WO2001014414A2 - Human abc2 transporter and uses thereof - Google Patents

Human abc2 transporter and uses thereof Download PDF

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Publication number
WO2001014414A2
WO2001014414A2 PCT/CA2000/000962 CA0000962W WO0114414A2 WO 2001014414 A2 WO2001014414 A2 WO 2001014414A2 CA 0000962 W CA0000962 W CA 0000962W WO 0114414 A2 WO0114414 A2 WO 0114414A2
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abc2 transporter
nucleic acid
polypeptide
abc2
protein
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PCT/CA2000/000962
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French (fr)
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WO2001014414A3 (en
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Stephane Le Bihan
Catriona Wilson
David L. Charest
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Activepass Pharmaceuticals, Inc.
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Priority to CA002383063A priority Critical patent/CA2383063A1/en
Priority to JP2001518743A priority patent/JP2003509017A/en
Priority to EP00954219A priority patent/EP1210422A2/en
Priority to AU66771/00A priority patent/AU6677100A/en
Publication of WO2001014414A2 publication Critical patent/WO2001014414A2/en
Publication of WO2001014414A3 publication Critical patent/WO2001014414A3/en

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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
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/14—Drugs for disorders of the nervous system for treating abnormal movements, e.g. chorea, dyskinesia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/14—Drugs for disorders of the nervous system for treating abnormal movements, e.g. chorea, dyskinesia
    • A61P25/16—Anti-Parkinson drugs
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/22—Anxiolytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/24—Antidepressants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P3/00—Drugs for disorders of the metabolism
    • A61P3/06—Antihyperlipidemics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2217/00—Genetically modified animals
    • A01K2217/07—Animals genetically altered by homologous recombination
    • A01K2217/075—Animals genetically altered by homologous recombination inducing loss of function, i.e. knock out
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides

Definitions

  • ABC transporter proteins represent a large superfamily of proteins with conserved features in both prokaryotes and eukaryotes. ABC transporters catalyze ATP-dependent transport of endogenous or exogenous substrates across biological membranes (Borst, P., (1997) Seminar in Cancer Biology 8:131-213) and/or allosterically modify the function of heterologous proteins (Higgins CF, 1995, Cell 82:693-696). Several ABC transporters have been associated with clinically relevant phenotypes including the phenomenon of multidrug resistance (Ambudkar S.V. et al., (1999), Annu. Rev.
  • the present invention is based, at least in part, on the discovery of a novel ATP Binding Cassette (ABC) transporter family member, referred to herein as ABC2 transporter nucleic acid and protein molecules
  • ABC2 transporter nucleic acid and protein molecules The ABC2 transporter molecules of the present invention are useful as targets for developing modulating agents to regulate a variety of cellular processes, particularly the transport of neurotoxic molecules, e.g., ⁇ -amyloid peptide, across cell membranes or, e.g., the blood-brain barrier (BBB).
  • Neurotoxic molecules such as ⁇ -amyloid peptide are involved in neurological disorders such as Alzheimer's disease (see, e.g., Goate et al. (1991) Nature 349:704; Games et al.
  • ABC2 transporter would be expected to modulate amyloid deposition and thus, Alzheimer's disease.
  • the ABC2 transporter molecules of the invention are useful as targets for developing modulating agents of multidrug resistance.
  • the molecules of the presen invention are useful as diagnostic and therapeutic tools.
  • this invention provides isolated nucleic acid molecules encoding ABC2 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection of ABC2-encoding nucleic acids.
  • an ABC2 transporter nucleic acid molecule of the invention is at least 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more identical to the nucleotide sequence (e.g., to the entire length of the nucleotide sequence) shown in SEQ ID NO: 1 or 3, or a complement thereof.
  • the isolated nucleic acid molecule includes the nucleotide sequence shown in SEQ ID NO: 1 or 3, or a complement thereof. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 1-90 of SEQ ID NO: 1. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 6097- 6792 of SEQ ID NO: 1.
  • an ABC2 transporter nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ID NO: 2.
  • an ABC2 transporter nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence at least 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to the entire length of the amino acid sequence of SEQ ID NO: 2.
  • an isolated nucleic acid molecule encodes the amino acid sequence of human ABC2 transporter having the amino acid sequence of SEQ ID NO: 2.
  • the nucleic acid molecule is at least 6006 nucleotides in length.
  • the nucleic acid molecule is at least 6792 nucleotides in length and encodes a protein having ABC2 transporter activity (as described herein).
  • Another embodiment of the invention features nucleic acid molecules, preferably ABC2 transporter nucleic acid molecules, which specifically detect ABC2 transporter nucleic acid molecules relative to nucleic acid molecules encoding non-ABC2 transporter proteins.
  • such a nucleic acid molecule is at least 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 500-1000, 1000-1500, 1500-2000, or 2000-2500 or more nucleotides in length and/or hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NO: 1, or a complement thereof.
  • the nucleic acid molecule can be of a length within a range having one of the numbers listed above as a lower limit and another number as the upper limit for the number of nucleotides in length, e.g., molecules that are 60-80, 300-1000, or 150-400 nucleotides in length.
  • the nucleic acid molecules are at least 15 (e.g., contiguous) nucleotides in length and hybridize under stringent conditions to nucleotides 91-6096 of SEQ
  • nucleic acid molecules comprise nucleotides
  • the nucleic acid molecule encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ED NO: 2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NO: 2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID NO: 2,
  • Another embodiment of the invention provides an isolated nucleic acid molecule which is antisense to an ABC2 transporter nucleic acid molecule, e.g., the coding strand of an ABC2 transporter nucleic acid molecule.
  • Another aspect of the invention provides a vector comprising an ABC2 transporter nucleic acid molecule.
  • the vector is a recombinant expression vector.
  • the invention provides a host cell containing a vector of the invention.
  • the invention provides a host cell containing a nucleic acid molecule of the invention.
  • the invention also provides a method for producing a protein, preferably an ABC2 transporter protein, by culturing in a suitable medium, a host cell, e.g., a mammalian host cell such as a non-human mammalian cell, of the invention containing a recombinant expression vector, such that the protein is produced.
  • the protein preferably an ABC2 transporter protein, includes at least one transmembrane domain and has an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,
  • the protein preferably an ABC2 transporter protein, includes at least one transmembrane domain and is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1.
  • the invention features fragments of the protein having the amino acid sequence of SEQ ID NO: 2, wherein the fragment comprises at least 15 amino acids
  • the protein preferably an ABC2 transporter protein
  • the invention features an isolated protein, preferably an ABC2 transporter protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to a nucleotide sequence of SEQ ID NO: 1 or 3, or a complement thereof.
  • This invention further features an isolated protein, preferably an ABC2 transporter protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1 or 3, or a complement thereof.
  • the proteins of the present invention or portions thereof, e.g., biologically active portions thereof, can be operatively linked to a non-ABC2 transporter polypeptide (e.g., heterologous amino acid sequences) to form fusion proteins.
  • the invention further features antibodies, such as monoclonal or polyclonal antibodies, that specifically bind proteins of the invention, preferably ABC2 transporter proteins.
  • the ABC2 transporter proteins, biologically active portions thereof, or expressible nucleic acids encoding the foregoing can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
  • the present invention provides a method for detecting the presence of an ABC2 transporter nucleic acid molecule, protein or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting an ABC2 transporter nucleic acid molecule, protein or polypeptide such that the presence of an ABC2 transporter nucleic acid molecule, protein or polypeptide is detected in the biological sample.
  • the present invention provides a method for detecting the presence of ABC2 transporter activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of ABC2 transporter activity such that the presence of ABC2 transporter activity is detected in the biological sample.
  • the invention provides a method for modulating ABC2 transporter activity comprising contacting a cell capable of expressing an ABC2 transporter with an agent that modulates ABC2 transporter activity such that ABC2 transporter activity in the cell is modulated.
  • the agent inhibits ABC2 transporter activity.
  • the agent modulates the ability of the ABC2 transporter to allosterically modify the function of other membrane proteins.
  • the agent stimulates ABC2 transporter activity.
  • the agent is an antibody that specifically binds to an ABC2 transporter protein.
  • the agent modulates expression of ABC2 transporter by modulating transcription of an ABC2 transporter gene or translation of an ABC2 transporter mRNA.
  • the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of an ABC2 transporter mRNA or an ABC2 transporter gene.
  • the methods of the present invention are used to treat a subject having a disorder characterized by aberrant or unwanted ABC2 transporter protein or nucleic acid expression or activity by administering an agent which is an ABC2 transporter modulator to the subject.
  • the ABC2 transporter modulator is an AB2C transporter protein.
  • the ABC2 transporter modulator is an ABC2 transporter nucleic acid molecule.
  • the ABC2 transporter modulator is a polypeptide antibody (or fragment thereof), peptide, peptidomimetic, or other small molecule, e.g. a molecule that is carbohydrate-based, lipid-based, nucleic acid-based, natural organic- based, or synthetically derived organic-based.
  • the present invention also provides a diagnostic assay for identifying the presence or absence of a genetic alteration characterized by at least one of (i) aberrant modification or mutation of a gene encoding an ABC2 transporter protein; (ii) mis-regulation of the gene; and (iii) aberrant post-translational modification of an ABC2 transporter protein, wherein a wild- type form of the gene encodes a protein with an ABC2 transporter activity.
  • the invention provides a method for identifying a compound that binds to or modulates the activity of an ABC2 transporter protein, by providing an indicator composition comprising an ABC2 transporter protein having ABC2 transporter activity, contacting the indicator composition with a test compound, and determining the effect of the test compound on ABC2 transporter activity in the indicator composition to identify a compound that modulates the activity of an ABC2 transporter protein, e.g., an ABC2 transporter protein associated with a membrane.
  • Figure 1 depicts the cDNA sequence and predicted amino acid sequence of a human ABC2 transporter.
  • the nucleotide sequence corresponds to nucleic acids 1 to 6792 of SEQ ED NO: 1.
  • the coding region without the 5' and 3' untranslated regions of the human ABC2 transporter gene is shown in SEQ ED NO: 3.
  • Figure 2 depicts the amino acid sequence of the ABC transporter molecule corresponding to amino acids 1 to 2001 of SEQ ED NO: 2.
  • Figure 3 depicts an amino acid sequence alignment of the human ABC2 transporter polypeptide compared with polypeptides found in various species.
  • the symbols (:) and (*) represent, respectively, amino acid residue positions having similarity or identity.
  • Figure 4 depicts hydrophobicity, hydrophilicity, and transmembrane plots for the human ABC2 transporter polypeptide.
  • Figure 5 depicts a transmembrane helix prediction plot for the human ABC2 transporter polypeptide.
  • Figure 6 depicts a schematic showing the map positions of various cDNA fragments and primer locations with respect to the full length ABC2 transporter clone (hsA2.2).
  • the present invention is based, at least in part, on the discovery of a novel ATP Binding
  • ABC transporter family member referred to herein as ABC2 transporter nucleic acid and protein molecules.
  • ABC transporter molecules are transmembrane proteins which catalyze ATP-dependent transport of endogenous or exogenous substrates across biological membranes.
  • ABC transporters have been associated with the transport of polypeptides, e.g., a neurotoxic polypeptide, such as ⁇ -amyloid, which is involved in Alzheimer's disease. Other neurological diseases caused by neurotoxic polypeptides include prion diseases, Parkinson's disease, Huntington's disease, etc. (for a review, see Hardy et al. (1998) Science 282: 1075-1079).
  • ABC transporters are associated with the transport of substrates across the blood- brain-barrier.
  • ABC transporters are associated with multidrug resistance found in cells especially, e.g., cells that are refractory to cytotoxic anti-cancer drugs (Borst, P. (1997) Sem. Cancer Bio. 8:131-134).
  • the ABC2 transporter molecules of the invention are suitable targets for developing novel diagnostic targets and therapeutic agents to control cellular transport in cells of the brain (e.g., neuronal cells) and transport across the blood-brain-barrier.
  • the ABC2 transporter molecules are suitable targets for developing diagnostic targets and therapeutic agents for detecting and/or treating cells or tissues having multidrug resistance, e.g., a cancer.
  • novel human ABC2 transporter molecules described herein are believed to have one or more of the following functions and/or applications: -ABC transporters expressed in the brain are implicated in the transport of substrates through the blood brain barrier (Schinkel A.H., et al, (1994) Cell, 77, 491) and therefore identification of the sequence of the human ABC2 transporter described herein affords the development of new strategies for altering the function of the blood brain barrier. Given that many drugs of potential utility in treating diseases of the brain are discarded because they do not enter the brain at therapeutically relevant concentrations, the present invention allows for the development of strategies to assist in the delivery of drugs to the brain.
  • -ABC transporters expressed in the brain are potential transporters for the ⁇ -amyloid peptide, a peptide whose deposition in senile plaques is a fundamental feature of Alzheimer's disease.
  • identifying novel transporters that regulate ⁇ -amyloid deposition is crucial in developing therapeutic treatment for Alzheimer's disease.
  • the human homologue of the Drosophila melanogaster white gene has been reported to be associated with mood and panic disorders (Nakamura M et al, (1999), Mol.
  • Psychiatry, 4, 155-162 is a member of the superfamily of ABC transporters.
  • the human ABC2 transporter of the invention is also expressed in the brain, and, accordingly, may be involved in mood and panic disorders. Identification of the sequence of human ABC transporter described herein allows for the development of new treatments for mood and panic disorders.
  • the human ABC1 protein has been shown to be associated with cholesterol efflux and mutated forms cause Tangier disease and familial high-density lipoprotein deficiency (Brooks- Wilson A. et al, Bodzioch M. et al. Rust S. et al, Nature Genetics, 22, 336-345, 347-351, 352- 355 respectively).
  • human ABC2 is likely to be a cholesterol transporter. Identification of the sequence of human ABC2 allows for the development of new treatments for diseases involving cholesterol misregulation.
  • the mouse Abel protein has been implicated in interleukin-l ⁇ (EL-l ⁇ ) secretion from macrophages (Hamon Y.
  • IL-l ⁇ is a mediator of inflammatory reactions, and agents able to impair its production or secretion are of potential therapeutic importance.
  • identification of the related sequence of human ABC2 allows for the development of new treatments for inflammatory diseases.
  • family when referring to the protein and nucleic acid molecules of the invention is intended to mean two or more proteins or nucleic acid molecules having a common structural domain or motif and having sufficient amino acid or nucleotide sequence homology as defined herein.
  • family members can be naturally or non-naturally occurring and can be from either the same or different species.
  • a family can contain a first protein of human origin, as well as other, distinct proteins of human origin or alternatively, can contain homologues of non-human origin.
  • Members of a family may also have common functional characteristics.
  • the family of. ABC transporter proteins comprise at least one "transmembrane domain” and preferably two transmembrane domains.
  • transmembrane domain includes an amino acid sequence of about 18 amino acid residues in length which spans the plasma membrane. More preferably, a transmembrane domain includes about at least 18, 20, 25, 30, 35, 40, or 45 residues or more and spans the plasma membrane. Transmembrane domains are described in, for example, Zaelles W.N. et a (1996) Annual Rev. Neuronsci. 19: 235-63, the contents of which are incorporated herein by reference.
  • the amino acid sequences of the human ABC2 transporter protein that comprise transmembrane domains are indicated in Fig. 2. One or more of these transmembrane domains may associate to form a membrane-spanning domain.
  • Isolated proteins of the present invention preferably ABC2 transporter proteins, have an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ED NO: 2 or are encoded by a nucleotide sequence sufficiently homologous to SEQ ED NO: 1 or 3.
  • the term "sufficiently homologous” refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences share common structural domains or motifs and/or a common functional activity.
  • amino acid or nucleotide sequences which share common structural domains have at least 60% homology, more preferably 70%-80%, and even more preferably 90-95% homology across the amino acid sequences of the domains and contain at least one and preferably two structural domains or motifs, are defined herein as sufficiently homologous.
  • amino acid or nucleotide sequences which share at least 60%, more preferably 70-80%, or 90-95% homology and share a common functional activity are defined herein as sufficiently homologous.
  • ABC2 transporter activity refers to an activity exerted by an ABC2 transporter protein, polypeptide or nucleic acid molecule on an ABC2 transporter responsive cell or on an ABC2 transporter protein substrate, as determined in vivo, or in vitro, according to standard techniques.
  • an ABC2 transporter activity has the ability to act as an energy-dependent (ATP) molecular pump.
  • an ABC2 activity is a direct activity, such as an association with a membrane associated protein and/or the transport of an endogenous or exogenous substrate across a biological membrane.
  • the ABC2 activity is the ability of the polypeptide to allosterically modify the function of other membrane proteins.
  • modulation of p- glycoprotein by an ABC transporter modulator has been shown to alter the magnitude of volume-activated chloride currents (reviewed in Higgins, C. F. Volume-activated chloride currents associated with the multidrug resistance P-glycoprotein, J. Physiol. 482:31S-36S (1995)).
  • p-glycoprotein and other ABC transporters have multiple functions, one of which is to allosterically modify the function of the other membrane proteins.
  • the present invention is consistent with a model in which the allosteric modification of other membrane proteins by e.g., an ABC2 transporter, is responsible for a change in the transport of a substrate, e.g., ⁇ -amyloid, a cytotoxic drug, or other small molecule.
  • a substrate e.g., ⁇ -amyloid, a cytotoxic drug, or other small molecule.
  • an ABC2 activity is at least one or more of the following activities: (i) activation of an ABC2-dependent signal transduction pathway; (ii) modulation of the transport of a substrate (e.g., a cytotoxic drug, ⁇ -amyloid) across a membrane; (iii) interaction of an ABC2 protein with a non-ABC2 membrane-associated molecule; (iv) modulation of the development or differentiation of an ABC2-expressing cell; (v) modulation of the development or differentiation of a non-ABC2- expressing cell; (vi) modulation of the homeostasis of an ABC2-expressing cell; and (vii) modulation of the homeostasis of a non-ABC2-expressing cell.
  • a substrate e.g., a cytotoxic drug, ⁇ -amyloid
  • another embodiment of the invention features isolated ABC2 transporter proteins and polypeptides having an ABC2 transporter activity.
  • Preferred proteins are ABC2 transporter proteins having at least one transmembrane domain, preferably two transmembrane domains, and, preferably, ABC2 transporter activity.
  • the nucleotide sequence of the isolated human ABC2 transporter protein cDNA and the predicted amino acid sequence of the human ABC2 transporter polypeptide are shown in Fig. 5 and in SEQ ID NOs: 1 and 2, respectively.
  • the human ABC2 transporter gene which is approximately 6792 nucleotides in length, encodes a protein having a molecular weight of approximately 223 kDa and which is approximately 2001 amino acid residues in length.
  • nucleic acid molecules that encode ABC2 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes to identify ABC2-encoding nucleic acid molecules (e.g., ABC2 transporter mRNA) and fragments for use as PCR primers for the amplification or mutation of ABC2 transporter nucleic acid molecules.
  • nucleic acid molecule is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs.
  • the nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
  • isolated nucleic acid molecule includes nucleic acid molecules which are separated from other nucleic acid molecules which are present in the natural source of the nucleic acid.
  • isolated includes nucleic acid molecules which are separated from the chromosome with which the genomic DNA is naturally associated.
  • an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived.
  • the isolated ABC2 transporter nucleic acid molecule can contain less than about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived.
  • an "isolated" nucleic acid molecule such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized.
  • a nucleic acid molecule of the present invention e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ED NO: 1 or 3, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or portion of the nucleic acid sequence of SEQ D NO: 1 or 3 as a hybridization probe, ABC2 transporter nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989).
  • nucleic acid molecule encompassing all or a portion of SEQ ED NO: 1 or 3 can be isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence of SEQ ED NO: 1 or 3.
  • PCR polymerase chain reaction
  • a nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques.
  • the nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
  • oligonucleotides corresponding to ABC2 transporter nucleotide sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer.
  • an isolated nucleic acid molecule of the invention comprises the nucleotide sequence shown in SEQ ID NO: 1.
  • the sequence of SEQ ID NO: 1 corresponds to the human ABC2 cDNA.
  • This cDNA comprises sequences encoding the human ABC2 protein (i.e., "the coding region", from nucleotides 91-6096), as well as 5' untranslated sequences (nucleotides 1-90) and 3' untranslated sequences (nucleotides 6097-6792).
  • the nucleic acid molecule can comprise only the coding region of SEQ ED NO: 1 (e.g., nucleotides 91-6096, corresponding to SEQ ED NO: 3).
  • an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of the nucleotide sequence shown in SEQ ID NO: 1 or 3, or a portion of any of these nucleotide sequences.
  • a nucleic acid molecule which is complementary to the nucleotide sequence shown in SEQ ID NO: 1 or 3 is one which is sufficiently complementary to the nucleotide sequence shown in SEQ ID NO: 1 or 3 such that it can hybridize to the nucleotide sequence shown in SEQ ED NO: 1 or 3, thereby forming a stable duplex.
  • an isolated nucleic acid molecule of the present invention comprises a nucleotide sequence which is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to the entire length of the nucleotide sequence shown in SEQ ED NO: 1 or 3, or a portion of any of these nucleotide sequences.
  • the nucleic acid molecule of the invention can comprise only a portion of the nucleic acid sequence of SEQ ED NO: 1 or 3, for example, a fragment which can be used as a probe or primer or a fragment encoding a portion of an ABC2 transporter protein, e.g., a biologically active portion of an ABC2 transporter protein.
  • the nucleotide sequence determined from the cloning of the ABC2 transporter gene allows for the generation of probes and primers designed for use in identifying and/or cloning other ABC2 transporter family members, as well as ABC2 transporter homologues from other species.
  • the probe/primer typically comprises substantially purified oligonucleotide.
  • the oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12 or 15, preferably about 20 or 25, more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 consecutive nucleotides of a sense sequence of SEQ ED NO: 1 or 3 of an anti-sense sequence of SEQ ID NO: 1 or 3, or of a naturally occurring allelic variant or mutant of SEQ ED NO: 1 or 3.
  • a nucleic acid molecule of the present invention comprises a nucleotide sequence which is greater than 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500-1000, 1000-1500, 1500-2000, or 2000-2500 or more nucleotides in length and hybridizes under stringent hybridization conditions to a nucleic acid molecule of SEQ ED NO: l or 3.
  • Probes based on the ABC2 transporter nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins.
  • the probe further comprises a label group attached thereto, e.g., the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Such probes can be used as a part of a diagnostic test kit for identifying cells or tissue which misexpress an ABC2 transporter protein, such as by measuring a level of an ABC2-encoding nucleic acid in a sample of cells from a subject e.g., detecting ABC2 transporter mRNA levels or determining whether a genomic ABC2 transporter gene has been mutated or deleted.
  • a nucleic acid fragment encoding a "biologically active portion of an ABC2 transporter protein” can be prepared by isolating a portion of the nucleotide sequence of SEQ ED NO: 1 or 3 which encodes a polypeptide having an ABC2 transporter biological activity (the biological activities of the ABC2 transporter proteins are described herein), expressing the encoded portion of the ABC2 transporter protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the ABC2 transporter protein.
  • the invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ED NO: 1 or 3 due to degeneracy of the genetic code and thus encode the same ABC2 transporter proteins as those encoded by the nucleotide sequence shown in SEQ ED NO: 1 or 3.
  • an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ED NO: 2.
  • DNA sequence polymorphisms that lead to changes in the amino acid sequences of the ABC2 transporter proteins may exist within a population (e.g., the human population). Such genetic polymorphism in the ABC2 transporter genes may exist among individuals within a population due to natural allelic variation.
  • the terms "gene” and “recombinant gene” refer to nucleic acid molecules which include an open reading frame encoding an ABC2 transporter protein, preferably a mammalian ABC2 transporter protein, and can further include non-coding regulatory sequences, and introns.
  • Allelic variants of a human ABC2 transporter include both functional and nonfunctional ABC2 transporter proteins.
  • Functional allelic variants are naturally occurring amino acid sequence variants of the human ABC2 transporter that maintain the ability to bind an ABC2 transporter ligand.
  • Functional allelic variants will typically contain only conservative substitution of one or more amino acids of SEQ ED NO: 2 or substitution, deletion or insertion of non-critical residues in non-critical regions of the protein.
  • Non-functional allelic variants are naturally occurring amino acid sequence variants of the human ABC2 transporter protein that do not have the ability to either bind an ABC2 transporter ligand. Non-functional allelic variants will typically contain a non-conservative substitution, a deletion, or insertion or premature truncation of the amino acid sequence of SEQ ID NO: 2 or a substitution, insertion or deletion in critical residues or critical regions.
  • the present invention further provides non-human orthologues of the human ABC2 transporter protein.
  • Orthologues of the human ABC2 transporter protein are proteins that are isolated from non-human organisms and possess the same ABC2 transporter activity as the human ABC2 transporter protein. Orthologues of the human ABC2 protein can readily be identified as comprising an amino acid sequence that is substantially homologous to SEQ ID NO: 2.
  • nucleic acid molecules encoding other ABC2 transporter family members and, thus, which have a nucleotide sequence which differs from the ABC2 transporter sequences of SEQ ED NO: 1 or 3 are intended to be within the scope of the invention.
  • another ABC2 transporter cDNA can be identified based on the nucleotide sequence of the human ABC2 transporter.
  • nucleic acid molecules encoding ABC2 transporter proteins from different species, e.g., mammals, and which, thus, have a nucleotide sequence which differs from the ABC2 transporter sequences of SEQ ED NO: 1 or 3 are intended to be within the scope of the invention.
  • a mouse ABC2 transporter cDNA can be identified based on the nucleotide sequence of the human ABC2 transporter.
  • Nucleic acid molecules corresponding to natural allelic variants and homologues of the ABC2 transporter cDNAs of the invention can be isolated based on their homology to the ABC2 transporter nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Nucleic acid molecules corresponding to natural allelic variants and homologues of the ABC2 transporter cDNAs of the invention can further be isolated by mapping to the same chromosome or locus as the ABC2 transporter gene.
  • an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ED NO: 1 or 3.
  • the nucleic acid is at least 30, 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2739 or more nucleotides in length.
  • hybridizes under stringent conditions is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 75% homologous to each other typically remain hybridized to each other.
  • the conditions are such that sequences at least about 80%, even more preferably at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% homologous to each other typically remain hybridized to each other.
  • stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6.
  • a preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50°C, preferably at 55°C, more preferably at 60°C, and even more preferably at 65°C.
  • SSC 6X sodium chloride/sodium citrate
  • 0.1% SDS 0.1% SDS at 50°C, preferably at 55°C, more preferably at 60°C, and even more preferably at 65°C.
  • an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ED NO: 1 or 3 corresponds to a naturally-occurring nucleic acid molecule.
  • a "naturally- occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
  • allelic variants of the ABC2 transporter sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ED NO: 1 or 3, thereby leading to changes in the amino acid sequence of the encoded ABC2 transporter proteins, without altering the functional ability of the ABC2 transporter proteins.
  • nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ID NO: 1 or 3.
  • non-essential amino acid residue is a residue that can be altered from the wild-type sequence of ABC2 transporter (e.g., the sequence of SEQ ID NO: 2) without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity.
  • nucleic acid molecules encoding ABC2 transporter proteins that contain changes in amino acid residues that are not essential for activity.
  • Such ABC2 transporter proteins differ in amino acid sequence from SEQ ED NO: 2, yet retain biological activity.
  • the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or more homologous to SEQ ED NO: 2.
  • An isolated nucleic acid molecule encoding an ABC2 transporter protein homologous to the protein of SEQ ED NO: 2 can be created by introducing one or more nucleotide substitutions, additions, or deletions into the nucleotide sequence of SEQ ED NO: 1 or 3, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ED NO: 1 or 3 by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g.
  • a predicted nonessential amino acid residue in an ABC2 transporter protein is preferably replaced with another amino acid residue from the same side chain family.
  • mutations can be introduced randomly along all or part of an ABC2 transporter coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for ABC2 transporter biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ED NO: 1 or 3 the encoded protein can be expressed recombinantly and the activity of the protein can be determined.
  • a mutant ABC2 transporter protein can be assayed for the ability to interact with a non-ABC2 transporter molecule, e.g., an ABC2 transporter ligand, e.g., a polypeptide or a small molecule.
  • a non-ABC2 transporter molecule e.g., an ABC2 transporter ligand, e.g., a polypeptide or a small molecule.
  • another aspect of the invention pertains to isolated nucleic acid molecules which are antisense thereto.
  • An "antisense" nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence.
  • an antisense nucleic acid can hydrogen bond to a sense nucleic acid.
  • the antisense nucleic acid can be complementary to an entire ABC2 transporter coding strand, or to only a portion thereof.
  • an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding ABC2.
  • the term "coding region” refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the coding region of human UMAT corresponds to SEQ ED NO: 3).
  • the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding ABC2.
  • noncoding region refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).
  • antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing.
  • the antisense nucleic acid molecule can be complementary to the entire coding region of ABC2 transporter mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of
  • the antisense oligonucleotide can be complementary to the region surrounding the translation start site of ABC2 transporter mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides or more in length.
  • An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used.
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5- iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5- methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-meth
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
  • the antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding an ABC2 transporter protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation.
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • An example of a route of administration of antisense nucleic acid molecules of the invention include direct injection at a tissue site.
  • antisense nucleic acid molecules can be modified to target selected cells and then administered systemically.
  • antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens.
  • the antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.
  • the antisense nucleic acid molecule of the invention is an ⁇ - anomeric nucleic acid molecule.
  • An cc-anomeric nucleic acid molecule forms specific double- stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641).
  • the antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • an antisense nucleic acid of the invention is a ribozyme.
  • Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region.
