Nucleotides and amino acids are represented in the manner recommended by the rUPAC-IUB Biochemical Nomenclature Commission or (for amino acids) by three letters code.
  • the present invention provides purified and isolated polynucleotides (e.g., DNA sequences and RNA transcripts, both sense and complementary antisense strands, both single- and double-stranded, including splice variants thereof) that encode unknown G protein-coupled receptors heretofore termed novel GPCRs, or nGPCRs.
  • polynucleotides e.g., DNA sequences and RNA transcripts, both sense and complementary antisense strands, both single- and double-stranded, including splice variants thereof
  • novel GPCRs heretofore termed novel GPCRs, or nGPCRs.
  • nGPCR-x genes are described herein and designated herein collectively as nGPCR-x (where x is 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049, 1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, and 1077).
  • nGPCR- 1011 nGPCR-1012
  • Table 1 identifies the novel gene sequence nGPCR-x designation, the SEQ ID NO: of the gene sequence, the SEQ ID NO: of the polypeptide encoded thereby, and the U.S. Provisional Application in which the gene sequence has been disclosed.
  • nGPCR- 1011 When a specific nGPCR is identified (for example nGPCR- 1011), it is understood that only that specific nGPCR is being referred to.
  • the invention provides purified and isolated polynucleotides (e.g., cDNA, genomic DNA, synthetic DNA, RNA, or combinations thereof, whether single- or double-stranded) that comprise a nucleotide sequence encoding the amino acid sequence of the polypeptides of the invention.
  • polynucleotides e.g., cDNA, genomic DNA, synthetic DNA, RNA, or combinations thereof, whether single- or double-stranded
  • Such polynucleotides are useful for recombinantly expressing the receptor and also for detecting expression of the receptor in cells (e.g. , using Northern hybridization and in situ hybridization assays).
  • polynucleotides also are useful in the design of antisense and other molecules for the suppression of the expression of nGPCR-x in a cultured cell, a tissue, or an animal; for therapeutic pu ⁇ oses; or to provide a model for diseases or conditions characterized by aberrant nGPCR-x expression.
  • polynucleotides of the invention are entire isolated, non-recombinant native chromosomes of host cells.
  • a preferred polynucleotide has a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, which correspond to naturally occurring nGPCR-x sequences.
  • the invention also provides a purified and isolated polynucleotide comprising a nucleotide sequence that encodes a mammalian polypeptide, wherein the polynucleotide hybridizes to a polynucleotide having the sequence set forth in sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, or the non-coding strand complementary thereto, under the following hybridization conditions: (a) hybridization for 16 hours at 42C in a hybridization solution comprising 50% formamide, 1% SDS, 1 M NaCI, 10% dextran sulfate; and (b) washing 2 times for 30 minutes each at 60C in a wash solution comprising 0.1% SSC,
  • the present invention relates to molecules which comprise the gene sequences that encode the nGPCRs; constructs and recombinant host cells inco ⁇ orating the gene sequences; the novel GPCR polypeptides encoded by the gene sequences; antibodies to the polypeptides and homologs; kits employing the polynucleotides and polypeptides, and methods of making and using all of the foregoing.
  • the present invention relates to homologs of the gene sequences and of the polypeptides and methods of making and using the same.
  • Genomic DNA of the invention comprises the protein-coding region for a polypeptide of the invention and is also intended to include allelic variants thereof.
  • RNA transcripts that undergo one or more splicing events wherein intron (i.e., non-coding regions) of the transcripts are removed, or "spliced out.”
  • RNA transcripts that can be spliced by alternative mechanisms, and therefore be subject to removal of different RNA sequences but still encode a nGPCR-x polypeptide are referred to in the art as splice variants which are embraced by the invention.
  • Splice variants comprehended by the invention therefore are encoded by the same original genomic DNA sequences but arise from distinct mRNA transcripts.
  • Allelic variants are modified forms of a wild-type gene sequence, the modification resulting from recombination during chromosomal segregation or exposure to conditions which give rise to genetic mutation. Allelic variants, like wild type genes, are naturally occurring sequences (as opposed to non-naturally occurring variants that arise from in vitro manipulation).
  • the invention also comprehends cDNA that is obtained through reverse transcription of an RNA polynucleotide encoding nGPCR-x (conventionally followed by second strand synthesis of a complementary strand to provide a double-stranded DNA).
  • Preferred DNA sequences encoding human nGPCR-x polypeptides are selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67.
  • a preferred DNA of the invention comprises a double stranded molecule along with the complementary molecule (the "non-coding strand” or “complement") having a sequence unambiguously deducible from the coding strand according to Watson-Crick base-pairing rules for DNA.
  • polynucleotides encoding the nGPCR-x polypeptide selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, which differ in sequence from the polynucleotides selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, by virtue of the well-known degeneracy of the universal nuclear genetic code.
  • the invention further embraces other species, preferably mammalian, homologs of the human nGPCR-x DNA.
  • Species homologs in general, share at least 35%, at least 40%, at least 45%, at least 50%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99% homology with human DNA of the invention.
  • percent sequence "homology" with respect to polynucleotides of the invention may be calculated as the percentage of nucleotide bases in the candidate sequence that are identical to nucleotides in the nGPCR-x sequence set forth in sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity.
  • Polynucleotides of the invention permit identification and isolation of polynucleotides encoding related nGPCR-x polypeptides, such as human allelic variants and species homologs, by well-known techniques including Southern and/or Northern hybridization, and polymerase chain reaction (PCR).
  • related polynucleotides include human and non-human genomic sequences, including allelic variants, as well as polynucleotides encoding polypeptides homologous to nGPCR-x and structurally related polypeptides sharing one or more biological, immunological, and/or physical properties of nGPCR-x.
  • Non-human species genes encoding proteins homologous to nGPCR-x can also be identified by Southern and/or PCR analysis and are useful in animal models for nGPCR-x disorders.
  • Knowledge of the sequence of a human nGPCR-x DNA also makes possible through use of Southern hybridization or polymerase chain reaction (PCR) the identification of genomic DNA sequences encoding nGPCR-x expression control regulatory sequences such as promoters, operators, enhancers, repressors, and the like.
  • Polynucleotides of the invention are also useful in hybridization assays to detect the capacity of cells to express nGPCR-x.
  • Polynucleotides of the invention may also provide a basis for diagnostic methods useful for identifying a genetic alteration(s) in a nGPCR-x locus that underlies a disease state or states, which information is useful both for diagnosis and for selection of therapeutic strategies.
  • the nGPCR-x nucleotide sequences disclosed herein may be used to identify homologs of the nGPCR-x, in other animals, including but not limited to humans and other mammals, and invertebrates. Any of the nucleotide sequences disclosed herein, or any portion thereof, can be used, for example, as probes to screen databases or nucleic acid libraries, such as, for example, genomic or cDNA libraries, to identify homologs, using screening procedures well known to those skilled in the art.
  • homologs having at least 50%, more preferably at least 60%, more preferably at least 70%, more preferably at least 80%, more preferably at least 90%, more preferably at least 95%, and most preferably at least 100% homology with nGPCR-x sequences can be identified.
  • the disclosure herein of full-length polynucleotides encoding nGPCR-x polypeptides makes readily available to the worker of ordinary skill in the art every possible fragment of the full-length polynucleotide.
  • One preferred embodiment of the present invention provides an isolated nucleic acid molecule comprising a sequence homologous sequences selected from the group consisting of SEQ ID NO: 1 to SEQ ID NO: 67, and fragments thereof.
  • Another preferred embodiment provides an isolated nucleic acid molecule comprising a sequence selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67, and fragments thereof.
  • fragments of nGPCR-x-encoding polynucleotides comprise at least 10, and preferably at least 12, 14, 16, 18, 20, 25, 50, or 75 consecutive nucleotides of a polynucleotide encoding nGPCR-x.
  • fragment polynucleotides of the invention comprise sequences unique to the nGPCR-x-encoding polynucleotide sequence, and therefore hybridize under highly stringent or moderately stringent conditions only (i.e., "specifically") to polynucleotides encoding nGPCR-x (or fragments thereof).
  • Polynucleotide fragments of genomic sequences of the invention comprise not only sequences unique to the coding region, but also include fragments of the full-length sequence derived from introns, regulatory regions, and/or other non-translated sequences. Sequences unique to polynucleotides of the invention are recognizable through sequence comparison to other known polynucleotides, and can be identified through use of alignment programs routinely utilized in the art, e.g., those made available in public sequence databases. Such sequences also are recognizable from Southern hybridization analyses to determine the number of fragments of genomic DNA to which a polynucleotide will hybridize.
  • Polynucleotides of the invention can be labeled in a manner that permits their detection, including radioactive, fluorescent, and enzymatic labeling. Fragment polynucleotides are particularly useful as probes for detection of full-length or fragments of nGPCR-x polynucleotides.
  • One or more polynucleotides can be included in kits that are used to detect the presence of a polynucleotide encoding nGPCR-x, or used to detect variations in a polynucleotide sequence encoding nGPCR-x.
  • the invention also embraces DNAs encoding nGPCR-x polypeptides that hybridize under moderately stringent or high stringency conditions to the non-coding strand, or complement, of the polynucleotides set forth in sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO:67.
  • Exemplary highly stringent hybridization conditions are as follows: hybridization at 42C in a hybridization solution comprising 50% formamide, 1% SDS, 1 M NaCI, 10% Dextran sulfate, and washing twice for 30 minutes at 60C in a wash solution comprising 0.1 X SSC and 1% SDS. It is understood in the art that conditions of equivalent stringency can be achieved through variation of temperature and buffer, or salt concentration as described Ausubel et al. (Eds.), Protocols in Molecular Biology, John Wiley & Sons (1994), pp. 6.0.3 to 6.4.10. Modifications in hybridization conditions can be empirically determined or precisely calculated based on the length and the percentage of guanosine/cytosine (GC) base pairing of the probe.
  • GC guanosine/cytosine
  • the hybridization conditions can be calculated as described in Sambrook, et al, (Eds.), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York (1989), pp. 9.47 to 9.51.
  • nucleotide sequence information disclosed in the present invention, one skilled in the art can identify and obtain nucleotide sequences which encode nGPCR-x from different sources (i.e., different tissues or different organisms) through a variety of means well known to the skilled artisan and as disclosed by, for example, Sambrook et al., "Molecular cloning: a laboratory manual", Second Edition, Cold Spring Harbor Press, Cold Spring Harbor, NY (1989), which is inco ⁇ orated herein by reference in its entirety.
  • DNA that encodes nGPCR-x may be obtained by screening of mRNA, cDNA, or genomic DNA with oligonucleotide probes generated from the nGPCR-x gene sequence information provided herein. Probes may be labeled with a detectable group, such as a fluorescent group, a radioactive atom or a chemiluminescent group in accordance with procedures known to the skilled artisan and used in conventional hybridization assays, as described by, for example, Sambrook et al.
  • a detectable group such as a fluorescent group, a radioactive atom or a chemiluminescent group
  • a nucleic acid molecule comprising any of the nGPCR-x nucleotide sequences described above can alternatively be synthesized by use of the polymerase chain reaction (PCR) procedure, with the PCR oligonucleotide primers produced from the nucleotide sequences provided herein. See U.S. Patent Numbers 4,683, 195 to Mullis et al. and 4,683,202 to MuUis.
  • the PCR reaction provides a method for selectively increasing the concentration of a particular nucleic acid sequence even when that sequence has not been previously purified and is present only in a single copy in a particular sample.
  • the method can be used to amplify either single- or double-stranded DNA.
  • the essence of the method involves the use of two oligonucleotide probes to serve as primers for the template-dependent, polymerase mediated replication of a desired nucleic acid molecule.
  • Automated sequencing methods can be used to obtain or verify the nucleotide sequence of nGPCR-x.
  • the nGPCR-x nucleotide sequences of the present invention are believed to be 100% accurate.
  • nucleotide sequence obtained by automated methods may contain some errors.
  • Nucleotide sequences determined by automation are typically at least about 90%, more typically at least about 95% to at least about 99.9% identical to the actual nucleotide sequence of a given nucleic acid molecule.
  • the actual sequence may be more precisely determined using manual sequencing methods, which are well known in the art.
  • An error in a sequence which results in an insertion or deletion of one or more nucleotides may result in a frame shift in translation such that the predicted amino acid sequence will differ from that which would be predicted from the actual nucleotide sequence of the nucleic acid molecule, starting at the point of the mutation.
  • nucleic acid molecules of the present invention are useful for screening for restriction fragment length polymo ⁇ hism (RFLP) associated with certain disorders, as well as for genetic mapping.
  • RFLP restriction fragment length polymo ⁇ hism
  • the polynucleotide sequence information provided by the invention makes possible large-scale expression of the encoded polypeptide by techniques well known and routinely practiced in the art.
  • vectors or recombinant expression vectors, comprising any of the nucleic acid molecules described above.
  • Vectors are used herein either to amplify DNA or RNA encoding nGPCR-x and/or to express DNA which encodes nGPCR-x.
  • Preferred vectors include, but are not limited to, plasmids, phages, cosmids, episomes, viral particles or viruses, and integratable DNA fragments (i.e., fragments integratable into the host genome by homologous recombination).
  • Preferred viral particles include, but are not limited to, adenoviruses, baculoviruses, parvoviruses, he ⁇ esviruses, poxviruses, adeno- associated viruses, Semliki Forest viruses, vaccinia viruses, and retroviruses.
  • Preferred expression vectors include, but are not limited to, pcDNA3 (Invitrogen) and pSVL (Pharmacia Biotech).
  • Expression constructs include, but are not limited to, pSPORTTM vectors, pGEMTM vectors (Promega), pPROEXvectorsTM (LTI, Bethesda, MD), BluescriptTM vectors (Stratagene), pQETM vectors (Qiagen), pSE420TM (Invitrogen), and pYES2TM(Invitrogen).