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)
  • a ribozyme having specificity for an ABC2-encoding nucleic acid can be designed based upon the nucleotide sequence of an ABC2 transporter cDNA disclosed herein (i.e., SEQ ED NO: 1).
  • SEQ ED NO: 1 a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an ABC2-encoding mRNA. See, e.g., Cech et al U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742.
  • ABC2 transporter mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261:1411-1418.
  • ABC2 transporter gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the ABC2 transporter (e.g., the ABC2 transporter promoter and/or enhancers) to form triple helical structures that prevent transcription of the ABC2 transporter gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the ABC2 transporter e.g., the ABC2 transporter promoter and/or enhancers
  • nucleotide sequences complementary to the regulatory region of the ABC2 transporter e.g., the ABC2 transporter promoter and/or enhancers
  • the ABC2 transporter nucleic acid molecules of the present invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule.
  • the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic & Medicinal Chemistry 4 (1): 5-23).
  • peptide nucleic acids refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained.
  • the neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength.
  • the synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra; Perry-OXeefe et al. Proc. Natl. Acad. Sci. 93: 14670-675.
  • PNAs of ABC2 transporter nucleic acid molecules can be used in therapeutic and diagnostic applications.
  • PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication.
  • PNAs of ABC2 transporter nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, (e.g., by PNA-directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, (e.g., SI nucleases (Hyrup B. (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al.
  • PNAs of ABC2 transporter nucleic acid molecules can be modified, (e.g., to enhance their stability or cellular uptake), by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art.
  • PNA-DNA chimeras of ABC2 transporter nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA.
  • DNA recognition enzymes e.g., RNAse H and DNA polymerases
  • PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup B. (1996) supra).
  • the synthesis of PNA- DNA chimeras can be performed as described in Hyrup B. (1996) supra and Finn P J. et al. (1996) Nucleic Acids Res. 24 (17): 3357-63.
  • a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used as a between the PNA and the 5' end of DNA (Mag, M. et al. (1989) Nucleic Acid Res. 17: 5973- 88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. (1996) supra).
  • chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser, K.H. et al. (1975) Bioorganic Med. Chem. Lett. 5: 1119-11124).
  • the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No.
  • peptides e.g., for targeting host cell receptors in vivo
  • agents facilitating transport across the cell membrane see, e.g., Letsinger et al. (1989) Proc. Natl Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No.
  • oligonucleotides can be modified with hybridization-triggered cleavage agents (See, e.g., Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating agents (See, e.g., Zon (1988) Pharm. Res. 5:539-549).
  • the oligonucleotide may be conjugated to another molecule, (e.g., a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent).
  • ABC2 Transporter Proteins and Anti-ABC2 Transporter Antibodies One aspect of the invention pertains to isolated ABC2 transporter proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti-ABC2 transporter antibodies.
  • native ABC2 transporter proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques.
  • ABC2 transporter proteins are produced by recombinant DNA techniques.
  • an ABC2 transporter protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.
  • an “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the ABC2 transporter protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular material” includes preparations of ABC2 transporter protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced.
  • the language "substantially free of cellular material” includes preparations of ABC2 transporter protein having less than about 30% (by dry weight) of non-ABC2 transporter protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-ABC2 transporter protein, still more preferably less than about 10% of non-ABC2 transporter protein, and most preferably less than about 5% non-ABC2 transporter protein.
  • non-ABC2 transporter protein also referred to herein as a "contaminating protein”
  • contaminating protein also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of ABC2 transporter protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein.
  • the language “substantially free of chemical precursors or other chemicals” includes preparations of ABC2 transporter protein having less than about 30% (by dry weight) of chemical precursors or non-ABC2 transporter chemicals, more preferably less than about 20% chemical precursors or non-ABC2 transporter chemicals, still more preferably less than about 10% chemical precursors or non-ABC2 transporter chemicals, and most preferably less than about 5% chemical precursors or non-ABC2 transporter chemicals.
  • a "biologically active portion" of an ABC2 transporter protein includes a fragment of an ABC2 transporter protein which participates in an interaction between an ABC2 transporter molecule and a non-ABC2 transporter molecule.
  • Biologically active portions of an ABC2 transporter protein include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequence of the ABC2 transporter protein, e.g., the amino acid sequence shown in SEQ ED NO: 2, which include less amino acids than the full length ABC2 transporter proteins, and exhibit at least one activity of an ABC2 transporter protein.
  • biologically active portions comprise a domain or motif with at least one activity of the ABC2 transporter protein.
  • a biologically active portion of an ABC2 transporter protein can be a polypeptide which is, for example, 10, 25, 50, 100, 200, 300, 400, 500, 600, 700, 800 or more amino acids in length.
  • Biologically active portions of an ABC2 transporter protein can be used as targets for developing agents which modulate an ABC2 transporter mediated activity.
  • a biologically active portion of an ABC2 transporter protein comprises at least one transmembrane domain. It is to be understood that a preferred biologically active portion of an ABC2 transporter protein of the present invention may contain at least one transmembrane domain. Another preferred biologically active portion of an ABC2 transporter protein may contain at least two transmembrane domains.
  • transmembrane domains may associate to form a membrane-spanning domain.
  • the biologically active portion of the ABC2 transporter protein may include multiple clusters of conserved residues that define an ATP binding domain.
  • the biologically active portion of the ABC2 transporter protein may comprise a Walker domain, e.g., a Walker A and/or Walker B domain (see Fig. 2.; Patel et al. (1998) Trends Cell Biol 8: 65-71). Identification of these domains may be facilitated using any of a number of art recognized molecular modeling techniques as described herein (see also Example 2).
  • other biologically active portions, in which other regions of the protein are deleted can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native ABC2 transporter protein.
  • the ABC2 transporter protein has an amino acid sequence shown in SEQ ED NO: 2.
  • the ABC2 transporter protein is substantially homologous to SEQ ED NO: 2, and retains the functional activity of the protein of SEQ ED NO: 2, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail in subsection I above.
  • the ABC2 transporter protein is a protein which comprises an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to SEQ ID NO: 2.
  • sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes).
  • the length of a reference sequence aligned for comparison purposes is at least 70%, preferably, 80%, 90% or 100% of the length of the reference sequence (e.g., when aligning a second sequence to the ABC2 transporter amino acid sequence of SEQ ED NO: 2 having 2001 amino acid residues, at least 600, preferably at least 800, more preferably at least 1000, even more preferably at least 1200, and even more preferably at least 1400, 1600, 1800, or 2001 amino acid residues are aligned).
  • the amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared.
  • amino acid or nucleic acid “identity” is equivalent to amino acid or nucleic acid "homology”).
  • the percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences.
  • a comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent identity between two amino acid sequences is determined using standard art recognized comparison software using standard parameter settings. For example, the Needleman and Wunsch (J.
  • Mol Biol (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package can be employed using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
  • the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • the nucleic acid and protein sequences of the present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences.
  • Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
  • Gapped BLAST can be utilized as described in Altschul et al, (1997) Nucleic Acids Res. 25(17):3389- 3402.
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • XBLAST and NBLAST See http://www.ncbi.nlm.nih.gov.
  • an ABC2 transporter chimeric or fusion protein comprises an ABC2 transporter polypeptide operatively linked to a non-ABC2 transporter polypeptide.
  • An “ABC2 transporter polypeptide” refers to a polypeptide having an amino acid sequence corresponding to ABC2
  • a “non-ABC2 transporter polypeptide” refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the ABC2 transporter protein, e.g., a protein which is different from the ABC2 transporter protein and which is derived from the same or a different organism.
  • an ABC2 transporter polypeptide can correspond to all or a portion of an ABC2 transporter protein.
  • an ABC2 transporter fusion protein comprises at least one biologically active portion of an ABC2 transporter protein.
  • an ABC2 transporter fusion protein comprises at least two biologically active portions of an ABC2 transporter protein.
  • the term "operatively linked" is intended to indicate that the ABC2 transporter polypeptide and the non-ABC2 transporter polypeptide are fused in-frame to each other.
  • the non-ABC2 transporter polypeptide can be fused to the N-terminus or C-terminus of the ABC2 transporter polypeptide.
  • the fusion protein is a GST-ABC2 transporter fusion protein in which the ABC2 transporter sequences are fused to the C-terminus of the GST sequences.
  • Such fusion proteins can facilitate the purification of recombinant ABC2.
  • the fusion protein is an ABC2 transporter protein containing a heterologous signal sequence at its N-terminus.
  • expression and/or secretion of ABC2 transporter can be increased through use of a heterologous signal sequence.
  • the ABC2 transporter fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo.
  • the ABC2 transporter fusion proteins can be used to affect the bioavailability of an ABC2 transporter substrate.
  • ABC2 transporter fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, (i) aberrant modification or mutation of a gene encoding an ABC2 transporter protein; (ii) mis-regulation of the ABC2 transporter gene; and (iii) aberrant post-translational modification of an ABC2 transporter protein.
  • ABC2-fusion proteins of the invention can be used as immunogens to produce anti-ABC2 transporter antibodies in a subject, to purify ABC2 transporter ligands and in screening assays to identify molecules which inhibit the interaction of an ABC2 transporter with an ABC2 transporter substrate.
  • an ABC2 transporter chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques.
  • DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation.
  • the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers.
  • PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992).
  • anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • An ABC2 transporter-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the ABC2 transporter protein.
  • the present invention also pertains to variants of the ABC2 transporter proteins which function as either ABC2 transporter agonists or as ABC2 transporter antagonists.
  • Variants of the ABC2 transporter proteins can be generated by mutagenesis, e.g., discrete point mutation or truncation of an ABC2 transporter protein.
  • An agonist of the ABC2 transporter proteins can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of an ABC2 transporter protein.
  • An antagonist of an ABC2 transporter protein can inhibit one or more of the activities of the naturally occurring form of the ABC2 transporter protein by, for example, competitively modulating an activity of an ABC2 transporter protein.
  • specific biological effects can be elicited by treatment with a variant of limited function.
  • treatment of a subject with a variant having a subset of the biological activities of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the ABC2 transporter protein.
  • variants of an ABC2 transporter protein which function as either ABC2 transporter agonists (mimetics) or as ABC2 transporter antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of an ABC2 transporter protein for ABC2 transporter protein agonist or antagonist activity.
  • a variegated library of ABC2 transporter variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library.
  • a variegated library of ABC2 transporter variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential ABC2 transporter sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of ABC2 transporter sequences therein.
  • methods which can be used to produce libraries of potential ABC2 transporter variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector.
  • degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential ABC2 transporter sequences.
  • Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3; Itakura et al (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11 :477.
  • libraries of fragments of an ABC2 transporter protein coding sequence can be used to generate a variegated population of ABC2 transporter fragments for screening and subsequent selection of variants of an ABC2 transporter protein.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an ABC2 transporter coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with SI nuclease, and ligating the resulting fragment library into an expression vector.
  • an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the ABC2 transporter protein.
  • REM Recursive ensemble mutagenesis
  • An isolated ABC2 transporter protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind ABC2 transporter using standard techniques for polyclonal and monoclonal antibody preparation.
  • a full-length ABC2 transporter protein can be used or, alternatively, the invention provides antigenic peptide fragments of ABC2 transporter for use as immunogens.
  • Preferred epitopes encompassed by the antigenic peptide are regions of ABC2 transporter that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity.
  • An ABC2 transporter immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen.
  • An appropriate immunogenic preparation can contain, for example, recombinantly expressed ABC2 transporter protein or a chemically synthesized ABC2 transporter polypeptide.
  • the preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic ABC2 transporter preparation induces a polyclonal anti- ABC2 transporter antibody response. Accordingly, another aspect of the invention pertains to anti-ABC2 transporter antibodies.
  • antibody refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as ABC2 transporter.
  • immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin.
  • the invention provides polyclonal and monoclonal antibodies that bind ABC2 transporter.
  • monoclonal antibody or “monoclonal antibody composition”, as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of ABC2 transporter.
  • a monoclonal antibody composition thus typically displays a single binding affinity for a particular ABC2 transporter protein with which it immunoreacts.
  • Polyclonal anti-ABC2 transporter antibodies can be prepared as described above by immunizing a suitable subject with an ABC2 transporter immunogen.
  • the anti-ABC2 transporter antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized ABC2 transporter.
  • ELISA enzyme linked immunosorbent assay
  • the antibody molecules directed against ABC2 transporter can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as protein A chromatography to obtain the IgG fraction.
  • antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem .255:4980-83; Yeh et al. (1976) Proc. Natl. Acad. Sci. USA 76:2927-31; and Yeh et al. (1982) Int. J.
  • an immortal cell line typically a myeloma
  • lymphocytes typically splenocytes
  • the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds ABC2 transporter.
  • the immortal cell line e.g., a myeloma cell line
  • the immortal cell line is derived from the same mammalian species as the lymphocytes.
  • murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line.
  • Preferred immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium").
  • HAT medium culture medium containing hypoxanthine, aminopterin and thymidine
  • Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e.g., the P3-NSl/l-Ag4-l, P3-x63-Ag8.653 or Sp2/O-Agl4 myeloma lines. These myeloma lines are available from ATCC.
  • HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG").
  • PEG polyethylene glycol
  • Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed).
  • Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind ABC2, e.g., using a standard ELISA assay.
  • a monoclonal anti- ABC2 transporter antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with ABC2 transporter to thereby isolate immunoglobulin library members that bind ABC2.
  • Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al.
  • recombinant anti-ABC2 transporter antibodies such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
  • Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US 86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al European Patent Application 173,494; Neuberger et al. PCT International Publication No.
  • An anti-ABC2 transporter antibody (e.g., monoclonal antibody) can be used to isolate ABC2 transporter by standard techniques, such as affinity chromatography or immunoprecipitation.
  • An anti-ABC2 transporter antibody can facilitate the purification of natural ABC2 transporter from cells and of recombinantly produced ABC2 transporter expressed in host cells.
  • an anti-ABC2 transporter antibody can be used to detect ABC2 transporter protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the ABC2 transporter protein.
  • Anti-ABC2 transporter antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance.
  • detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, -galactosidase, or acetylcholinesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin;
  • suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin;
  • an example of a luminescent material includes luminol;
  • examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125 I, 131 1, 35 S, 33 P, 32 P, or 3 H.
  • vectors preferably expression vectors, containing a nucleic acid encoding an ABC2 transporter protein (or a portion thereof).
  • vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked.
  • plasmid refers to a circular double stranded DNA loop into which additional DNA segments can be ligated.
  • viral vector Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome.
  • Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors).
  • vectors e.g., non-episomal mammalian vectors
  • Other vectors are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome.
  • certain vectors are capable of directing the expression of genes to which they are operatively linked.
  • Such vectors are referred to herein as "expression vectors".
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.
  • plasmid and vector can be used interchangeably as the plasmid is the most commonly used form of vector.
  • the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.
  • the recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed.
  • operably linked is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).
  • regulatory sequence is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology
  • Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cells and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like.
  • the expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., ABC2 transporter proteins, mutant forms of ABC2 transporter proteins, fusion proteins, and the like).
  • the recombinant expression vectors of the invention can be designed for expression of ABC2 transporter proteins in prokaryotic or eukaryotic cells.
  • ABC2 transporter proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990).
  • the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase. Expression of proteins in prokaryotes is most often carried out in E.
  • Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein.
  • Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification.
  • a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein.
  • enzymes, and their cognate recognition sequences include Factor Xa, thrombin and enterokinase.
  • Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S.
  • an ABC2 transporter fusion protein expressed in a retroviral expression vector of the present invention can be utilized to infect bone marrow cells which are subsequently transplanted into irradiated recipients.
  • E. coli expression vectors include pTrc (Amann et al, (1988) Gene 69:301-315) and pET l id (Studier et al, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60- 89).
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter.
  • Target gene expression from the pET 1 Id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl).
  • This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter.
  • One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128).
  • Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al
  • nucleic Acids Res. 20:2111-2118 Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
  • the ABC2 transporter expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et al, (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al, (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, CA), and picZ (InVitrogen Corp, San Diego, CA).
  • ABC2 transporter proteins can be expressed in insect cells using baculovirus expression vectors.
  • Baculovirus vectors available for expression of proteins in cultured insect cells include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
  • a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector.
  • mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al (1987) EMBO J. 6:187-195).
  • the expression vector's control functions are often provided by viral regulatory elements.
  • commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalo virus and Simian Virus 40.
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol.
  • promoters of T cell receptors Winoto and Baltimore (1989) EMBO J. 8:729-733 and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S.
  • Patent No. 4,873,316 and European Application Publication No. 264,166 Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the ⁇ -fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
  • the invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to ABC2 transporter mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA.
  • the antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced.
  • a high efficiency regulatory region the activity of which can be determined by the cell type into which the vector is introduced.
  • Another aspect of the invention pertains to host cells into which an ABC2 transporter nucleic acid molecule of the invention is introduced, e.g., an ABC2 transporter nucleic acid molecule within a recombinant expression vector or an ABC2 transporter nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome.
  • the terms "host cell” and “recombinant host cell” are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
  • a host cell can be any prokaryotic or eukaryotic cell.
  • an ABC2 transporter protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • mammalian cells such as Chinese hamster ovary cells (CHO) or COS cells.
  • Other suitable host cells are known to those skilled in the art.
  • Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques.
  • transformation and “transfection” are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, D ⁇ A ⁇ -dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.
  • a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest.
  • selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate.
  • Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding an ABC2 transporter protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
  • a host cell of the invention such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) an ABC2 transporter protein.
  • the invention further provides methods for producing an ABC2 transporter protein using the host cells of the invention.
  • the method comprises culturing the host cell of the invention (into which a recombinant expression vector encoding an ABC2 transporter protein has been introduced) in a suitable medium such that an ABC2 transporter protein is produced.
  • the method further comprises isolating an ABC2 transporter protein from the medium or the host cell.
  • transgenic animal is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.
  • transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like.
  • a transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal.
  • a "homologous recombinant animal” is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous ABC2 transporter gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
  • a transgenic animal of the invention can be created by introducing an ABC2-encoding nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal.
  • the ABC2 transporter cDNA sequence of SEQ ED NO: 1 can be introduced as a transgene into the genome of a non-human animal.
  • a nonhuman homologue of a human ABC2 transporter gene such as a mouse or rat ABC2 transporter gene, can be used as a transgene.
  • an ABC2 transporter gene homologue such as another ABC2 transporter family member, can be isolated based on hybridization to the ABC2 transporter cDNA sequences of SEQ ID NO: 1 or 3 (described further in subsection I above) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene.
  • a tissue-specific regulatory sequence(s) can be operably linked to an ABC2 transporter transgene to direct expression of an ABC2 transporter protein to particular cells.
  • a transgenic founder animal can be identified based upon the presence of an ABC2 transporter transgene in its genome and/or expression of ABC2 transporter mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene.
  • transgenic animals carrying a transgene encoding an ABC2 transporter protein can further be bred to other transgenic animals carrying other transgenes, for example, animals carrying a transgene encoding a neurotoxic polypeptide such as ⁇ -amyloid.
  • a vector is prepared which contains at least a portion of an ABC2 transporter gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the ABC2 transporter gene.
  • the ABC2 transporter gene can be a human gene (e.g., the cDNA of SEQ ED NO: 3), but more preferably, is a non-human homologue of a human ABC2 transporter gene (e.g., a cDNA isolated by stringent hybridization with the nucleotide sequence of SEQ ED NO: 1).
  • a mouse ABC2 transporter gene can be used to construct a homologous recombination nucleic acid molecule, e.g., a vector, suitable for altering an endogenous ABC2 transporter gene in the mouse genome.
  • the homologous recombination nucleic acid molecule is designed such that, upon homologous recombination, the endogenous ABC2 transporter gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector).
  • the homologous recombination nucleic acid molecule can be designed such that, upon homologous recombination, the endogenous ABC2 transporter gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous ABC2 transporter protein).
  • the altered portion of the ABC2 transporter gene is flanked at its 5' and 3' ends by additional nucleic acid sequence of the ABC2 transporter gene to allow for homologous recombination to occur between the exogenous ABC2 transporter gene carried by the homologous recombination nucleic acid molecule and an endogenous ABC2 transporter gene in a cell, e.g., an embryonic stem cell.
  • the additional flanking ABC2 transporter nucleic acid sequence is of sufficient length for successful homologous recombination with the endogenous gene.
  • homologous recombination nucleic acid molecule typically, several kilobases of flanking DNA (both at the 5' and 3 'ends) are included in the homologous recombination nucleic acid molecule (see, e.g., Thomas, K.R. and Capecchi, M. R. (1987) Cell 51:503 for a description of homologous recombination vectors).
  • the homologous recombination nucleic acid molecule is introduced into a cell, e.g., an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced ABC2 transporter gene has homologously recombined with the endogenous ABC2 transporter gene are selected (see e.g., Li, E. et /.
  • the selected cells can then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A. in Ter ⁇ toc ⁇ rcinom ⁇ s and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152).
  • aggregation chimeras see e.g., Bradley, A. in Ter ⁇ toc ⁇ rcinom ⁇ s and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152).
  • a chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term.
  • Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene.
  • Methods for constructing homologous recombination nucleic acid molecules, e.g., vectors, or homologous recombinant animals are described further in Bradley, A. (1991) Current Opinion in Biotechnology 2:823-829 and in PCT International Publication Nos.: WO 90/11354 by Le Mouellec et al; WO 91/01140 by Smithies et al; WO 92/0968 by Zijlsira et al. ; and WO 93/04169 by Berns et al.
  • transgenic non-human animals can be produced which contain selected systems which allow for regulated expression of the transgene.
  • a system is the cre/loxP recombinase system of bacteriophage PI.
  • cre/loxP recombinase system of bacteriophage PI.
  • FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355.
  • mice containing transgenes encoding both the Cre recombinase and a selected protein are required.
  • Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
  • Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al (1997) Nature 385:810-813 and PCT International Publication Nos. WO 97/07668 and WO 97/07669.
  • a cell e.g., a somatic cell
  • the quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated.
  • the reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal.
  • the offspring borne of this female foster animal will be a clone of the animal from which the cell, e.g., the somatic cell, is isolated.
  • compositions suitable for administration can be incorporated into pharmaceutical compositions suitable for administration.
  • Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
  • a pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral, e.g. , intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants
  • compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a fragment of an ABC2 transporter protein or an anti-ABC2 transporter antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • the active compound e.g., a fragment of an ABC2 transporter protein or an anti-ABC2 transporter antibody
  • dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic ABC2 transporter dispersion medium and the required other ingredients from those enumerated above.
  • the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets.
  • the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed.
  • Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition.
  • the tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a suitable propellant e.g., a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositories.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • the compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
  • the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
  • Dosage unit form refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier.
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
  • Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50.
  • Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC50 i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • the nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors.
  • Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057).
  • the pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded.
  • the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
  • compositions can be included in a container, pack, or dispenser together with instructions for administration.
  • nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: a) screening assays; b) predictive medicine (e.g., diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics); and c) methods of treatment (e.g., therapeutic and prophylactic).
  • the isolated nucleic acid molecules of the invention can be used, for example, to express ABC2 transporter protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect ABC2 transporter mRNA (e.g., in a biological sample) or a genetic alteration in an ABC2 transporter gene, and to modulate ABC2 transporter activity, as described further below.
  • the ABC2 transporter proteins can be used to treat disorders characterized by insufficient or excessive production of an ABC2 transporter substrate or production of ABC2 transporter inhibitors.
  • ABC2 transporter proteins can be used to screen for naturally occurring ABC2 transporter substrates, to screen for drugs or compounds which modulate ABC2 transporter activity, as well as to treat disorders characterized by insufficient or excessive production of ABC2 transporter protein or production of ABC2 transporter protein forms which have decreased, aberrant or unwanted activity compared to ABC2 transporter wild type protein.
  • anti-ABC2 transporter antibodies of the invention can be used to detect and isolate ABC2 transporter proteins, regulate the bioavailability of ABC2 transporter proteins, and modulate ABC2 transporter activity.
  • the invention provides a method (also referred to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to ABC2 transporter proteins, have a stimulatory or inhibitory effect on, for example, ABC2 transporter expression or ABC2 transporter activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of an ABC2 transporter substrate.
  • modulators i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to ABC2 transporter proteins, have a stimulatory or inhibitory effect on, for example, ABC2 transporter expression or ABC2 transporter activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of an ABC2 transporter substrate.
  • the invention provides assays for screening candidate or test compounds which are substrates of an ABC2 transporter protein or polypeptide or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of an ABC2 transporter protein or polypeptide or biologically active portion thereof.
  • the test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12:145).
  • Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al.
  • an assay is a cell-based assay in which a cell which expresses an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate ABC2 transporter activity is determined. Determining the ability of the test compound to modulate ABC2 transporter activity can be accomplished by monitoring, for example, cellular transport of organic anions, organic cations, cytotoxic anti-cancer drugs, intracellular calcium, potassium, phosphatidylcholine, sodium concentration, neuronal membrane depolarization, a neurotoxic polypeptide (e.g., ⁇ -amyloid), or the activity of an ABC2 transporter-regulated transcription factor.
  • a neurotoxic polypeptide e.g., ⁇ -amyloid
  • the cell for example, can be of mammalian origin, e.g., a neuronal cell.
  • the ability of the test compound to modulate ABC2 transporter binding to a substrate or to bind to ABC2 transporter can also be determined. Determining the ability of the test compound to modulate ABC2 transporter binding to a substrate can be accomplished, for example, by coupling the ABC2 transporter substrate with a radioisotope or enzymatic label such that binding of the ABC2 transporter substrate to ABC2 transporter can be determined by detecting the labeled ABC2 transporter substrate in a complex.
  • Determining the ability of the test compound to bind ABC2 transporter can be accomplished, for example, by coupling the compound with a radioisotope or enzymatic label such that binding of the compound to ABC2 transporter can be determined by detecting the labeled ABC2 transporter compound in a complex.
  • compounds e.g., ABC2 transporter substrates
  • compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.
  • suitable compounds include, but are not limited to, verapamil, desmethoxyverapamil, chloroquine, quinine, chinchonidine, primaquine, tamoxifen, dihydrocyclosporin, yohimbine, corynanthine, reserpine, physostigmine, acridine, acridine orange, quinacrine, trifluoroperazine chlorpromazine, propanolol, atropine, tryptamine, forskolin, 1,9-dideoxyforskolin, cyclosporin, (US Patent 4,117,118 (1978)), PSC-833 (cyclosporin D, 6-[(2S, 4R, 6E)-4-methyl-2-(methylamino)-3-oxo-6-octenoic acid]-(9CI)), [US Patent 5,525,590] [ACS 121584-18-7], Keller et al, "S Z PSC 833, a non-
  • a microphysiometer can be used to detect the interaction of a compound with ABC2 transporter without the labeling of either the compound or the ABC2. McConnell, H. M. et al. (1992) Science 257:1906-1912.
  • a "microphysiometer” e.g., Cytosensor
  • LAPS light-addressable potentiometric sensor
  • an assay is a cell-based assay comprising contacting a cell expressing an ABC2 transporter target molecule (e.g., an ABC2 transporter substrate) with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of the ABC2 transporter target molecule. Determining the ability of the test compound to modulate the activity of an ABC2 transporter target molecule can be accomplished, for example, by determining the ability of the ABC2 transporter protein to bind to or interact with the ABC2 transporter target molecule.
  • an ABC2 transporter target molecule e.g., an ABC2 transporter substrate
  • Determining the ability of the test compound to modulate the activity of an ABC2 transporter target molecule can be accomplished, for example, by determining the ability of the ABC2 transporter protein to bind to or interact with the ABC2 transporter target molecule.
  • Determining the ability of the ABC2 transporter protein or a biologically active fragment thereof, to bind to or interact with an ABC2 transporter target molecule can be accomplished by one of the methods described above for determining direct binding. In a preferred embodiment, determining the ability of the ABC2 transporter protein to bind to or interact with an ABC2 transporter target molecule can be accomplished by determining the activity of the target molecule.
  • the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (i.e., intracellular Ca2+, diacylglycerol, IP3, and the like), detecting catalytic/enzymatic activity of the target an appropriate substrate, detecting the induction of a reporter gene (comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), cellular transport of, e.g., a reference compound or, e.g., a neurotoxic polypeptide (e.g., ⁇ -amyloid) or detecting a target-regulated cellular response.
  • a reporter gene comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase
  • an assay of the present invention is a cell-free assay in which an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the ABC2 transporter protein or biologically active portion thereof is determined.
  • Preferred biologically active portions of the ABC2 transporter proteins to be used in assays of the present invention include fragments which participate in interactions with non-ABC2 transporter molecules, e.g., fragments with high surface probability scores (see, for example, Figure 2). Binding of the test compound to the ABC2 transporter protein can be determined either directly or indirectly as described above.
  • the assay includes contacting the ABC2 transporter protein or biologically active portion thereof with a known compound which binds ABC2 transporter to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an ABC2 transporter protein, wherein determining the ability of the test compound to interact with an ABC2 transporter protein comprises determining the ability of the test compound to preferentially bind to ABC2 transporter or biologically active portion thereof as compared to the known compound.
  • the assay is a cell-free assay in which an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the ABC2 transporter protein or biologically active portion thereof is determined.
  • Determining the ability of the test compound to modulate the activity of an ABC2 transporter protein can be accomplished, for example, by determining the ability of the ABC2 transporter protein to bind to an ABC2 transporter target molecule by one of the methods described above for determining direct binding. Alternatively, for example, ATP binding can be measured. Determining the ability of the ABC2 transporter protein to bind to an ABC2 transporter target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis
  • BIOA surface plasmon resonance
  • determining the ability of the test compound to modulate the activity of an ABC2 transporter protein can be accomplished by determining the ability of the ABC2 transporter protein to further modulate the activity of a downstream effector of an ABC2 transporter target molecule.