  • Expression constructs preferably comprise GPCR-x-encoding polynucleotides operatively linked to an endogenous or exogenous expression control DNA sequence and a transcription terminator.
  • Expression control DNA sequences include promoters, enhancers, operators, and regulatory element binding sites generally, and are typically selected based on the expression systems in which the expression construct is to be utilized.
  • Preferred promoter and enhancer sequences are generally selected for the ability to increase gene expression, while operator sequences are generally selected for the ability to regulate gene expression.
  • Expression constructs of the invention may also include sequences encoding one or more selectable markers that permit identification of host cells bearing the construct.
  • Expression constructs may also include sequences that facilitate, and preferably promote, homologous recombination in a host cell.
  • Preferred constructs of the invention also include sequences necessary for replication in a host cell.
  • Expression constructs are preferably utilized for production of an encoded protein, but may also be utilized simply to amplify a nGPCR-x-encoding polynucleotide sequence.
  • the vector is an expression vector wherein the polynucleotide of the invention is operatively linked to a polynucleotide comprising an expression control sequence.
  • Autonomously replicating recombinant expression constructs such as plasmid and viral DNA vectors inco ⁇ orating polynucleotides of the invention are also provided.
  • Preferred expression vectors are replicable DNA constructs in which a DNA sequence encoding nGPCR-x is operably linked or connected to suitable control sequences capable of effecting the expression of the nGPCR-x in a suitable host.
  • DNA regions are operably linked or connected when they are functionally related to each other.
  • a promoter is operably linked or connected to a coding sequence if it controls the transcription of the sequence.
  • Amplification vectors do not require expression control domains, but rather need only the ability to replicate in a host, usually conferred by an origin of replication, and a selection gene to facilitate recognition of transformants. The need for control sequences in the expression vector will vary depending upon the host selected and the transformation method chosen. Generally, control sequences include a transcriptional promoter, an optional operator sequence to control transcription, a sequence encoding suitable mRNA ribosomal binding and sequences which control the termination of transcription and translation.
  • Preferred vectors preferably contain a promoter that is recognized by the host organism.
  • the promoter sequences of the present invention may be prokaryotic, eukaryotic or viral.
  • suitable prokaryotic sequences include the P R and P promoters of bacteriophage lambda (The bacteriophage Lambda, Hershey, A. D., Ed., Cold Spring Harbor Press, Cold Spring Harbor, NY (1973), which is inco ⁇ orated herein by reference in its entirety; Lambda II, Hendrix, R. W., Ed., Cold Spring Harbor Press, Cold Spring Harbor, NY (1980), which is inco ⁇ orated herein by reference in its entirety); the t ⁇ , recA, heat shock, and lacZ promoters of E.
  • Additional promoters include, but are not limited to, mouse mammary tumor virus, long terminal repeat of human immunodeficiency virus, maloney virus, cytomegalovirus immediate early promoter, Epstein Barr virus, Rous sarcoma virus, human actin, human myosin, human hemoglobin, human muscle creatine, and human metalothionein.
  • Additional regulatory sequences can also be included in preferred vectors.
  • Preferred examples of suitable regulatory sequences are represented by the Shine-Dalgarno of the replicase gene of the phage MS-2 and of the gene ell of bacteriophage lambda.
  • the Shine- Dalgarno sequence may be directly followed by DNA encoding nGPCR-x and result in the expression of the mature nGPCR-x protein.
  • suitable expression vectors can include an appropriate marker that allows the screening of the transformed host cells.
  • the transformation of the selected host is carried out using any one of the various techniques well known to the expert in the art and described in Sambrook et ah, supra.
  • An origin of replication can also be provided either by construction of the vector to include an exogenous origin or may be provided by the host cell chromosomal replication mechanism. If the vector is integrated into the host cell chromosome, the latter may be sufficient.
  • one skilled in the art can transform mammalian cells by the method of co-transformation with a selectable marker and nGPCR-x DNA.
  • An example of a suitable marker is dihydrofolate reductase (DHFR) or thymidine kinase (see, U.S. Patent No. 4,399,216).
  • DHFR dihydrofolate reductase
  • thymidine kinase see, U.S. Patent No. 4,399,216.
  • Nucleotide sequences encoding GPCR-x may be recombined with vector DNA in accordance with conventional techniques, including blunt-ended or staggered-ended termini for ligation, restriction enzyme digestion to provide appropriate termini, filling in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesiderable joining, and ligation with appropriate ligases. Techniques for such manipulation are disclosed by Sambrook et al., supra and are well known in the art. Methods for construction of mammalian expression vectors are disclosed in, for example, Okayama et al, Mol. Cell.
  • host cells including prokaryotic and eukaryotic cells, comprising a polynucleotide of the invention (or vector of the invention) in a manner that permits expression of the encoded nGPCR-x polypeptide.
  • Polynucleotides of the invention may be introduced into the host cell as part of a circular plasmid, or as linear DNA comprising an isolated protein coding region or a viral vector.
  • Methods for introducing DNA into the host cell that are well known and routinely practiced in the art include transformation, transfection, electroporation, nuclear injection, or fusion with carriers such as liposomes, micelles, ghost cells, and protoplasts.
  • Expression systems of the invention include bacterial, yeast, fungal, plant, insect, invertebrate, vertebrate, and mammalian cells systems.
  • the invention provides host cells that are transformed or transfected (stably or transiently) with polynucleotides of the invention or vectors of the invention. As stated above, such host cells are useful for amplifying the polynucleotides and also for expressing the nGPCR-x polypeptide or fragment thereof encoded by the polynucleotide.
  • the invention provides a method for producing a nGPCR-x polypeptide (or fragment thereof) comprising the steps of growing a host cell of the invention in a nutrient medium and isolating the polypeptide or variant thereof from the cell or the medium.
  • nGPCR-x is a seven transmembrane receptor, it will be appreciated that, for some applications, such as certain activity assays, the preferable isolation may involve isolation of cell membranes containing the polypeptide embedded therein, whereas for other applications a more complete isolation may be preferable.
  • transformed host cells having an expression vector comprising any of the nucleic acid molecules described above are provided.
  • Suitable host cells for expression of the polypeptides of the invention include, but are not limited to, prokaryotes, yeast, and eukaryotes. If a prokaryotic expression vector is employed, then the appropriate host cell would be any prokaryotic cell capable of expressing the cloned sequences. Suitable prokaryotic cells include, but are not limited to, bacteria of the genera Escherichia, Bacillus, Salmonella, Pseudomonas, Streptomyces, and Staphylococcus. If an eukaryotic expression vector is employed, then the appropriate host cell would be any eukaryotic cell capable of expressing the cloned sequence.
  • eukaryotic cells are cells of higher eukaryotes.
  • Suitable eukaryotic cells include, but are not limited to, non-human mammalian tissue culture cells and human tissue culture cells.
  • Preferred host cells include, but are not limited to, insect cells, HeLa cells, Chinese hamster ovary cells (CHO cells), African green monkey kidney cells (COS cells), human 293 cells, and murine 3T3 fibroblasts. Propagation of such cells in cell culture has become a routine procedure (see, Tissue Culture, Academic Press, Kruse and Patterson, eds. (1973), which is inco ⁇ orated herein by reference in its entirety).
  • a yeast host may be employed as a host cell.
  • Preferred yeast cells include, but are not limited to, the genera Saccharomyces, Pichia, and Kluveromyces.
  • Preferred yeast hosts are S. cerevisiae and P. pastoris.
  • Preferred yeast vectors can contain an origin of replication sequence from a 2T yeast plasmid, an autonomously replication sequence (ARS), a promoter region, sequences for polyadenylation, sequences for transcription termination, and a selectable marker gene.
  • ARS autonomously replication sequence
  • Shuttle vectors for replication in both yeast and E. coli are also included herein.
  • insect cells may be used as host cells.
  • the polypeptides of the invention are expressed using a baculovirus expression system (see, Luckow et al, Bio/Technology, 1988, 6, 47, Baculovirus Expression Vectors: A Laboratory Manual, O'Rielly et al (Eds.), W.H. Freeman and Company, New York, 1992, and U.S. Patent No. 4,879,236, each of which is inco ⁇ orated herein by reference in its entirety).
  • the MAXBACTM complete baculovirus expression system can, for example, be used for production in insect cells.
  • Host cells of the invention are a valuable source of immunogen for development of antibodies specifically immunoreactive with nGPCR-x.
  • Host cells of the invention are also useful in methods for the large-scale production of nGPCR-x polypeptides wherein the cells are grown in a suitable culture medium and the desired polypeptide products are isolated from the cells, or from the medium in which the cells are grown, by purification methods known in the art, e.g., conventional chromatographic methods including immunoaffinity chromatography, receptor affinity chromatography, hydrophobic interaction chromatography, lectin affinity chromatography, size exclusion filtration, cation or anion exchange chromatography, high pressure liquid chromatography (HPLC), reverse phase HPLC, and the like.
  • HPLC high pressure liquid chromatography
  • Still other methods of purification include those methods wherein the desired protein is expressed and purified as a fusion protein having a specific tag, label, or chelating moiety that is recognized by a specific binding partner or agent.
  • the purified protein can be cleaved to yield the desired protein, or can be left as an intact fusion protein. Cleavage of the fusion component may produce a form of the desired protein having additional amino acid residues as a result of the cleavage process.
  • Knowledge of nGPCR-x DNA sequences allows for modification of cells to permit, or increase, expression of endogenous nGPCR-x.
  • Cells can be modified (e.g., by homologous recombination) to provide increased expression by replacing, in whole or in part, the naturally occurring nGPCR-x promoter with all or part of a heterologous promoter so that the cells express nGPCR-x at higher levels.
  • the heterologous promoter is inserted in such a manner that it is operatively linked to endogenous nGPCR-x encoding sequences.
  • amplifiable marker DNA e.g., ada, dhfr, and the multifunctional CAD gene which encodes carbamoyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase
  • intron DNA may be inserted along with the heterologous promoter DNA. If linked to the nGPCR-x coding sequence, amplification of the marker DNA by standard selection methods results in co-amplification of the nGPCR-x coding sequences in the cells.
  • Knock-outs The DNA sequence information provided by the present invention also makes possible the development (e.g., by homologous recombination or "knock-out” strategies; see Capecchi, Science 244:1288-1292 (1989), which is inco ⁇ orated herein by reference in its entirety) of animals that fail to express functional nGPCR-x or that express a variant of nGPCR-x. Such animals (especially small laboratory animals such as rats, rabbits, and mice) are useful as models for studying the in vivo activities of nGPCR-x and modulators of nGPCR-x. Antisense
  • anti-sense polynucleotides that recognize and hybridize to polynucleotides encoding nGPCR-x.
  • Full-length and fragment anti-sense polynucleotides are provided.
  • Fragment antisense molecules of the invention include (i) those that specifically recognize and hybridize to nGPCR-x RNA (as determined by sequence comparison of DNA encoding nGPCR-x to DNA encoding other known molecules). Identification of sequences unique to nGPCR-x encoding polynucleotides can be deduced through use ofany publicly available sequence database, and/or through use of commercially available sequence comparison programs.
  • Anti-sense polynucleotides are particularly relevant to regulating expression of nGPCR-x by those cells expressing nGPCR-x mRNA.
  • Antisense nucleic acids preferably 10 to 30 base-pair oligonucleotides
  • capable of specifically binding to nGPCR-x expression control sequences or nGPCR-x RNA are introduced into cells (e.g., by a viral vector or colloidal dispersion system such as a liposome).
  • the antisense nucleic acid binds to the nGPCR-x target nucleotide sequence in the cell and prevents transcription and/or translation of the target sequence.
  • Phosphorothioate and methylphosphonate antisense oligonucleotides are specifically contemplated for therapeutic use by the invention.
  • the antisense oligonucleotides may be further modified by adding poly-L-lysine, transferrin polylysine, or cholesterol moieties at their 5' end. Suppression of nGPCR-x expression at either the transcriptional or translational level is useful to generate cellular or animal models for diseases/conditions characterized by aberrant nGPCR-x expression.
  • Antisense oligonucleotides, or fragments of sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67, or sequences complementary or homologous thereto, derived from the nucleotide sequences of the present invention encoding nGPCR-x are useful as diagnostic tools for probing gene expression in various tissues.
  • tissue can be probed in situ with oligonucleotide probes carrying detectable groups by conventional autoradiography techniques to investigate native expression of this enzyme or pathological conditions relating thereto.
  • Antisense oligonucleotides are preferably directed to regulatory regions of sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67, or mRNA corresponding thereto, including, but not limited to, the initiation codon, TATA box, enhancer sequences, and the like. Transcription factors
  • nGPCR-x sequences taught in the present invention facilitate the design of novel transcription factors for modulating nGPCR-x expression in native cells and animals, and cells transformed or transfected with nGPCR-x polynucleotides.
  • the Cys 2 -His zinc finger proteins which bind DNA via their zinc finger domains, have been shown to be amenable to structural changes that lead to the recognition of different target sequences.
  • These artificial zinc finger proteins recognize specific target sites with high affinity and low dissociation constants, and are able to act as gene switches to modulate gene expression.
  • nGPCR-x target sequence of the present invention facilitates the engineering of zinc finger proteins specific for the target sequence using known methods such as a combination of structure-based modeling and screening of phage display libraries (Segal et al, Proc. Natl Acad. Sci. USA 96:2758-2763 (1999); Liu et al, Proc. Natl. Acad. Sci. USA 94:5525-5530 (1997); Greisman et al, Science 275:657-661 (1997); Choo et al, J. Mol. Biol. 273:525-532 (1997)).
  • Each zinc finger domain usually recognizes three or more base pairs.
  • a zinc finger protein consisting of 6 tandem repeats of zinc fingers would be expected to ensure specificity for a particular sequence (Segal et al).
  • the artificial zinc finger repeats designed based on nGPCR-x sequences, are fused to activation or repression domains to promote or suppress nGPCR-x expression (Liu et al).
  • the zinc finger domains can be fused to the TATA box-binding factor (TBP) with varying lengths of linker region between the zinc finger peptide and the TBP to create either transcriptional activators or repressors (Kim et al, Proc. Natl Acad. Sci.
  • Such proteins and polynucleotides that encode them have utility for modulating nGPCR-x expression in vivo in both native cells, animals and humans; and/or cells transfected with nGPCR-x-encoding sequences.
  • the novel transcription factor can be delivered to the target cells by transfecting constructs that express the transcription factor (gene therapy), or by introducing the protein.
  • Engineered zinc finger proteins can also be designed to bind RNA sequences for use in therapeutics as alternatives to antisense or catalytic RNA methods (McColl et al, Proc. Natl Acad. Sci. USA 96:9521-9526 (1997); Wu et al. , Proc. Natl. Acad. Sci.
  • the present invention contemplates methods of designing such transcription factors based on the gene sequence of the invention, as well as customized zinc finger proteins, that are useful to modulate nGPCR-x expression in cells (native or transformed) whose genetic complement includes these sequences.
  • Polypeptides The invention also provides purified and isolated mammalian nGPCR-x polypeptides encoded by a polynucleotide of the invention. Presently preferred is a human nGPCR-x polypeptide comprising the amino acid sequence set out in sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, or fragments thereof comprising an epitope specific to the polypeptide.
  • epitope specific to is meant a portion of the nGPCR receptor that is recognizable by an antibody that is specific for the nGPCR, as defined in detail below.
  • sequences provided are particular human sequences, the invention is intended to include within its scope other human allelic variants; non-human mammalian forms of nGPCR-x, and other vertebrate forms of nGPCR-x. It will be appreciated that extracellular epitopes are particularly useful for generating and screening for antibodies and other binding compounds that bind to receptors such as nGPCR-x.
  • the invention provides a purified and isolated polypeptide comprising at least one extracellular domain (e.g., the N-terminal extracellular domain or one of the three extracellular loops) of nGPCR-x.
  • a purified and isolated polypeptide comprising the N-terminal extracellular domain of nGPCR-x are highly preferred.
  • a purified and isolated polypeptide comprising a nGPCR-x fragment selected from the group consisting of the N-terminal extracellular domain of nGPCR-x, transmembrane domains of nGPCR-x, an extracellular loop connecting transmembrane domains of nGPCR-x, an intracellular loop connecting transmembrane domains of nGPCR-x, the C-terminal cytoplasmic region of nGPCR-x, and fusions thereof.
  • Such fragments may be continuous portions of the native receptor.
  • knowledge of the nGPCR-x gene and protein sequences as provided herein permits recombining of various domains that are not contiguous in the native protein.
  • nGPCR-x was shown to contain transmembrane-spanning domains.
  • the invention also embraces polypeptides that have at least 99%, at least 95%, at least 90%, at least 85%, at least 80%, at least 75%, at least 70%, at least 65%, at least 60%, at least 55% or at least 50% identity and/or homology to the preferred polypeptide of the invention.
  • Percent amino acid sequence "identity" with respect to the preferred polypeptide of the invention is defined herein as the percentage of amino acid residues in the candidate sequence that are identical with the residues in the nGPCR-x sequence after aligning both sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • Percent sequence "homology" with respect to the preferred polypeptide of the invention is defined herein as the percentage of amino acid residues in the candidate sequence that are identical with the residues in the nGPCR-x sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and also considering any conservative substitutions as part of the sequence identity.
  • percent homology is calculated as the percentage of amino acid residues in the smaller of two sequences which align with identical amino acid residue in the sequence being compared, when four gaps in a length of 100 amino acids may be introduced to maximize alignment (Dayhoff, m. Atlas of Protein Sequence and Structure, Vol. 5, p. 124, National Biochemical Research Foundation, Washington, D.C. (1972), inco ⁇ orated herein by reference in its entirety).
  • Polypeptides of the invention may be isolated from natural cell sources or may be chemically synthesized, but are preferably produced by recombinant procedures involving host cells of the invention. Use of mammalian host cells is expected to provide for such post-translational modifications (e.g., glycosylation, truncation, lipidation, and phosphorylation) as may be needed to confer optimal biological activity on recombinant expression products of the invention. Glycosylated and non-glycosylated forms of nGPCR-x polypeptides are embraced by the invention. The invention also embraces variant (or analog) nGPCR-x polypeptides.
  • Insertions are provided wherein one or more amino acid residues supplement a nGPCR-x amino acid sequence. Insertions may be located at either or both termini of the protein, or may be positioned within internal regions of the nGPCR-x amino acid sequence. Insertional variants with additional residues at either or both termini can include, for example, fusion proteins and proteins including amino acid tags or labels.
  • Insertion variants include nGPCR-x polypeptides wherein one or more amino acid residues are added to a nGPCR-x acid sequence or to a biologically active fragment thereof.
  • Variant products of the invention also include mature nGPCR-x products, i.e., nGPCR-x products wherein leader or signal sequences are removed, with additional amino terminal residues.
  • the additional amino terminal residues may be derived from another protein, or may include one or more residues that are not identifiable as being derived from specific proteins.
  • nGPCR-x products with an additional methionine residue at position -1 (Met _1 -nGPCR-x) are contemplated, as are variants with additional methionine and lysine residues at positions -2 and -1 (Met "2 -Lys _1 -nGPCR-x).
  • Variants of nGPCR-x with additional Met, Met-Lys, Lys residues are particularly useful for enhanced recombinant protein production in bacterial host cells.
  • the invention also embraces nGPCR-x variants having additional amino acid residues that result from use of specific expression systems.
  • use of commercially available vectors that express a desired polypeptide as part of a glutathione-S-transferase (GST) fusion product provides the desired polypeptide having an additional glycine residue at position -1 after cleavage of the GST component from the desired polypeptide.
  • GST glutathione-S-transferase
  • Variants that result from expression in other vector systems are also contemplated.
  • Insertional variants also include fusion proteins wherein the amino terminus and/or the carboxy terminus of nGPCR-x is/are fused to another polypeptide.
  • the invention provides deletion variants wherein one or more amino acid residues in a nGPCR-x polypeptide are removed.
  • Deletions can be effected at one or both termini of the nGPCR-x polypeptide, or with removal of one or more non-terminal amino acid residues of nGPCR-x.
  • Deletion variants therefore, include all fragments of a nGPCR-x polypeptide.
  • the invention also embraces polypeptide fragments of sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, wherein the fragments maintain biological (e.g. , ligand binding and/or intracellular signaling) immunological properties of a nGPCR-x polypeptide.
  • biological e.g. , ligand binding and/or intracellular signaling
  • an isolated nucleic acid molecule comprises a nucleotide sequence that encodes a polypeptide comprising an amino acid sequence homologous to sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, and fragments thereof, wherein the nucleic acid molecule encoding at least a portion of nGPCR-x.
  • the isolated nucleic acid molecule comprises a sequence that encodes a polypeptide comprising sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, and fragments thereof.
  • polypeptide fragments comprise at least 5, 10, 15, 20, 25, 30, 35, or 40 consecutive amino acids of sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136.
  • Preferred polypeptide fragments display antigenic properties unique to, or specific for, human nGPCR-x and its allelic and species homologs. Fragments of the invention having the desired biological and immunological properties can be prepared by any of the methods well known and routinely practiced in the art.
  • the invention provides substitution variants of nGPCR-x polypeptides. Substitution variants include those polypeptides wherein one or more amino acid residues of a nGPCR-x polypeptide are removed and replaced with alternative residues. In one aspect, the substitutions are conservative in nature; however, the invention embraces substitutions that are also non-conservative. Conservative substitutions for this pu ⁇ ose may be defined as set out in Tables 2, 3, or 4 below.
  • Variant polypeptides include those wherein conservative substitutions have been introduced by modification of polynucleotides encoding polypeptides of the invention.
  • Amino acids can be classified according to physical properties and contribution to secondary and tertiary protein structure.
  • a conservative substitution is recognized in the art as a substitution of one amino acid for another amino acid that has similar properties.
  • Exemplary conservative substitutions are set out in Table 2 (from WO 97/09433, page 10, published March 13, 1997 (PCT/GB96/02197, filed 9/6/96), immediately below.
  • conservative amino acids can be grouped as described in Lehninger,
  • polypeptides of the invention is intended to include polypeptides bearing modifications other than insertion, deletion, or substitution of amino acid residues.
  • the modifications may be covalent in nature, and include for example, chemical bonding with polymers, lipids, other organic, and inorganic moieties.
  • Such derivatives may be prepared to increase circulating half-life of a polypeptide, or may be designed to improve the targeting capacity of the polypeptide for desired cells, tissues, or organs.
  • the invention further embraces nGPCR-x polypeptides that have been covalently modified to include one or more water-soluble polymer attachments such as polyethylene glycol, polyoxyethylene glycol, or polypropylene glycol.
  • Variants that display ligand binding properties of native nGPCR-x and are expressed at higher levels, as well as variants that provide for constitutively active receptors, are particularly useful in assays of the invention; the variants are also useful in providing cellular, tissue and animal models of diseases/conditions characterized by aberrant nGPCR-x activity.
  • compositions comprising purified polypeptides of the invention.
  • Preferred compositions comprise, in addition to the polypeptide of the invention, a pharmaceutically acceptable (i.e., sterile and non-toxic) liquid, semisolid, or solid diluent that serves as a pharmaceutical vehicle, excipient, or medium. Any diluent known in the art may be used.
  • Exemplary diluents include, but are not limited to, water, saline solutions, polyoxyethylene sorbitan monolaurate, magnesium stearate, methyl- and propylhydroxybenzoate, talc, alginates, starches, lactose, sucrose, dextrose, sorbitol, mannitol, glycerol, calcium phosphate, mineral oil, and cocoa butter.
  • Variants that display ligand binding properties of native nGPCR-x and are expressed at higher levels, as well as variants that provide for constitutively active receptors, are particularly useful in assays of the invention; the variants are also useful in assays of the invention and in providing cellular, tissue and animal models of diseases/conditions characterized by aberrant nGPCR-x activity.
  • the G protein-coupled receptor functions through a specific heterotrimeric guanine-nucleotide-binding regulatory protein (G-protein) coupled to the intracellular portion of the G protein-coupled receptor molecule. Accordingly, the G protein-coupled receptor has a specific affinity to G protein. G proteins specifically bind to guanine nucleotides. Isolation of G proteins provides a means to isolate guanine nucleotides. G Proteins may be isolated using commercially available anti-G protein antibodies or isolated G protein-coupled receptors. Similarly, G proteins may be detected in a sample isolated using commercially available detectable anti-G protein antibodies or isolated G protein-coupled receptors.
  • G-protein guanine-nucleotide-binding regulatory protein
  • the isolated n-GPCR-x proteins of the present invention are useful to isolate and purify G proteins from samples such as cell lysates.
  • Example 14 below sets forth an example of isolation of G proteins using isolated n-GPCR-x proteins.
  • Such methodolgy may be used in place of the use of commercially available anti-G protein antibodies which are used to isolate G proteins.
  • G proteins may be detected using n- GPCR-x proteins in place of commercially available detectable anti-G protein antibodies. Since n-GPCR-x proteins specifically bind to G proteins, they can be employed in any specific use where G protein specific affinity is required such as those uses where commercially available anti-G protein antibodies are employed.
  • Antibodies specifically bind to G proteins, they can be employed in any specific use where G protein specific affinity is required such as those uses where commercially available anti-G protein antibodies are employed.
  • antibodies e.g., monoclonal and polyclonal antibodies, single chain antibodies, chimeric antibodies, bifunctional/bispecific antibodies, humanized antibodies, human antibodies, and complementary determining region (CDR)-grafted antibodies, including compounds which include CDR sequences which specifically recognize a polypeptide of the invention) specific for nGPCR-x or fragments thereof.
  • Preferred antibodies of the invention are human antibodies that are produced and identified according to methods described in WO93/11236, published June 20, 1993, which is inco ⁇ orated herein by reference in its entirety.
  • Antibody fragments, including Fab, Fab', F(ab') , and F v are also provided by the invention.
  • variable regions of the antibodies of the invention recognize and bind nGPCR-x polypeptides exclusively (i.e., axe able to distinguish nGPCR-x polypeptides from other known GPCR polypeptides by virtue of measurable differences in binding affinity, despite the possible existence of localized sequence identity, homology, or similarity between nGPCR-x and such polypeptides).
  • specific antibodies may also interact with other proteins (for example, S. ⁇ ureus protein A or other antibodies in ELISA techniques) through interactions with sequences outside the variable region of the antibodies, and, in particular, in the constant region of the molecule.
  • the invention provides an antibody that is specific for the nGPCR-x of the invention.
  • Antibody specificity is described in greater detail below.
  • antibodies that can be generated from polypeptides that have previously been described in the literature and that are capable of fortuitously cross-reacting with nGPCR-x are considered “cross-reactive" antibodies.
  • Such cross-reactive antibodies are not antibodies that are "specific" for nGPCR-x.
  • the determination of whether an antibody is specific for nGPCR-x or is cross-reactive with another known receptor is made using any of several assays, such as Western blotting assays, that are well known in the art.
  • assays such as Western blotting assays, that are well known in the art.
  • antibodies that specifically bind to an extracellular epitope of the nGPCR-x are preferred.
  • the invention provides monoclonal antibodies. Hybridomas that produce such antibodies also are intended as aspects of the invention.
  • the invention provides a humanized antibody. Humanized antibodies are useful for in vivo therapeutic indications.
  • the invention provides a cell-free composition comprising polyclonal antibodies, wherein at least one of the antibodies is an antibody of the invention specific for nGPCR-x.
  • Antisera isolated from an animal is an exemplary composition, as is a composition comprising an antibody fraction of an antisera that has been resuspended in water or in another diluent, excipient, or carrier.