  • the activity of the effector molecule on an appropriate target can be determined or the binding of the effector to an appropriate target can be determined as previously described.
  • the cell-free assay involves contacting an ABC2 transporter protein or biologically active portion thereof with a known compound which binds the ABC2 transporter protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the ABC2 transporter protein, wherein determining the ability of the test compound to interact with the ABC2 transporter protein comprises determining the ability of the ABC2 transporter protein to preferentially bind to or modulate the activity of an ABC2 transporter target molecule.
  • the cell-free assays of the present invention are amenable to use of both soluble and/or membrane-bound forms of isolated proteins (e.g., ABC2 transporter proteins or biologically active portions thereof ).
  • isolated proteins e.g., ABC2 transporter proteins or biologically active portions thereof.
  • non-ionic detergents such as n-octy
  • binding of a test compound to an ABC2 transporter protein, or interaction of an ABC2 transporter protein with a target molecule in the presence and absence of a candidate compound can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes.
  • a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix.
  • glutathione-S-transferase/ABC2 transporter fusion proteins or glutathione-S-transferase/target fusion proteins can be adsorbed onto glutathione Sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtiter plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or ABC2 transporter protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above.
  • glutathione Sepharose beads Sigma Chemical, St. Louis, MO
  • glutathione derivatized microtiter plates which are then combined with the test compound or the test compound and either the non-adsorbed target protein or ABC2 transporter protein, and the
  • the complexes can be dissociated from the matrix, and the level of ABC2 transporter binding or activity determined using standard techniques.
  • Other techniques for immobilizing proteins on matrices can also be used in the screening assays of the invention.
  • an ABC2 transporter protein or an ABC2 transporter target molecule can be immobilized utilizing conjugation of biotin and streptavidin.
  • Biotinylated ABC2 transporter protein or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, EL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • antibodies reactive with ABC2 transporter protein or target molecules but which do not interfere with binding of the ABC2 transporter protein to its target molecule can be derivatized to the wells of the plate, and unbound target or ABC2 transporter protein trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies reactive with the ABC2 transporter protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the ABC2 transporter protein or target molecule.
  • modulators of ABC2 transporter expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of ABC2 transporter mRNA or protein in the cell is determined.
  • the level of expression of ABC2 transporter mRNA or protein in the presence of the candidate compound is compared to the level of expression of ABC2 transporter mRNA or protein in the absence of the candidate compound.
  • the candidate compound can then be identified as a modulator of ABC2 transporter expression based on this comparison. For example, when expression of ABC2 transporter mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of ABC2 transporter mRNA or protein expression.
  • the candidate compound when expression of ABC2 transporter mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of ABC2 transporter mRNA or protein expression.
  • the level of ABC2 transporter mRNA or protein expression in the cells can be determined by methods described herein for detecting ABC2 transporter mRNA or protein.
  • the ABC2 transporter proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol Chem.
  • ABC2-binding proteins bind to or interact with ABC2 transporter
  • ABC2-binding proteins bind to or interact with ABC2 transporter
  • Such ABC2-binding proteins are also likely to be involved in the propagation of signals by the ABC2 transporter proteins or ABC2 transporter targets as, for example, downstream elements of an ABC2-mediated signaling pathway.
  • ABC2-binding proteins are likely to be ABC2 transporter inhibitors.
  • the two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains.
  • the assay utilizes two different DNA constructs.
  • the gene that codes for an ABC2 transporter protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4).
  • a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein (“prey" or "sample”) is fused to a gene that codes for the activation domain of the known transcription factor.
  • the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the ABC2 transporter protein.
  • a reporter gene e.g., LacZ
  • the invention pertains to a combination of two or more of the assays described herein.
  • a modulating agent can be identified using a cell-based or a cell free assay, and the ability of the agent to modulate the activity of an ABC2 transporter protein can be confirmed in vivo, e.g., in an animal.
  • This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model.
  • an agent identified as described herein e.g., an ABC2 transporter modulating agent, an antisense ABC2 transporter nucleic acid molecule, an ABC2-specific antibody, or an ABC2-binding partner
  • an agent identified as described herein can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent.
  • an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent.
  • this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.
  • cDNA sequences identified herein can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.
  • this sequence can be used to map the location of the gene on a chromosome.
  • This process is called chromosome mapping.
  • portions or fragments of the ABC2 transporter nucleotide sequences, described herein can be used to map the location of the ABC2 transporter genes on a chromosome.
  • the mapping of the ABC2 transporter sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease. Briefly, ABC2 transporter genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the ABC2 transporter nucleotide sequences.
  • ABC2 transporter sequences can be used to predict primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the ABC2 transporter sequences will yield an amplified fragment.
  • Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes. By using media in which mouse cells cannot grow, because they lack a particular enzyme, but human cells can, the one human chromosome that contains the gene encoding the needed enzyme, will be retained. By using various media, panels of hybrid cell lines can be established. Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. (D ⁇ ustachio P.
  • Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.
  • PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler.
  • Using the ABC2 transporter nucleotide sequences to design oligonucleotide primers sublocalization can be achieved with panels of fragments from specific chromosomes.
  • Other mapping strategies which can similarly be used to map an ABC2 transporter sequence to its chromosome include in situ hybridization (described in Fan, Y. et al.
  • FISH Fluorescence in situ hybridization
  • a pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually.
  • the FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. Preferably 1,000 bases, and more preferably 2,000 bases will suffice to get good results at a reasonable amount of time. For a review of this technique, see Verma et al, Human Chromosomes: A Manual of BABC transporter Techniques (Pergamon Press, New York 1988).
  • Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.
  • differences in the D ⁇ A sequences between individuals affected and unaffected with a disease associated with the ABC2 transporter gene can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.
  • the ABC2 transporter sequences of the present invention can also be used to identify individuals from minute biological samples.
  • the United States military for example, is considering the use of restriction fragment length polymo ⁇ hism (RFLP) for identification of its personnel.
  • RFLP restriction fragment length polymo ⁇ hism
  • an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification.
  • This method does not suffer from the current limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult.
  • the sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057).
  • sequences of the present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome.
  • the ABC2 transporter nucleotide sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
  • Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences.
  • the sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue.
  • the ABC2 transporter nucleotide sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases.
  • Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification pu ⁇ oses.
  • the noncoding sequences of SEQ ED NO: 1 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers which each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ED NO: 3 are used, a more appropriate number of primers for positive individual identification would be 500-2,000. If a panel of reagents from ABC2 transporter nucleotide sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual. Using the unique identification database, positive identification of the individual, living or dead, can be made from extremely small tissue samples.
  • DNA-based identification techniques can also be used in forensic biology. Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a pe ⁇ etrator of a crime.
  • PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample.
  • sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual).
  • an "identification marker” i.e. another DNA sequence that is unique to a particular individual.
  • actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments.
  • Sequences targeted to noncoding regions of SEQ ED NO: 1 are particularly appropriate for this use as greater numbers of polymo ⁇ hisms occur in the noncoding regions, making it easier to differentiate individuals using this technique.
  • polynucleotide reagents include the ABC2 transporter nucleotide sequences or portions thereof, e.g., fragments derived from the noncoding regions of SEQ ID NO: 1 having a length of at least 20 bases, preferably at least 30 bases.
  • the ABC2 transporter nucleotide sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such ABC2 transporter probes can be used to identify tissue by species and/or by organ type.
  • these reagents e.g., ABC2 transporter primers or probes can be used to screen tissue culture for contamination (i.e. screen for the presence of a mixture of different types of cells in a culture).
  • the present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, and monitoring clinical trials are used for prognostic (predictive) pu ⁇ oses to thereby treat an individual prophylactically. Accordingly, one aspect of the present invention relates to diagnostic assays for determining ABC2 transporter protein and/or nucleic acid expression as well as ABC2 transporter activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant or unwanted ABC2 transporter expression or activity.
  • a biological sample e.g., blood, serum, cells, tissue
  • the invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with ABC2 transporter protein, nucleic acid expression or activity. For example, mutations in an ABC2 transporter gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive pu ⁇ ose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with ABC2 transporter protein, nucleic acid expression or activity.
  • Another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of ABC2 transporter in clinical trials. These and other agents are described in further detail in the following sections.
  • An exemplary method for detecting the presence or absence of ABC2 transporter protein or nucleic acid in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting ABC2 transporter protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes ABC2 transporter protein such that the presence of ABC2 transporter protein or nucleic acid is detected in the biological sample.
  • a preferred agent for detecting ABC2 transporter mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to ABC2 transporter mRNA or genomic DNA.
  • the nucleic acid probe can be, for example, a full-length ABC2 transporter nucleic acid, such as the nucleic acid of SEQ ID NO: 1, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to ABC2 transporter mRNA or genomic DNA.
  • a preferred agent for detecting ABC2 transporter protein is an antibody capable of binding to ABC2 transporter protein, preferably an antibody with a detectable label.
  • Antibodies can be polyclonal, or more preferably, monoclonal.
  • an intact antibody, or a fragment thereof can be used.
  • labeled with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled.
  • indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.
  • biological sample is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect ABC2 transporter mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo.
  • in vitro techniques for detection of ABC2 transporter mRNA include Northern hybridizations and in situ hybridizations.
  • in vitro techniques for detection of ABC2 transporter protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence.
  • In vitro techniques for detection of ABC2 transporter genomic DNA include Southern hybridizations.
  • in vivo techniques for detection of ABC2 transporter protein include introducing into a subject a labeled anti-ABC2 transporter antibody.
  • the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
  • the biological sample contains protein molecules from the test subject.
  • the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject.
  • a preferred biological sample is a serum sample isolated by conventional means from a subject.
  • the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting ABC2 transporter protein, mRNA, or genomic DNA, such that the presence of ABC2 transporter protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of ABC2 transporter protein, mRNA or genomic DNA in the control sample with the presence of ABC2 transporter protein, mRNA or genomic DNA in the test sample.
  • kits for detecting the presence of ABC2 transporter in a biological sample can comprise a labeled compound or agent capable of detecting ABC2 transporter protein or mRNA in a biological sample; means for determining the amount of ABC2 transporter in the sample; and means for comparing the amount of ABC2 transporter in the sample with a standard.
  • the compound or agent can be packaged in a suitable container.
  • the kit can further comprise instructions for using the kit to detect an ABC2 transporter protein or nucleic acid.
  • the diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity.
  • aberrant includes an ABC2 transporter expression or activity which deviates from the wild type ABC2 transporter expression or activity.
  • Aberrant expression or activity includes increased or decreased expression or activity, as well as expression or activity which does not follow the wild type developmental pattern of expression or the subcellular pattern of expression.
  • aberrant ABC2 transporter expression or activity is intended to include the cases in which a mutation in the ABC2 transporter gene causes the ABC2 transporter gene to be under- expressed or over-expressed and situations in which such mutations result in a non-functional ABC2 transporter protein or a protein which does not function in a wild-type fashion, e.g., a protein which does not interact with an ABC2 transporter ligand or one which interacts with a non-ABC2 transporter ligand.
  • the term "unwanted” includes an unwanted phenomenon involved in a biological response.
  • unwanted includes an ABC2 transporter expression or activity which is undesirable in a subject.
  • the assays described herein can be utilized to identify a subject having or at risk of developing a disorder associated with a misregulation in ABC2 transporter protein activity or nucleic acid expression.
  • the prognostic assays can be utilized to identify a subject having or at risk for developing a disorder associated with a misregulation in ABC2 transporter protein activity or nucleic acid expression.
  • the present invention provides a method for identifying a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity in which a test sample is obtained from a subject and ABC2 transporter protein or nucleic acid (e.g., mRNA or genomic DNA) is detected, wherein the presence of ABC2 transporter protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity.
  • a test sample refers to a biological sample obtained from a subject of interest.
  • a test sample can be a biological fluid (e.g., serum), cell sample, or tissue.
  • the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity, e.g., a cancer where the cells of the cancer have developed multidrug resistance.
  • an agent e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate
  • the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant or unwanted ABC2 transporter expression or activity in which a test sample is obtained and ABC2 transporter protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of ABC2 transporter protein or nucleic acid expression or activity is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant or unwanted ABC2 transporter expression or activity).
  • the methods of the invention can also be used to detect genetic alterations in an ABC2 transporter gene, thereby determining if a subject with the altered gene is at risk for a disorder characterized by misregulation in ABC2 transporter protein activity or nucleic acid expression.
  • the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characterized by at least one of an alteration affecting the integrity of a gene encoding an ABC2 protein, or the mis-expression of the ABC2 transporter gene.
  • such genetic alterations can be detected by ascertaining the existence of at least one of 1) a deletion of one or more nucleotides from an ABC2 transporter gene; 2) an addition of one or more nucleotides to an ABC2 transporter gene; 3) a substitution of one or more nucleotides of an ABC2 transporter gene, 4) a chromosomal rearrangement of an ABC2 transporter gene; 5) an alteration in the level of a messenger RNA transcript of an ABC2 transporter gene, 6) aberrant modification of an ABC2 transporter gene, such as of the methylation pattern of the genomic DNA, 7) the presence of a non-wild type splicing pattern of a messenger RNA transcript of an ABC2 transporter gene, 8) a non-wild type level of an ABC2-protein, 9) allelic loss of an ABC2 transporter gene, and 10) inappropriate post- translational modification of an ABC2-protein.
  • assays known in the art which can be used for detecting alterations
  • detection of the alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91:360-364), the latter of which can be particularly useful for detecting point mutations in the ABC2-gene (see Abravaya et al.
  • PCR polymerase chain reaction
  • LCR ligation chain reaction
  • This method can include the steps of collecting a sample of cells from a subject, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to an ABC2 transporter gene under conditions such that hybridization and amplification of the ABC2-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
  • nucleic acid e.g., genomic, mRNA or both
  • Alternative amplification methods include: self sustained sequence replication (Guatelli, J.C. et al, (1990) Proc. Natl Acad. Sci. USA 87:1874-1878), iranscriptional amplification system (Kwoh, D.Y. et al, (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q- Beta Replicase (Lizardi, P.M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
  • mutations in an ABC2 transporter gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns.
  • sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA.
  • sequence specific ribozymes see, for example, U.S. Patent No. 5,498,531 can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
  • genetic mutations in ABC2 transporter can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin, M.T. et al. (1996) Human Mutation 1: 244-255; Kozal, M.J. et al (1996) Nature Medicine 2: 753-759).
  • genetic mutations in ABC2 transporter can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, M.T. et al. supra.
  • a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected.
  • Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
  • any of a variety of sequencing reactions known in the art can be used to directly sequence the ABC2 transporter gene and detect mutations by comparing the sequence of the sample ABC2 transporter with the corresponding wild-type (control) sequence.
  • Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Biotechniques
  • RNA/RNA or RNA/DNA heteroduplexes Other methods for detecting mutations in the ABC2 transporter gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science 230: 1242).
  • the art technique of "mismatch cleavage" starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type ABC2 transporter sequence with potentially mutant RNA or DNA obtained from a tissue sample.
  • the double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to base pair mismatches between the control and sample strands.
  • RNA DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with SI nuclease to enzymatically digesting the mismatched regions.
  • either DNA DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton et al. (1988) Proc. Natl Acad Sci USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217:286-295.
  • the control DNA or RNA can be labeled for detection.
  • the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in ABC2 transporter cDNAs obtained from samples of cells.
  • DNA mismatch repair enzymes
  • the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662).
  • a probe based on an ABC2 transporter sequence e.g., a wild-type ABC2 transporter sequence
  • a probe based on an ABC2 transporter sequence is hybridized to a cDNA or other DNA product from a test cell(s).
  • the duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, for example, U.S. Patent No. 5,459,039.
  • alterations in electrophoretic mobility will be used to identify mutations in ABC2 transporter genes.
  • single strand conformation polymo ⁇ hism may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al.
  • Single-stranded DNA fragments of sample and control ABC2 transporter nucleic acids will be denatured and allowed to renature.
  • the secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change.
  • the DNA fragments may be labeled or detected with labeled probes.
  • the sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence.
  • the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet 7:5).
  • the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495).
  • DGGE denaturing gradient gel electrophoresis
  • DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DNA by PCR.
  • a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem 265:12753).
  • oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki et al (1989) Proc. Natl Acad. Sci USA 86:6230).
  • Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
  • Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11:238).
  • amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
  • the methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving an ABC2 transporter gene.
  • any cell type or tissue in which ABC2 transporter is expressed may be utilized in the prognostic assays described herein.
  • ABC2 transporter protein can be applied not only in ABC2 transporter drug screening, but also in clinical trials.
  • the effectiveness of an agent determined by a screening assay as described herein to increase ABC2 transporter gene expression, protein levels, or upregulate ABC2 transporter activity can be monitored in clinical trials of subjects exhibiting decreased ABC2 transporter gene expression, protein levels, or downregulated ABC2 transporter activity.
  • the effectiveness of an agent determined by a screening assay to decrease ABC2 transporter gene expression, protein levels, or downregulate ABC2 transporter activity can be monitored in clinical trials of subjects exhibiting increased ABC2 transporter gene expression, protein levels, or upregulated ABC2 transporter activity.
  • the expression or activity of an ABC2 transporter gene, and preferably, other genes that have been implicated in, for example, an ABC2-associated disorder can be used as a "read out" or markers of the phenotype of a particular cell.
  • genes, including ABC2 that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates ABC2 transporter activity (e.g., identified in a screening assay as described herein) can be identified.
  • an agent e.g., compound, drug or small molecule
  • ABC2 transporter activity e.g., identified in a screening assay as described herein
  • cells can be isolated and RNA prepared and analyzed for the levels of expression of ABC2 transporter and other genes implicated in the ABC2-associated disorder, respectively.
  • the levels of gene expression can be quantified by northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of ABC2 transporter or other genes.
  • the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during treatment of the individual with the agent.
  • the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) including the steps of (i) obtaining a preadministration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of an ABC2 transporter protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the ABC2 transporter protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the ABC2 transporter protein, mRNA, or genomic DNA in the preadministration sample with the ABC2 transporter protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly.
  • an agent e.
  • increased administration of the agent may be desirable to increase the expression or activity of ABC2 transporter to higher levels than detected, i.e., to increase the effectiveness of the agent.
  • decreased administration of the agent may be desirable to decrease expression or activity of ABC2 transporter to lower levels than detected, i.e. to decrease the effectiveness of the agent.
  • ABC2 transporter expression or activity may be used as an indicator of the effectiveness of an agent, even in the absence of an observable phenotypic response.
  • the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant or unwanted ABC2 transporter expression or activity.
  • treatments may be specifically tailored or modified, based on knowledge obtained from the field of pharmacogenomics.
  • “Pharmacogenomics”, as used herein, refers to the application of genomics technologies such as gene sequencing, statistical genetics, and gene expression analysis to drugs in clinical development and on the market.
  • the term refers the study of how a patient's genes determine his or her response to a drug (e.g., a patient's "drug response phenotype", or "drug response genotype”.)
  • another aspect of the invention provides methods for tailoring an individual's prophylactic or therapeutic treatment with either the ABC2 transporter molecules of the present invention or ABC2 transporter modulators according to that individual's drug response genotype.
  • Pharmacogenomics allows a clinician or physician to target prophylactic or therapeutic treatments to patients who will most benefit from the treatment and to avoid treatment of patients who will experience toxic drug-related side effects.
  • the invention provides a method for preventing in a subject, a disease or condition associated with an aberrant or unwanted ABC2 transporter expression or activity, by administering to the subject an ABC2 transporter or an agent which modulates ABC2 transporter expression or at least one ABC2 transporter activity.
  • Subjects at risk for a disease which is caused or contributed to by aberrant or unwanted ABC2 transporter expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein.
  • Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the ABC2 transporter aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
  • an ABC2 transporter agonist or ABC2 transporter antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein.
  • the modulatory method of the invention involves contacting a cell with an ABC2 transporter or agent that modulates one or more of the activities of ABC2 transporter protein activity associated with the cell.
  • An agent that modulates ABC2 transporter protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring target molecule of an ABC2 transporter protein (e.g., an ABC2 transporter substrate), an ABC2 transporter antibody, an ABC2 transporter agonist or antagonist, a peptidomimetic of an ABC2 transporter agonist or antagonist, or other small molecule.
  • the agent stimulates one or more ABC2 transporter activities.
  • stimulatory agents include active ABC2 transporter protein and a nucleic acid molecule encoding an ABC2 transporter that has been introduced into the cell.
  • the agent inhibits one or more ABC2 transporter activities.
  • inhibitory agents include antisense ABC2 transporter nucleic acid molecules, anti-ABC2 transporter antibodies, and ABC2 transporter inhibitors.
  • the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant or unwanted expression or activity of an ABC2 transporter protein or nucleic acid molecule.
  • the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., upregulates or downregulates) ABC2 transporter expression or activity.
  • the method involves administering an ABC2 transporter protein or nucleic acid molecule as therapy to compensate for reduced, aberrant, or unwanted ABC2 transporter expression or activity.
  • Stimulation of ABC2 transporter activity is desirable in situations in which ABC2 transporter is abnormally downregulated and/or in which increased ABC2 transporter activity is likely to have a beneficial effect.
  • stimulation of ABC2 transporter activity is desirable in situations in which an ABC2 transporter is downregulated and/or in which increased ABC2 transporter activity is likely to have a beneficial effect.
  • inhibition of ABC2 transporter activity is desirable in situations in which ABC2 transporter is abnormally upregulated and/or in which decreased ABC2 transporter activity is likely to have a beneficial effect.
  • an agent found to inhibit ABC2 transporter activity is used in combination with another therapy such that the targeting of that therapy across the blood-brain- barrier is achieved.
  • ABC2 transporter molecules of the present invention as well as agents, or modulators which have a stimulatory or inhibitory effect on ABC2 transporter activity (e.g., ABC2 transporter gene expression) as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) ABC2-associated disorders associated with aberrant or unwanted ABC2 transporter activity.
  • pharmacogenomics i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug
  • Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug.
  • a physician or clinician may consider applying knowledge obtained in relevant pharmacogenomics studies in determining whether to administer an ABC2 transporter molecule or ABC2 transporter modulator as well as tailoring the dosage and/or therapeutic regimen of treatment with an ABC2 transporter molecule or ABC2 transporter modulator.
  • Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, for example, Eichelbaum, M. et al (1996) Clin. Exp. Pharmacol. Physiol 23(10-11) :983-985 and Linder, M.W. et al (1997) Clin. Chem. 43(2):254-266.
  • two types of pharmacogenetic conditions can be differentiated.
  • G6PD glucose-6-phosphate dehydrogenase deficiency
  • a genome-wide association relies primarily on a high-resolution map of the human genome consisting of already known gene-related markers (e.g., a "bi-allelic” gene marker map which consists of 60,000-100,000 polymo ⁇ hic or variable sites on the human genome, each of which has two variants.)
  • gene-related markers e.g., a "bi-allelic” gene marker map which consists of 60,000-100,000 polymo ⁇ hic or variable sites on the human genome, each of which has two variants.
  • Such a high-resolution genetic map can be compared to a map of the genome of each of a statistically significant number of patients taking part in a Phase II/III drug trial to identify markers associated with a particular observed drug response or side effect.
  • such a high resolution map can be generated from a combination of some ten- million known single nucleotide polymo ⁇ hisms (SNPs) in the human genome.
  • SNP single nucleotide polymo ⁇ hisms
  • a "SNP" is a common alteration that occurs in a single nucleotide base in a stretch of DNA. For example, a SNP may occur once per every 1000 bases of DNA.
  • a SNP may be involved in a disease process, however, the vast majority may not be disease-associated. Given a genetic map based on the occurrence of such SNPs, individuals can be grouped into genetic categories depending on a particular pattern of SNPs in their individual genome.
  • treatment regimens can be tailored to groups of genetically similar individuals, taking into account traits that may be common among such genetically similar individuals.
  • a method termed the "candidate gene approach” can be utilized to identify genes that predict drug response.
  • a gene that encodes a drugs target e.g., an ABC2 transporter protein of the present invention
  • all common variants of that gene can be fairly easily identified in the population and it can be determined if having one version of the gene versus another is associated with a particular drug response.
  • the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action.
  • the gene coding for CYP2D6 is highly polymo ⁇ hic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite mo ⁇ hine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra- rapid metabolism has been identified to be due to CYP2D6 gene amplification.
  • a method termed the "gene expression profiling" can be utilized to identify genes that predict drug response.
  • a drug e.g., an ABC2 transporter molecule or ABC2 transporter modulator of the present invention
  • the gene expression of an animal dosed with a drug can give an indication whether gene pathways related to toxicity have been turned on.
  • Information generated from more than one of the above pharmacogenomics approaches can be used to determine appropriate dosage and treatment regimens for prophylactic or therapeutic treatment an individual. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with an ABC2 transporter molecule or ABC2 transporter modulator, such as a modulator identified by one of the exemplary screening assays described herein.
  • the human ABC2 transporter cDNA i.e., ABC2 was isolated using polymerase chain reaction (PCR) and primers designed (described below) from a mouse nucleotide sequence (mouse ortholog) containing a partial coding sequence for an ATP binding cassette transporter named abc2 (Gene Bank accession number X75927, Luciani M.F.
  • the first ABC2 cDNA fragment isolated was a 5096 base pair (bp) C-terminal fragment obtained by polymerase chain reaction (PCR) conducted on a human normal fetal brain cDNA library (Origene Technologies No. LLFB-1001) using oligonucleotides PI and P2 (as defined below; see also Fig. 6).
  • the PCR reaction was carried out in a final volume of 25 ⁇ l using 5 ⁇ l (master plate) or 1 ⁇ l (sub plate) of the cDNA library in an appropriate reaction mixture (10 mM Tris-HCl pH 8.3, 50 mM KC1, 1.5 mM MgC12, 0.2 mM each dNTP, 0.1 ⁇ M each primer PI and P2, 2% DMSO, 1.25 unit of AmpliTaq DNA Polymerase (Perkin Elmer)).
  • an appropriate reaction mixture 10 mM Tris-HCl pH 8.3, 50 mM KC1, 1.5 mM MgC12, 0.2 mM each dNTP, 0.1 ⁇ M each primer PI and P2, 2% DMSO, 1.25 unit of AmpliTaq DNA Polymerase (Perkin Elmer)).
  • the cycling parameters were: denaturation at 94°C for 2 min; denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec, elongation step at 72°C for 1 min for 30 cycles; followed by a final elongation at 72°C for 5 min).
  • the resultant nucleotide sequence was obtained using an automated DNA sequencing engine (LICOR).
  • LICOR automated DNA sequencing engine
  • the second ABC2 cDNA fragment (A2R1, See Fig.
  • the oligonucleotides P4 and P5 were used to demonstrate that the A2R1 fragment is contiguous to and represents the direct upstream sequence of the hsA2.0 cDNA fragment.
  • the normal fetal brain double-strand (ds) cDNA library mentioned above was made by subjecting 1 ⁇ g of normal human fetal brain poly(A) + RNA (Invitrogen #D6030-25) to first and second strand synthesis according to the Clontech MARATHON cDNA Amplification Kit (#K1802-1). Resultant double stranded cDNA was then phenol-chloroform extracted, alcohol precipitated, and ligated to a double-stranded cDNA adaptor according to the manufacturer's instructions.
  • the PCR reaction used to isolate A2R1 was carried out in a final volume of 20 ⁇ l using 2 ⁇ l of the ds cDNA and reagents provided by and according to the Clontech Advantage cDNA PCR kit (#K1905-1).
  • the cycling parameters were: denaturation at 94°C for 1 min; denaturation at 94°C for 30 sec, annealing at 60°C (P4, P5, P8 and P9) or 70°C (P3, P7 and adaptor specific primer) for 30 sec, elongation at 72°C for 2 min for 30 cycles, followed by a final elongation step at 72°C for 5 min.
  • the third ABC2 cDNA fragment (A2R2) isolated was a 1109 bp fragment obtained by screening a pBlueScript II cDNA library containing 5' RACE PCR products.
  • the 5' RACE PCR products were generated from a human normal brain ds cDNA library using the oligonucleotides P6 and API and the PCR conditions described above.
  • the human normal adult brain double-strand (ds) cDNA library was made by subjecting 2.5 ⁇ g of normal human normal adult brain total RNA (Invitrogen #D6030-01) to first strand synthesis using the oligonucleotide P5 and second strand synthesis according to the Clontech MARATHON cDNA Amplification Kit (#K1802-1).
  • Double stranded cDNA was phenol-chloroform extracted and alcohol precipitated prior ligation to a double-stranded cDNA adaptor according to the manufacturer's instructions.
  • the oligonucleotides P7 and P8 were then used to demonstrate that the A2R2 fragment is contiguous to, and represents the direct upstream sequence of, the A2R1 cDNA fragment.
  • A2R2 and A2R1 were determined to overlap by 471 bp (see Fig. 6). Table 1.
  • hsA2.2 6792 bp cDNA named hsA2.2, the complete fragment described herein as the invention.
  • Oligonucleotides P9 and P10 were used to generate a bp fragment (A2R1R2) that overlaps hsA2.0.
  • A2R1R2 and hsA2.0 were fused using a convenient endonuclease restriction site.
  • the resultant clone of a 6792 bp was determined to contain the human ABC2 transporter gene coding sequence in addition to 5' and the 3' untranslated regions (UTRs).
  • the nucleotide sequence encoding the human ABC2 transporter protein is shown in Figure 1 and is set forth as SEQ ED NO: 1.