  • the invention provides an anti-idiotypic antibody specific for an antibody that is specific for nGPCR-x.
  • the invention provides a polypeptide comprising a fragment of a nGPCR-x-specific antibody, wherein the fragment and the polypeptide bind to the nGPCR-x.
  • the invention provides polypeptides that are single chain antibodies and CDR-grafted antibodies.
  • Non-human antibodies may be humanized by any of the methods known in the art. In one method, the non-human CDRs are inserted into a human antibody or consensus antibody framework sequence. Further changes can then be introduced into the antibody framework to modulate affinity or immunogenicity.
  • Antibodies of the invention are useful for, e.g., therapeutic pu ⁇ oses (by modulating activity of nGPCR-x), diagnostic pu ⁇ oses to detect or quantitate nGPCR-x, and purification of nGPCR-x.
  • Kits comprising an antibody of the invention for any of the pu ⁇ oses described herein are also comprehended.
  • a kit of the invention also includes a control antigen for which the antibody is immunospecific.
  • the invention comprehends gene therapy to restore nGPCR-x activity to treat those disease states.
  • nGPCR-x gene Delivery of a functional nGPCR-x gene to appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments).
  • viral vectors e.g., adenovirus, adeno-associated virus, or a retrovirus
  • physical DNA transfer methods e.g., liposomes or chemical treatments.
  • compositions including pharmaceutical compositions, comprising any of the nucleic acid molecules or recombinant expression vectors described above and an acceptable carrier or diluent.
  • the carrier or diluent is pharmaceutically acceptable. Suitable carriers are described in the most recent edition of Remington's Pharmaceutical Sciences, A. Osol, a standard reference text in this field, which is inco ⁇ orated herein by reference in its entirety.
  • Preferred examples of such carriers or diluents include, but are not limited to, water, saline, Ringer's solution, dextrose solution, and 5% human serum albumin. Liposomes and nonaqueous vehicles such as fixed oils may also be used. The formulations are sterilized by commonly used techniques.
  • compositions comprising polypeptides, polynucleotides, or antibodies of the invention that have been formulated with, e.g., a pharmaceutically acceptable carrier.
  • the invention also provides methods of using antibodies of the invention.
  • the invention provides a method for modulating ligand binding of a nGPCR-x comprising the step of contacting the nGPCR-x with an antibody specific for the nGPCR-x, under conditions wherein the antibody binds the receptor.
  • GPCRs that may be expressed in the brain provide an indication that aberrant nGPCR-x signaling activity may correlate with one or more neurological or psychological disorders.
  • the invention also provides a method for treating a neurological or psychiatric disorder comprising the step of administering to a mammal in need of such treatment an amount of an antibody-like polypeptide of the invention that is sufficient to modulate ligand binding to a nGPCR-x in neurons of the mammal.
  • nGPCR-x may also be expressed in other tissues, including but not limited to, peripheral blood lymphocytes, pancreas, ovary, uterus, testis, salivary gland, thyroid gland, kidney, adrenal gland, liver, bone marrow, prostate, fetal liver, colon, muscle, and fetal brain, and may be found in many other tissues.
  • nGPCR-x mRNA transcripts may be found in many tissues, including, but not limited to, frontal lobe, hypothalamus, pons, cerebellum, caudate nucleus, and medulla. Tissues and brain regions where specific nGPCRs of the present invention are expressed are identified in the Examples below. Kits The present invention is also directed to kits, including pharmaceutical kits.
  • kits can comprise any of the nucleic acid molecules described above, any of the polypeptides described above, or any antibody which binds to a polypeptide of the invention as described above, as well as a negative control.
  • the kit preferably comprises additional components, such as, for example, instructions, solid support, reagents helpful for quantification, and the like.
  • the invention features methods for detection of a polypeptide in a sample as a diagnostic tool for diseases or disorders, wherein the method comprises the steps of: (a) contacting the sample with a nucleic acid probe which hybridizes under hybridization assay conditions to a nucleic acid target region of a polypeptide having sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136, said probe comprising the nucleic acid sequence encoding the polypeptide, fragments thereof, and the complements of the sequences and fragments; and (b) detecting the presence or amount of the probe:target region hybrid as an indication of the disease.
  • the disease is selected from the group consisting of thyroid disorders (e.g. thyreotoxicosis, myxoedema); renal failure; inflammatory conditions (e.g., Crohn's disease); diseases related to cell differentiation and homeostasis; rheumatoid arthritis; autoimmune disorders; movement disorders; CNS disorders (e.g., pain including migraine; stroke; psychotic and neurological disorders, including anxiety, mental disorder, manic depression, anxiety, generalized anxiety disorder, post-traumatic-stress disorder, depression, bipolar disorder, delirium, dementia, severe mental retardation; dyskinesias, such as Huntington's disease or Tourette's Syndrome; attention disorders including attention deficit disorder (ADD) and attention deficit-hyperactivity disorder (ADHD), and degenerative disorders such as Parkinson's, Alzheimer's; movement disorders, including ataxias, supranuclear palsy, etc.); infections, such as viral infections caused by HIV-1 or HIV-2; metabolic and cardiovascular diseases and disorders (e.g.,
  • Kits may be designed to detect either expression of polynucleotides encoding these proteins or the proteins themselves in order to identify tissue as being neurological.
  • oligonucleotide hybridization kits can be provided which include a container having an oligonucleotide probe specific for the n-GPCR-x-specific DNA and optionally, containers with positive and negative controls and/or instructions.
  • PCR kits can be provided which include a container having primers specific for the n-GPCR-x-specific sequences, DNA and optionally, containers with size markers, positive and negative controls and/or instructions.
  • Hybridization conditions should be such that hybridization occurs only with the genes in the presence of other nucleic acid molecules. Under stringent hybridization conditions only highly complementary nucleic acid sequences hybridize. Preferably, such conditions prevent hybridization of nucleic acids having 1 or 2 mismatches out of 20 contiguous nucleotides. Such conditions are defined supra.
  • the diseases for which detection of genes in a sample could be diagnostic include diseases in which nucleic acid (DNA and/or RNA) is amplified in comparison to normal cells. By “amplification” is meant increased numbers of DNA or RNA in a cell compared with normal cells.
  • the diseases that could be diagnosed by detection of nucleic acid in a sample preferably include central nervous system and metabolic diseases.
  • the test samples suitable for nucleic acid probing methods of the present invention include, for example, cells or nucleic acid extracts of cells, or biological fluids. The samples used in the above-described methods will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts to be assayed. Methods for preparing nucleic acid extracts of cells are well known in the art and can be readily adapted in order to obtain a sample that is compatible with the method utilized.
  • immunoassay kits can be provided which have containers container having antibodies specific for the n-GPCR-x-protein and optionally, containers with positive and negative controls and/or instructions. Kits may also be provided useful in the identification of GPCR binding partners such as natural ligands or modulators (agonists or antagonists).
  • Substances useful for treatment of disorders or diseases preferably show positive results in one or more in vitro assays for an activity corresponding to treatment of the disease or disorder in question.
  • Substances that modulate the activity of the polypeptides preferably include, but are not limited to, antisense oligonucleotides, agonists and antagonists, and inhibitors of protein kinases.
  • Another aspect of the present invention is directed to methods of inducing an immune response in a mammal against a polypeptide of the invention by administering to the mammal an amount of the polypeptide sufficient to induce an immune response.
  • the amount will be dependent on the animal species, size of the animal, and the like but can be determined by those skilled in the art.
  • Methods of identifying ligands The invention also provides assays to identify compounds that bind nGPCR-x.
  • One such assay comprises the steps of: (a) contacting a composition comprising a nGPCR-x with a compound suspected of binding nGPCR-x; and (b) measuring binding between the compound and nGPCR-x.
  • the composition comprises a cell expressing nGPCR-x on its surface.
  • isolated nGPCR-x or cell membranes comprising nGPCR-x are employed.
  • the binding may be measured directly, e.g., by using a labeled compound, or may be measured indirectly by several techniques, including measuring intracellular signaling of nGPCR-x induced by the compound (or measuring changes in the level of nGPCR-x signaling).
  • compounds identified as binding nGPCR-x can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate binding to nGPCR-x.
  • binding molecules including natural ligands and synthetic compounds, can be identified or developed using isolated or recombinant nGPCR-x products, nGPCR-x variants, or preferably, cells expressing such products. Binding partners are useful for purifying nGPCR-x products and detection or quantification of nGPCR-x products in fluid and tissue samples using known immunological procedures. Binding molecules are also manifestly useful in modulating (i.e., blocking, inhibiting or stimulating) biological activities of nGPCR-x, especially those activities involved in signal transduction.
  • the DNA and amino acid sequence information provided by the present invention also makes possible identification of binding partner compounds with which a nGPCR-x polypeptide or polynucleotide will interact.
  • Methods to identify binding partner compounds include solution assays, in vitro assays wherein nGPCR-x polypeptides are immobilized, and cell-based assays. Identification of binding partner compounds of nGPCR-x polypeptides provides candidates for therapeutic or prophylactic intervention in pathologies associated with nGPCR-x normal and aberrant biological activity.
  • the invention includes several assay systems for identifying nGPCR-x binding partners.
  • methods of the invention comprise the steps of (a) contacting a nGPCR-x polypeptide with one or more candidate binding partner compounds and (b) identifying the compounds that bind to the nGPCR-x polypeptide. Identification of the compounds that bind the nGPCR-x polypeptide can be achieved by isolating the nGPCR-x polypeptide/binding partner complex, and separating the binding partner compound from the nGPCR-x polypeptide.
  • nGPCR-x polypeptide/binding partner complex is isolated using an antibody immunospecific for either the nGPCR-x polypeptide or the candidate binding partner compound.
  • either the nGPCR-x polypeptide or the candidate binding partner compound comprises a label or tag that facilitates its isolation
  • methods of the invention to identify binding partner compounds include a step of isolating the nGPCR-x polypeptide/binding partner complex through interaction with the label or tag.
  • An exemplary tag of this type is a poly-histidine sequence, generally around six histidine residues, that permits isolation of a compound so labeled using nickel chelation.
  • Other labels and tags such as the FLAG® tag (Eastman Kodak, Rochester, NY), well known and routinely used in the art, are embraced by the invention.
  • the invention provides a method comprising the steps of (a) contacting an immobilized nGPCR-x polypeptide with a candidate binding partner compound and (b) detecting binding of the candidate compound to the nGPCR-x polypeptide.
  • the candidate binding partner compound is immobilized and binding of nGPCR-x is detected. Immobilization is accomplished using any of the methods well known in the art, including covalent bonding to a support, a bead, or a chromatographic resin, as well as non-covalent, high affinity interactions such as antibody binding, or use of streptavidin/biotin binding wherein the immobilized compound includes a biotin moiety.
  • Detection of binding can be accomplished (i) using a radioactive label on the compound that is not immobilized, (ii) using of a fluorescent label on the non-immobilized compound, (iii) using an antibody immunospecific for the non-immobilized compound, (iv) using a label on the non-immobilized compound that excites a fluorescent support to which the immobilized compound is attached, as well as other techniques well known and routinely practiced in the art.
  • the invention also provides cell-based assays to identify binding partner compounds of a nGPCR-x polypeptide.
  • the invention provides a method comprising the steps of contacting a nGPCR-x polypeptide expressed on the surface of a cell with a candidate binding partner compound and detecting binding of the candidate binding partner compound to the nGPCR-x polypeptide.
  • the detection comprises detecting a calcium flux or other physiological event in the cell caused by the binding of the molecule.
  • Another aspect of the present invention is directed to methods of identifying compounds that bind to either nGPCR-x or nucleic acid molecules encoding nGPCR-x, comprising contacting nGPCR-x, or a nucleic acid molecule encoding the same, with a compound, and determining whether the compound binds nGPCR-x or a nucleic acid molecule encoding the same.
  • Binding can be determined by binding assays which are well known to the skilled artisan, including, but not limited to, gel-shift assays, Western blots, radiolabeled competition assay, phage-based expression cloning, co-fractionation by chromatography, co-precipitation, cross linking, interaction trap/two-hybrid analysis, southwestern analysis, ELISA, and the like, which are described in, for example, Current Protocols in Molecular Biology, 1999, John Wiley & Sons, NY, which is inco ⁇ orated herein by reference in its entirety.
  • the compounds to be screened include (which may include compounds which are suspected to bind nGPCR-x, or a nucleic acid molecule encoding the same), but are not limited to, extracellular, intracellular, biologic or chemical origin.
  • the methods of the invention also embrace ligands, especially neuropeptides, that are attached to a label, such as a radiolabel (e.g., I, S, P, P, H), a fluorescence label, a chemiluminescent label, an enzymic label and an immunogenic label.
  • a radiolabel e.g., I, S, P, P, H
  • Modulators falling within the scope of the invention include, but are not limited to, non-peptide molecules such as non-peptide mimetics, non-peptide allosteric effectors, and peptides.
  • nGPCR-x polypeptide or polynucleotide employed in such a test may either be free in solution, attached to a solid support, borne on a cell surface or located intracellularly or associated with a portion of a cell.
  • One skilled in the art can, for example, measure the formation of complexes between nGPCR-x and the compound being tested.
  • one skilled in the art can examine the diminution in complex formation between nGPCR-x and its substrate caused by the compound being tested. -
  • nGPCR-x high throughput screening for compounds having suitable binding affinity to nGPCR-x is employed. Briefly, large numbers of different test compounds are synthesized on a solid substrate. The peptide test compounds are contacted with nGPCR-x and washed. Bound nGPCR-x is then detected by methods well known in the art. Purified polypeptides of the invention can also be coated directly onto plates for use in the aforementioned drug screening techniques. In addition, non-neutralizing antibodies can be used to capture the protein and immobilize it on the solid support. Generally, an expressed nGPCR-x can be used for HTS binding assays in conjunction with its defined ligand, in this case the corresponding neuropeptide that activates it.