  • the longest open reading frame of the human ABC2 transporter begins with the sequence AACATGA which matches the consensus eukaryotic translation initiation motif at nucleotide position 91 (ATG) and ends with a TGA termination signal at position 6094.
  • the coding region (open reading frame) of SEQ ED NO: 1 is set forth as SEQ ID NO: 3.
  • a putative polyadenylation signal (AATAAATAA) is located in the 3' untranslated region at nucleotide position 6772 (Fig. 1). Starting from the first in-frame ATG, the open reading frame is predicted to encode a polypeptide of 2001 amino acids with a molecular weight of 223 kDa. The amino acid sequence of the full length polypeptide is shown in Figure 2 and provided in SEQ ED NO: 2.
  • amino acid sequences of the human ABC2 transporter polypeptide was compared to amino acid sequences of known polypeptides and various motifs were identified.
  • nucleic acid sequence (and predicted amino acid sequence) of the isolated clone was determined to share homology with the nucleotide sequence of mouse abc2, human ABCR, and human ABCl (85%, 65%, and 67% respectively; BLASTn program against non- redundant GenBank+EMBL+DDBJ+PDB sequences).
  • the translation product of hsA2.0 is a polypeptide which shares from 92% to 96% amino acid identity with the mouse abc2 (Global Pairwise ClustalW Alignment and BLASTp program against non-redundant SwissProt sequences, respectively). Therefore, the clone hsA2.0 was determined to encode part of the human ABC2 transporter and 3' UTR sequence. This 3' fragment of the human ABC2 gene (hsA2.0, see Fig. 6) finds identity with the sequence of at least 32 human expressed sequence tags (ESTs) using the BLASTn program against the non-redundant Database of GenBank EST Division.
  • ESTs human expressed sequence tags
  • GenBank accession numbers of these ESTs are AI139808, T33919, W69928, R85265, H39045, R44798, F12829, T74974, R61688, H14465, R83132, AI491962, T31574, M78056, W69747, T65432, AI247203, H05244, H14299, Z19133, AA573061, R19133, R61689, AA351626, R20481, AA351625, AA324817, AA702968, M78484, R45304, AI567619 and AI085673 and these sequences are inco ⁇ orated in their entireties by reference herein.
  • the region of the human ABC2 clone represented by the cDNA fragment A2R1 is novel and shares homology with human ABCl and ABCR (62% and 58% respectively, BLASTn program against non-redundant GenBank+EMBL+DDBJ+PDB sequences).
  • the region of the human ABC2 transporter clone represented by the cDNA fragment A2R2, in particular, the first 638 bp, is a novel sequence and does not share homology with previously identified ABC2 transporter proteins (using the BLASTn program against non- redundant GenBank+EMBL+DDBJ+PDB sequences; BLASTx against non-redundant
  • the 1721 bp region of the ABC2 clone represented by A2R1 and A2R2 shares homology with 9 human EST nucleotide sequences (using the BLASTn program against the non-redundant Database of GenBank EST Division).
  • GenBank accession numbers of these ESTs are AI039834, AA772600, AA748768, AI050892, AA725355, AI089785, AI603917, AI174196 and AI344681 and these sequences are inco ⁇ orated in their entireties by reference herein.
  • the human ABC2 transporter of the invention belongs to the ATP-binding cassette (ABC) superfamily. Members of this family are structurally and functionally related in their ability to catalyze the translocation of substrates across biological membranes.
  • the deduced sequence of 2001 amino acids comprises, from N-terminus to C-terminus, an N-terminal membrane anchor domain, a transmembrane domain, and a second conserved nucleotide binding fold, specifying the human ABC2 polypeptide as a full-transporter (see Fig. 2 and SEQ ED NO: 2).
  • the human ABC2 transporter was determined to have partial sequence identity with a polypeptide in the HUGE database (human unidentified gene-encoded large proteins) maintained by the Kazusa DNA Research Institute (see http://www.kazusa.or.jp/). The next greatest sequence homology between ABC2 and other gene products was observed with the human ABC transporter polypeptide termed "ABCl" (51% similarity). lesser homologies were noted between ABC2 (HsA2.2) and other transporters (see Table 2 and Fig. 3).
  • the human ABC2 transporter polypeptide was also analyzed with respect to potential membrane spanning segments. Hydropathy plots and 2D fold models obtained using publicly available bioinformatic tools (Heidelberg, Germany, http://dodo.cpmc.columbia.edu/predictprotein/) defined 12 putative transmembrane spanning regions (TMH). Six TMH are in the N-terminal sequence of the protein, five TMH are in the C-terminal sequence of the protein and one TMH (hinge) is in the middle region. All TMH have a helical 2D fold structure, which indicate that human ABC2 is a membrane anchored protein (see Figs. 4 and 5). Therefore, the human ABC2 transporter polypeptide exhibits the typical features conserved among ABC transporters. ABC transporter proteins structural organization represents variations on common themes. One common theme is the basic structure of those transporters with twelve hydrophobic transmembrane segments and two hydrophilic ATP binding sites, either present in a single polypeptide chain or assembled from half or quarter molecules.
  • human ABC2 defines it as a novel full transporter.
  • Art recognized bioinformatic modeling tools indicate that the N-terminal part is in an "outside conformation, while the ATP binding cassettes of the predicted ABC2 protein are in an "inside” conformation.
  • human ABC2 transporter can be associated with an intracellular membrane structure or with a cytoplasmic membrane.
  • EXAMPLE 3 TISSUE DISTRIBUTION OF HUMAN ABC2 TRANSPORTER mRNA This example describes the tissue distribution of ABC2 transporter mRNA, as can be determined by Northern blot hybridization and in situ hybridization.
  • Northern blot hybridizations with the various RNA samples are performed under standard conditions and washed under stringent conditions, i.e., 0.2XSSC at 65°C.
  • the DNA probe is radioactively labeled with ⁇ P-dCIP using the Prime-It kit (Stratagene, La Jolla, CA) according to the instructions of the supplier.
  • Filters containing human mRNA are probed in ExpressHyb hybridization solution (Clontech) and washed at high stringency according to manufacturer's recommendations.
  • tissues obtained from brains are first frozen on dry ice.
  • Ten-micrometer-thick coronal sections of the tissues are postfixed with 4% formaldehyde in DEPC treated IX phosphate- buffered saline at room temperature for 10 minutes before being rinsed twice in DEPC IX phosphate-buffered saline and once in 0.1 M triethanolamine-HCl (pH 8.0).
  • sections are rinsed in DEPC 2X SSC (IX SSC is 0.15M NaCl plus 0.015M sodium citrate).
  • Tissue is then dehydrated through a series of ethanol washes, incubated in 100% chloroform for 5 minutes, and then rinsed in 100% ethanol for 1 minute and 95% ethanol for 1 minute and allowed to air dry.
  • Hybridizations are performed with 35s-radiolabeled (5 x i()7 cpm/ml) cRNA probes. Probes are incubated in the presence of a solution containing 600 mM NaCl, 10 mM Tris (pH 7.5), 1 mM EDTA, 0.01% sheared salmon sperm DNA, 0.01% yeast tRNA, 0.05% yeast total RNA type XI, IX Denhardt's solution, 50% formamide, 10% dextran sulfate, 100 mM dithiothreitol, 0.1% sodium dodecyl sulfate (SDS), and 0.1% sodium thiosulfate for 18 hours at 55°C.
  • SDS sodium dodecyl sulfate
  • slides are washed with 2X SSC. Sections are then sequentially incubated at 37°C in TNE (a solution containing 10 mM Tris-HCl (pH 7.6), 500 mM NaCl, and 1 mM EDTA), for 10 minutes, in TNE with 10 ⁇ g of RNase A per ml for 30 minutes, and finally in TNE for 10 minutes. Slides are then rinsed with 2X SSC at room temperature, washed with 2X SSC at 50°C for 1 hour, washed with 0.2X SSC at 55°C for 1 hour, and 0.2X SSC at 60°C for 1 hour.
  • TNE a solution containing 10 mM Tris-HCl (pH 7.6), 500 mM NaCl, and 1 mM EDTA
  • Sections are then dehydrated rapidly through serial ethanol-0.3 M sodium acetate concentrations before being air dried and exposed to Kodak Biomax MR scientific imaging film for 24 hours and subsequently dipped in NB-2 photoemulsion and exposed at 4°C for 7 days before being developed and counter stained.
  • Electronic Northern analysis has indicated that the ABC2 transporter mRNA are fairly neuron-specific.
  • the human ABC2 transporter is expressed as a recombinant glutathione-S-transferase (GST) fusion polypeptide in E. coli and the fusion polypeptide is isolated and characterized. Specifically, the human ABC2 transporter is fused to GST and this fusion polypeptide is expressed in E. coli, e.g., strain PEB199. As the human ABC2 transporter polypeptide is predicted to be approximately 223 kDa and GST is predicted to be 26 kDa, the fusion polypeptide is predicted to be approximately 249 kDa in molecular weight. Expression of the GST-ABC2 transporter fusion protein in PEB199 is induced with EPTG.
  • GST glutathione-S-transferase
  • the recombinant fusion polypeptide is purified from crude bacterial lysates of the induced PEB199 strain by affinity chromatography on glutathione beads. Using polyacrylamide gel electrophoretic analysis of the polypeptide purified from the bacterial lysates, the molecular weight of the resultant fusion polypeptide is determined. If desired, the polypeptide may be prepared in association with a membrane, such as, e.g., a micelle or membrane vesicle using art recognized techniques.
  • a membrane such as, e.g., a micelle or membrane vesicle using art recognized techniques.
  • the pcDNA/Amp vector by Invitrogen Co ⁇ oration (San Diego, CA) is used.
  • This vector contains an SV40 origin of replication, an ampicillin resistance gene, an E. coli replication origin, a CMV promoter followed by a polylinker region, and an SV40 intron and polyadenylation site.
  • a DNA fragment encoding the entire ABC2 transporter protein and an HA tag Wang et al.
  • the 5' primer contains the restriction site of interest followed by approximately twenty nucleotides of the ABC2 transporter coding sequence starting from the initiation codon; the 3' end sequence contains complementary sequences to the other restriction site of interest, a translation stop codon, the HA tag or FLAG tag and the last 20 nucleotides of the ABC2 transporter coding sequence.
  • the PCR amplified fragment and the pCDNA/Amp vector are digested with the appropriate restriction enzymes and the vector is dephosphorylated using the CIAP enzyme (New England Biolabs, Beverly, MA).
  • the two restriction sites chosen are different so that the ABC2 transporter gene is inserted in the correct orientation.
  • the ligation mixture is transformed into E.
  • coli cells strains HB101, DH5 ⁇ , SURE, available from Stratagene Cloning Systems, La Jolla, CA, can be used
  • the transformed culture is plated on ampicillin media plates, and resistant colonies are selected.
  • Plasmid DNA is isolated from transformants and examined by restriction analysis for the presence of the correct fragment.
  • Eukaryotic cells e.g., COS cells are subsequently transfected with the ABC2 transporter-pcDNA/Amp plasmid DNA using the calcium phosphate or calcium chloride co- precipitation methods, DEAE-dextran-mediated transfection, lipofection, or electroporation.
  • Other suitable methods for transfecting host cells can be found in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989.
  • the expression of the ABC2 transporter polypeptide is detected by radiolabelling (35s-methionine or 35s-cysteine available from NEN, Boston, MA, can be used) and immunoprecipitation (Harlow, E. and Lane, D. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988) using an HA specific monoclonal antibody. Briefly, the cells are labeled for 8 hours with 35s-methionine (or 35s-cysteine). The culture media are then collected and the cells are lysed using detergents (RIPA buffer, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM Tris, pH 7.5). Both the cell lysate and the culture media are precipitated with an HA specific monoclonal antibody. Precipitated polypeptides are then analyzed by SDS-PAGE.
  • DNA containing the ABC2 transporter coding sequence is cloned directly into the polylinker of the pCDNA/Amp vector using the appropriate restriction sites.
  • the resulting plasmid is transfected into COS cells in the manner described above, and the expression of the ABC2 transporter polypeptide is detected by radiolabelling and immunoprecipitation using an ABC2 transporter specific monoclonal antibody.
  • the ABC2 transporter is expressed in a mammalian cell line as described above and a base line for the cellular transport of a reference molecule, e.g., ⁇ -amyloid or other small molecule, is established.
  • a reference molecule e.g., ⁇ -amyloid or other small molecule
  • Cells are then incubated with a test compound and a change in the level of the cellular transport of the reference molecule is determined using standards techniques.
  • a test compound that changes the transport of the detectable reference molecule is then identified as a candidate compound that alters ABC2 transporter activity.
  • Lead compounds may then be tested on, e.g., cells of neuronal origin or, alternatively, on brain tissue from a test animal. Methods for conducting such an assay are known in the art.
  • lead test compounds that inhibit ABC2-mediated transport of, e.g., ⁇ -amyloid are further tested in vivo.
  • Mouse models for various neurological diseases, e.g., amyloid disease are also known in the art (see, e.g., Hardy et al, (1998) Science 282:1075-1079; Goate, et al, (1991) N ⁇ twre 349: 704; Games, et al, (1995) Nature 373: 523; and Suzuki, et al, (1994) Science 264: 1336).
  • a transgenic mouse model overexpressing an ABC2 transporter polypeptide e.g., the human ABC2 transporter polypeptide or corresponding murine polypeptide is generated using the techniques described herein.
  • This animal may then be tested directly or used as a cell or tissue source, e.g., brain tissue source, for testing modulators of the human ABC2 transporter polypeptide.
  • the animal is directly tested with a test compound and monitored for a physiological result, e.g., presence of ⁇ -amyloid in the cerebral spinal fluid (CSF).
  • CSF cerebral spinal fluid
  • the animal may be breed with an animal overexpressing a undesired polypeptide, e.g., an amyloid polypeptide, and a change in the transport of the polypeptide is measured (e.g., in the CSF) as compared to a control.
  • a undesired polypeptide e.g., an amyloid polypeptide
  • test animals are further monitored in the presence or absence of a modulator of the ABC2 transporter.
  • the activity of the ABC2 transporter is determined regarding the ability of a detectable reference molecule to cross the blood-brain barrier.
  • the animal is examined for the prevalence of multidrug resistant cells or tissues, and/or the sensitivity of the animal to cytotoxic drugs suitable for treating a neoplasm. Accordingly, these animals represent in vivo assay systems in which to test the ability of an ABC2 transporter and/or ABC2 transporter modulator to prevent, treat, or delay the onset of disease.

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Abstract

The invention provides isolated nucleic acid molecules, designated ABC2 transporter nucleic acid molecules, which encode novel ABC transporter family members. The invention also provides antisense nucleic acid molecules, recombinant expression vectors containing ABC2 transporter nucleic acid molecules, host cells into which the expression vectors have been introduced, and nonhuman transgenic animals in which an ABC2 transporter gene has been introduced or disrupted. The invention still further provides isolated ABC2 transporter proteins, fusion proteins, antigenic peptides, anti-ABC2 transporter antibodies, and screening assays for ABC2 transporter modulators. Diagnostic and therapeutic methods utilizing compositions of the invention are also provided.

Description

NOVEL ABC2 TRANSPORTER AND USES THEREOF
BACKGROUND OF THE INVENTION
ABC transporter proteins represent a large superfamily of proteins with conserved features in both prokaryotes and eukaryotes. ABC transporters catalyze ATP-dependent transport of endogenous or exogenous substrates across biological membranes (Borst, P., (1997) Seminar in Cancer Biology 8:131-213) and/or allosterically modify the function of heterologous proteins (Higgins CF, 1995, Cell 82:693-696). Several ABC transporters have been associated with clinically relevant phenotypes including the phenomenon of multidrug resistance (Ambudkar S.V. et al., (1999), Annu. Rev. Toxicol., 39:361-398), cystic fibrosis (Riordin JR et al., (1989) Science 245:1066-1073), atherosclerosis (Brooks-Wilson A et al., (1999) Nature Genetics 22:336-345), hyperinsulinemic hypoglycemia (Thomas PM et al., (1995) Science 268:46-429), macular degeneration (Allikmets R et al., (1997) Science 277:1805-1807), and adrenoleukodystrophy (Mosser J et al, (1993) Nature 361:726-730), to name but a few.
While the genes associated with these disease phenotypes have been identified to some degree, it is clear that a large number of putative ABC transporters exist in the human genome, as evidenced by the partial sequences noted in various EST databases (Allikmets et al, (1996) Hum Mol Genet 5:1649-1655). However, the utility of such information is compromised by the absence of the full-length nucleotide sequence of the coding region of the relevant gene and its translated protein product.
SUMMARY OF THE INVENTION
The present invention is based, at least in part, on the discovery of a novel ATP Binding Cassette (ABC) transporter family member, referred to herein as ABC2 transporter nucleic acid and protein molecules The ABC2 transporter molecules of the present invention are useful as targets for developing modulating agents to regulate a variety of cellular processes, particularly the transport of neurotoxic molecules, e.g., β-amyloid peptide, across cell membranes or, e.g., the blood-brain barrier (BBB). Neurotoxic molecules such as β-amyloid peptide are involved in neurological disorders such as Alzheimer's disease (see, e.g., Goate et al. (1991) Nature 349:704; Games et al. (1995) Nature 373:523; and Suzuki et al. (1994) Science 264:1336). Other neurological disease involving toxic polypeptides include, e.g., prion diseases, Huntington's disease, Parkinson's disease, etc. (for a review see Hardy et al. (1998) Science 282:1075-1079. Accordingly, modulation of amyloid-β protein export with a modulator of the human
ABC2 transporter would be expected to modulate amyloid deposition and thus, Alzheimer's disease. In addition, the ABC2 transporter molecules of the invention are useful as targets for developing modulating agents of multidrug resistance. Moreover, the molecules of the presen invention are useful as diagnostic and therapeutic tools.
Accordingly, in one aspect, this invention provides isolated nucleic acid molecules encoding ABC2 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as primers or hybridization probes for the detection of ABC2-encoding nucleic acids.
In one embodiment, an ABC2 transporter nucleic acid molecule of the invention is at least 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more identical to the nucleotide sequence (e.g., to the entire length of the nucleotide sequence) shown in SEQ ID NO: 1 or 3, or a complement thereof.
In a preferred embodiment, the isolated nucleic acid molecule includes the nucleotide sequence shown in SEQ ID NO: 1 or 3, or a complement thereof. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 1-90 of SEQ ID NO: 1. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 6097- 6792 of SEQ ID NO: 1.
In another embodiment, an ABC2 transporter nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ID NO: 2. In a preferred embodiment, an ABC2 transporter nucleic acid molecule includes a nucleotide sequence encoding a protein having an amino acid sequence at least 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to the entire length of the amino acid sequence of SEQ ID NO: 2.
In another preferred embodiment, an isolated nucleic acid molecule encodes the amino acid sequence of human ABC2 transporter having the amino acid sequence of SEQ ID NO: 2. In yet another preferred embodiment, the nucleic acid molecule is at least 6006 nucleotides in length. In a further preferred embodiment, the nucleic acid molecule is at least 6792 nucleotides in length and encodes a protein having ABC2 transporter activity (as described herein). Another embodiment of the invention features nucleic acid molecules, preferably ABC2 transporter nucleic acid molecules, which specifically detect ABC2 transporter nucleic acid molecules relative to nucleic acid molecules encoding non-ABC2 transporter proteins. For example, in one embodiment, such a nucleic acid molecule is at least 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 500-1000, 1000-1500, 1500-2000, or 2000-2500 or more nucleotides in length and/or hybridizes under stringent conditions to a nucleic acid molecule comprising the nucleotide sequence shown in SEQ ID NO: 1, or a complement thereof. It should be understood that the nucleic acid molecule can be of a length within a range having one of the numbers listed above as a lower limit and another number as the upper limit for the number of nucleotides in length, e.g., molecules that are 60-80, 300-1000, or 150-400 nucleotides in length.
In preferred embodiments, the nucleic acid molecules are at least 15 (e.g., contiguous) nucleotides in length and hybridize under stringent conditions to nucleotides 91-6096 of SEQ
ID NO: 1. In other preferred embodiments, the nucleic acid molecules comprise nucleotides
91-6096 of SEQ ID NO: 1.
In other preferred embodiments, the nucleic acid molecule encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ED NO: 2, wherein the nucleic acid molecule hybridizes to a nucleic acid molecule comprising SEQ ID
NO: 1 or 3 under stringent conditions.
Another embodiment of the invention provides an isolated nucleic acid molecule which is antisense to an ABC2 transporter nucleic acid molecule, e.g., the coding strand of an ABC2 transporter nucleic acid molecule. Another aspect of the invention provides a vector comprising an ABC2 transporter nucleic acid molecule. In certain embodiments, the vector is a recombinant expression vector.
In another embodiment, the invention provides a host cell containing a vector of the invention.
In yet another embodiment, the invention provides a host cell containing a nucleic acid molecule of the invention. The invention also provides a method for producing a protein, preferably an ABC2 transporter protein, by culturing in a suitable medium, a host cell, e.g., a mammalian host cell such as a non-human mammalian cell, of the invention containing a recombinant expression vector, such that the protein is produced.
Another aspect of this invention features isolated or recombinant ABC2 transporter proteins and polypeptides. In a preferred embodiment, the protein, preferably an ABC2 transporter protein, includes at least one transmembrane domain and has an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%,
91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to the amino acid sequence of SEQ ID NO: 2. In yet another preferred embodiment, the protein, preferably an ABC2 transporter protein, includes at least one transmembrane domain and is encoded by a nucleic acid molecule having a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1. In another embodiment, the invention features fragments of the protein having the amino acid sequence of SEQ ID NO: 2, wherein the fragment comprises at least 15 amino acids
(e.g., contiguous amino acids) of the amino acid sequence of SEQ ID NO: 2. In another embodiment, the protein, preferably an ABC2 transporter protein, has the amino acid sequence of SEQ ID NO: 2. In another embodiment, the invention features an isolated protein, preferably an ABC2 transporter protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence at least 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to a nucleotide sequence of SEQ ID NO: 1 or 3, or a complement thereof. This invention further features an isolated protein, preferably an ABC2 transporter protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence which hybridizes under stringent hybridization conditions to a nucleic acid molecule comprising the nucleotide sequence of SEQ ID NO: 1 or 3, or a complement thereof.
The proteins of the present invention or portions thereof, e.g., biologically active portions thereof, can be operatively linked to a non-ABC2 transporter polypeptide (e.g., heterologous amino acid sequences) to form fusion proteins. The invention further features antibodies, such as monoclonal or polyclonal antibodies, that specifically bind proteins of the invention, preferably ABC2 transporter proteins. In addition, the ABC2 transporter proteins, biologically active portions thereof, or expressible nucleic acids encoding the foregoing, can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable carriers.
In another aspect, the present invention provides a method for detecting the presence of an ABC2 transporter nucleic acid molecule, protein or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting an ABC2 transporter nucleic acid molecule, protein or polypeptide such that the presence of an ABC2 transporter nucleic acid molecule, protein or polypeptide is detected in the biological sample.
In another aspect, the present invention provides a method for detecting the presence of ABC2 transporter activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of ABC2 transporter activity such that the presence of ABC2 transporter activity is detected in the biological sample.
In another aspect, the invention provides a method for modulating ABC2 transporter activity comprising contacting a cell capable of expressing an ABC2 transporter with an agent that modulates ABC2 transporter activity such that ABC2 transporter activity in the cell is modulated. In one embodiment, the agent inhibits ABC2 transporter activity. In another embodiment, the agent modulates the ability of the ABC2 transporter to allosterically modify the function of other membrane proteins. In another embodiment, the agent stimulates ABC2 transporter activity. In one embodiment, the agent is an antibody that specifically binds to an ABC2 transporter protein. In another embodiment, the agent modulates expression of ABC2 transporter by modulating transcription of an ABC2 transporter gene or translation of an ABC2 transporter mRNA. In yet another embodiment, the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of an ABC2 transporter mRNA or an ABC2 transporter gene. In one embodiment, the methods of the present invention are used to treat a subject having a disorder characterized by aberrant or unwanted ABC2 transporter protein or nucleic acid expression or activity by administering an agent which is an ABC2 transporter modulator to the subject. In one embodiment, the ABC2 transporter modulator is an AB2C transporter protein. In another embodiment the ABC2 transporter modulator is an ABC2 transporter nucleic acid molecule. In yet another embodiment, the ABC2 transporter modulator is a polypeptide antibody (or fragment thereof), peptide, peptidomimetic, or other small molecule, e.g. a molecule that is carbohydrate-based, lipid-based, nucleic acid-based, natural organic- based, or synthetically derived organic-based. The present invention also provides a diagnostic assay for identifying the presence or absence of a genetic alteration characterized by at least one of (i) aberrant modification or mutation of a gene encoding an ABC2 transporter protein; (ii) mis-regulation of the gene; and (iii) aberrant post-translational modification of an ABC2 transporter protein, wherein a wild- type form of the gene encodes a protein with an ABC2 transporter activity. In another aspect the invention provides a method for identifying a compound that binds to or modulates the activity of an ABC2 transporter protein, by providing an indicator composition comprising an ABC2 transporter protein having ABC2 transporter activity, contacting the indicator composition with a test compound, and determining the effect of the test compound on ABC2 transporter activity in the indicator composition to identify a compound that modulates the activity of an ABC2 transporter protein, e.g., an ABC2 transporter protein associated with a membrane.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 depicts the cDNA sequence and predicted amino acid sequence of a human ABC2 transporter. The nucleotide sequence corresponds to nucleic acids 1 to 6792 of SEQ ED NO: 1. The coding region without the 5' and 3' untranslated regions of the human ABC2 transporter gene is shown in SEQ ED NO: 3.
Figure 2 depicts the amino acid sequence of the ABC transporter molecule corresponding to amino acids 1 to 2001 of SEQ ED NO: 2. Figure 3 depicts an amino acid sequence alignment of the human ABC2 transporter polypeptide compared with polypeptides found in various species. The symbols (:) and (*) represent, respectively, amino acid residue positions having similarity or identity.
Figure 4 depicts hydrophobicity, hydrophilicity, and transmembrane plots for the human ABC2 transporter polypeptide. Figure 5 depicts a transmembrane helix prediction plot for the human ABC2 transporter polypeptide. Figure 6 depicts a schematic showing the map positions of various cDNA fragments and primer locations with respect to the full length ABC2 transporter clone (hsA2.2).
DETAILED DESCRIPTION OF THE INVENTION The present invention is based, at least in part, on the discovery of a novel ATP Binding
Cassette (ABC) transporter family member, referred to herein as ABC2 transporter nucleic acid and protein molecules. ABC transporter molecules are transmembrane proteins which catalyze ATP-dependent transport of endogenous or exogenous substrates across biological membranes. ABC transporters have been associated with the transport of polypeptides, e.g., a neurotoxic polypeptide, such as β-amyloid, which is involved in Alzheimer's disease. Other neurological diseases caused by neurotoxic polypeptides include prion diseases, Parkinson's disease, Huntington's disease, etc. (for a review, see Hardy et al. (1998) Science 282: 1075-1079). In particular, ABC transporters are associated with the transport of substrates across the blood- brain-barrier. In addition, ABC transporters are associated with multidrug resistance found in cells especially, e.g., cells that are refractory to cytotoxic anti-cancer drugs (Borst, P. (1997) Sem. Cancer Bio. 8:131-134).
Accordingly, the ABC2 transporter molecules of the invention are suitable targets for developing novel diagnostic targets and therapeutic agents to control cellular transport in cells of the brain (e.g., neuronal cells) and transport across the blood-brain-barrier. Moreover, the ABC2 transporter molecules are suitable targets for developing diagnostic targets and therapeutic agents for detecting and/or treating cells or tissues having multidrug resistance, e.g., a cancer.
In particular, the novel human ABC2 transporter molecules described herein are believed to have one or more of the following functions and/or applications: -ABC transporters expressed in the brain are implicated in the transport of substrates through the blood brain barrier (Schinkel A.H., et al, (1994) Cell, 77, 491) and therefore identification of the sequence of the human ABC2 transporter described herein affords the development of new strategies for altering the function of the blood brain barrier. Given that many drugs of potential utility in treating diseases of the brain are discarded because they do not enter the brain at therapeutically relevant concentrations, the present invention allows for the development of strategies to assist in the delivery of drugs to the brain.
-ABC transporters expressed in the brain (as described in, e.g., U.S. Patent Application No. 08/847,616 and PCT/US98/08463, the text of which is incorporated herein) are potential transporters for the β-amyloid peptide, a peptide whose deposition in senile plaques is a fundamental feature of Alzheimer's disease. Thus, identifying novel transporters that regulate β-amyloid deposition is crucial in developing therapeutic treatment for Alzheimer's disease. -The human homologue of the Drosophila melanogaster white gene has been reported to be associated with mood and panic disorders (Nakamura M et al, (1999), Mol. Psychiatry, 4, 155-162), and this gene is a member of the superfamily of ABC transporters. The human ABC2 transporter of the invention is also expressed in the brain, and, accordingly, may be involved in mood and panic disorders. Identification of the sequence of human ABC transporter described herein allows for the development of new treatments for mood and panic disorders.