  • the identified peptide is labeled with a suitable radioisotope, including, but not limited to, 125 1, 3 H, 35 S or 32 P, by methods that are well known to those skilled in the art.
  • the peptides may be labeled by well-known methods with a suitable fluorescent derivative (Baindur et al , Drug Dev. Res., 1994, 33, 373-398; Rogers, Drug Discovery Today, 1997, 2, 156-160).
  • Radioactive ligand specifically bound to the receptor in membrane preparations made from the cell line expressing the recombinant protein can be detected in HTS assays in one of several standard ways, including filtration of the receptor-ligand complex to separate bound ligand from unbound ligand (Williams, Med. Res. Rev., 1991, 11, 147-184; Sweetnam et al, J. Natural
  • assays may be used to identify specific ligands of a nGPCR-x receptor, including assays that identify ligands of the target protein through measuring direct binding of test ligands to the target protein, as well as assays that identify ligands of target proteins through affinity ultrafiltration with ion spray mass spectroscopy/HPLC methods or other physical and analytical methods.
  • binding interactions are evaluated indirectly using the yeast two- hybrid system described in Fields et al, Nature, 340:245-246 (1989), and Fields et al., Trends in Genetics, 10:286-292 (1994), both of which are inco ⁇ orated herein by reference in its entirety.
  • the two-hybrid system is a genetic assay for detecting interactions between two proteins or polypeptides. It can be used to identify proteins that bind to a known protein of interest, or to delineate domains or residues critical for an interaction. Variations on this methodology have been developed to clone genes that encode DNA binding proteins, to identify peptides that bind to a protein, and to screen for drugs.
  • the two-hybrid system exploits the ability of a pair of interacting proteins to bring a transcription activation domain into close proximity with a DNA binding domain that binds to an upstream activation sequence (UAS) of a reporter gene, and is generally performed in yeast.
  • UAS upstream activation sequence
  • the assay requires the construction of two hybrid genes encoding (1) a DNA-binding domain that is fused to a first protein and (2) an activation domain fused to a second protein.
  • the DNA-binding domain targets the first hybrid protein to the UAS of the reporter gene; however, because most proteins lack an activation domain, this DNA-binding hybrid protein does not activate transcription of the reporter gene.
  • the second hybrid protein which contains the activation domain, cannot by itself activate expression of the reporter gene because it does not bind the UAS. However, when both hybrid proteins are present, the noncovalent interaction of the first and second proteins tethers the activation domain to the UAS, activating transcription of the reporter gene.
  • this assay can be used to detect agents that interfere with the binding interaction.
  • Expression of the reporter gene is monitored as different test agents are added to the system. The presence of an inhibitory agent results in lack of a reporter signal.
  • the yeast two-hybrid assay can also be used to identify proteins that bind to the gene product.
  • a fusion polynucleotide encoding both a nGPCR-x receptor (or fragment) and a UAS binding domain i.e., a first protein
  • a large number of hybrid genes each encoding a different second protein fused to an activation domain are produced and screened in the assay.
  • the second protein is encoded by one or more members of a total cDNA or genomic DNA fusion library, with each second protein-coding region being fused to the activation domain.
  • This system is applicable to a wide variety of proteins, and it is not even necessary to know the identity or function of the second binding protein.
  • the system is highly sensitive and can detect interactions not revealed by other methods; even transient interactions may trigger transcription to produce a stable mRNA that can be repeatedly translated to yield the reporter protein.
  • test ligands may be used to search for agents that bind to the target protein.
  • One such screening method to identify direct binding of test ligands to a target protein is described in U.S. Patent No. 5,585,277, inco ⁇ orated herein by reference in its entirety. This method relies on the principle that proteins generally exist as a mixture of folded and unfolded states, and continually alternate between the two states.
  • the target protein molecule bound by the ligand remains in its folded state.
  • the folded target protein is present to a greater extent in the presence of a test ligand which binds the target protein, than in the absence of a ligand. Binding of the ligand to the target protein can be determined by any method that distinguishes between the folded and unfolded states of the target protein. The function of the target protein need not be known in order for this assay to be performed. Virtually any agent can be assessed by this method as a test ligand, including, but not limited to, metals, polypeptides, proteins, lipids, polysaccharides, polynucleotides and small organic molecules.
  • Determining whether a test compound binds to nGPCR-x can also be accomplished by measuring the intrinsic fluorescence of nGPCR-x and determining whether the intrinsic fluorescence is modulated in the presence of the test compound.
  • the intrinsic fluorescence of nGPCR-x is measured as a function of the tryptophan residue(s) of nGPCR-x.
  • fluorescence of nGPCR-x is measured and compared to the fluorescence intensity of nGPCR-x in the presence of the test compound, wherein a decrease in fluorescence intensity indicates binding of the test compound to nGPCR-x.
  • Preferred methodology is set forth in "Principles of Fluorescence Specfroscopy" by Joseph R.
  • inventions comprise using competitive screening assays in which neutralizing antibodies capable of binding a polypeptide of the invention specifically compete with a test compound for binding to the polypeptide.
  • the antibodies can be used to detect the presence ofany peptide that shares one or more antigenic determinants with nGPCR-x.
  • Radiolabeled competitive binding studies are described in A.H. Lin et al. Antimicrobial Agents and Chemotherapy, 1997, vol. 41, no. 10. pp. 2127-2131, the disclosure of which is inco ⁇ orated herein by reference in its entirety. Identification of modulating agents
  • the invention also provides methods for identifying a modulator of binding between a nGPCR-x and a nGPCR-x binding partner, comprising the steps of: (a) contacting a nGPCR-x binding partner and a composition comprising a nGPCR-x in the presence and in the absence of a putative modulator compound; (b) detecting binding between the binding partner and the nGPCR-x; and (c) identifying a putative modulator compound or a modulator compound in view of decreased or increased binding between the binding partner and the nGPCR-x in the presence of the putative modulator, as compared to binding in the absence of the putative modulator.
  • nGPCR-x binding partners that stimulate nGPCR-x activity are useful as agonists in disease states or conditions characterized by insufficient nGPCR-x signaling (e.g., as a result of insufficient activity of a nGPCR-x ligand).
  • nGPCR-x binding partners that block ligand- mediated nGPCR-x signaling are useful as nGPCR-x antagonists to treat disease states or conditions characterized by excessive nGPCR-x signaling.
  • nGPCR-x modulators in general, as well as nGPCR-x polynucleotides and polypeptides, are useful in diagnostic assays for such diseases or conditions.
  • the invention provides methods for treating a disease or abnormal condition by administering to a patient in need of such treatment a substance that modulates the activity or expression of a polypeptide having sequences selected from the group consisting of SEQ ID NO:68 to SEQ ID NO: 136.
  • Agents that modulate (i.e., increase, decrease, or block) nGPCR-x activity or expression may be identified by incubating a putative modulator with a cell containing a nGPCR-x polypeptide or polynucleotide and determining the effect of the putative modulator on nGPCR-x activity or expression.
  • nGPCR-x The selectivity of a compound that modulates the activity of nGPCR-x can be evaluated by comparing its effects on nGPCR-x to its effect on other GPCR compounds. Following identification of compounds that modulate nGPCR-x activity or expression, such compounds can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate their activity.
  • Selective modulators may include, for example, antibodies and other proteins, peptides, or organic molecules that specifically bind to a nGPCR- x polypeptide or a nGPCR-x-encoding nucleic acid. Modulators of nGPCR-x activity will be therapeutically useful in treatment of diseases and physiological conditions in which normal or aberrant nGPCR-x activity is involved.
  • nGPCR-x polynucleotides, polypeptides, and modulators may be used in the freatment of such diseases and conditions as infections, such as viral infections caused by HJN-1 or HIN-2; pain; cancers; metabolic and cardiovascular diseases and disorders (e.g., type 2 diabetes, impaired glucose tolerance, dyslipidemia, obesity, anorexia, hypotension, hypertension, thrombosis, myocardial infarction, cardiomyopathies, atherosclerosis, etc.); Parkinson's disease; and psychotic and neurological disorders, including anxiety, mental disorder, manic depression, schizophrenia, migraine, major depression, attention disorders including ADD and ADHD, delirium, dementia* severe mental retardation and dyskinesias, such as Huntington's disease or Tourette's Syndrome, among others.
  • nGPCR-x polynucleotides and polypeptides, as well as nGPCR-x modulators may also be used in diagnostic assays for such diseases or conditions.
  • Methods of the invention to identify modulators include variations on any of the methods described above to identify binding partner compounds, the variations including techniques wherein a binding partner compound has been identified and the binding assay is carried out in the presence and absence of a candidate modulator.
  • a modulator is identified in those instances where binding between the nGPCR-x polypeptide and the binding partner compound changes in the presence of the candidate modulator compared to binding in the absence of the candidate modulator compound.
  • a modulator that increases binding between the nGPCR-x polypeptide and the binding partner compound is described as an enhancer or activator, and a modulator that decreases binding between the nGPCR-x polypeptide and the binding partner compound is described as an inhibitor.
  • such compounds can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate their activity as modulators.
  • the invention also comprehends high-throughput screening (HTS) assays to identify compounds that interact with or inhibit biological activity (i.e., affect enzymatic activity, binding activity, etc.) of a nGPCR-x polypeptide.
  • HTS assays permit screening of large numbers of compounds in an efficient manner.
  • Cell-based HTS systems are contemplated to investigate nGPCR-x receptor-ligand interaction.
  • HTS assays are designed to identify "hits” or "lead compounds” having the desired property, from which modifications can be designed to improve the desired property. Chemical modification of the "hit” or “lead compound” is often based on an identifiable structure/activity relationship between the "hit” and the nGPCR-x polypeptide.
  • Another aspect of the present invention is directed to methods of identifying compounds which modulate (i.e., increase or decrease) activity of nGPCR-x comprising contacting nGPCR- x with a compound, and determining whether the compound modifies activity of nGPCR-x.
  • the activity in the presence of the test compared is measured to the activity in the absence of the test compound. Where the activity of the sample containing the test compound is higher than the activity in the sample lacking the test compound, the compound will have increased activity. Similarly, where the activity of the sample containing the test compound is lower than the activity in the sample lacking the test compound, the compound will have inhibited activity.
  • such compounds can be further tested in other assays including, but not limited to, in vivo models, in order to confirm or quantitate their activity.
  • the present invention is particularly useful for screening compounds by using nGPCR-x in any of a variety of drug screening techniques.
  • the compounds to be screened include (which may include compounds which are suspected to modulate nGPCR-x activity), but are not limited to, extracellular, intracellular, biologic or chemical origin.
  • the nGPCR-x polypeptide employed in such a test may be in any form, preferably, free in solution, attached to a solid support, borne on a cell surface or located intracellularly.
  • One skilled in the art can, for example, measure the formation of complexes between nGPCR-x and the compound being tested. Alternatively, one skilled in the art can examine the diminution in complex formation between nGPCR-x and its substrate caused by the compound being tested.
  • nGPCR-x polypeptides of the invention can be determined by, for example, examining the ability to bind or be activated by chemically synthesized peptide ligands.
  • the activity of nGPCR-x polypeptides can be assayed by examining their ability to bind calcium ions, hormones, chemokines, neuropeptides, neurotransmitters, nucleotides, lipids, odorants, and photons.
  • the activity of the nGPCR-x polypeptides can be determined by examining the activity of effector molecules including, but not limited to, adenylate cyclase, phospholipases and ion channels.
  • modulators of nGPCR-x polypeptide activity may alter a GPCR receptor function, such as a binding property of a receptor or an activity such as G protein-mediated signal transduction or membrane localization.
  • the assay may take the form of an ion flux assay, a yeast growth assay, a non-hydrolyzable GTP assay such as a [ 35 S]-GTP ⁇ S assay, a cAMP assay, an inositol triphosphate assay, a diacylglycerol assay, an Aequorin assay, a Luciferase assay, a FLIPR assay for intracellular Ca 2+ concentration, a mitogenesis assay, a MAP Kinase activity assay, an arachidonic acid release assay (e.g., using [ 3 H]-arachidonic acid), and an assay for extracellular acidification rates, as well as other binding or function-based assays of nGPCR-
  • the invention comprehends the inclusion ofany of the G proteins known in the art, such as G 16 , G 15 , or chimeric G q d 5 , G qS 5, G q05 , G q25 , and the like.
  • nGPCR-x activity can be determined by methodologies that are used to assay for FaRP activity, which is well known to those skilled in the art.
  • Biological activities of nGPCR-x receptors according to the invention include, but are not limited to, the binding of a natural or an unnatural ligand, as well as any one of the functional activities of GPCRs known in the art.
  • Non-limiting examples of GPCR activities include transmembrane signaling of various forms, which may involve G protein association and/or the exertion of an influence over G protein binding of various guanidylate nucleotides; another exemplary activity of GPCRs is the binding of accessory proteins or polypeptides that differ from known G proteins.
  • the modulators of the invention exhibit a variety of chemical structures, which can be generally grouped into non-peptide mimetics of natural GPCR receptor ligands, peptide and non-peptide allosteric effectors of GPCR receptors, and peptides that may function as activators or inhibitors (competitive, uncompetitive and non-competitive) (e.g., antibody products) of GPCR receptors.
  • the invention does not restrict the sources for suitable modulators, which may be obtained from natural sources such as plant, animal or mineral extracts, or non-natural sources such as small molecule libraries, including the products of combinatorial chemical approaches to library construction, and peptide libraries.
  • Examples of peptide modulators of GPCR receptors exhibit the following primary structures: GLGPRPLRFamide, GNSFLRFamide, GGPQGPLRFamide, GPSGPLRFamide, PDVDHVFLRFamide, and pyro- EDVDHVFLRFamide.
  • Other assays can be used to examine enzymatic activity including, but not limited to, photometric, radiometric, HPLC, electrochemical, and the like, which are described in, for example, Enzyme Assays: A Practical Approach, eds. R. Eisenthal and M. J. Danson, 1992, Oxford University Press, which is inco ⁇ orated herein by reference in its entirety.
  • Recombinant receptors are preferred for binding assay HTS because they allow for better specificity (higher relative purity), provide the ability to generate large amounts of receptor material, and can be used in a broad variety of formats (see Hodgson, Bio/Technology, 1992, 10, 973-980; each of which is inco ⁇ orated herein by reference in its entirety).
  • a variety of heterologous systems is available for functional expression of recombinant receptors that are well known to those skilled in the art. Such systems include bacteria (Strosberg, et al, Trends in Pharmacological Sciences, 1992, 13, 95-98), yeast (Pausch, Trends in Biotechnology, 1997, 15, 487-494), several kinds of insect cells (Vanden Broeck, Int. Rev. Cytology, 1996, 164, 189-268), amphibian cells (Jayawickreme et al, Current Opinion in
  • methods of screening for compounds that modulate nGPCR-x activity comprise contacting test compounds with nGPCR-x and assaying for the presence of a complex between the compound and nGPCR-x.
  • the ligand is typically labeled. After suitable incubation, free ligand is separated from that present in bound form, and the amount of free or uncomplexed label is a measure of the ability of the particular compound to bind to nGPCR-x.
  • the G proteins required for functional expression of heterologous GPCRs can be native constituents of the host cell or can be introduced through well-known recombinant technology.
  • the G proteins can be intact or chimeric.
  • a nearly universally competent G protein e.g., G ⁇ i ⁇
  • G protein activation results in the stimulation or inhibition of other native proteins, events that can be linked to a measurable response.
  • Such biological responses include, but are not limited to, the following: the ability to survive in the absence of a limiting nutrient in specifically engineered yeast cells (Pausch, Trends in Biotechnology, 1997, 15, 487-494); changes in intracellular Ca 2+ concentration as measured by fluorescent dyes (Mu ⁇ hy, et al, Cur. Opinion Drug Disc. Dev., 1998, 1, 192-199). Fluorescence changes can also be used to monitor ligand-induced changes in membrane potential or intracellular pH; an automated system suitable for HTS has been described for these pu ⁇ oses (Schroeder, et al, J. Biomolecular Screening, 1996, 1, 75-80).
  • HTS HTS employing these receptors
  • permanently transfected CHO cells in which agonists and antagonists can be identified by the ability to specifically alter the binding of GTP ⁇ [ 35 S] in membranes prepared from these cells.
  • permanently transfected CHO cells could be used for the preparation of membranes which contain significant amounts of the recombinant receptor proteins; these membrane preparations would then be used in receptor binding assays, employing the radiolabelled ligand specific for the particular receptor.
  • a functional assay such as fluorescent monitoring of ligand-induced changes in internal Ca 2+ concentration or membrane potential in permanently transfected CHO cells containing each of these receptors individually or in combination would be preferred for HTS.
  • Equally preferred would be an alternative type of mammalian cell, such as HEK293 or COS cells, in similar formats. More preferred would be permanently transfected insect cell lines, such as Drosophila S2 cells. Even more preferred would be recombinant yeast cells expressing the Drosophila melanogaster receptors in HTS formats well known to those skilled in the art (e.g., Pausch, Trends in Biotechnology, 1997, 15, 487-494).
  • the invention contemplates a multitude of assays to screen and identify inhibitors of ligand binding to nGPCR-x receptors.
  • the nGPCR-x receptor is immobilized and interaction with a binding partner is assessed in the presence and absence of a candidate modulator such as an inhibitor compound.
  • interaction between the nGPCR- x receptor and its binding partner is assessed in a solution assay, both in the presence and absence of a candidate inhibitor compound.
  • an inhibitor is identified as a compound that decreases binding between the nGPCR-x receptor and its binding partner.
  • Another contemplated assay involves a variation of the dihybrid assay wherein an inhibitor of protein/protein interactions is identified by detection of a positive signal in a transformed or transfected host cell, as described in PCT publication number WO 95/20652, published August 3, 1995.
  • Candidate modulators contemplated by the invention include compounds selected from libraries of either potential activators or potential inhibitors. There are a number of different libraries used for the identification of small molecule modulators, including: (1) chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules. Chemical libraries consist of random chemical structures, some of which are analogs of known compounds or analogs of compounds that have been identified as "hits" or "leads" in other drug discovery screens, some of which are derived from natural products, and some of which arise from non-directed synthetic organic chemistry.
  • Natural product libraries are collections of microorganisms, animals, plants, or marine organisms which are used to create mixtures for screening by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of plants or marine organisms. Natural product libraries include polyketides, non-ribosomal peptides, and variants (non-naturally occurring) thereof. For a review, see Science 282:63-68 (1998). Combinatorial libraries are composed of large numbers of peptides, oligonucleotides, or organic compounds as a mixture. These libraries are relatively easy to prepare by traditional automated synthesis methods, PCR, cloning, or proprietary synthetic methods. Of particular interest are non-peptide combinatorial libraries.
  • Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries.
  • combinatorial chemistry and libraries created therefrom see Myers, Curr. Opin. Biotechnol 8:701-707 (1997). Identification of modulators through use of the various libraries described herein permits modification of the candidate "hit” (or “lead”) to optimize the capacity of the "hit” to modulate activity.
  • binding partners can be designed and include soluble forms of binding partners, as well as such binding partners as chimeric, or fusion, proteins.
  • polypeptides of the invention are employed as a research tool for identification, characterization and purification of interacting, regulatory proteins.
  • Appropriate labels are inco ⁇ orated into the polypeptides of the invention by various methods known in the art and the polypeptides are used to capture interacting molecules. For example, molecules are incubated with the labeled polypeptides, washed to remove unbound polypeptides, and the polypeptide complex is quantified. Data obtained using different concentrations of polypeptide are used to calculate values for the number, affinity, and association of polypeptide with the protein complex.
  • Labeled polypeptides are also useful as reagents for the purification of molecules with which the polypeptide interacts including, but not limited to, inhibitors.
  • affinity purification a polypeptide is covalently coupled to a chromatography column. Cells and their membranes are extracted, and various cellular subcomponents are passed over the column. Molecules bind to the column by virtue of their affinity to the polypeptide. The polypeptide- complex is recovered from the column, dissociated and the recovered molecule is subjected to protein sequencing. This amino acid sequence is then used to identify the captured molecule or to design degenerate oligonucleotides for cloning the corresponding gene from an appropriate cDNA library.
  • compounds may be identified which exhibit similar properties to the ligand for the nGPCR-x of the invention, but which are smaller and exhibit a longer half time than the endogenous ligand in a human or animal body.
  • a molecule according to the invention is used as a "lead” compound.
  • the design of mimetics to known pharmaceutically active compounds is a well-known approach in the development of pharmaceuticals based on such "lead” compounds. Mimetic design, synthesis and testing are generally used to avoid randomly screening a large number of molecules for a target property.
  • structural data deriving from the analysis of the deduced amino acid sequences encoded by the DNAs of the present invention are useful to design new drugs, more specific and therefore with a higher pharmacological potency.
  • the novel molecules identified by the screening methods according to the invention are low molecular weight organic molecules, in which case a composition or pharmaceutical composition can be prepared thereof for oral intake, such as in tablets.
  • a composition or pharmaceutical composition comprising the nucleic acid molecules, vectors, polypeptides, antibodies and compounds identified by the screening methods described herein, can be prepared for any route of administration including, but not limited to, oral, intravenous, cutaneous, subcutaneous, nasal, intramuscular or infraperitoneal.
  • the nature of the carrier or other ingredients will depend on the specific route of administration and particular embodiment of the invention to be administered.
  • the present compounds and methods including nucleic acid molecules, polypeptides, antibodies, compounds identified by the screening methods described herein, have a variety of pharmaceutical applications and may be used, for example, to treat or prevent unregulated cellular growth, such as cancer cell and tumor growth.
  • the present molecules are used in gene therapy.
  • gene therapy procedures see e.g. Anderson, Science, 1992, 256, 808-813, which is inco ⁇ orated herein by reference in its entirety.
  • the present invention also encompasses a method of agonizing (stimulating) or antagonizing a nGPCR-x natural binding partner associated activity in a mammal comprising administering to said mammal an agonist or antagonist to one of the above disclosed polypeptides in an amount sufficient to effect said agonism or antagonism.
  • One embodiment of the present invention is a method of treating diseases in a mammal with an agonist or antagonist of the protein of the present invention comprises administering the agonist or antagonist to a mammal in an amount sufficient to agonize or antagonize nGPCR-x-associated functions.
  • exemplary diseases and conditions amenable to treatment based on the present invention include, but are not limited to, thyroid disorders (e.g.
  • thyreotoxicosis myxoedema
  • renal failure inflammatory conditions (e.g., Crohn's disease); diseases related to cell differentiation and homeostasis; rheumatoid arthritis; autoimmune disorders; movement disorders; CNS disorders (e.g., pain including migraine; stroke; psychotic and neurological disorders, including anxiety, mental disorder, manic depression, anxiety, generalized anxiety disorder, post- traumatic-stress disorder, Schizophrenia, depression, bipolar disorder, delirium, dementia, severe mental retardation; dyskinesias, such as Huntington's disease or Tourette's Syndrome; attention disorders including ADD and ADHD, and degenerative disorders such as Parkinson's, Alzheimer's; movement disorders, including ataxias, supranuclear palsy, etc.); infections, such as viral infections caused by HIV-1 or HIV-2; metabolic and cardiovascular diseases and disorders (e.g., type 2 diabetes, impaired glucose tolerance, dyslipidemia, obesity, anorexia, hypotension, hypertension, thrombosis,
  • the proper dosage depends on various factors such as the type of disease being treated, the particular composition being used and the size and physiological condition of the patient, including such factors as, for example, weight, age, sex, disease state, etc.
  • Therapeutically effective doses for the compounds described herein can be estimated initially from cell culture and animal models. For example, a dose can be formulated in animal models to achieve a circulating concentration range that initially takes into account the IC 50 as determined in cell culture assays. The animal model data can be used to more accurately determine useful doses in humans.
  • Plasma half-life and biodistribution of the drug and metabolites in the plasma, tumors and major organs can also be determined to facilitate the selection of drugs most appropriate to inhibit a disorder. Such measurements can be carried out.
  • HPLC analysis can be performed on the plasma of animals treated with the drug and the location of radiolabeled compounds can be determined using detection methods such as X-ray, CAT scan and MRI.
  • Compounds that show potent inhibitory activity in the screening assays, but have poor pharm- acokinetic characteristics, can be optimized by altering the chemical structure and retesting. In this regard, compounds displaying good pharmacokinetic characteristics can be used as a model.
  • Toxicity studies can also be carried out by measuring the blood cell composition.
  • toxicity studies can be carried out in a suitable animal model as follows: 1) the compound is administered to mice (an untreated control mouse should also be used); 2) blood samples are periodically obtained via the tail vein from one mouse in each treatment group; and 3) the samples are analyzed for red and white blood cell counts, blood cell composition and the percent of lymphocytes versus polymo ⁇ honuclear cells. A comparison of results for each dosing regime with the controls indicates if toxicity is present.
  • the expected daily dose of a hydrophobic pharmaceutical agent is between 1 to 500 mg/day, preferably 1 to 250 mg/day, and most preferably 1 to 50 mg/day.
  • Drugs can be delivered less frequently provided plasma levels of the active moiety are sufficient to maintain therapeutic effectiveness. Plasma levels should reflect the potency of the drug. Generally, the more potent the compound the lower the plasma levels necessary to achieve efficacy.
  • Sequences selected from the group consisting of SEQ ID NO:l to SEQ ID NO: 67 will, as detailed above, enable screening the endogenous neurofransmitters/hormones/ligands which activate, agonize, or antagonize nGPCR-x and for compounds with potential utility in treating disorders including, but not limited to, thyroid disorders (e.g.
  • thyreotoxicosis myxoedema
  • renal failure inflammatory conditions (e.g., Crohn's disease); diseases related to cell differentiation and homeostasis; rheumatoid arthritis; autoimmune disorders; movement disorders; CNS disorders (e.g., pain including migraine; stroke; psychotic and neurological disorders, including anxiety, mental disorder, manic depression, anxiety, generalized anxiety disorder, post-traumatic-stress disorder, Schizophrenia, depression, bipolar disorder, delirium, dementia, severe mental retardation; dyskinesias, such as Huntington's disease or Tourette's Syndrome; attention disorders including ADD and ADHD, and degenerative disorders such as Parkinson's, Alzheimer's; movement disorders, including ataxias, supranuclear palsy, etc.); infections, such as viral infections caused by HJV-1 or HIV-2; metabolic and cardiovascular diseases and disorders (e.g., type 2 diabetes, impaired glucose tolerance, dyslipidemia, obesity, anorexia, hypotension, hypertension, thrombosis
  • nGPCR-x may be useful in the treatment of respiratory ailments such as asthma, where T cells are implicated by the disease. Contraction of airway smooth muscle is stimulated by thrombin. Cicala et al (1999) Br J Pharmacol 126:478-484. Additionally, in bronchiolitis obliterans, it has been noted that activation of thrombin receptors may be deleterious. Hauck et al. (1999) Am J Physiol 277:L22-L29. Furthermore, mast cells have also been shown to have thrombin receptors. Cirino et al (1996) J Exp Med 183:821-827.
  • nGPCR-x may also be useful in remodeling of airway structures in chronic pulmonary inflammation via stimulation of fibroblast procollagen synthesis. See, e.g., Chambers et al. (1998) Biochem J 333:121-127; Trejo et al. (1996) J Biol Chem 271:21536-21541.
  • nGPCR-x may be useful in the treatment of unstable angina due to the role of T cells and inflammation. See Aukrust et al. (1999) Circulation 100:614-620.