-ABC transporters have been shown to be involved in the phenomenon of multidrug resistance (Ling, V., (1997) Cancer Chemother Pharmacol 40:S3-S8), and overexpression of human ABC2 has been shown to be associated with a multidrug phenotype (Naomi, M., et α/.,(1998) Cancer Research, 58: 1332-1337). The present invention will allow precise determination of the ability of ABC2 to contribute to the multidrug resistance phenotype and the design of agents capable of ameliorating multidrug resistance using techniques similar to those described by Boer, R., et al. ((1996) European Journal of Cancer, 32A: 857-861). -The human ABC1 protein has been shown to be associated with cholesterol efflux and mutated forms cause Tangier disease and familial high-density lipoprotein deficiency (Brooks- Wilson A. et al, Bodzioch M. et al. Rust S. et al, Nature Genetics, 22, 336-345, 347-351, 352- 355 respectively). As the ABC1 protein is a close homologue of the ABC2 protein, human ABC2 is likely to be a cholesterol transporter. Identification of the sequence of human ABC2 allows for the development of new treatments for diseases involving cholesterol misregulation. -The mouse Abel protein has been implicated in interleukin-lβ (EL-lβ) secretion from macrophages (Hamon Y. et al, 1997, Blood, 90, 2911-2915). IL-lβ is a mediator of inflammatory reactions, and agents able to impair its production or secretion are of potential therapeutic importance. Thus, identification of the related sequence of human ABC2 allows for the development of new treatments for inflammatory diseases.
The term "family" when referring to the protein and nucleic acid molecules of the invention is intended to mean two or more proteins or nucleic acid molecules having a common structural domain or motif and having sufficient amino acid or nucleotide sequence homology as defined herein. Such family members can be naturally or non-naturally occurring and can be from either the same or different species. For example, a family can contain a first protein of human origin, as well as other, distinct proteins of human origin or alternatively, can contain homologues of non-human origin. Members of a family may also have common functional characteristics.
For example, the family of. ABC transporter proteins comprise at least one "transmembrane domain" and preferably two transmembrane domains. As used herein, the term "transmembrane domain" includes an amino acid sequence of about 18 amino acid residues in length which spans the plasma membrane. More preferably, a transmembrane domain includes about at least 18, 20, 25, 30, 35, 40, or 45 residues or more and spans the plasma membrane. Transmembrane domains are described in, for example, Zagotta W.N. et a (1996) Annual Rev. Neuronsci. 19: 235-63, the contents of which are incorporated herein by reference. The amino acid sequences of the human ABC2 transporter protein that comprise transmembrane domains are indicated in Fig. 2. One or more of these transmembrane domains may associate to form a membrane-spanning domain.
Isolated proteins of the present invention, preferably ABC2 transporter proteins, have an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ED NO: 2 or are encoded by a nucleotide sequence sufficiently homologous to SEQ ED NO: 1 or 3. As used herein, the term "sufficiently homologous" refers to a first amino acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an amino acid residue which has a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences share common structural domains or motifs and/or a common functional activity. For example, amino acid or nucleotide sequences which share common structural domains have at least 60% homology, more preferably 70%-80%, and even more preferably 90-95% homology across the amino acid sequences of the domains and contain at least one and preferably two structural domains or motifs, are defined herein as sufficiently homologous. Furthermore, amino acid or nucleotide sequences which share at least 60%, more preferably 70-80%, or 90-95% homology and share a common functional activity are defined herein as sufficiently homologous.
As used interchangeably herein, "ABC2 transporter activity", "biological activity of an ABC2 transporter" or "functional activity of an ABC2 transporter ", refers to an activity exerted by an ABC2 transporter protein, polypeptide or nucleic acid molecule on an ABC2 transporter responsive cell or on an ABC2 transporter protein substrate, as determined in vivo, or in vitro, according to standard techniques. Preferably, an ABC2 transporter activity has the ability to act as an energy-dependent (ATP) molecular pump. In one embodiment, an ABC2 activity is a direct activity, such as an association with a membrane associated protein and/or the transport of an endogenous or exogenous substrate across a biological membrane. In another embodiment, the ABC2 activity is the ability of the polypeptide to allosterically modify the function of other membrane proteins. For example, in some cells, modulation of p- glycoprotein by an ABC transporter modulator has been shown to alter the magnitude of volume-activated chloride currents (reviewed in Higgins, C. F. Volume-activated chloride currents associated with the multidrug resistance P-glycoprotein, J. Physiol. 482:31S-36S (1995)). Thus, in this model, p-glycoprotein and other ABC transporters have multiple functions, one of which is to allosterically modify the function of the other membrane proteins. The present invention is consistent with a model in which the allosteric modification of other membrane proteins by e.g., an ABC2 transporter, is responsible for a change in the transport of a substrate, e.g., β-amyloid, a cytotoxic drug, or other small molecule. Accordingly, an ABC2 activity is at least one or more of the following activities: (i) activation of an ABC2-dependent signal transduction pathway; (ii) modulation of the transport of a substrate (e.g., a cytotoxic drug, β-amyloid) across a membrane; (iii) interaction of an ABC2 protein with a non-ABC2 membrane-associated molecule; (iv) modulation of the development or differentiation of an ABC2-expressing cell; (v) modulation of the development or differentiation of a non-ABC2- expressing cell; (vi) modulation of the homeostasis of an ABC2-expressing cell; and (vii) modulation of the homeostasis of a non-ABC2-expressing cell. Accordingly, another embodiment of the invention features isolated ABC2 transporter proteins and polypeptides having an ABC2 transporter activity. Preferred proteins are ABC2 transporter proteins having at least one transmembrane domain, preferably two transmembrane domains, and, preferably, ABC2 transporter activity.
The nucleotide sequence of the isolated human ABC2 transporter protein cDNA and the predicted amino acid sequence of the human ABC2 transporter polypeptide are shown in Fig. 5 and in SEQ ID NOs: 1 and 2, respectively.The human ABC2 transporter gene, which is approximately 6792 nucleotides in length, encodes a protein having a molecular weight of approximately 223 kDa and which is approximately 2001 amino acid residues in length. Various aspects of the invention are described in further detail in the following subsections:
I. Isolated Nucleic Acid Molecules
One aspect of the invention pertains to isolated nucleic acid molecules that encode ABC2 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hybridization probes to identify ABC2-encoding nucleic acid molecules (e.g., ABC2 transporter mRNA) and fragments for use as PCR primers for the amplification or mutation of ABC2 transporter nucleic acid molecules. As used herein, the term "nucleic acid molecule" is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
The term "isolated nucleic acid molecule" includes nucleic acid molecules which are separated from other nucleic acid molecules which are present in the natural source of the nucleic acid. For example, with regards to genomic DNA, the term "isolated" includes nucleic acid molecules which are separated from the chromosome with which the genomic DNA is naturally associated. Preferably, an "isolated" nucleic acid is free of sequences which naturally flank the nucleic acid (i.e., sequences located at the 5' and 3' ends of the nucleic acid) in the genomic DNA of the organism from which the nucleic acid is derived. For example, in various embodiments, the isolated ABC2 transporter nucleic acid molecule can contain less than about 5 kb, 4kb, 3kb, 2kb, 1 kb, 0.5 kb or 0.1 kb of nucleotide sequences which naturally flank the nucleic acid molecule in genomic DNA of the cell from which the nucleic acid is derived. Moreover, an "isolated" nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. A nucleic acid molecule of the present invention, e.g., a nucleic acid molecule having the nucleotide sequence of SEQ ED NO: 1 or 3, or a portion thereof, can be isolated using standard molecular biology techniques and the sequence information provided herein. Using all or portion of the nucleic acid sequence of SEQ D NO: 1 or 3 as a hybridization probe, ABC2 transporter nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989). Moreover, a nucleic acid molecule encompassing all or a portion of SEQ ED NO: 1 or 3 can be isolated by the polymerase chain reaction (PCR) using synthetic oligonucleotide primers designed based upon the sequence of SEQ ED NO: 1 or 3.
A nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The nucleic acid so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis. Furthermore, oligonucleotides corresponding to ABC2 transporter nucleotide sequences can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer. In a preferred embodiment, an isolated nucleic acid molecule of the invention comprises the nucleotide sequence shown in SEQ ID NO: 1. The sequence of SEQ ID NO: 1 corresponds to the human ABC2 cDNA. This cDNA comprises sequences encoding the human ABC2 protein (i.e., "the coding region", from nucleotides 91-6096), as well as 5' untranslated sequences (nucleotides 1-90) and 3' untranslated sequences (nucleotides 6097-6792). Alternatively, the nucleic acid molecule can comprise only the coding region of SEQ ED NO: 1 (e.g., nucleotides 91-6096, corresponding to SEQ ED NO: 3).
In another preferred embodiment, an isolated nucleic acid molecule of the invention comprises a nucleic acid molecule which is a complement of the nucleotide sequence shown in SEQ ID NO: 1 or 3, or a portion of any of these nucleotide sequences. A nucleic acid molecule which is complementary to the nucleotide sequence shown in SEQ ID NO: 1 or 3 is one which is sufficiently complementary to the nucleotide sequence shown in SEQ ID NO: 1 or 3 such that it can hybridize to the nucleotide sequence shown in SEQ ED NO: 1 or 3, thereby forming a stable duplex.
In still another preferred embodiment, an isolated nucleic acid molecule of the present invention comprises a nucleotide sequence which is at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to the entire length of the nucleotide sequence shown in SEQ ED NO: 1 or 3, or a portion of any of these nucleotide sequences.
Moreover, the nucleic acid molecule of the invention can comprise only a portion of the nucleic acid sequence of SEQ ED NO: 1 or 3, for example, a fragment which can be used as a probe or primer or a fragment encoding a portion of an ABC2 transporter protein, e.g., a biologically active portion of an ABC2 transporter protein. The nucleotide sequence determined from the cloning of the ABC2 transporter gene allows for the generation of probes and primers designed for use in identifying and/or cloning other ABC2 transporter family members, as well as ABC2 transporter homologues from other species. The probe/primer typically comprises substantially purified oligonucleotide. The oligonucleotide typically comprises a region of nucleotide sequence that hybridizes under stringent conditions to at least about 12 or 15, preferably about 20 or 25, more preferably about 30, 35, 40, 45, 50, 55, 60, 65, or 75 consecutive nucleotides of a sense sequence of SEQ ED NO: 1 or 3 of an anti-sense sequence of SEQ ID NO: 1 or 3, or of a naturally occurring allelic variant or mutant of SEQ ED NO: 1 or 3. In an exemplary embodiment, a nucleic acid molecule of the present invention comprises a nucleotide sequence which is greater than 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500-1000, 1000-1500, 1500-2000, or 2000-2500 or more nucleotides in length and hybridizes under stringent hybridization conditions to a nucleic acid molecule of SEQ ED NO: l or 3. Probes based on the ABC2 transporter nucleotide sequences can be used to detect transcripts or genomic sequences encoding the same or homologous proteins. In preferred embodiments, the probe further comprises a label group attached thereto, e.g., the label group can be a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as a part of a diagnostic test kit for identifying cells or tissue which misexpress an ABC2 transporter protein, such as by measuring a level of an ABC2-encoding nucleic acid in a sample of cells from a subject e.g., detecting ABC2 transporter mRNA levels or determining whether a genomic ABC2 transporter gene has been mutated or deleted.
A nucleic acid fragment encoding a "biologically active portion of an ABC2 transporter protein" can be prepared by isolating a portion of the nucleotide sequence of SEQ ED NO: 1 or 3 which encodes a polypeptide having an ABC2 transporter biological activity (the biological activities of the ABC2 transporter proteins are described herein), expressing the encoded portion of the ABC2 transporter protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the ABC2 transporter protein.
The invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ED NO: 1 or 3 due to degeneracy of the genetic code and thus encode the same ABC2 transporter proteins as those encoded by the nucleotide sequence shown in SEQ ED NO: 1 or 3. In another embodiment, an isolated nucleic acid molecule of the invention has a nucleotide sequence encoding a protein having an amino acid sequence shown in SEQ ED NO: 2.
In addition to the ABC2 transporter nucleotide sequences shown in SEQ ED NO: 1 or 3, it will be appreciated by those skilled in the art that DNA sequence polymorphisms that lead to changes in the amino acid sequences of the ABC2 transporter proteins may exist within a population (e.g., the human population). Such genetic polymorphism in the ABC2 transporter genes may exist among individuals within a population due to natural allelic variation. As used herein, the terms "gene" and "recombinant gene" refer to nucleic acid molecules which include an open reading frame encoding an ABC2 transporter protein, preferably a mammalian ABC2 transporter protein, and can further include non-coding regulatory sequences, and introns.
Allelic variants of a human ABC2 transporter include both functional and nonfunctional ABC2 transporter proteins. Functional allelic variants are naturally occurring amino acid sequence variants of the human ABC2 transporter that maintain the ability to bind an ABC2 transporter ligand. Functional allelic variants will typically contain only conservative substitution of one or more amino acids of SEQ ED NO: 2 or substitution, deletion or insertion of non-critical residues in non-critical regions of the protein.
Non-functional allelic variants are naturally occurring amino acid sequence variants of the human ABC2 transporter protein that do not have the ability to either bind an ABC2 transporter ligand. Non-functional allelic variants will typically contain a non-conservative substitution, a deletion, or insertion or premature truncation of the amino acid sequence of SEQ ID NO: 2 or a substitution, insertion or deletion in critical residues or critical regions.
The present invention further provides non-human orthologues of the human ABC2 transporter protein. Orthologues of the human ABC2 transporter protein are proteins that are isolated from non-human organisms and possess the same ABC2 transporter activity as the human ABC2 transporter protein. Orthologues of the human ABC2 protein can readily be identified as comprising an amino acid sequence that is substantially homologous to SEQ ID NO: 2.
Moreover, nucleic acid molecules encoding other ABC2 transporter family members and, thus, which have a nucleotide sequence which differs from the ABC2 transporter sequences of SEQ ED NO: 1 or 3 are intended to be within the scope of the invention. For example, another ABC2 transporter cDNA can be identified based on the nucleotide sequence of the human ABC2 transporter. Moreover, nucleic acid molecules encoding ABC2 transporter proteins from different species, e.g., mammals, and which, thus, have a nucleotide sequence which differs from the ABC2 transporter sequences of SEQ ED NO: 1 or 3 are intended to be within the scope of the invention. For example, a mouse ABC2 transporter cDNA can be identified based on the nucleotide sequence of the human ABC2 transporter.
Nucleic acid molecules corresponding to natural allelic variants and homologues of the ABC2 transporter cDNAs of the invention can be isolated based on their homology to the ABC2 transporter nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hybridization probe according to standard hybridization techniques under stringent hybridization conditions. Nucleic acid molecules corresponding to natural allelic variants and homologues of the ABC2 transporter cDNAs of the invention can further be isolated by mapping to the same chromosome or locus as the ABC2 transporter gene.
Accordingly, in another embodiment, an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hybridizes under stringent conditions to the nucleic acid molecule comprising the nucleotide sequence of SEQ ED NO: 1 or 3. En other embodiment, the nucleic acid is at least 30, 50, 100, 150, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1250, 1500, 1750, 2000, 2250, 2500, 2739 or more nucleotides in length. As used herein, the term "hybridizes under stringent conditions" is intended to describe conditions for hybridization and washing under which nucleotide sequences at least 75% homologous to each other typically remain hybridized to each other. Preferably, the conditions are such that sequences at least about 80%, even more preferably at least about 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 98% homologous to each other typically remain hybridized to each other. Such stringent conditions are known to those skilled in the art and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.1-6.3.6. A preferred, non-limiting example of stringent hybridization conditions are hybridization in 6X sodium chloride/sodium citrate (SSC) at about 45°C, followed by one or more washes in 0.2 X SSC, 0.1% SDS at 50°C, preferably at 55°C, more preferably at 60°C, and even more preferably at 65°C. Preferably, an isolated nucleic acid molecule of the invention that hybridizes under stringent conditions to the sequence of SEQ ED NO: 1 or 3 corresponds to a naturally-occurring nucleic acid molecule. As used herein, a "naturally- occurring" nucleic acid molecule refers to an RNA or DNA molecule having a nucleotide sequence that occurs in nature (e.g., encodes a natural protein).
In addition to naturally-occurring allelic variants of the ABC2 transporter sequences that may exist in the population, the skilled artisan will further appreciate that changes can be introduced by mutation into the nucleotide sequences of SEQ ED NO: 1 or 3, thereby leading to changes in the amino acid sequence of the encoded ABC2 transporter proteins, without altering the functional ability of the ABC2 transporter proteins. For example, nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ID NO: 1 or 3. A "non-essential" amino acid residue is a residue that can be altered from the wild-type sequence of ABC2 transporter (e.g., the sequence of SEQ ID NO: 2) without altering the biological activity, whereas an "essential" amino acid residue is required for biological activity.
Accordingly, another aspect of the invention pertains to nucleic acid molecules encoding ABC2 transporter proteins that contain changes in amino acid residues that are not essential for activity. Such ABC2 transporter proteins differ in amino acid sequence from SEQ ED NO: 2, yet retain biological activity. En one embodiment, the isolated nucleic acid molecule comprises a nucleotide sequence encoding a protein, wherein the protein comprises an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or more homologous to SEQ ED NO: 2.
An isolated nucleic acid molecule encoding an ABC2 transporter protein homologous to the protein of SEQ ED NO: 2 can be created by introducing one or more nucleotide substitutions, additions, or deletions into the nucleotide sequence of SEQ ED NO: 1 or 3, such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ED NO: 1 or 3 by standard techniques, such as site-directed mutagenesis and PCR-mediated mutagenesis. Preferably, conservative amino acid substitutions are made at one or more predicted non-essential amino acid residues. A "conservative amino acid substitution" is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in an ABC2 transporter protein is preferably replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of an ABC2 transporter coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for ABC2 transporter biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ED NO: 1 or 3 the encoded protein can be expressed recombinantly and the activity of the protein can be determined. En a preferred embodiment, a mutant ABC2 transporter protein can be assayed for the ability to interact with a non-ABC2 transporter molecule, e.g., an ABC2 transporter ligand, e.g., a polypeptide or a small molecule. In addition to the nucleic acid molecules encoding ABC2 transporter proteins described above, another aspect of the invention pertains to isolated nucleic acid molecules which are antisense thereto. An "antisense" nucleic acid comprises a nucleotide sequence which is complementary to a "sense" nucleic acid encoding a protein, e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can hydrogen bond to a sense nucleic acid. The antisense nucleic acid can be complementary to an entire ABC2 transporter coding strand, or to only a portion thereof. In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding ABC2. The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues (e.g., the coding region of human UMAT corresponds to SEQ ED NO: 3). In another embodiment, the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding ABC2. The term "noncoding region" refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).
Given the coding strand sequences encoding ABC2 transporter disclosed herein (e.g., SEQ ED NO: 3), antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of ABC2 transporter mRNA, but more preferably is an oligonucleotide which is antisense to only a portion of the coding or noncoding region of
ABC2 transporter mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of ABC2 transporter mRNA. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides or more in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5- iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1- methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5- methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4- thiouracil, 5-methyluracil, uracil-5- oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5- methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following subsection).
The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding an ABC2 transporter protein to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention include direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient intracellular concentrations of the antisense molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred. In yet another embodiment, the antisense nucleic acid molecule of the invention is an α- anomeric nucleic acid molecule. An cc-anomeric nucleic acid molecule forms specific double- stranded hybrids with complementary RNA in which, contrary to the usual β-units, the strands run parallel to each other (Gaultier et al. (1987) Nucleic Acids. Res. 15:6625-6641). The antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (Inoue et al (1987) Nucleic Acids Res. 15:6131-6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
In still another embodiment, an antisense nucleic acid of the invention is a ribozyme. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave ABC2 transporter mRNA transcripts to thereby inhibit translation of ABC2 transporter mRNA. A ribozyme having specificity for an ABC2-encoding nucleic acid can be designed based upon the nucleotide sequence of an ABC2 transporter cDNA disclosed herein (i.e., SEQ ED NO: 1). For example, a derivative of a Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in an ABC2-encoding mRNA. See, e.g., Cech et al U.S. Patent No. 4,987,071; and Cech et al. U.S. Patent No. 5,116,742. Alternatively, ABC2 transporter mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261:1411-1418.
Alternatively, ABC2 transporter gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the ABC2 transporter (e.g., the ABC2 transporter promoter and/or enhancers) to form triple helical structures that prevent transcription of the ABC2 transporter gene in target cells. See generally, Helene, C. (1991) Anticancer Drug Des. 6(6):569-84; Helene, C. et al. (1992) Ann. NY. Acad. Sci. 660:27-36; and Maher, L.J. (1992) Bioassays 14(12):807-15. In yet another embodiment, the ABC2 transporter nucleic acid molecules of the present invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acid molecules can be modified to generate peptide nucleic acids (see Hyrup B. et al. (1996) Bioorganic & Medicinal Chemistry 4 (1): 5-23). As used herein, the terms "peptide nucleic acids" or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup B. et al. (1996) supra; Perry-OXeefe et al. Proc. Natl. Acad. Sci. 93: 14670-675.
PNAs of ABC2 transporter nucleic acid molecules can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, for example, inducing transcription or translation arrest or inhibiting replication. PNAs of ABC2 transporter nucleic acid molecules can also be used in the analysis of single base pair mutations in a gene, (e.g., by PNA-directed PCR clamping); as 'artificial restriction enzymes' when used in combination with other enzymes, (e.g., SI nucleases (Hyrup B. (1996) supra)); or as probes or primers for DNA sequencing or hybridization (Hyrup B. et al. (1996) supra; Perry-OXeefe supra). In another embodiment, PNAs of ABC2 transporter nucleic acid molecules can be modified, (e.g., to enhance their stability or cellular uptake), by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras of ABC2 transporter nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, (e.g., RNAse H and DNA polymerases), to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup B. (1996) supra). The synthesis of PNA- DNA chimeras can be performed as described in Hyrup B. (1996) supra and Finn P J. et al. (1996) Nucleic Acids Res. 24 (17): 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5'-deoxy-thymidine phosphoramidite, can be used as a between the PNA and the 5' end of DNA (Mag, M. et al. (1989) Nucleic Acid Res. 17: 5973- 88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. (1996) supra). Alternatively, chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment (Peterser, K.H. et al. (1975) Bioorganic Med. Chem. Lett. 5: 1119-11124).
In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al. (1989) Proc. Natl Acad. Sci. USA 86:6553-6556; Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT Publication No.
W088/09810) or the blood-brain barrier (see, e.g., PCT Publication No. W089/10134). In addition, oligonucleotides can be modified with hybridization-triggered cleavage agents (See, e.g., Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating agents (See, e.g., Zon (1988) Pharm. Res. 5:539-549). To this end, the oligonucleotide may be conjugated to another molecule, (e.g., a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent).
II. Isolated ABC2 Transporter Proteins and Anti-ABC2 Transporter Antibodies One aspect of the invention pertains to isolated ABC2 transporter proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise anti-ABC2 transporter antibodies. In one embodiment, native ABC2 transporter proteins can be isolated from cells or tissue sources by an appropriate purification scheme using standard protein purification techniques. In another embodiment, ABC2 transporter proteins are produced by recombinant DNA techniques. Alternative to recombinant expression, an ABC2 transporter protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques. An "isolated" or "purified" protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the ABC2 transporter protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language "substantially free of cellular material" includes preparations of ABC2 transporter protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language "substantially free of cellular material" includes preparations of ABC2 transporter protein having less than about 30% (by dry weight) of non-ABC2 transporter protein (also referred to herein as a "contaminating protein"), more preferably less than about 20% of non-ABC2 transporter protein, still more preferably less than about 10% of non-ABC2 transporter protein, and most preferably less than about 5% non-ABC2 transporter protein. When the ABC2 transporter protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation.
The language "substantially free of chemical precursors or other chemicals" includes preparations of ABC2 transporter protein in which the protein is separated from chemical precursors or other chemicals which are involved in the synthesis of the protein. In one embodiment, the language "substantially free of chemical precursors or other chemicals" includes preparations of ABC2 transporter protein having less than about 30% (by dry weight) of chemical precursors or non-ABC2 transporter chemicals, more preferably less than about 20% chemical precursors or non-ABC2 transporter chemicals, still more preferably less than about 10% chemical precursors or non-ABC2 transporter chemicals, and most preferably less than about 5% chemical precursors or non-ABC2 transporter chemicals. As used herein, a "biologically active portion" of an ABC2 transporter protein includes a fragment of an ABC2 transporter protein which participates in an interaction between an ABC2 transporter molecule and a non-ABC2 transporter molecule. Biologically active portions of an ABC2 transporter protein include peptides comprising amino acid sequences sufficiently homologous to or derived from the amino acid sequence of the ABC2 transporter protein, e.g., the amino acid sequence shown in SEQ ED NO: 2, which include less amino acids than the full length ABC2 transporter proteins, and exhibit at least one activity of an ABC2 transporter protein. Typically, biologically active portions comprise a domain or motif with at least one activity of the ABC2 transporter protein. A biologically active portion of an ABC2 transporter protein can be a polypeptide which is, for example, 10, 25, 50, 100, 200, 300, 400, 500, 600, 700, 800 or more amino acids in length. Biologically active portions of an ABC2 transporter protein can be used as targets for developing agents which modulate an ABC2 transporter mediated activity. In one embodiment, a biologically active portion of an ABC2 transporter protein comprises at least one transmembrane domain. It is to be understood that a preferred biologically active portion of an ABC2 transporter protein of the present invention may contain at least one transmembrane domain. Another preferred biologically active portion of an ABC2 transporter protein may contain at least two transmembrane domains. One or more of these transmembrane domains may associate to form a membrane-spanning domain. In addition, or alternatively, the biologically active portion of the ABC2 transporter protein may include multiple clusters of conserved residues that define an ATP binding domain. In addition, or alternatively, the biologically active portion of the ABC2 transporter protein may comprise a Walker domain, e.g., a Walker A and/or Walker B domain (see Fig. 2.; Patel et al. (1998) Trends Cell Biol 8: 65-71). Identification of these domains may be facilitated using any of a number of art recognized molecular modeling techniques as described herein (see also Example 2). Moreover, other biologically active portions, in which other regions of the protein are deleted, can be prepared by recombinant techniques and evaluated for one or more of the functional activities of a native ABC2 transporter protein.
In a preferred embodiment, the ABC2 transporter protein has an amino acid sequence shown in SEQ ED NO: 2. In other embodiments, the ABC2 transporter protein is substantially homologous to SEQ ED NO: 2, and retains the functional activity of the protein of SEQ ED NO: 2, yet differs in amino acid sequence due to natural allelic variation or mutagenesis, as described in detail in subsection I above. Accordingly, in another embodiment, the ABC2 transporter protein is a protein which comprises an amino acid sequence at least about 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or more homologous to SEQ ID NO: 2.
To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second amino acid or nucleic acid sequence for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). In a preferred embodiment, the length of a reference sequence aligned for comparison purposes is at least 70%, preferably, 80%, 90% or 100% of the length of the reference sequence (e.g., when aligning a second sequence to the ABC2 transporter amino acid sequence of SEQ ED NO: 2 having 2001 amino acid residues, at least 600, preferably at least 800, more preferably at least 1000, even more preferably at least 1200, and even more preferably at least 1400, 1600, 1800, or 2001 amino acid residues are aligned). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position (as used herein amino acid or nucleic acid "identity" is equivalent to amino acid or nucleic acid "homology"). The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which need to be introduced for optimal alignment of the two sequences. A comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In a preferred embodiment, the percent identity between two amino acid sequences is determined using standard art recognized comparison software using standard parameter settings. For example, the Needleman and Wunsch (J. Mol Biol (48):444-453 (1970)) algorithm which has been incorporated into the GAP program in the GCG software package (available at http://www.gcg.com) can be employed using either a Blossum 62 matrix or a PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred embodiment, the percent identity between two nucleotide sequences is determined using the GAP program in the GCG software package (available at http://www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40, 50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6. In another embodiment, the percent identity between two amino acid or nucleotide sequences is determined using the algorithm of E. Meyers and W. Miller (CABIOS, 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
The nucleic acid and protein sequences of the present invention can further be used as a "query sequence" to perform a search against public databases to, for example, identify other family members or related sequences. Such searches can be performed using the NBLAST and XBLAST programs (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10. BLAST nucleotide searches can be performed with the NBLAST program, score = 100, wordlength = 12 to obtain nucleotide sequences homologous to ABC2 transporter nucleic acid molecules of the invention. BLAST protein searches can be performed with the XBLAST program, score = 50, wordlength = 3 to obtain amino acid sequences homologous to ABC2 transporter protein molecules of the invention. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al, (1997) Nucleic Acids Res. 25(17):3389- 3402. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov.
The invention also provides ABC2 transporter chimeric or fusion proteins. As used herein, an ABC2 transporter "chimeric protein" or "fusion protein" comprises an ABC2 transporter polypeptide operatively linked to a non-ABC2 transporter polypeptide. An "ABC2 transporter polypeptide" refers to a polypeptide having an amino acid sequence corresponding to ABC2, whereas a "non-ABC2 transporter polypeptide" refers to a polypeptide having an amino acid sequence corresponding to a protein which is not substantially homologous to the ABC2 transporter protein, e.g., a protein which is different from the ABC2 transporter protein and which is derived from the same or a different organism. Within an ABC2 transporter fusion protein the ABC2 transporter polypeptide can correspond to all or a portion of an ABC2 transporter protein. In a preferred embodiment, an ABC2 transporter fusion protein comprises at least one biologically active portion of an ABC2 transporter protein. In another preferred embodiment, an ABC2 transporter fusion protein comprises at least two biologically active portions of an ABC2 transporter protein. Within the fusion protein, the term "operatively linked" is intended to indicate that the ABC2 transporter polypeptide and the non-ABC2 transporter polypeptide are fused in-frame to each other. The non-ABC2 transporter polypeptide can be fused to the N-terminus or C-terminus of the ABC2 transporter polypeptide. For example, in one embodiment, the fusion protein is a GST-ABC2 transporter fusion protein in which the ABC2 transporter sequences are fused to the C-terminus of the GST sequences. Such fusion proteins can facilitate the purification of recombinant ABC2.
In another embodiment, the fusion protein is an ABC2 transporter protein containing a heterologous signal sequence at its N-terminus. In certain host cells (e.g., mammalian host cells), expression and/or secretion of ABC2 transporter can be increased through use of a heterologous signal sequence. The ABC2 transporter fusion proteins of the invention can be incorporated into pharmaceutical compositions and administered to a subject in vivo. The ABC2 transporter fusion proteins can be used to affect the bioavailability of an ABC2 transporter substrate. Use of ABC2 transporter fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, (i) aberrant modification or mutation of a gene encoding an ABC2 transporter protein; (ii) mis-regulation of the ABC2 transporter gene; and (iii) aberrant post-translational modification of an ABC2 transporter protein.
Moreover, the ABC2-fusion proteins of the invention can be used as immunogens to produce anti-ABC2 transporter antibodies in a subject, to purify ABC2 transporter ligands and in screening assays to identify molecules which inhibit the interaction of an ABC2 transporter with an ABC2 transporter substrate.
Preferably, an ABC2 transporter chimeric or fusion protein of the invention is produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different polypeptide sequences are ligated together in-frame in accordance with conventional techniques, for example by employing blunt-ended or stagger-ended termini for ligation, restriction enzyme digestion to provide for appropriate termini, filling-in of cohesive ends as appropriate, alkaline phosphatase treatment to avoid undesirable joining, and enzymatic ligation. In another embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chimeric gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide). An ABC2 transporter-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the ABC2 transporter protein.
The present invention also pertains to variants of the ABC2 transporter proteins which function as either ABC2 transporter agonists or as ABC2 transporter antagonists. Variants of the ABC2 transporter proteins can be generated by mutagenesis, e.g., discrete point mutation or truncation of an ABC2 transporter protein. An agonist of the ABC2 transporter proteins can retain substantially the same, or a subset, of the biological activities of the naturally occurring form of an ABC2 transporter protein. An antagonist of an ABC2 transporter protein can inhibit one or more of the activities of the naturally occurring form of the ABC2 transporter protein by, for example, competitively modulating an activity of an ABC2 transporter protein. Thus, specific biological effects can be elicited by treatment with a variant of limited function. In one embodiment, treatment of a subject with a variant having a subset of the biological activities of the naturally occurring form of the protein has fewer side effects in a subject relative to treatment with the naturally occurring form of the ABC2 transporter protein.
In one embodiment, variants of an ABC2 transporter protein which function as either ABC2 transporter agonists (mimetics) or as ABC2 transporter antagonists can be identified by screening combinatorial libraries of mutants, e.g., truncation mutants, of an ABC2 transporter protein for ABC2 transporter protein agonist or antagonist activity. In one embodiment, a variegated library of ABC2 transporter variants is generated by combinatorial mutagenesis at the nucleic acid level and is encoded by a variegated gene library. A variegated library of ABC2 transporter variants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential ABC2 transporter sequences is expressible as individual polypeptides, or alternatively, as a set of larger fusion proteins (e.g., for phage display) containing the set of ABC2 transporter sequences therein. There are a variety of methods which can be used to produce libraries of potential ABC2 transporter variants from a degenerate oligonucleotide sequence. Chemical synthesis of a degenerate gene sequence can be performed in an automatic DNA synthesizer, and the synthetic gene then ligated into an appropriate expression vector. Use of a degenerate set of genes allows for the provision, in one mixture, of all of the sequences encoding the desired set of potential ABC2 transporter sequences. Methods for synthesizing degenerate oligonucleotides are known in the art (see, e.g., Narang, S.A. (1983) Tetrahedron 39:3; Itakura et al (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11 :477.
In addition, libraries of fragments of an ABC2 transporter protein coding sequence can be used to generate a variegated population of ABC2 transporter fragments for screening and subsequent selection of variants of an ABC2 transporter protein. In one embodiment, a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an ABC2 transporter coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denaturing the double stranded DNA, renaturing the DNA to form double stranded DNA which can include sense/antisense pairs from different nicked products, removing single stranded portions from reformed duplexes by treatment with SI nuclease, and ligating the resulting fragment library into an expression vector. By this method, an expression library can be derived which encodes N-terminal, C-terminal and internal fragments of various sizes of the ABC2 transporter protein.
Several techniques are known in the art for screening gene products of combinatorial libraries made by point mutations or truncation, and for screening cDNA libraries for gene products having a selected property. Such techniques are adaptable for rapid screening of the gene libraries generated by the combinatorial mutagenesis of ABC2 transporter proteins. The most widely used techniques, which are amenable to high through-put analysis, for screening large gene libraries typically include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the combinatorial genes under conditions in which detection of a desired activity facilitates isolation of the vector encoding the gene whose product was detected. Recursive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the libraries, can be used in combination with the screening assays to identify ABC2 transporter variants (Arkin and Yourvan (1992) Proc. Natl Acad. Sci. USA 59:7811-7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
An isolated ABC2 transporter protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind ABC2 transporter using standard techniques for polyclonal and monoclonal antibody preparation. A full-length ABC2 transporter protein can be used or, alternatively, the invention provides antigenic peptide fragments of ABC2 transporter for use as immunogens. Preferred epitopes encompassed by the antigenic peptide are regions of ABC2 transporter that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity.
An ABC2 transporter immunogen typically is used to prepare antibodies by immunizing a suitable subject, (e.g., rabbit, goat, mouse or other mammal) with the immunogen. An appropriate immunogenic preparation can contain, for example, recombinantly expressed ABC2 transporter protein or a chemically synthesized ABC2 transporter polypeptide. The preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an immunogenic ABC2 transporter preparation induces a polyclonal anti- ABC2 transporter antibody response. Accordingly, another aspect of the invention pertains to anti-ABC2 transporter antibodies. The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e., molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as ABC2 transporter. Examples of immunologically active portions of immunoglobulin molecules include F(ab) and F(ab')2 fragments which can be generated by treating the antibody with an enzyme such as pepsin. The invention provides polyclonal and monoclonal antibodies that bind ABC2 transporter. The term "monoclonal antibody" or "monoclonal antibody composition", as used herein, refers to a population of antibody molecules that contain only one species of an antigen binding site capable of immunoreacting with a particular epitope of ABC2 transporter. A monoclonal antibody composition thus typically displays a single binding affinity for a particular ABC2 transporter protein with which it immunoreacts.
Polyclonal anti-ABC2 transporter antibodies can be prepared as described above by immunizing a suitable subject with an ABC2 transporter immunogen. The anti-ABC2 transporter antibody titer in the immunized subject can be monitored over time by standard techniques, such as with an enzyme linked immunosorbent assay (ELISA) using immobilized ABC2 transporter. If desired, the antibody molecules directed against ABC2 transporter can be isolated from the mammal (e.g., from the blood) and further purified by well known techniques, such as protein A chromatography to obtain the IgG fraction. At an appropriate time after immunization, e.g., when the anti-ABC2 transporter antibody titers are highest, antibody-producing cells can be obtained from the subject and used to prepare monoclonal antibodies by standard techniques, such as the hybridoma technique originally described by Kohler and Milstein (1975) Nature 256:495-497) (see also, Brown et al. (1981) J. Immunol. 127:539-46; Brown et al. (1980) J. Biol. Chem .255:4980-83; Yeh et al. (1976) Proc. Natl. Acad. Sci. USA 76:2927-31; and Yeh et al. (1982) Int. J. Cancer 29:269-75), the more recent human B cell hybridoma technique (Xozbor et al. (1983) Immunol Today 4:72), the EBV- hybridoma technique (Cole et al. (1985), Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96) or trioma techniques. The technology for producing monoclonal antibody hybridomas is well known (see generally R. H. Kenneth, in Monoclonal Antibodies: A New Dimension In Biological Analyses, Plenum Publishing Corp., New York, New York (1980); E. A. Lerner (1981) Yale J. Biol Med., 54:387-402; M. L. Gefter et al. (1977) Somatic Cell
Genet. 3:231-36). Briefly, an immortal cell line (typically a myeloma) is fused to lymphocytes (typically splenocytes) from a mammal immunized with an ABC2 transporter immunogen as described above, and the culture supernatants of the resulting hybridoma cells are screened to identify a hybridoma producing a monoclonal antibody that binds ABC2 transporter.
Any of the many well known protocols used for fusing lymphocytes and immortalized cell lines can be applied for the purpose of generating an anti-ABC2 transporter monoclonal antibody (see, e.g., G. Galfre et al (1977) Nature 266:55052; Gefter et al Somatic Cell Genet., cited supra; Earner, Yale J. Biol. Med., cited supra; Kenneth, Monoclonal Antibodies, cited supra). Moreover, the ordinarily skilled worker will appreciate that there are many variations of such methods which also would be useful. Typically, the immortal cell line (e.g., a myeloma cell line) is derived from the same mammalian species as the lymphocytes. For example, murine hybridomas can be made by fusing lymphocytes from a mouse immunized with an immunogenic preparation of the present invention with an immortalized mouse cell line. Preferred immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopterin and thymidine ("HAT medium"). Any of a number of myeloma cell lines can be used as a fusion partner according to standard techniques, e.g., the P3-NSl/l-Ag4-l, P3-x63-Ag8.653 or Sp2/O-Agl4 myeloma lines. These myeloma lines are available from ATCC. Typically, HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG"). Hybridoma cells resulting from the fusion are then selected using HAT medium, which kills unfused and unproductively fused myeloma cells (unfused splenocytes die after several days because they are not transformed). Hybridoma cells producing a monoclonal antibody of the invention are detected by screening the hybridoma culture supernatants for antibodies that bind ABC2, e.g., using a standard ELISA assay.
Alternative to preparing monoclonal antibody-secreting hybridomas, a monoclonal anti- ABC2 transporter antibody can be identified and isolated by screening a recombinant combinatorial immunoglobulin library (e.g., an antibody phage display library) with ABC2 transporter to thereby isolate immunoglobulin library members that bind ABC2. Kits for generating and screening phage display libraries are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAP™ Phage Display Kit, Catalog No. 240612). Additionally, examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S. Patent No. 5,223,409; Kang et al. PCT International Publication No. WO 92/18619; Dower et al. PCT International Publication No. WO 91/17271; Winter et al. PCT International Publication WO 92/20791; Markland et al PCT International Publication No. WO 92/15679; Breitling et al. PCT International Publication WO 93/01288; McCafferty et al PCT International Publication No. WO 92/01047; Garrard et al. PCT International Publication No. WO 92/09690; Ladner et al. PCT International Publication No. WO 90/02809; Fuchs et al. (1991) Bio/Technology 9:1370-1372; Hay et al. (1992) Hum. Antibod. Hybridomas 3:81-85; Huse et al. (1989) Science 246:1275-1281; Griffiths et al. (1993) EMBO J 12:725-734; Hawkins et al. (1992) J. Mol Biol 226:889-896; Clarkson et al. (1991) Nature 352:624-628; Gram et al. (1992) Proc. Natl Acad. Sci. USA 89:3576-3580; Garrad et al (1991) Bio/Technology 9:1373-1377; Hoogenboom et al. (1991) Nuc. Acid Res. 19:4133-4137; Barbas et al. (1991) Proc. Natl. Acad. Sci. USA 88:7978-7982; and McCafferty et al. Nature (1990) 348:552-554.
Additionally, recombinant anti-ABC2 transporter antibodies, such as chimeric and humanized monoclonal antibodies, comprising both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention. Such chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in Robinson et al. International Application No. PCT/US 86/02269; Akira, et al. European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison et al European Patent Application 173,494; Neuberger et al. PCT International Publication No. WO 86/01533; Cabilly et al. U.S. Patent No. 4,816,567; Cabilly et al European Patent Application 125,023; Better et al. (1988) Science 240:1041-1043; Liu et al. (1987) Proc. Natl. Acad. Sci. USA 84:3439-3443; Liu et al (1987) J. Immunol. 139:3521-3526; Sun et al. (1987) Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al. (1987) Cane. Res. 47:999-1005; Wood et al (1985) Nature 314:446-449; and Shaw et al. (1988) J. Natl. Cancer Inst. 80:1553-1559); Morrison, S. L. (1985) Science 229:1202-1207; Oi et al. (1986) BioTechniques 4:214; Winter U.S. Patent 5,225,539; Jones et al. (1986) Nature 321:552-525; Verhoeyan et al. (1988) Science 239:1534; and Beidler et al. (1988) J. Immunol. 141:4053-4060.
An anti-ABC2 transporter antibody (e.g., monoclonal antibody) can be used to isolate ABC2 transporter by standard techniques, such as affinity chromatography or immunoprecipitation. An anti-ABC2 transporter antibody can facilitate the purification of natural ABC2 transporter from cells and of recombinantly produced ABC2 transporter expressed in host cells. Moreover, an anti-ABC2 transporter antibody can be used to detect ABC2 transporter protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the ABC2 transporter protein. Anti-ABC2 transporter antibodies can be used diagnostically to monitor protein levels in tissue as part of a clinical testing procedure, e.g., to, for example, determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling (i.e., physically linking) the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, and radioactive materials. Examples of suitable enzymes include horseradish peroxidase, alkaline phosphatase, -galactosidase, or acetylcholinesterase; examples of suitable prosthetic group complexes include streptavidin/biotin and avidin/biotin; examples of suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride or phycoerythrin; an example of a luminescent material includes luminol; examples of bioluminescent materials include luciferase, luciferin, and aequorin, and examples of suitable radioactive material include 125I, 1311, 35S, 33P, 32P, or 3H.
III. Recombinant Expression Vectors and Host Cells
Another aspect of the invention pertains to vectors, preferably expression vectors, containing a nucleic acid encoding an ABC2 transporter protein (or a portion thereof). As used herein, the term "vector" refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments can be ligated. Another type of vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "expression vectors". In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" can be used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions. The recombinant expression vectors of the invention comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory sequences, selected on the basis of the host cells to be used for expression, which is operatively linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, "operably linked" is intended to mean that the nucleotide sequence of interest is linked to the regulatory sequence(s) in a manner which allows for expression of the nucleotide sequence (e.g., in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell). The term "regulatory sequence" is intended to include promoters, enhancers and other expression control elements (e.g., polyadenylation signals). Such regulatory sequences are described, for example, in Goeddel; Gene Expression Technology: Methods in Enzymology
185, Academic Press, San Diego, CA (1990). Regulatory sequences include those which direct constitutive expression of a nucleotide sequence in many types of host cells and those which direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein desired, and the like. The expression vectors of the invention can be introduced into host cells to thereby produce proteins or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., ABC2 transporter proteins, mutant forms of ABC2 transporter proteins, fusion proteins, and the like).
The recombinant expression vectors of the invention can be designed for expression of ABC2 transporter proteins in prokaryotic or eukaryotic cells. For example, ABC2 transporter proteins can be expressed in bacterial cells such as E. coli, insect cells (using baculovirus expression vectors) yeast cells or mammalian cells. Suitable host cells are discussed further in Goeddel, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, CA (1990). Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase. Expression of proteins in prokaryotes is most often carried out in E. coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non- fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, usually to the amino terminus of the recombinant protein. Such fusion vectors typically serve three purposes: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Typical fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith, D.B. and Johnson, K.S. (1988) Gene 67:31-40), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S- transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein. Purified fusion proteins can be utilized in ABC2 transporter activity assays, (e.g., direct assays or competitive assays described in detail below), or to generate antibodies specific for ABC2 transporter proteins, for example. In a preferred embodiment, an ABC2 transporter fusion protein expressed in a retroviral expression vector of the present invention can be utilized to infect bone marrow cells which are subsequently transplanted into irradiated recipients. The pathology of the subject recipient is then examined after sufficient time has passed (e.g., six (6) weeks). Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amann et al, (1988) Gene 69:301-315) and pET l id (Studier et al, Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 60- 89). Target gene expression from the pTrc vector relies on host RNA polymerase transcription from a hybrid trp-lac fusion promoter. Target gene expression from the pET 1 Id vector relies on transcription from a T7 gnlO-lac fusion promoter mediated by a coexpressed viral RNA polymerase (T7 gnl). This viral polymerase is supplied by host strains BL21(DE3) or HMS174(DE3) from a resident prophage harboring a T7 gnl gene under the transcriptional control of the lacUV 5 promoter. One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, California (1990) 119-128). Another strategy is to alter the nucleic acid sequence of the nucleic acid to be inserted into an expression vector so that the individual codons for each amino acid are those preferentially utilized in E. coli (Wada et al, (1992)
Nucleic Acids Res. 20:2111-2118). Such alteration of nucleic acid sequences of the invention can be carried out by standard DNA synthesis techniques.
In another embodiment, the ABC2 transporter expression vector is a yeast expression vector. Examples of vectors for expression in yeast S. cerevisiae include pYepSecl (Baldari, et al, (1987) Embo J. 6:229-234), pMFa (Kurjan and Herskowitz, (1982) Cell 30:933-943), pJRY88 (Schultz et al, (1987) Gene 54:113-123), pYES2 (Invitrogen Corporation, San Diego, CA), and picZ (InVitrogen Corp, San Diego, CA).
Alternatively, ABC2 transporter proteins can be expressed in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., Sf 9 cells) include the pAc series (Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL series (Lucklow and Summers (1989) Virology 170:31-39).
In yet another embodiment, a nucleic acid of the invention is expressed in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman et al (1987) EMBO J. 6:187-195). When used in mammalian cells, the expression vector's control functions are often provided by viral regulatory elements. For example, commonly used promoters are derived from polyoma, Adenovirus 2, cytomegalo virus and Simian Virus 40. For other suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, e<£, Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989. In another embodiment, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue- specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J. 8:729-733) and immunoglobulins (Banerji et al. (1983) Cell 33:729-740; Queen and Baltimore (1983) Cell 33:741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle (1989) Proc. Natl. Acad. Sci. USA 86:5473-5477), pancreas-specific promoters (Edlund et al. (1985) Science 230:912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Patent No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, for example the murine hox promoters (Kessel and Gruss (1990) Science 249:374-379) and the α-fetoprotein promoter (Campes and Tilghman (1989) Genes Dev. 3:537-546).
The invention further provides a recombinant expression vector comprising a DNA molecule of the invention cloned into the expression vector in an antisense orientation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcription of the DNA molecule) of an RNA molecule which is antisense to ABC2 transporter mRNA. Regulatory sequences operatively linked to a nucleic acid cloned in the antisense orientation can be chosen which direct the continuous expression of the antisense RNA molecule in a variety of cell types, for instance viral promoters and/or enhancers, or regulatory sequences can be chosen which direct constitutive, tissue specific or cell type specific expression of antisense RNA. The antisense expression vector can be in the form of a recombinant plasmid, phagemid or attenuated virus in which antisense nucleic acids are produced under the control of a high efficiency regulatory region, the activity of which can be determined by the cell type into which the vector is introduced. For a discussion of the regulation of gene expression using antisense genes see Weintraub, H. et al, Antisense RNA as a molecular tool for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) 1986. Another aspect of the invention pertains to host cells into which an ABC2 transporter nucleic acid molecule of the invention is introduced, e.g., an ABC2 transporter nucleic acid molecule within a recombinant expression vector or an ABC2 transporter nucleic acid molecule containing sequences which allow it to homologously recombine into a specific site of the host cell's genome. The terms "host cell" and "recombinant host cell" are used interchangeably herein. It is understood that such terms refer not only to the particular subject cell but to the progeny or potential progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term as used herein.
A host cell can be any prokaryotic or eukaryotic cell. For example, an ABC2 transporter protein can be expressed in bacterial cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells). Other suitable host cells are known to those skilled in the art.
Vector DNA can be introduced into prokaryotic or eukaryotic cells via conventional transformation or transfection techniques. As used herein, the terms "transformation" and "transfection" are intended to refer to a variety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chloride co-precipitation, DΕAΕ-dextran-mediated transfection, lipofection, or electroporation. Suitable methods for transforming or transfecting host cells can be found in Sambrook, et al. (Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989), and other laboratory manuals.
For stable transfection of mammalian cells, it is known that, depending upon the expression vector and transfection technique used, only a small fraction of cells may integrate the foreign DNA into their genome. In order to identify and select these integrants, a gene that encodes a selectable marker (e.g., resistance to antibiotics) is generally introduced into the host cells along with the gene of interest. Preferred selectable markers include those which confer resistance to drugs, such as G418, hygromycin and methotrexate. Nucleic acid encoding a selectable marker can be introduced into a host cell on the same vector as that encoding an ABC2 transporter protein or can be introduced on a separate vector. Cells stably transfected with the introduced nucleic acid can be identified by drug selection (e.g., cells that have incorporated the selectable marker gene will survive, while the other cells die).
A host cell of the invention, such as a prokaryotic or eukaryotic host cell in culture, can be used to produce (i.e., express) an ABC2 transporter protein. Accordingly, the invention further provides methods for producing an ABC2 transporter protein using the host cells of the invention. In one embodiment, the method comprises culturing the host cell of the invention (into which a recombinant expression vector encoding an ABC2 transporter protein has been introduced) in a suitable medium such that an ABC2 transporter protein is produced. In another embodiment, the method further comprises isolating an ABC2 transporter protein from the medium or the host cell.
The host cells of the invention can also be used to produce non-human transgenic animals. For example, in one embodiment, a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which ABC2-coding sequences have been introduced. Such host cells can then be used to create non-human transgenic animals in which exogenous ABC2
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SUBSTITUTΕ SHEET (RULE 26) transporter sequences have been introduced into their genome or homologous recombinant animals in which endogenous ABC2 transporter sequences have been altered. Such animals are useful for studying the function and/or activity of an ABC2 transporter and for identifying and/or evaluating modulators of ABC2 transporter activity. As used herein, a "transgenic animal" is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene. Other examples of transgenic animals include non-human primates, sheep, dogs, cows, goats, chickens, amphibians, and the like. A transgene is exogenous DNA which is integrated into the genome of a cell from which a transgenic animal develops and which remains in the genome of the mature animal, thereby directing the expression of an encoded gene product in one or more cell types or tissues of the transgenic animal. As used herein, a "homologous recombinant animal" is a non-human animal, preferably a mammal, more preferably a mouse, in which an endogenous ABC2 transporter gene has been altered by homologous recombination between the endogenous gene and an exogenous DNA molecule introduced into a cell of the animal, e.g., an embryonic cell of the animal, prior to development of the animal.
A transgenic animal of the invention can be created by introducing an ABC2-encoding nucleic acid into the male pronuclei of a fertilized oocyte, e.g., by microinjection, retroviral infection, and allowing the oocyte to develop in a pseudopregnant female foster animal. The ABC2 transporter cDNA sequence of SEQ ED NO: 1 can be introduced as a transgene into the genome of a non-human animal. Alternatively, a nonhuman homologue of a human ABC2 transporter gene, such as a mouse or rat ABC2 transporter gene, can be used as a transgene. Alternatively, an ABC2 transporter gene homologue, such as another ABC2 transporter family member, can be isolated based on hybridization to the ABC2 transporter cDNA sequences of SEQ ID NO: 1 or 3 (described further in subsection I above) and used as a transgene. Intronic sequences and polyadenylation signals can also be included in the transgene to increase the efficiency of expression of the transgene. A tissue-specific regulatory sequence(s) can be operably linked to an ABC2 transporter transgene to direct expression of an ABC2 transporter protein to particular cells. Methods for generating transgenic animals via embryo manipulation and microinjection, particularly animals such as mice, have become conventional in the art and are described, for example, in U.S. Patent Nos. 4,736,866 and 4,870,009, both by Leder et al, U.S. Patent No. 4,873,191 by Wagner et al. and in Hogan, B., Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1986). Similar methods are used for production of other transgenic animals. A transgenic founder animal can be identified based upon the presence of an ABC2 transporter transgene in its genome and/or expression of ABC2 transporter mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals carrying the transgene. Moreover, transgenic animals carrying a transgene encoding an ABC2 transporter protein can further be bred to other transgenic animals carrying other transgenes, for example, animals carrying a transgene encoding a neurotoxic polypeptide such as β-amyloid.
To create a homologous recombinant animal, a vector is prepared which contains at least a portion of an ABC2 transporter gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the ABC2 transporter gene. The ABC2 transporter gene can be a human gene (e.g., the cDNA of SEQ ED NO: 3), but more preferably, is a non-human homologue of a human ABC2 transporter gene (e.g., a cDNA isolated by stringent hybridization with the nucleotide sequence of SEQ ED NO: 1). For example, a mouse ABC2 transporter gene can be used to construct a homologous recombination nucleic acid molecule, e.g., a vector, suitable for altering an endogenous ABC2 transporter gene in the mouse genome. In a preferred embodiment, the homologous recombination nucleic acid molecule is designed such that, upon homologous recombination, the endogenous ABC2 transporter gene is functionally disrupted (i.e., no longer encodes a functional protein; also referred to as a "knock out" vector). Alternatively, the homologous recombination nucleic acid molecule can be designed such that, upon homologous recombination, the endogenous ABC2 transporter gene is mutated or otherwise altered but still encodes functional protein (e.g., the upstream regulatory region can be altered to thereby alter the expression of the endogenous ABC2 transporter protein). In the homologous recombination nucleic acid molecule, the altered portion of the ABC2 transporter gene is flanked at its 5' and 3' ends by additional nucleic acid sequence of the ABC2 transporter gene to allow for homologous recombination to occur between the exogenous ABC2 transporter gene carried by the homologous recombination nucleic acid molecule and an endogenous ABC2 transporter gene in a cell, e.g., an embryonic stem cell. The additional flanking ABC2 transporter nucleic acid sequence is of sufficient length for successful homologous recombination with the endogenous gene. Typically, several kilobases of flanking DNA (both at the 5' and 3 'ends) are included in the homologous recombination nucleic acid molecule (see, e.g., Thomas, K.R. and Capecchi, M. R. (1987) Cell 51:503 for a description of homologous recombination vectors). The homologous recombination nucleic acid molecule is introduced into a cell, e.g., an embryonic stem cell line (e.g., by electroporation) and cells in which the introduced ABC2 transporter gene has homologously recombined with the endogenous ABC2 transporter gene are selected (see e.g., Li, E. et /. (1992) Cell 69:915). The selected cells can then injected into a blastocyst of an animal (e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A. in Terαtocαrcinomαs and Embryonic Stem Cells: A Practical Approach, E.J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152). A chimeric embryo can then be implanted into a suitable pseudopregnant female foster animal and the embryo brought to term. Progeny harboring the homologously recombined DNA in their germ cells can be used to breed animals in which all cells of the animal contain the homologously recombined DNA by germline transmission of the transgene. Methods for constructing homologous recombination nucleic acid molecules, e.g., vectors, or homologous recombinant animals are described further in Bradley, A. (1991) Current Opinion in Biotechnology 2:823-829 and in PCT International Publication Nos.: WO 90/11354 by Le Mouellec et al; WO 91/01140 by Smithies et al; WO 92/0968 by Zijlsira et al. ; and WO 93/04169 by Berns et al.
In another embodiment, transgenic non-human animals can be produced which contain selected systems which allow for regulated expression of the transgene. One example of such a system is the cre/loxP recombinase system of bacteriophage PI. For a description of the cre/loxP recombinase system, see, e.g., Lakso et al. (1992) Proc. Natl. Acad. Sci. USA 89:6232-6236. Another example of a recombinase system is the FLP recombinase system of Saccharomyces cerevisiae (O'Gorman et al. (1991) Science 251:1351-1355. If a cre/loxP recombinase system is used to regulate expression of the transgene, animals containing transgenes encoding both the Cre recombinase and a selected protein are required. Such animals can be provided through the construction of "double" transgenic animals, e.g., by mating two transgenic animals, one containing a transgene encoding a selected protein and the other containing a transgene encoding a recombinase.
Clones of the non-human transgenic animals described herein can also be produced according to the methods described in Wilmut, I. et al (1997) Nature 385:810-813 and PCT International Publication Nos. WO 97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic cell, from the transgenic animal can be isolated and induced to exit the growth cycle and enter G0 phase. The quiescent cell can then be fused, e.g., through the use of electrical pulses, to an enucleated oocyte from an animal of the same species from which the quiescent cell is isolated. The reconstructed oocyte is then cultured such that it develops to morula or blastocyte and then transferred to pseudopregnant female foster animal. The offspring borne of this female foster animal will be a clone of the animal from which the cell, e.g., the somatic cell, is isolated.
IV. Pharmaceutical Compositions
The ABC2 transporter nucleic acid molecules, fragments of ABC2 transporter proteins, anti-ABC2 transporter antibodies (also referred to herein as "active compounds"), expressible nucleic acids encoding ABC2 transporters (or fragments thereof), or any compound identified as a modulator of an ABC2 transporter (as described herein) can be incorporated into pharmaceutical compositions suitable for administration. Such compositions typically comprise the nucleic acid molecule, protein, or antibody and a pharmaceutically acceptable carrier. As used herein the language "pharmaceutically acceptable carrier" is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, use thereof in the compositions is contemplated. Supplementary active compounds can also be incorporated into the compositions.
A pharmaceutical composition of the invention is formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral, e.g. , intravenous, intradermal, subcutaneous, oral (e.g., inhalation), transdermal (topical), transmucosal, and rectal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, Cremophor EL™ (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be sterile and should be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyetheylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols such as manitol, sorbitol, sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound (e.g., a fragment of an ABC2 transporter protein or an anti-ABC2 transporter antibody) in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a basic ABC2 transporter dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Oral compositions generally include an inert diluent or an edible carrier. They can be enclosed in gelatin capsules or compressed into tablets. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, oral compositions can also be prepared using a fluid carrier for use as a mouthwash, wherein the compound in the fluid carrier is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or corn starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring. For administration by inhalation, the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., a gas such as carbon dioxide, or a nebulizer.
Systemic administration can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art. The compounds can also be prepared in the form of suppositories (e.g., with conventional suppository bases such as cocoa butter and other glycerides) or retention enemas for rectal delivery.