  • a further example is the treatment of inflammatory diseases, such as psoriasis, inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, and thyroiditis.
  • inflammatory diseases such as psoriasis, inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, and thyroiditis.
  • thrombin receptors Due to the tissue expression profile of nGPCR-x, inhibition of thrombin receptors may be beneficial for these diseases. See, e.g., Morris et al. (1996) Ann Rheum Dis 55:841-843.
  • NK cells and monocytes are also critical cell types which contribute to the pathogenesis of these diseases. See, e.g., Naldini & Carney (1996) Cell Immunol 172:35-42; Hoffman & Cooper (1995) Blood Cells Mol Dis 21:156-167; Colotta et al. (1994) Am J Pafhol 144:975-985.
  • nGPCR-x in bone marrow and spleen may suggest that it may play a role in the proliferation of hematopoietic progenitor cells. See DiCuccio et al. (1996) Exp Hematol 24:914-918.
  • nGPCR-x may be useful in the treatment of acute and/or traumatic brain injury.
  • Asfrocytes have been demonstrated to express thrombin receptors. Activation of thrombin receptors may be involved in astrogliosis following brain injury. Therefore, inhibition of receptor activity may be beneficial for limiting neuroinflammation.
  • Scar formation mediated by asfrocytes may also be limited by inhibiting thrombin receptors. See, e.g, Pindon et al. (1998) Eur J Biochem 255:766-774; Ubi & Reiser. (1997) Glia 21:361-369; Grabham & Cunningham (1995) J Neurochem 64:583-591.
  • nGPCR-x receptor activation may mediate neuronal and asfrocyte apoptosis and prevention of neurite outgrowth. Inhibition would be beneficial in both chronic and acute brain injury. See, e.g., Donovan et al. (1997) J Neurosci 17:5316-5326; Turgeon et al (1998) J
  • Such neurological diseases and disorders including but are not limited to, mental disorder, affective disorders, ADHD/ADD, and neural disorders such as Alzheimer's disease, Parkinson's disease, migraine, schizophrenia, and senile dementia as well as depression, anxiety, bipolar disease, epilepsy, neuritis, neurasthenia, neuropathy, neuroses, and the like.
  • the invention provides genetic screening procedures that entail analyzing a person's genome — in particular their alleles for GPCRs of the invention - - to determine whether the individual possesses a genetic characteristic found in other individuals that are considered to be afflicted with, or at risk for, developing a mental disorder or disease of the brain that is suspected of having a hereditary component.
  • the invention provides a method for determining a potential for developing a disorder affecting the brain in a human subject comprising the steps of analyzing the coding sequence of one or more GPCR genes from the human subject; and determining development potential for the disorder in said human subject from the analyzing step.
  • the invention provides a method of screening a human subject to diagnose a disorder affecting the brain or genetic predisposition therefor, comprising the steps of: (a) assaying nucleic acid of a human subject to determine a presence or an absence of a mutation altering the amino acid sequence, expression, or biological activity of at least one seven transmembrane receptor that is expressed in the brain, wherein the nucleic acid corresponds to the gene encoding the seven transmembrane receptor; and (b) diagnosing the disorder or predisposition from the presence or absence of said mutation, wherein the presence of a mutation altering the amino acid sequence, expression, or biological activity of allele in the nucleic acid correlates with an increased risk of developing the disorder.
  • the seven transmembrane receptor is nGPCR-x, or an allelic variant thereof, and the disease is mental disorder.
  • human subject is meant any human being, human embryo, or human fetus. It will be apparent that methods of the present invention will be of particular interest to individuals that have themselves been diagnosed with a disorder affecting the brain or have relatives that have been diagnosed with a disorder affecting the brain.
  • screening for an increased risk is meant determination of whether a genetic variation exists in the human subject that correlates with a greater likelihood of developing a disorder affecting the brain than exists for the human population as a whole, or for a relevant racial or ethnic human sub-population to which the individual belongs. Both positive and negative determinations (i.e., determinations that a genetic predisposition marker is present or is absent) are intended to fall within the scope of screening methods of the invention.
  • the presence of a mutation altering the sequence or expression of at least one nGPCR-x seven fransmembrane receptor allele in the nucleic acid is correlated with an increased risk of developing mental disorder, whereas the absence of such a mutation is reported as a negative determination.
  • the "assaying" step of the invention may involve any techniques available for analyzing nucleic acid to determine its characteristics, including but not limited to well-known techniques such as single-strand conformation polymo ⁇ hism analysis (SSCP) (Orita et al, Proc Natl. Acad. Sci.
  • the assaying step comprises at least one procedure selected from the group consisting of: (a) determining a nucleotide sequence of at least one codon of at least one nGPCR-x allele of the human subject; (b) performing a hybridization assay to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences; (c) performing a polynucleotide migration assay to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences; and (d) performing a restriction endonuclease digestion to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences.
  • the assaying involves sequencing of nucleic acid to determine nucleotide sequence thereof, using any available sequencing technique.
  • any available sequencing technique See, e.g., Sanger et al, Proc. Natl. Acad. Sci. (USA), 74: 5463-5467 (1977) (dideoxy chain termination method); Mirzabekov, TIBTECH, 12: 27-32 (1994) (sequencing by hybridization); Drmanac et al, Nature Biotechnology, 16: 54-58 (1998); U.S. Patent No.
  • the analysis may entail sequencing of the entire nGPCR gene genomic DNA sequence, or portions thereof; or sequencing of the entire seven transmembrane receptor coding sequence or portions thereof. In some circumstances, the analysis may involve a determination of whether an individual possesses a particular allelic variant, in which case sequencing of only a small portion of nucleic acid ⁇ enough to determine the sequence of a particular codon characterizing the allelic variant ⁇ is sufficient.
  • the assaying step comprises performing a hybridization assay to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences.
  • the hybridization involves a determination of whether nucleic acid derived from the human subject will hybridize with one or more oligonucleotides, wherein the oligonucleotides have nucleotide sequences that correspond identically to a portion of the GPCR gene sequence taught herein, such as the nGPCR-x coding sequence, or that correspond identically except for one mismatch.
  • the hybridization conditions are selected to differentiate between perfect sequence complementarity and imperfect matches differing by one or more bases.
  • Such hybridization experiments thereby can provide single nucleotide polymo ⁇ hism sequence information about the nucleic acid from the human subject, by virtue of knowing the sequences of the oligonucleotides used in the experiments.
  • nucleic acid derived from the human subject is subjected to gel electrophoresis, usually adjacent to (or co-loaded with) one or more reference nucleic acids.
  • the nucleic acid from the human subject and the reference sequence(s) are subjected to similar chemical or enzymatic treatments and then elecfrophoresed under conditions whereby the polynucleotides will show a differential migration pattern, unless they contain identical sequences.
  • nucleic acid of a human subject is intended to include nucleic acid obtained directly from the human subject (e.g., DNA or RNA obtained from a biological sample such as a blood, tissue, or other cell or fluid sample); and also nucleic acid derived from nucleic acid obtained directly from the human subject.
  • cDNA that is complementary to RNA derived from a biological sample from a human subject
  • amplifying e.g., via polymerase chain reaction (PCR)
  • PCR polymerase chain reaction
  • Any such derived polynucleotide which retains relevant nucleotide sequence information of the human subject's own DNA/RNA is intended to fall within the definition of "nucleic acid of a human subject" for the pu ⁇ oses of the present invention.
  • mutation includes addition, deletion, and/or substitution of one or more nucleotides in the GPCR gene sequence (e.g., as compared to the seven transmembrane receptor-encoding sequences) and other polymo ⁇ hisms that occur in introns (where introns exist) and that are identifiable via sequencing, restriction fragment length polymo ⁇ hism, or other techniques.
  • the various activity examples provided herein permit determination of whether a mutation modulates activity of the relevant receptor in the presence or absence of various test substances.
  • the invention provides methods of screening a person's genotype with respect to GPCRs of the invention, and correlating such genotypes with diagnoses for disease or with predisposition for disease (for genetic counseling).
  • the invention provides a method of screening for an nGPCR-x hereditary mental disorder genotype in a human patient, comprising the steps of: (a) providing a biological sample comprising nucleic acid from the patient, the nucleic acid including sequences corresponding to said patient's nGPCR-x alleles; (b) analyzing the nucleic acid for the presence of a mutation or mutations; (c) determining an nGPCR-x genotype from the analyzing step; and (d) correlating the presence of a mutation in an nGPCR-x allele with a hereditary mental disorder genotype.
  • the biological sample is a cell sample containing human cells that contain genomic DNA of the human subject.
  • the analyzing can be performed analogously to the assaying described in preceding paragraphs.
  • the analyzing comprises sequencing a portion of the nucleic acid (e.g., DNA or RNA), the portion comprising at least one codon of the nGPCR-x alleles.
  • the invention also may be practiced by assaying protein of a human subject to determine the presence or absence of an amino acid sequence variation in GPCR protein from the human subject. Such protein analyses may be performed, e.g., by fragmenting GPCR protein via chemical or enzymatic methods and sequencing the resultant peptides; or by Western analyses using an antibody having specificity for a particular allelic variant of the GPCR.
  • the invention also provides materials that are useful for performing methods of the invention. For example, the present invention provides oligonucleotides useful as probes in the many analyzing techniques described above.
  • oligonucleotide probes comprise 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 nucleotides that have a sequence that is identical, or exactly complementary, to a portion of a human GPCR gene sequence taught herein (or allelic variant thereof), or that is identical or exactly complementary except for one nucleotide substitution.
  • the oligonucleotides have a sequence that corresponds in the foregoing manner to a human GPCR coding sequence taught herein.
  • an oligonucleotide probe of the invention is purified and isolated.
  • the oligonucleotide probe is labeled, e.g., with a radioisotope, chromophore, or fluorophore.
  • the probe is covalently attached to a solid support. (See generally Ausubel et al. and Sambrook et al, supra.)
  • kits comprising reagents that are useful for practicing methods of the invention.
  • the invention provides a kit for screening a human subject to diagnose a mental disorder or a genetic predisposition therefor, comprising, in association: (a) an oligonucleotide useful as a probe for identifying polymo ⁇ hisms in a human nGPCR-x seven fransmembrane receptor gene, the oligonucleotide comprising 6-50 nucleotides that have a sequence that is identical or exactly complementary to a portion of a human nGPCR-x gene sequence or nGPCR-x coding sequence, except for one sequence difference selected from the group consisting of a nucleotide addition, a nucleotide deletion, or nucleotide substitution; and (b) a media packaged with the oligonucleotide containing information identifying polymo ⁇ hisms identifiable with the probe that correlate with mental disorder or a genetic predisposition therefor
  • Exemplary information-containing media include printed paper package inserts or packaging labels; and magnetic and optical storage media that are readable by computers or machines used by practitioners who perform genetic screening and counseling services.
  • the practitioner uses the information provided in the media to correlate the results of the analysis with the oligonucleotide with a diagnosis.
  • the oligonucleotide is labeled.
  • the invention provides methods of identifying those allelic variants of GPCRs of the invention that correlate with mental disorders.
  • the invention provides a method of identifying a seven transmembrane allelic variant that correlates with a mental disorder, comprising steps of: (a) providing a biological sample comprising nucleic acid from a human patient diagnosed with a mental disorder, or from the patient's genetic progenitors or progeny; (b) analyzing the nucleic acid for the presence of a mutation or mutations in at least one seven transmembrane receptor that is expressed in the brain, wherein the nucleic acid includes sequence corresponding to the gene or genes encoding the at least one seven fransmembrane receptor; (c) determining a genotype for the patient for the at least one seven fransmembrane receptor from said analyzing step; and (d) identifying an allelic variant that correlates with the mental disorder from the determining step.
  • the chromosomal localization data facilitates identifying an involved GPCR with a chromosomal marker.
  • the foregoing method can be performed to correlate GPCRs of the invention to a number of disorders having hereditary components that are causative or that predispose persons to the disorder.
  • the disorder is a mental disorder
  • the at least one seven fransmembrane receptor comprises nGPCR-x or an allelic variant thereof.
  • polynucleotides that comprise the allelic variant sequences identified by such methods, and polypeptides encoded by the allelic variant sequences, and oligonucleotide and oligopeptide fragments thereof that embody the mutations that have been identified.
  • Such materials are useful in in vitro cell-free and cell-based assays for identifying lead compounds and therapeutics for freatment of the disorders.
  • the variants are used in activity assays, binding assays, and assays to screen for activity modulators described herein.
  • the invention provides a purified and isolated polynucleotide comprising a nucleotide sequence encoding a nGPCR-x receptor allelic variant identified according to the methods described above; and an oligonucleotide that comprises the sequences that differentiate the allelic variant from the nGPCR-x sequences.
  • the invention also provides a vector comprising the polynucleotide (preferably an expression vector); and a host cell transformed or transfected with the polynucleotide or vector.
  • the invention also provides an isolated cell line that is expressing the allelic variant GPCR polypeptide; purified cell membranes from such cells; purified polypeptide; and synthetic peptides that embody the allelic variation amino acid sequence.
  • the invention provides a purified polynucleotide comprising a nucleotide sequence encoding a nGPCR-x seven transmembrane receptor protein of a human that is affected with a mental disorder; wherein said polynucleotide hybridizes to the complement of nGPCR-x under the following hybridization conditions: (a) hybridization for 16 hours at 42C in a hybridization solution comprising 50% formamide, 1% SDS, 1 M NaCI, 10% dexfran sulfate and (b) washing 2 times for 30 minutes at 60C in a wash solution comprising O.lx SSC and 1% SDS; and wherein the polynucleotide encodes a nGPCR- x amino acid sequence that differs by at least one residue.
  • An exemplary assay for using the allelic variants is a method for identifying a modulator of nGPCR-x biological activity, comprising the steps of: (a) contacting a cell expressing the allelic variant in the presence and in the absence of a putative modulator compound; (b) measuring nGPCR-x biological activity in the cell; and (c) identifying a putative modulator compound in view of decreased or increased nGPCR-x biological activity in the presence versus absence of the putative modulator.