In one embodiment, the active compounds are prepared with carriers that will protect the compound against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art. The materials can also be obtained commercially from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Patent No. 4,522,811.
It is especially advantageous to formulate oral or parenteral compositions in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique characteristics of the active compound and the particular therapeutic effect to be achieved, and the limitations inherent in the art of compounding such an active compound for the treatment of individuals.
Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects. The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.
The nucleic acid molecules of the invention can be inserted into vectors and used as gene therapy vectors. Gene therapy vectors can be delivered to a subject by, for example, intravenous injection, local administration (see U.S. Patent 5,328,470) or by stereotactic injection (see e.g., Chen et al. (1994) Proc. Natl. Acad. Sci. USA 91:3054-3057). The pharmaceutical preparation of the gene therapy vector can include the gene therapy vector in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is imbedded. Alternatively, where the complete gene delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the gene delivery system.
The pharmaceutical compositions can be included in a container, pack, or dispenser together with instructions for administration.
V. Uses and Methods of the Invention
The nucleic acid molecules, proteins, protein homologues, and antibodies described herein can be used in one or more of the following methods: a) screening assays; b) predictive medicine (e.g., diagnostic assays, prognostic assays, monitoring clinical trials, and pharmacogenetics); and c) methods of treatment (e.g., therapeutic and prophylactic).
The isolated nucleic acid molecules of the invention can be used, for example, to express ABC2 transporter protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect ABC2 transporter mRNA (e.g., in a biological sample) or a genetic alteration in an ABC2 transporter gene, and to modulate ABC2 transporter activity, as described further below. The ABC2 transporter proteins can be used to treat disorders characterized by insufficient or excessive production of an ABC2 transporter substrate or production of ABC2 transporter inhibitors. In addition, the ABC2 transporter proteins can be used to screen for naturally occurring ABC2 transporter substrates, to screen for drugs or compounds which modulate ABC2 transporter activity, as well as to treat disorders characterized by insufficient or excessive production of ABC2 transporter protein or production of ABC2 transporter protein forms which have decreased, aberrant or unwanted activity compared to ABC2 transporter wild type protein. Moreover, the anti-ABC2 transporter antibodies of the invention can be used to detect and isolate ABC2 transporter proteins, regulate the bioavailability of ABC2 transporter proteins, and modulate ABC2 transporter activity.
A. Screening Assays:
The invention provides a method (also referred to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to ABC2 transporter proteins, have a stimulatory or inhibitory effect on, for example, ABC2 transporter expression or ABC2 transporter activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of an ABC2 transporter substrate.
In one embodiment, the invention provides assays for screening candidate or test compounds which are substrates of an ABC2 transporter protein or polypeptide or biologically active portion thereof. In another embodiment, the invention provides assays for screening candidate or test compounds which bind to or modulate the activity of an ABC2 transporter protein or polypeptide or biologically active portion thereof. The test compounds of the present invention can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12:145). Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt et al. (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6909; Erb et al. (1994) Proc. Natl Acad. Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678; Cho et al. (1993) Science 261:1303; Carrell et al (1994) Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem. Int. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med. Chem. 37:1233.
Libraries of compounds may be presented in solution (e.g., Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991) Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556), bacteria (Ladner USP 5,223,409), spores (Ladner USP '409), plasmids (Cull et al. (1992) Proc Natl Acad Sci USA 89: 1865-1869) or on phage (Scott and Smith (1990) Science 249:386-390); (Devlin (1990) Science 249:404-406); (Cwiria et al (1990) Proc. Natl. Acad. Sci. 87:6378-6382); (Felici (1991) J. Mol Biol 222:301-310); (Ladner supra.).
In one embodiment, an assay is a cell-based assay in which a cell which expresses an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate ABC2 transporter activity is determined. Determining the ability of the test compound to modulate ABC2 transporter activity can be accomplished by monitoring, for example, cellular transport of organic anions, organic cations, cytotoxic anti-cancer drugs, intracellular calcium, potassium, phosphatidylcholine, sodium concentration, neuronal membrane depolarization, a neurotoxic polypeptide (e.g., β-amyloid), or the activity of an ABC2 transporter-regulated transcription factor. The cell, for example, can be of mammalian origin, e.g., a neuronal cell. The ability of the test compound to modulate ABC2 transporter binding to a substrate or to bind to ABC2 transporter can also be determined. Determining the ability of the test compound to modulate ABC2 transporter binding to a substrate can be accomplished, for example, by coupling the ABC2 transporter substrate with a radioisotope or enzymatic label such that binding of the ABC2 transporter substrate to ABC2 transporter can be determined by detecting the labeled ABC2 transporter substrate in a complex. Determining the ability of the test compound to bind ABC2 transporter can be accomplished, for example, by coupling the compound with a radioisotope or enzymatic label such that binding of the compound to ABC2 transporter can be determined by detecting the labeled ABC2 transporter compound in a complex. For example, compounds (e.g., ABC2 transporter substrates) can be labeled with l251, 35S, 14C, 33P, 32P, or 3H, either directly or indirectly, and the radioisotope detected by direct counting of radioemmission or by scintillation counting. Alternatively, compounds can be enzymatically labeled with, for example, horseradish peroxidase, alkaline phosphatase, or luciferase, and the enzymatic label detected by determination of conversion of an appropriate substrate to product.
In one embodiment, suitable compounds include, but are not limited to, verapamil, desmethoxyverapamil, chloroquine, quinine, chinchonidine, primaquine, tamoxifen, dihydrocyclosporin, yohimbine, corynanthine, reserpine, physostigmine, acridine, acridine orange, quinacrine, trifluoroperazine chlorpromazine, propanolol, atropine, tryptamine, forskolin, 1,9-dideoxyforskolin, cyclosporin, (US Patent 4,117,118 (1978)), PSC-833 (cyclosporin D, 6-[(2S, 4R, 6E)-4-methyl-2-(methylamino)-3-oxo-6-octenoic acid]-(9CI)), [US Patent 5,525,590] [ACS 121584-18-7], Keller et al, "S Z PSC 833, a non-immunosuppressive cylcosporine: its potency in overcoming p-glycoprotein-mediated multidrug resistance of murine leukemia", Int J Cancer 50:593-597 (1992)), RU-486 (17β-hydroxy-l lβ-[4- dimethylaminophenyl]-17α prop-l-ynyl estra-4, 9-dien-3 one), RU-49953 (17β-hydroxy-llβ, 17α-[4-dimethylaminophenyl] - 17α prop-1-ynyl estra-4, 9 dien-3 one), S9778 (6-{4-[2,2-di( )- ethylamino]-l-piperidinyl}-NN', di-2-propenyl-l,3,5-triazine-2,4-diamine, bismethane sulfonate, [US patent 5,225,411; EP 466586] [ACS # 140945-01-3]; Dhainaut et al, "New iriazine derivatives as potent modulators of multidrug resistance," J Medicinal Chemistry 35:2481-2496 (1992)), MS-209 (5-[3-[4-(2,2-diphenylacetyl)piperazin-l-yl]-2- hydroxypropoxy]quinoline sesquifumarate, [US patent 5,405,843 (continuation of 5,112,817)], [ACS # 158681-49-3], Sato et al, "Reversal of multidrug resistance by a novel quinoline derivative, MS-209, Cancer Chemother Pharmacol 35:271-277 (1995)), MS-073 (Fukazawa et al, European Patent Application 0363212 (1989)), FK-506 (Tanaka et al, M. Physicochemical properties of FK-506, a novel immunosuppressant isolated from Streptomyces tsukubaensis" Transplantation Proceedings. 19(5 Suppl 6): 11-6, (1987); Naito et al, "Reversal of multidrug resistance by an immunosuppressive agent FK-506," Cancer Chemother & Pharmacol. 29:195-200 (1992); Pourtier-Manzanedo et al, "FK-506 (fujimycin) reverses the multidrug resistance of tumor cells in vitro," Anti-Cancer Drugs 2:279-83 (1991); Epand & Epand, "The new potent immunosuppressant FK-506 reverses multidrug resistance in Chinese hamster ovary cells," Anti-Cancer Drug Design 6:189-93 (1991)), VX-710 (2- peperidinecarboxylic acid, l-[oxo(3,4,5-trimethoxyphenyl)acetyl]-3-(3-pyridinyl)-l-[3-(3- pyridinyl)proρyl]butyl ester [ACS 159997-94-1] [US patent number 5,620,971] Germann et al, "Chemosensitization and drug accumulation effects of VX-710, verapamil, cyclosporin A, MS- 209 and GF120918 in multidrug resistance-associated protein MRP" Anti-Cancer Drugs 8, 141-155 (1997) ; Germann et al, "Cellular and biochemical characterization of VX-710 as a chemosensitizer: reversal of P-glycoprotein-mediated multidrug resistance in vitro" Anti- Cancer Drugs 8, 125-140 (1997)), VX-853 ([US patent number 5,543,423] [ACS # 190454-58- 1), AHC-52 (methyl 2-(N-benzyl-N-methylamino)ethyl-2, 6-dimethyl-4-(2- isopropylpyrazolo[l,5-a]pyridine-3-yl)-l,4-dihyropyridine-3,5-dicarboxylate; [Japanese Patent 63-135381; European Patent 0270926] [ACS 119666-09-0] Shinoda et al, "In vivo circumvention of vincristine resistance in mice with P388 leukemia using a novel compound, AHC-52," Cancer Res 49: 1722-6 (1989)), GF-120918 (9,10-dihydro-5-methoxy-9-oxo-N-[4- [2-(l,2,3,4-tetrahydro-6,7-dimethoxyisoquinol-2-yl) ethyl]phenyl]-4 acridinecarboxamide,[US patent 5,604,237] [ACS # 143664-11-3] Hyafil et al, "In vitro and in vivo reversal of multidrug resistance by GF120918, an acridonecarboxamide derivative," Cancer Res 53:4595- 4602 (1993)), and XR-9051 ( 3-[(3Z, 6Z)-6-Benzylidene-l-methyl-2,5-dioxopiperazin-3- ylidenemethyl]-N-[4-[2-(6,7-dimethoxy-l,2,3,4-tetrahydroisoquinolin-2- yl)ethyl]phenyl]benzamide hydrochloride, [ACS#57-22-7]). It is also within the scope of this invention to determine the ability of a compound (e.g., an ABC2 transporter substrate) to interact with ABC2 transporter without the labeling of any of the interactants. For example, a microphysiometer can be used to detect the interaction of a compound with ABC2 transporter without the labeling of either the compound or the ABC2. McConnell, H. M. et al. (1992) Science 257:1906-1912. As used herein, a "microphysiometer" (e.g., Cytosensor) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between a compound and ABC2.
In another embodiment, an assay is a cell-based assay comprising contacting a cell expressing an ABC2 transporter target molecule (e.g., an ABC2 transporter substrate) with a test compound and determining the ability of the test compound to modulate (e.g. stimulate or inhibit) the activity of the ABC2 transporter target molecule. Determining the ability of the test compound to modulate the activity of an ABC2 transporter target molecule can be accomplished, for example, by determining the ability of the ABC2 transporter protein to bind to or interact with the ABC2 transporter target molecule.
Determining the ability of the ABC2 transporter protein or a biologically active fragment thereof, to bind to or interact with an ABC2 transporter target molecule can be accomplished by one of the methods described above for determining direct binding. In a preferred embodiment, determining the ability of the ABC2 transporter protein to bind to or interact with an ABC2 transporter target molecule can be accomplished by determining the activity of the target molecule. For example, the activity of the target molecule can be determined by detecting induction of a cellular second messenger of the target (i.e., intracellular Ca2+, diacylglycerol, IP3, and the like), detecting catalytic/enzymatic activity of the target an appropriate substrate, detecting the induction of a reporter gene (comprising a target-responsive regulatory element operatively linked to a nucleic acid encoding a detectable marker, e.g., luciferase), cellular transport of, e.g., a reference compound or, e.g., a neurotoxic polypeptide (e.g., β-amyloid) or detecting a target-regulated cellular response.
In yet another embodiment, an assay of the present invention is a cell-free assay in which an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the ABC2 transporter protein or biologically active portion thereof is determined. Preferred biologically active portions of the ABC2 transporter proteins to be used in assays of the present invention include fragments which participate in interactions with non-ABC2 transporter molecules, e.g., fragments with high surface probability scores (see, for example, Figure 2). Binding of the test compound to the ABC2 transporter protein can be determined either directly or indirectly as described above. In a preferred embodiment, the assay includes contacting the ABC2 transporter protein or biologically active portion thereof with a known compound which binds ABC2 transporter to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with an ABC2 transporter protein, wherein determining the ability of the test compound to interact with an ABC2 transporter protein comprises determining the ability of the test compound to preferentially bind to ABC2 transporter or biologically active portion thereof as compared to the known compound.
In another embodiment, the assay is a cell-free assay in which an ABC2 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate (e.g., stimulate or inhibit) the activity of the ABC2 transporter protein or biologically active portion thereof is determined. Determining the ability of the test compound to modulate the activity of an ABC2 transporter protein can be accomplished, for example, by determining the ability of the ABC2 transporter protein to bind to an ABC2 transporter target molecule by one of the methods described above for determining direct binding. Alternatively, for example, ATP binding can be measured. Determining the ability of the ABC2 transporter protein to bind to an ABC2 transporter target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis
(BIA). Sjolander, S. and Urbaniczky, C. (1991) Anal Chem. 63:2338-2345 and Szabo et al. (1995) Curr. Opin. Struct. Biol. 5:699-705. As used herein, "BIA" is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore). Changes in the optical phenomenon of surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.
In an alternative embodiment, determining the ability of the test compound to modulate the activity of an ABC2 transporter protein can be accomplished by determining the ability of the ABC2 transporter protein to further modulate the activity of a downstream effector of an ABC2 transporter target molecule. For example, the activity of the effector molecule on an appropriate target can be determined or the binding of the effector to an appropriate target can be determined as previously described. In yet another embodiment, the cell-free assay involves contacting an ABC2 transporter protein or biologically active portion thereof with a known compound which binds the ABC2 transporter protein to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with the ABC2 transporter protein, wherein determining the ability of the test compound to interact with the ABC2 transporter protein comprises determining the ability of the ABC2 transporter protein to preferentially bind to or modulate the activity of an ABC2 transporter target molecule.
The cell-free assays of the present invention are amenable to use of both soluble and/or membrane-bound forms of isolated proteins (e.g., ABC2 transporter proteins or biologically active portions thereof ). In the case of cell-free assays in which a membrane-bound form of an isolated protein is used it may be desirable to utilize a solubilizing agent such that the membrane-bound form of the isolated protein is maintained in solution. Examples of such solubilizing agents include non-ionic detergents such as n-octylglucoside, n-dodecylglucoside, n-dodecylmaltoside, octanoyl-N-methylglucamide, decanoyl-N-methylglucamide, Triton® X- 100, Triton® X-114, Thesit®, Isotridecypoly(ethylene glycol ether)n, 3-[(3- cholamidopropyl)dimethylamminio]-l -propane sulfonate (CHAPS), 3-[(3- cholamidopropyl)dimethylamminio]-2-hydroxy-l-propane sulfonate (CHAPSO), or N- dodecyl=N,N-dimethyl-3-ammonio-l-propane sulfonate.
In more than one embodiment of the above assay methods of the present invention, it may be desirable to immobilize either ABC2 transporter or its target molecule to facilitate separation of complexed from uncomplexed forms of one or both of the proteins, as well as to accommodate automation of the assay. Binding of a test compound to an ABC2 transporter protein, or interaction of an ABC2 transporter protein with a target molecule in the presence and absence of a candidate compound, can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro-centrifuge tubes. In one embodiment, a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matrix. For example, glutathione-S-transferase/ABC2 transporter fusion proteins or glutathione-S-transferase/target fusion proteins can be adsorbed onto glutathione Sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione derivatized microtiter plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or ABC2 transporter protein, and the mixture incubated under conditions conducive to complex formation (e.g., at physiological conditions for salt and pH). Following incubation, the beads or microtiter plate wells are washed to remove any unbound components, the matrix immobilized in the case of beads, complex determined either directly or indirectly, for example, as described above. Alternatively, the complexes can be dissociated from the matrix, and the level of ABC2 transporter binding or activity determined using standard techniques. Other techniques for immobilizing proteins on matrices can also be used in the screening assays of the invention. For example, either an ABC2 transporter protein or an ABC2 transporter target molecule can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated ABC2 transporter protein or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, EL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies reactive with ABC2 transporter protein or target molecules but which do not interfere with binding of the ABC2 transporter protein to its target molecule can be derivatized to the wells of the plate, and unbound target or ABC2 transporter protein trapped in the wells by antibody conjugation. Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies reactive with the ABC2 transporter protein or target molecule, as well as enzyme-linked assays which rely on detecting an enzymatic activity associated with the ABC2 transporter protein or target molecule.
In another embodiment, modulators of ABC2 transporter expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of ABC2 transporter mRNA or protein in the cell is determined. The level of expression of ABC2 transporter mRNA or protein in the presence of the candidate compound is compared to the level of expression of ABC2 transporter mRNA or protein in the absence of the candidate compound. The candidate compound can then be identified as a modulator of ABC2 transporter expression based on this comparison. For example, when expression of ABC2 transporter mRNA or protein is greater (statistically significantly greater) in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of ABC2 transporter mRNA or protein expression. Alternatively, when expression of ABC2 transporter mRNA or protein is less (statistically significantly less) in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of ABC2 transporter mRNA or protein expression. The level of ABC2 transporter mRNA or protein expression in the cells can be determined by methods described herein for detecting ABC2 transporter mRNA or protein.
In yet another aspect of the invention, the ABC2 transporter proteins can be used as "bait proteins" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent No. 5,283,317; Zervos et al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol Chem.
268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924; Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO94/10300), to identify other proteins, which bind to or interact with ABC2 transporter (" ABC2-binding proteins" or " ABC2-bp") and are involved in ABC2 transporter activity. Such ABC2-binding proteins are also likely to be involved in the propagation of signals by the ABC2 transporter proteins or ABC2 transporter targets as, for example, downstream elements of an ABC2-mediated signaling pathway. Alternatively, such ABC2-binding proteins are likely to be ABC2 transporter inhibitors.
The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. In one construct, the gene that codes for an ABC2 transporter protein is fused to a gene encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct, a DNA sequence, from a library of DNA sequences, that encodes an unidentified protein ("prey" or "sample") is fused to a gene that codes for the activation domain of the known transcription factor. If the "bait" and the "prey" proteins are able to interact, in vivo, forming an ABC2-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ) which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcription factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the ABC2 transporter protein.
In another aspect, the invention pertains to a combination of two or more of the assays described herein. For example, a modulating agent can be identified using a cell-based or a cell free assay, and the ability of the agent to modulate the activity of an ABC2 transporter protein can be confirmed in vivo, e.g., in an animal.
This invention further pertains to novel agents identified by the above-described screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., an ABC2 transporter modulating agent, an antisense ABC2 transporter nucleic acid molecule, an ABC2-specific antibody, or an ABC2-binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.
B. Detection Assays:
Portions or fragments of the cDNA sequences identified herein (and the corresponding complete gene sequences) can be used in numerous ways as polynucleotide reagents. For example, these sequences can be used to: (i) map their respective genes on a chromosome; and, thus, locate gene regions associated with genetic disease; (ii) identify an individual from a minute biological sample (tissue typing); and (iii) aid in forensic identification of a biological sample. These applications are described in the subsections below.
1. Chromosome Mapping
Once the sequence (or a portion of the sequence) of a gene has been isolated, this sequence can be used to map the location of the gene on a chromosome. This process is called chromosome mapping. Accordingly, portions or fragments of the ABC2 transporter nucleotide sequences, described herein, can be used to map the location of the ABC2 transporter genes on a chromosome. The mapping of the ABC2 transporter sequences to chromosomes is an important first step in correlating these sequences with genes associated with disease. Briefly, ABC2 transporter genes can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp in length) from the ABC2 transporter nucleotide sequences. Computer analysis of the ABC2 transporter sequences can be used to predict primers that do not span more than one exon in the genomic DNA, thus complicating the amplification process. These primers can then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the ABC2 transporter sequences will yield an amplified fragment.
Somatic cell hybrids are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hybrids of human and mouse cells grow and divide, they gradually lose human chromosomes in random order, but retain the mouse chromosomes. By using media in which mouse cells cannot grow, because they lack a particular enzyme, but human cells can, the one human chromosome that contains the gene encoding the needed enzyme, will be retained. By using various media, panels of hybrid cell lines can be established. Each cell line in a panel contains either a single human chromosome or a small number of human chromosomes, and a full set of mouse chromosomes, allowing easy mapping of individual genes to specific human chromosomes. (DΕustachio P. et al. (1983) Science 220:919-924). Somatic cell hybrids containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions. PCR mapping of somatic cell hybrids is a rapid procedure for assigning a particular sequence to a particular chromosome. Three or more sequences can be assigned per day using a single thermal cycler. Using the ABC2 transporter nucleotide sequences to design oligonucleotide primers, sublocalization can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map an ABC2 transporter sequence to its chromosome include in situ hybridization (described in Fan, Y. et al. (1990) Proc. Natl. Acad. Sci. USA, 87:6223-27), pre-screening with labeled flow-sorted chromosomes, and pre-selection by hybridization to chromosome specific cDNA libraries. Fluorescence in situ hybridization (FISH) of a DNA sequence to a metaphase chromosomal spread can further be used to provide a precise chromosomal location in one step. Chromosome spreads can be made using cells whose division has been blocked in metaphase by a chemical such as colcemid that disrupts the mitotic spindle. The chromosomes can be treated briefly with trypsin, and then stained with Giemsa. A pattern of light and dark bands develops on each chromosome, so that the chromosomes can be identified individually. The FISH technique can be used with a DNA sequence as short as 500 or 600 bases. However, clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection. Preferably 1,000 bases, and more preferably 2,000 bases will suffice to get good results at a reasonable amount of time. For a review of this technique, see Verma et al, Human Chromosomes: A Manual of BABC transporter Techniques (Pergamon Press, New York 1988).
Reagents for chromosome mapping can be used individually to mark a single chromosome or a single site on that chromosome, or panels of reagents can be used for marking multiple sites and/or multiple chromosomes. Reagents corresponding to noncoding regions of the genes actually are preferred for mapping purposes. Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hybridizations during chromosomal mapping.
Once a sequence has been mapped to a precise chromosomal location, the physical position of the sequence on the chromosome can be correlated with genetic map data. (Such data are found, for example, in V. McKusick, Mendelian Inheritance in Man, available on-line through Johns Hopkins University Welch Medical Library). The relationship between a gene and a disease, mapped to the same chromosomal region, can then be identified through linkage analysis (co-inheritance of physically adjacent genes), described in, for example, Egeland, J. et al (1987) Nαtwre, 325:783-787.
Moreover, differences in the DΝA sequences between individuals affected and unaffected with a disease associated with the ABC2 transporter gene, can be determined. If a mutation is observed in some or all of the affected individuals but not in any unaffected individuals, then the mutation is likely to be the causative agent of the particular disease. Comparison of affected and unaffected individuals generally involves first looking for structural alterations in the chromosomes, such as deletions or translocations that are visible from chromosome spreads or detectable using PCR based on that DNA sequence. Ultimately, complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymorphisms.
2. Tissue Typing
The ABC2 transporter sequences of the present invention can also be used to identify individuals from minute biological samples. The United States military, for example, is considering the use of restriction fragment length polymoφhism (RFLP) for identification of its personnel. In this technique, an individual's genomic DNA is digested with one or more restriction enzymes, and probed on a Southern blot to yield unique bands for identification. This method does not suffer from the current limitations of "Dog Tags" which can be lost, switched, or stolen, making positive identification difficult. The sequences of the present invention are useful as additional DNA markers for RFLP (described in U.S. Patent 5,272,057). Furthermore, the sequences of the present invention can be used to provide an alternative technique which determines the actual base-by-base DNA sequence of selected portions of an individual's genome. Thus, the ABC2 transporter nucleotide sequences described herein can be used to prepare two PCR primers from the 5' and 3' ends of the sequences. These primers can then be used to amplify an individual's DNA and subsequently sequence it.
Panels of corresponding DNA sequences from individuals, prepared in this manner, can provide unique individual identifications, as each individual will have a unique set of such DNA sequences due to allelic differences. The sequences of the present invention can be used to obtain such identification sequences from individuals and from tissue. The ABC2 transporter nucleotide sequences of the invention uniquely represent portions of the human genome. Allelic variation occurs to some degree in the coding regions of these sequences, and to a greater degree in the noncoding regions. It is estimated that allelic variation between individual humans occurs with a frequency of about once per each 500 bases. Each of the sequences described herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification puφoses. Because greater numbers of polymoφhisms occur in the noncoding regions, fewer sequences are necessary to differentiate individuals. The noncoding sequences of SEQ ED NO: 1 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 primers which each yield a noncoding amplified sequence of 100 bases. If predicted coding sequences, such as those in SEQ ED NO: 3 are used, a more appropriate number of primers for positive individual identification would be 500-2,000. If a panel of reagents from ABC2 transporter nucleotide sequences described herein is used to generate a unique identification database for an individual, those same reagents can later be used to identify tissue from that individual. Using the unique identification database, positive identification of the individual, living or dead, can be made from extremely small tissue samples.
3. Use of ABC2 Transporter Sequences in Forensic Biology
DNA-based identification techniques can also be used in forensic biology. Forensic biology is a scientific field employing genetic typing of biological evidence found at a crime scene as a means for positively identifying, for example, a peφetrator of a crime. To make such an identification, PCR technology can be used to amplify DNA sequences taken from very small biological samples such as tissues, e.g., hair or skin, or body fluids, e.g., blood, saliva, or semen found at a crime scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the origin of the biological sample. The sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR primers, targeted to specific loci in the human genome, which can enhance the reliability of DNA-based forensic identifications by, for example, providing another "identification marker" (i.e. another DNA sequence that is unique to a particular individual). As mentioned above, actual base sequence information can be used for identification as an accurate alternative to patterns formed by restriction enzyme generated fragments. Sequences targeted to noncoding regions of SEQ ED NO: 1 are particularly appropriate for this use as greater numbers of polymoφhisms occur in the noncoding regions, making it easier to differentiate individuals using this technique. Examples of polynucleotide reagents include the ABC2 transporter nucleotide sequences or portions thereof, e.g., fragments derived from the noncoding regions of SEQ ID NO: 1 having a length of at least 20 bases, preferably at least 30 bases.
The ABC2 transporter nucleotide sequences described herein can further be used to provide polynucleotide reagents, e.g., labeled or labelable probes which can be used in, for example, an in situ hybridization technique, to identify a specific tissue, e.g., brain tissue. This can be very useful in cases where a forensic pathologist is presented with a tissue of unknown origin. Panels of such ABC2 transporter probes can be used to identify tissue by species and/or by organ type.
In a similar fashion, these reagents, e.g., ABC2 transporter primers or probes can be used to screen tissue culture for contamination (i.e. screen for the presence of a mixture of different types of cells in a culture).
C. Predictive Medicine: The present invention also pertains to the field of predictive medicine in which diagnostic assays, prognostic assays, and monitoring clinical trials are used for prognostic (predictive) puφoses to thereby treat an individual prophylactically. Accordingly, one aspect of the present invention relates to diagnostic assays for determining ABC2 transporter protein and/or nucleic acid expression as well as ABC2 transporter activity, in the context of a biological sample (e.g., blood, serum, cells, tissue) to thereby determine whether an individual is afflicted with a disease or disorder, or is at risk of developing a disorder, associated with aberrant or unwanted ABC2 transporter expression or activity. The invention also provides for prognostic (or predictive) assays for determining whether an individual is at risk of developing a disorder associated with ABC2 transporter protein, nucleic acid expression or activity. For example, mutations in an ABC2 transporter gene can be assayed in a biological sample. Such assays can be used for prognostic or predictive puφose to thereby prophylactically treat an individual prior to the onset of a disorder characterized by or associated with ABC2 transporter protein, nucleic acid expression or activity. Another aspect of the invention pertains to monitoring the influence of agents (e.g., drugs, compounds) on the expression or activity of ABC2 transporter in clinical trials. These and other agents are described in further detail in the following sections.
1. Diagnostic Assays An exemplary method for detecting the presence or absence of ABC2 transporter protein or nucleic acid in a biological sample involves obtaining a biological sample from a test subject and contacting the biological sample with a compound or an agent capable of detecting ABC2 transporter protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes ABC2 transporter protein such that the presence of ABC2 transporter protein or nucleic acid is detected in the biological sample. A preferred agent for detecting ABC2 transporter mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to ABC2 transporter mRNA or genomic DNA. The nucleic acid probe can be, for example, a full-length ABC2 transporter nucleic acid, such as the nucleic acid of SEQ ID NO: 1, or a portion thereof, such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to ABC2 transporter mRNA or genomic DNA. Other suitable probes for use in the diagnostic assays of the invention are described herein. A preferred agent for detecting ABC2 transporter protein is an antibody capable of binding to ABC2 transporter protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab')2) can be used. The term "labeled", with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin. The term "biological sample" is intended to include tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. That is, the detection method of the invention can be used to detect ABC2 transporter mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of ABC2 transporter mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detection of ABC2 transporter protein include enzyme linked immunosorbent assays (ELISAs), Western blots, immunoprecipitations and immunofluorescence. In vitro techniques for detection of ABC2 transporter genomic DNA include Southern hybridizations. Furthermore, in vivo techniques for detection of ABC2 transporter protein include introducing into a subject a labeled anti-ABC2 transporter antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
In one embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a serum sample isolated by conventional means from a subject.