  • Example 1 is actual, while the remaining Examples are prophetic. Additional features and variations of the invention will be apparent to those skilled in the art from the entirety of this application, including the detailed description, and all such features are intended as aspects of the invention. Likewise, features of the invention described herein can be re-combined into additional embodiments that also are intended as aspects of the invention, irrespective of whether the combination of features is specifically mentioned above as an aspect or embodiment of the invention. Also, only such limitations which are described herein as critical to the invention should be viewed as such; variations of the invention lacking limitations which have not been described herein as critical are intended as aspects of the invention. EXAMPLES Example 1 : Identification of nGPCR-x A. Database search
  • the Celera database was searched using known GPCR receptors as query sequences to find patterns suggestive of novel G protein-coupled receptors. Positive hits were further analyzed with the GCG program BLAST to determine which ones were the most likely candidates to encode G protein-coupled receptors, using the standard (default) alignment produced by BLAST as a guide.
  • BLAST algorithm which stands for Basic Local Alignment Search Tool is suitable for determining sequence similarity (Altschul et al, J. Mol. Biol., 1990, 215, 403-410, which is inco ⁇ orated herein by reference in its entirety).
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information through the world wide web of the Internet (ncbi.nlm.nih.gov/).
  • This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence.
  • HSPs high scoring sequence pair
  • T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighbourhood word hits act as seeds for initiating searches to find HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extension for the word hits in each direction are halted when: 1) the cumulative alignment score falls off by the quantity X from its maximum achieved value; 2) the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or 3) the end of either sequence is reached.
  • the Blast algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • the BLAST algorithm Kerlin et al, Proc. Natl. Acad. Sci. USA, 1993, 90, 5873-5787, which is inco ⁇ orated herein by reference in its entirety
  • Gapped BLAST perform a statistical analysis of the similarity between two sequences.
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • a nucleic acid is considered similar to a GPCR gene or cDNA if the smallest sum probability in comparison of the test nucleic acid to a GPCR nucleic acid is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • Homology searches are performed with the program BLAST version 2.08.
  • a collection of about 200 to about 350 query amino acid sequences derived from GPCRs was used to search the genomic DNA sequence using TBLASTN and alignments with an E- value lower than 0.01 were collected from each BLAST search.
  • the amino acid sequences have been edited to remove regions in the sequence that produce non-significant alignments with proteins that are not related to GPCRs.
  • Multiple query sequences may have a significant alignment to the same genomic region, although each alignment may not cover exactly the same DNA region.
  • a procedure is used to determine the region of maximum common overlap between the alignments from several query sequences. This region is called the consensus DNA region.
  • the procedure for determining this consensus involves the automatic parsing of the BLAST output files using the program MSPcrunch to produce a tabular report. From this tabular report the start and end of each alignment in the genomic DNA is extracted. This information is used by a PERL script to derive the maximum common overlap. These regions are reported in the form of a unique sequence identifier, a start and the end position in the sequence. The sequences defined by these regions were extracted from the original genomic sequence file using the program fetchdb.
  • the consensus regions are assembled into a non-redundant set by using the program phrap. After assembly with phrap a set of contigs and singletons were defined as candidate DNA regions coding for nGPCRs. These sequences were then submitted for further sequence analysis. Further sequence analysis involves the removal of sequences previously isolated and removal of sequences that are related to olfactory GPCRs. The transmembrane regions for the sequences that remained were determined using a FORTRAN computer program called "tmtrest.aH" (Parodi etal, Comput.Appl.Biosci. 5:527-535(1994)). Only sequences that contained transmembrane regions in a pattern found in GPCRs were retained.
  • nGPRCR-x cDNAs were sequenced directly using an ABI377 fluorescence-based sequencer (Perkin-Elmer/Applied Biosystems Division, PE/ABD, Foster City, CA) and the ABI PRISMTM Ready Dye-Deoxy Terminator kit with Taq FSTM polymerase.
  • Each ABI cycle sequencing reaction contained about 0.5 ⁇ g of plasmid DNA. Cycle-sequencing was performed using an initial denaturation at 98C for 1 minute, followed by 50 cycles using the following parameters: 98C for 30 seconds, annealing at 50C for 30 seconds, and extension at 60C for 4 minutes. Temperature cycles and times were controlled by a Perkin-Elmer 9600 thermocycler.
  • Extension products were purified using CentriflexTM gel filtration cartridges (Advanced Genetic Technologies Co ⁇ ., Gaithersburg, MD). Each reaction product was loaded by pipette onto the column, which is then centrifuged in a swinging bucket centrifuge (Sorvall model RT6000B tabletop centrifuge) at 1500 x g for 4 minutes at room temperature. Column-purified samples were dried under vacuum for about 40 minutes and then dissolved in 5 ⁇ l of a DNA loading solution (83% deionized formamide, 8.3 mM EDTA, and 1.6 mg/ml Blue Dexfran). The samples were then heated to 90C for three minutes and loaded into the gel sample wells for sequence analysis using the ABI377 sequencer.
  • a DNA loading solution 83% deionized formamide, 8.3 mM EDTA, and 1.6 mg/ml Blue Dexfran.
  • Sequence analysis was performed by importing ABI377 files into the Sequencer program (Gene Codes, Ann Arbor, MI). Generally, sequence reads of 700 bp were obtained. Potential sequencing errors were minimized by obtaining sequence information from both DNA strands and by re-sequencing difficult areas using primers annealing at different locations until all sequencing ambiguities were removed.
  • Table 5 contains the sequences of the polynucleotides and polypeptides of the invention. Start and stop codons within the polynucleotide sequence are identified by boldface type. The fransmembrane domains within the polypeptide sequence are identified by underlining.
  • amino acid sequence ⁇ SEQ ID NO. 68> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 1:
  • amino acid sequence ⁇ SEQ ID NO. 69> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 2:
  • the following amino acid sequence ⁇ SEQ ID NO. 70> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 3:
  • amino acid sequence ⁇ SEQ ID NO. 71> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 4:
  • the following amino acid sequence ⁇ SEQ ID NO. 72> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 5: QGSCLCTLAWTTE*DPSLNT*K*KKRV ⁇ GN ⁇
  • amino acid sequence ⁇ SEQ ID NO. 73> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 6:
  • the following amino acid sequence ⁇ SEQ ID NO. 74> is a predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 7:
  • amino acid sequence ⁇ SEQ ID NO. 76> is a predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 9:
  • amino acid sequence ⁇ SEQ ID NO. 77> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 10:
  • the following amino acid sequence ⁇ SEQ ID NO. 78> is a predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 11 :
  • amino acid sequence ⁇ SEQ ID NO. 135> is another predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 11 :
  • amino acid sequence ⁇ SEQ ID NO. 79> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 12:
  • amino acid sequence ⁇ SEQ ID NO. 80> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 13:
  • amino acid sequence ⁇ SEQ ID NO. 81> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 14:
  • the following amino acid sequence ⁇ SEQ ID NO. 82> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 15: TCAMLV ⁇ GDVPENQLKWTWVRALINDSLFILCAISLVCYICKITKMSSANVYLESKGMSLCO ⁇ VNGSVVILLYSSRACYNLvNVTISQDTLESPFNYGWDNLSDKAHVEDISGEEYIVFGMvXFLWEH VPAWSVVLFFRAQRLNQNLAPAGMINSHSYSSRAYFFDNPRRYDSDDDLPRLGSSREGSLPNSQSL GV ⁇ GTMTGCGSSSYTVTPHLNGPMTDTAPLLFTCSNLDLNNHHSLYVTPQN
  • amino acid sequence ⁇ SEQ ID NO. 83> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 16:
  • amino acid sequence ⁇ SEQ ID NO. 84> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 17:
  • amino acid sequence ⁇ SEQ ID NO. 85> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 18:
  • amino acid sequence ⁇ SEQ ID NO. 86> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 19:
  • amino acid sequence ⁇ SEQ ID NO. 88> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 21:
  • amino acid sequence ⁇ SEQ ID NO. 89> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 22:
  • the following amino acid sequence ⁇ SEQ ID NO. 90> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 23 :
  • amino acid sequence ⁇ SEQ ID NO. 91> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 24:
  • amino acid sequence ⁇ SEQ ID NO. 92> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 25:
  • amino acid sequence ⁇ SEQ ID NO. 93> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 26:
  • amino acid sequence ⁇ SEQ ID NO. 94> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 27:
  • the following amino acid sequence ⁇ SEQ ID NO. 95> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 28:
  • amino acid sequence ⁇ SEQ ID NO. 96> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 29:
  • amino acid sequence ⁇ SEQ ID NO. 97> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 30:
  • amino acid sequence ⁇ SEQ ID NO. 98> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 31 :
  • amino acid sequence ⁇ SEQ ID NO. 99> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 32:
  • the following amino acid sequence ⁇ SEQ ID NO. 100> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 33:
  • amino acid sequence ⁇ SEQ ID NO. 101> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 34:
  • the following amino acid sequence ⁇ SEQ ID NO. 102> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 35: YLFCLTCLMTFAALVGSrYSLISLLKMQNRTVNSMLVASWSVT>DLMSVLSVTffMF QWPNEVP GYFQFLCTTSALlVr ⁇ CQGLSSNLKATLLVSYNFYTMFiRGVGSQTASRRSGQvXGv ⁇ TVWAASL LLSALPLCG GAFVRTPWGCLVTJCSSSYVLFLSlV ⁇ ALAFGLLVGLSWLTHRLLCSEEPPRLHSN YQEISRGASEPGTPPTAGRWSLSPEDAPGPSLRRSG
  • the following amino acid sequence ⁇ SEQ TD NO. 104> is die predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 37:
  • amino acid sequence ⁇ SEQ ID NO. 105> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 38:
  • amino acid sequence ⁇ SEQ ID NO. 106> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 39:
  • amino acid sequence ⁇ SEQ ID NO. 107> is the predicted amino acid sequence derived from the DNA sequence of SEQ ID NO. 40:
  • amino acid sequence ⁇ SEQ D NO. 108> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 41:
  • amino acid sequence ⁇ SEQ ED NO. 109> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 42:
  • the following amino acid sequence ⁇ SEQ ED NO. 110> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 43:
  • amino acid sequence ⁇ SEQ ED NO. 111> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 44:
  • amino acid sequence ⁇ SEQ ED NO. 112> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 45:
  • amino acid sequence ⁇ SEQ ED NO. 113> is the predicted amino acid sequence derived from the DNA sequence of SEQ ED NO. 46:

Abstract

L'invention concerne un gène codant pour un récepteur couplé à la protéine G, ce récepteur s'appelant nGPCR-x; des constructions et des cellules hôtes de recombinaison incorporant ledit gène; les polypeptides nGPCR-x codés par ledit gène; des anticorps contre les polypeptides nGPCR-x; et des méthodes de préparation et d'utilisation de tous les éléments précités.
PCT/US2001/014050 2000-05-03 2001-05-01 Nouveaux recepteurs couples a la proteine g WO2001083553A2 (fr)

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WO2001072295A2 (fr) * 2000-03-29 2001-10-04 Corixa Corporation Compositions et methodes pouvant traiter ou diagnostiquer le cancer du poumon
WO2002000701A2 (fr) * 2000-06-26 2002-01-03 Bayer Aktiengesellschaft Regulation du recepteur humain couple a la proteine g semblable au recepteur de l'hormone liberant la gonadotropine
US6759508B2 (en) 2000-09-01 2004-07-06 Corixa Corporation Compositions and methods for the therapy and diagnosis of lung cancer
EP1506306A2 (fr) * 2002-01-04 2005-02-16 Metabolex, Inc. Acides nucleiques codant une proteine g couplee a un recepteur implique dans un signalement de cellules d'ilots pancreatiques
WO2005024057A1 (fr) * 2003-09-10 2005-03-17 Galapagos Genomics N.V. Procede pour identifier un compose qui modifie le traitement d'une proteine precurseur de la beta-amyloide dans une cellule

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WO1999037679A1 (fr) * 1998-01-26 1999-07-29 Millennium Pharmaceuticals, Inc. Recepteurs de ligands et leurs utilisations
WO2001027158A2 (fr) * 1999-10-08 2001-04-19 Digiscents Sequences de recepteurs olfactifs
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Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001072295A2 (fr) * 2000-03-29 2001-10-04 Corixa Corporation Compositions et methodes pouvant traiter ou diagnostiquer le cancer du poumon
WO2001072295A3 (fr) * 2000-03-29 2002-08-22 Corixa Corp Compositions et methodes pouvant traiter ou diagnostiquer le cancer du poumon
WO2002000701A2 (fr) * 2000-06-26 2002-01-03 Bayer Aktiengesellschaft Regulation du recepteur humain couple a la proteine g semblable au recepteur de l'hormone liberant la gonadotropine
WO2002000701A3 (fr) * 2000-06-26 2002-06-13 Bayer Ag Regulation du recepteur humain couple a la proteine g semblable au recepteur de l'hormone liberant la gonadotropine
US6759508B2 (en) 2000-09-01 2004-07-06 Corixa Corporation Compositions and methods for the therapy and diagnosis of lung cancer
EP1506306A2 (fr) * 2002-01-04 2005-02-16 Metabolex, Inc. Acides nucleiques codant une proteine g couplee a un recepteur implique dans un signalement de cellules d'ilots pancreatiques
EP1506306A4 (fr) * 2002-01-04 2006-02-15 Metabolex Inc Acides nucleiques codant une proteine g couplee a un recepteur implique dans un signalement de cellules d'ilots pancreatiques
WO2005024057A1 (fr) * 2003-09-10 2005-03-17 Galapagos Genomics N.V. Procede pour identifier un compose qui modifie le traitement d'une proteine precurseur de la beta-amyloide dans une cellule

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