In another embodiment, the methods further involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting ABC2 transporter protein, mRNA, or genomic DNA, such that the presence of ABC2 transporter protein, mRNA or genomic DNA is detected in the biological sample, and comparing the presence of ABC2 transporter protein, mRNA or genomic DNA in the control sample with the presence of ABC2 transporter protein, mRNA or genomic DNA in the test sample.
The invention also encompasses kits for detecting the presence of ABC2 transporter in a biological sample. For example, the kit can comprise a labeled compound or agent capable of detecting ABC2 transporter protein or mRNA in a biological sample; means for determining the amount of ABC2 transporter in the sample; and means for comparing the amount of ABC2 transporter in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect an ABC2 transporter protein or nucleic acid.
Prognostic Assays The diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity. As used herein, the term "aberrant" includes an ABC2 transporter expression or activity which deviates from the wild type ABC2 transporter expression or activity. Aberrant expression or activity includes increased or decreased expression or activity, as well as expression or activity which does not follow the wild type developmental pattern of expression or the subcellular pattern of expression. For example, aberrant ABC2 transporter expression or activity is intended to include the cases in which a mutation in the ABC2 transporter gene causes the ABC2 transporter gene to be under- expressed or over-expressed and situations in which such mutations result in a non-functional ABC2 transporter protein or a protein which does not function in a wild-type fashion, e.g., a protein which does not interact with an ABC2 transporter ligand or one which interacts with a non-ABC2 transporter ligand. As used herein, the term "unwanted" includes an unwanted phenomenon involved in a biological response. For example, the term unwanted includes an ABC2 transporter expression or activity which is undesirable in a subject.
The assays described herein, such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disorder associated with a misregulation in ABC2 transporter protein activity or nucleic acid expression. Alternatively, the prognostic assays can be utilized to identify a subject having or at risk for developing a disorder associated with a misregulation in ABC2 transporter protein activity or nucleic acid expression. Thus, the present invention provides a method for identifying a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity in which a test sample is obtained from a subject and ABC2 transporter protein or nucleic acid (e.g., mRNA or genomic DNA) is detected, wherein the presence of ABC2 transporter protein or nucleic acid is diagnostic for a subject having or at risk of developing a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity. As used herein, a "test sample" refers to a biological sample obtained from a subject of interest. For example, a test sample can be a biological fluid (e.g., serum), cell sample, or tissue. Furthermore, the prognostic assays described herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with aberrant or unwanted ABC2 transporter expression or activity, e.g., a cancer where the cells of the cancer have developed multidrug resistance. Thus, the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with aberrant or unwanted ABC2 transporter expression or activity in which a test sample is obtained and ABC2 transporter protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of ABC2 transporter protein or nucleic acid expression or activity is diagnostic for a subject that can be administered the agent to treat a disorder associated with aberrant or unwanted ABC2 transporter expression or activity).
The methods of the invention can also be used to detect genetic alterations in an ABC2 transporter gene, thereby determining if a subject with the altered gene is at risk for a disorder characterized by misregulation in ABC2 transporter protein activity or nucleic acid expression. In preferred embodiments, the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characterized by at least one of an alteration affecting the integrity of a gene encoding an ABC2 protein, or the mis-expression of the ABC2 transporter gene. For example, such genetic alterations can be detected by ascertaining the existence of at least one of 1) a deletion of one or more nucleotides from an ABC2 transporter gene; 2) an addition of one or more nucleotides to an ABC2 transporter gene; 3) a substitution of one or more nucleotides of an ABC2 transporter gene, 4) a chromosomal rearrangement of an ABC2 transporter gene; 5) an alteration in the level of a messenger RNA transcript of an ABC2 transporter gene, 6) aberrant modification of an ABC2 transporter gene, such as of the methylation pattern of the genomic DNA, 7) the presence of a non-wild type splicing pattern of a messenger RNA transcript of an ABC2 transporter gene, 8) a non-wild type level of an ABC2-protein, 9) allelic loss of an ABC2 transporter gene, and 10) inappropriate post- translational modification of an ABC2-protein. As described herein, there are a large number of assays known in the art which can be used for detecting alterations in an ABC2 transporter gene. A preferred biological sample is a tissue or serum sample isolated by conventional means from a subject.
In certain embodiments, detection of the alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Patent Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91:360-364), the latter of which can be particularly useful for detecting point mutations in the ABC2-gene (see Abravaya et al. (1995) Nucleic Acids Res .23:675-682). This method can include the steps of collecting a sample of cells from a subject, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to an ABC2 transporter gene under conditions such that hybridization and amplification of the ABC2-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein. Alternative amplification methods include: self sustained sequence replication (Guatelli, J.C. et al, (1990) Proc. Natl Acad. Sci. USA 87:1874-1878), iranscriptional amplification system (Kwoh, D.Y. et al, (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q- Beta Replicase (Lizardi, P.M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
In an alternative embodiment, mutations in an ABC2 transporter gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA. Moreover, the use of sequence specific ribozymes (see, for example, U.S. Patent No. 5,498,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
In other embodiments, genetic mutations in ABC2 transporter can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotides probes (Cronin, M.T. et al. (1996) Human Mutation 1: 244-255; Kozal, M.J. et al (1996) Nature Medicine 2: 753-759). For example, genetic mutations in ABC2 transporter can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, M.T. et al. supra. Briefly, a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
In yet another embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence the ABC2 transporter gene and detect mutations by comparing the sequence of the sample ABC2 transporter with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Biotechniques
19:448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993) Appl. Biochem. Biotechnol. 38:147-159).
Other methods for detecting mutations in the ABC2 transporter gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science 230: 1242). In general, the art technique of "mismatch cleavage" starts by providing heteroduplexes of formed by hybridizing (labeled) RNA or DNA containing the wild-type ABC2 transporter sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to base pair mismatches between the control and sample strands. For instance, RNA DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with SI nuclease to enzymatically digesting the mismatched regions. In other embodiments, either DNA DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton et al. (1988) Proc. Natl Acad Sci USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217:286-295. In a preferred embodiment, the control DNA or RNA can be labeled for detection.
In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called "DNA mismatch repair" enzymes) in defined systems for detecting and mapping point mutations in ABC2 transporter cDNAs obtained from samples of cells. For example, the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662). According to an exemplary embodiment, a probe based on an ABC2 transporter sequence, e.g., a wild-type ABC2 transporter sequence, is hybridized to a cDNA or other DNA product from a test cell(s). The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, for example, U.S. Patent No. 5,459,039. In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in ABC2 transporter genes. For example, single strand conformation polymoφhism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sci USA: 86:2766, see also Cotton (1993) Mutat. Res. 285:125-144; and Hayashi (1992) Genet. Anal Tech. Appl. 9:73-79). Single-stranded DNA fragments of sample and control ABC2 transporter nucleic acids will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence, the resulting alteration in electrophoretic mobility enables the detection of even a single base change. The DNA fragments may be labeled or detected with labeled probes. The sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In a preferred embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet 7:5).
In yet another embodiment the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495). When DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DNA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem 265:12753). Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki et al (1989) Proc. Natl Acad. Sci USA 86:6230). Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
Alternatively, allele specific amplification technology which depends on selective PCR amplification may be used in conjunction with the instant invention. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner (1993) Tibtech 11:238). In addition it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection (Gasparini et al. (1992) Mol. Cell Probes 6:1). It is anticipated that in certain embodiments amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3' end of the 5' sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification. The methods described herein may be performed, for example, by utilizing prepackaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving an ABC2 transporter gene.
Furthermore, any cell type or tissue in which ABC2 transporter is expressed may be utilized in the prognostic assays described herein.
3. Monitoring of Effects During Clinical Trials Monitoring the influence of agents (e.g., drugs) on the expression or activity of an
ABC2 transporter protein can be applied not only in ABC2 transporter drug screening, but also in clinical trials. For example, the effectiveness of an agent determined by a screening assay as described herein to increase ABC2 transporter gene expression, protein levels, or upregulate ABC2 transporter activity, can be monitored in clinical trials of subjects exhibiting decreased ABC2 transporter gene expression, protein levels, or downregulated ABC2 transporter activity. Alternatively, the effectiveness of an agent determined by a screening assay to decrease ABC2 transporter gene expression, protein levels, or downregulate ABC2 transporter activity, can be monitored in clinical trials of subjects exhibiting increased ABC2 transporter gene expression, protein levels, or upregulated ABC2 transporter activity. In such clinical trials, the expression or activity of an ABC2 transporter gene, and preferably, other genes that have been implicated in, for example, an ABC2-associated disorder can be used as a "read out" or markers of the phenotype of a particular cell.
For example, and not by way of limitation, genes, including ABC2, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates ABC2 transporter activity (e.g., identified in a screening assay as described herein) can be identified. Thus, to study the effect of agents on ABC2-associated disorders, for example, in a clinical trial, cells can be isolated and RNA prepared and analyzed for the levels of expression of ABC2 transporter and other genes implicated in the ABC2-associated disorder, respectively. The levels of gene expression (e.g., a gene expression pattern) can be quantified by northern blot analysis or RT-PCR, as described herein, or alternatively by measuring the amount of protein produced, by one of the methods as described herein, or by measuring the levels of activity of ABC2 transporter or other genes. In this way, the gene expression pattern can serve as a marker, indicative of the physiological response of the cells to the agent. Accordingly, this response state may be determined before, and at various points during treatment of the individual with the agent.
In a preferred embodiment, the present invention provides a method for monitoring the effectiveness of treatment of a subject with an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate identified by the screening assays described herein) including the steps of (i) obtaining a preadministration sample from a subject prior to administration of the agent; (ii) detecting the level of expression of an ABC2 transporter protein, mRNA, or genomic DNA in the preadministration sample; (iii) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the ABC2 transporter protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the ABC2 transporter protein, mRNA, or genomic DNA in the preadministration sample with the ABC2 transporter protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the agent to the subject accordingly. For example, increased administration of the agent may be desirable to increase the expression or activity of ABC2 transporter to higher levels than detected, i.e., to increase the effectiveness of the agent. Alternatively, decreased administration of the agent may be desirable to decrease expression or activity of ABC2 transporter to lower levels than detected, i.e. to decrease the effectiveness of the agent. According to such an embodiment, ABC2 transporter expression or activity may be used as an indicator of the effectiveness of an agent, even in the absence of an observable phenotypic response.
D. Methods of Treatment: The present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant or unwanted ABC2 transporter expression or activity. With regards to both prophylactic and therapeutic methods of treatment, such treatments may be specifically tailored or modified, based on knowledge obtained from the field of pharmacogenomics. "Pharmacogenomics", as used herein, refers to the application of genomics technologies such as gene sequencing, statistical genetics, and gene expression analysis to drugs in clinical development and on the market. More specifically, the term refers the study of how a patient's genes determine his or her response to a drug (e.g., a patient's "drug response phenotype", or "drug response genotype".) Thus, another aspect of the invention provides methods for tailoring an individual's prophylactic or therapeutic treatment with either the ABC2 transporter molecules of the present invention or ABC2 transporter modulators according to that individual's drug response genotype. Pharmacogenomics allows a clinician or physician to target prophylactic or therapeutic treatments to patients who will most benefit from the treatment and to avoid treatment of patients who will experience toxic drug-related side effects. 1. Prophylactic Methods
In one aspect, the invention provides a method for preventing in a subject, a disease or condition associated with an aberrant or unwanted ABC2 transporter expression or activity, by administering to the subject an ABC2 transporter or an agent which modulates ABC2 transporter expression or at least one ABC2 transporter activity. Subjects at risk for a disease which is caused or contributed to by aberrant or unwanted ABC2 transporter expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a prophylactic agent can occur prior to the manifestation of symptoms characteristic of the ABC2 transporter aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression. Depending on the type of ABC2 transporter aberrancy, for example, an ABC2, ABC2 transporter agonist or ABC2 transporter antagonist agent can be used for treating the subject. The appropriate agent can be determined based on screening assays described herein.
2. Therapeutic Methods
Another aspect of the invention pertains to methods of modulating ABC2 transporter expression or activity for therapeutic puφoses. Accordingly, in an exemplary embodiment, the modulatory method of the invention involves contacting a cell with an ABC2 transporter or agent that modulates one or more of the activities of ABC2 transporter protein activity associated with the cell. An agent that modulates ABC2 transporter protein activity can be an agent as described herein, such as a nucleic acid or a protein, a naturally-occurring target molecule of an ABC2 transporter protein (e.g., an ABC2 transporter substrate), an ABC2 transporter antibody, an ABC2 transporter agonist or antagonist, a peptidomimetic of an ABC2 transporter agonist or antagonist, or other small molecule. In one embodiment, the agent stimulates one or more ABC2 transporter activities. Examples of such stimulatory agents include active ABC2 transporter protein and a nucleic acid molecule encoding an ABC2 transporter that has been introduced into the cell. In another embodiment, the agent inhibits one or more ABC2 transporter activities. Examples of such inhibitory agents include antisense ABC2 transporter nucleic acid molecules, anti-ABC2 transporter antibodies, and ABC2 transporter inhibitors. These modulatory methods can be performed in vitro (e.g., by culturing the cell with the agent) or, alternatively, in vivo (e.g., by administering the agent to a subject). As such, the present invention provides methods of treating an individual afflicted with a disease or disorder characterized by aberrant or unwanted expression or activity of an ABC2 transporter protein or nucleic acid molecule. In one embodiment, the method involves administering an agent (e.g., an agent identified by a screening assay described herein), or combination of agents that modulates (e.g., upregulates or downregulates) ABC2 transporter expression or activity. In another embodiment, the method involves administering an ABC2 transporter protein or nucleic acid molecule as therapy to compensate for reduced, aberrant, or unwanted ABC2 transporter expression or activity.
Stimulation of ABC2 transporter activity is desirable in situations in which ABC2 transporter is abnormally downregulated and/or in which increased ABC2 transporter activity is likely to have a beneficial effect. For example, stimulation of ABC2 transporter activity is desirable in situations in which an ABC2 transporter is downregulated and/or in which increased ABC2 transporter activity is likely to have a beneficial effect. Likewise, inhibition of ABC2 transporter activity is desirable in situations in which ABC2 transporter is abnormally upregulated and/or in which decreased ABC2 transporter activity is likely to have a beneficial effect.
In one embodiment, an agent found to inhibit ABC2 transporter activity is used in combination with another therapy such that the targeting of that therapy across the blood-brain- barrier is achieved.
3. Pharmaco genomic s
The ABC2 transporter molecules of the present invention, as well as agents, or modulators which have a stimulatory or inhibitory effect on ABC2 transporter activity (e.g., ABC2 transporter gene expression) as identified by a screening assay described herein can be administered to individuals to treat (prophylactically or therapeutically) ABC2-associated disorders associated with aberrant or unwanted ABC2 transporter activity. In conjunction with such treatment, pharmacogenomics (i.e., the study of the relationship between an individual's genotype and that individual's response to a foreign compound or drug) may be considered. Differences in metabolism of therapeutics can lead to severe toxicity or therapeutic failure by altering the relation between dose and blood concentration of the pharmacologically active drug. Thus, a physician or clinician may consider applying knowledge obtained in relevant pharmacogenomics studies in determining whether to administer an ABC2 transporter molecule or ABC2 transporter modulator as well as tailoring the dosage and/or therapeutic regimen of treatment with an ABC2 transporter molecule or ABC2 transporter modulator. Pharmacogenomics deals with clinically significant hereditary variations in the response to drugs due to altered drug disposition and abnormal action in affected persons. See, for example, Eichelbaum, M. et al (1996) Clin. Exp. Pharmacol. Physiol 23(10-11) :983-985 and Linder, M.W. et al (1997) Clin. Chem. 43(2):254-266. In general, two types of pharmacogenetic conditions can be differentiated. Genetic conditions transmitted as a single factor altering the way drugs act on the body (altered drug action) or genetic conditions transmitted as single factors altering the way the body acts on drugs (altered drug metabolism). These pharmacogenetic conditions can occur either as rare genetic defects or as naturally- occurring polymoφhisms. For example, glucose-6-phosphate dehydrogenase deficiency (G6PD) is a common inherited enzymopathy in which the main clinical complication is haemolysis after ingestion of oxidant drugs (anti-malarials, sulfonamides, analgesics, nitrofurans) and consumption of fava beans.
One pharmacogenomics approach to identifying genes that predict drug response, known as "a genome-wide association", relies primarily on a high-resolution map of the human genome consisting of already known gene-related markers (e.g., a "bi-allelic" gene marker map which consists of 60,000-100,000 polymoφhic or variable sites on the human genome, each of which has two variants.) Such a high-resolution genetic map can be compared to a map of the genome of each of a statistically significant number of patients taking part in a Phase II/III drug trial to identify markers associated with a particular observed drug response or side effect. Alternatively, such a high resolution map can be generated from a combination of some ten- million known single nucleotide polymoφhisms (SNPs) in the human genome. As used herein, a "SNP" is a common alteration that occurs in a single nucleotide base in a stretch of DNA. For example, a SNP may occur once per every 1000 bases of DNA. A SNP may be involved in a disease process, however, the vast majority may not be disease-associated. Given a genetic map based on the occurrence of such SNPs, individuals can be grouped into genetic categories depending on a particular pattern of SNPs in their individual genome. In such a manner, treatment regimens can be tailored to groups of genetically similar individuals, taking into account traits that may be common among such genetically similar individuals. Alternatively, a method termed the "candidate gene approach", can be utilized to identify genes that predict drug response. According to this method, if a gene that encodes a drugs target is known (e.g., an ABC2 transporter protein of the present invention), all common variants of that gene can be fairly easily identified in the population and it can be determined if having one version of the gene versus another is associated with a particular drug response. As an illustrative embodiment, the activity of drug metabolizing enzymes is a major determinant of both the intensity and duration of drug action. The discovery of genetic polymoφhisms of drug metabolizing enzymes (e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19) has provided an explanation as to why some patients do not obtain the expected drug effects or show exaggerated drug response and serious toxicity after taking the standard and safe dose of a drug. These polymoφhisms are expressed in two phenotypes in the population, the extensive metabolizer (EM) and poor metabolizer (PM). The prevalence of PM is different among different populations. For example, the gene coding for CYP2D6 is highly polymoφhic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6. Poor metabolizers of CYP2D6 and CYP2C19 quite frequently experience exaggerated drug response and side effects when they receive standard doses. If a metabolite is the active therapeutic moiety, PM show no therapeutic response, as demonstrated for the analgesic effect of codeine mediated by its CYP2D6-formed metabolite moφhine. The other extreme are the so called ultra-rapid metabolizers who do not respond to standard doses. Recently, the molecular basis of ultra- rapid metabolism has been identified to be due to CYP2D6 gene amplification.
Alternatively, a method termed the "gene expression profiling", can be utilized to identify genes that predict drug response. For example, the gene expression of an animal dosed with a drug (e.g., an ABC2 transporter molecule or ABC2 transporter modulator of the present invention) can give an indication whether gene pathways related to toxicity have been turned on.
Information generated from more than one of the above pharmacogenomics approaches can be used to determine appropriate dosage and treatment regimens for prophylactic or therapeutic treatment an individual. This knowledge, when applied to dosing or drug selection, can avoid adverse reactions or therapeutic failure and thus enhance therapeutic or prophylactic efficiency when treating a subject with an ABC2 transporter molecule or ABC2 transporter modulator, such as a modulator identified by one of the exemplary screening assays described herein.
This invention is further illustrated by the following examples which should not be construed as limiting.
EXEMPLIFICA TION
EXAMPLE 1 ISOLATION AND CLONING OF THE HUMAN ABC2 TRANSPORTER cDNA
In this example, the isolation and cloning of the gene encoding a novel human ABC2 transporter (i.e., human ABC2) is described. The human ABC2 transporter cDNA (i.e., ABC2) was isolated using polymerase chain reaction (PCR) and primers designed (described below) from a mouse nucleotide sequence (mouse ortholog) containing a partial coding sequence for an ATP binding cassette transporter named abc2 (Gene Bank accession number X75927, Luciani M.F. et al, (1994) Genomics, 21, 150-159) and two human partial nucleotide sequences (Gene Bank accession numbers U18235 and AB028985, the latter being described by Kikuno et al, (1999) DNA Res. 6, 197-205.
The first ABC2 cDNA fragment isolated (hsA2.0, See Fig. 6) was a 5096 base pair (bp) C-terminal fragment obtained by polymerase chain reaction (PCR) conducted on a human normal fetal brain cDNA library (Origene Technologies No. LLFB-1001) using oligonucleotides PI and P2 (as defined below; see also Fig. 6). The PCR reaction was carried out in a final volume of 25 μl using 5 μl (master plate) or 1 μl (sub plate) of the cDNA library in an appropriate reaction mixture (10 mM Tris-HCl pH 8.3, 50 mM KC1, 1.5 mM MgC12, 0.2 mM each dNTP, 0.1 μM each primer PI and P2, 2% DMSO, 1.25 unit of AmpliTaq DNA Polymerase (Perkin Elmer)). The cycling parameters were: denaturation at 94°C for 2 min; denaturation at 94°C for 30 sec, annealing at 60°C for 30 sec, elongation step at 72°C for 1 min for 30 cycles; followed by a final elongation at 72°C for 5 min). The resultant nucleotide sequence was obtained using an automated DNA sequencing engine (LICOR). The second ABC2 cDNA fragment (A2R1, See Fig. 6) isolated was a 1249 bp fragment obtained by 5' RACE PCR (rapid amplification of cDNA ends polymerase chain reaction) conducted on a human normal fetal brain double-strand (ds) cDNA library using the oligonucleotide P3 and an oligonucleotide specific to the adaptor linked to the 5' and 3' end of the cDNA library (API, from Clontech). The oligonucleotides P4 and P5 were used to demonstrate that the A2R1 fragment is contiguous to and represents the direct upstream sequence of the hsA2.0 cDNA fragment. The A2R1 and hsA2.0 clones overlap by 166 bp.
The normal fetal brain double-strand (ds) cDNA library mentioned above was made by subjecting 1 μg of normal human fetal brain poly(A)+ RNA (Invitrogen #D6030-25) to first and second strand synthesis according to the Clontech MARATHON cDNA Amplification Kit (#K1802-1). Resultant double stranded cDNA was then phenol-chloroform extracted, alcohol precipitated, and ligated to a double-stranded cDNA adaptor according to the manufacturer's instructions.
The PCR reaction used to isolate A2R1 was carried out in a final volume of 20 μl using 2 μl of the ds cDNA and reagents provided by and according to the Clontech Advantage cDNA PCR kit (#K1905-1). The cycling parameters were: denaturation at 94°C for 1 min; denaturation at 94°C for 30 sec, annealing at 60°C (P4, P5, P8 and P9) or 70°C (P3, P7 and adaptor specific primer) for 30 sec, elongation at 72°C for 2 min for 30 cycles, followed by a final elongation step at 72°C for 5 min.
The third ABC2 cDNA fragment (A2R2) isolated was a 1109 bp fragment obtained by screening a pBlueScript II cDNA library containing 5' RACE PCR products. The 5' RACE PCR products were generated from a human normal brain ds cDNA library using the oligonucleotides P6 and API and the PCR conditions described above. The human normal adult brain double-strand (ds) cDNA library was made by subjecting 2.5 μg of normal human normal adult brain total RNA (Invitrogen #D6030-01) to first strand synthesis using the oligonucleotide P5 and second strand synthesis according to the Clontech MARATHON cDNA Amplification Kit (#K1802-1). Double stranded cDNA was phenol-chloroform extracted and alcohol precipitated prior ligation to a double-stranded cDNA adaptor according to the manufacturer's instructions. The oligonucleotides P7 and P8 were then used to demonstrate that the A2R2 fragment is contiguous to, and represents the direct upstream sequence of, the A2R1 cDNA fragment. A2R2 and A2R1 were determined to overlap by 471 bp (see Fig. 6). Table 1. Oligonucleotide primers used in the isolation of human ABC2
Primers
5 ' -TCACTGGTGCAGACATTGTCGG-3 ' PI nucleotide 96 to 117 of U18235, 2141 to 2162 of hsA2.2 5' -CCTGGCTTGTACTTCAGGATGAGG-3 ' P2 nucleotide 253 to 230 of U18235, 2278 to 2301 of hsA2.2
5'-TGGTCTTGCCCGCCCCGTTGTGG-3' P3 nucleotide 1887 to 1866 of hsA2.2
5 ' -GTGCAGATGTTCCCCTACCCCTGCTACACACG-3 ' P4 nucleotide 851 to 882 of hsA2.2
5'-ATGGTGGTGGTCTTGCCCG-3' P5 nucleotide 1893 to 1875 of hsA2.2
5'- TCAGGATGGCGGTGAGTGCTGTCACGG-3 ' P6 nucleotide 1109 to 1083 of hsA2.2 5'-CAACAACCGCACCATTGAACCC-3' P7 nucleotide 49 to 70 of hsA2.2
5 ' -TTCTCCGCCACGATGTGCTGGATGG P8 nucleotide 984 to 960 of hsA2.2
5 ' -GACCTCGAGATGAGCTCCCTGGGCTTCACGAG P9 nucleotide 92 to 114 of hsA2.2 (contains GACCTCGAG Xho I)
5 ' -ATCCTTCCTGGACTCCTTCACATCGG-3 ' P10 nucleotide 2812 to 2787 of hsA2.2
Next, the three cDNA fragments described above were linked together in order to generate a 6792 bp cDNA named hsA2.2, the complete fragment described herein as the invention. Oligonucleotides P9 and P10 were used to generate a bp fragment (A2R1R2) that overlaps hsA2.0. A2R1R2 and hsA2.0 were fused using a convenient endonuclease restriction site.
The resultant clone of a 6792 bp was determined to contain the human ABC2 transporter gene coding sequence in addition to 5' and the 3' untranslated regions (UTRs). The nucleotide sequence encoding the human ABC2 transporter protein is shown in Figure 1 and is set forth as SEQ ED NO: 1. The longest open reading frame of the human ABC2 transporter begins with the sequence AACATGA which matches the consensus eukaryotic translation initiation motif at nucleotide position 91 (ATG) and ends with a TGA termination signal at position 6094. The coding region (open reading frame) of SEQ ED NO: 1 is set forth as SEQ ID NO: 3. A putative polyadenylation signal (AATAAATAA) is located in the 3' untranslated region at nucleotide position 6772 (Fig. 1). Starting from the first in-frame ATG, the open reading frame is predicted to encode a polypeptide of 2001 amino acids with a molecular weight of 223 kDa. The amino acid sequence of the full length polypeptide is shown in Figure 2 and provided in SEQ ED NO: 2.
EXAMPLE 2
CHARACTERIZATION OF THE NOVEL HUMAN ABC2 TRANSPORTER
MOLECULES
In this example, the amino acid sequences of the human ABC2 transporter polypeptide was compared to amino acid sequences of known polypeptides and various motifs were identified.
In particular, by comparing the nucleic acid sequence (and predicted amino acid sequence) of the isolated clone to other sequences found in publicly available databases (e.g., GenBank). The region of the human ABC2 clone represented by the cDNA fragment hsA2.0, was determined to share homology with the nucleotide sequence of mouse abc2, human ABCR, and human ABCl (85%, 65%, and 67% respectively; BLASTn program against non- redundant GenBank+EMBL+DDBJ+PDB sequences). The translation product of hsA2.0 is a polypeptide which shares from 92% to 96% amino acid identity with the mouse abc2 (Global Pairwise ClustalW Alignment and BLASTp program against non-redundant SwissProt sequences, respectively). Therefore, the clone hsA2.0 was determined to encode part of the human ABC2 transporter and 3' UTR sequence. This 3' fragment of the human ABC2 gene (hsA2.0, see Fig. 6) finds identity with the sequence of at least 32 human expressed sequence tags (ESTs) using the BLASTn program against the non-redundant Database of GenBank EST Division. The GenBank accession numbers of these ESTs are AI139808, T33919, W69928, R85265, H39045, R44798, F12829, T74974, R61688, H14465, R83132, AI491962, T31574, M78056, W69747, T65432, AI247203, H05244, H14299, Z19133, AA573061, R19133, R61689, AA351626, R20481, AA351625, AA324817, AA702968, M78484, R45304, AI567619 and AI085673 and these sequences are incoφorated in their entireties by reference herein.
The region of the human ABC2 clone represented by the cDNA fragment A2R1 is novel and shares homology with human ABCl and ABCR (62% and 58% respectively, BLASTn program against non-redundant GenBank+EMBL+DDBJ+PDB sequences).
The region of the human ABC2 transporter clone represented by the cDNA fragment A2R2, in particular, the first 638 bp, is a novel sequence and does not share homology with previously identified ABC2 transporter proteins (using the BLASTn program against non- redundant GenBank+EMBL+DDBJ+PDB sequences; BLASTx against non-redundant
GenBank CDS translations + PDB + SwissProt + Spupdate + PIR). Therefore, the most 5' end of the ABC2 clone (hsA2.2) is unclassified and is likely to represent either the less conserved 5' end of the coding sequence or a part of the 5' UTR of human ABC2.
The 1721 bp region of the ABC2 clone represented by A2R1 and A2R2 shares homology with 9 human EST nucleotide sequences (using the BLASTn program against the non-redundant Database of GenBank EST Division). The GenBank accession numbers of these ESTs are AI039834, AA772600, AA748768, AI050892, AA725355, AI089785, AI603917, AI174196 and AI344681 and these sequences are incoφorated in their entireties by reference herein.
The human ABC2 transporter of the invention belongs to the ATP-binding cassette (ABC) superfamily. Members of this family are structurally and functionally related in their ability to catalyze the translocation of substrates across biological membranes. The deduced sequence of 2001 amino acids comprises, from N-terminus to C-terminus, an N-terminal membrane anchor domain, a transmembrane domain, and a second conserved nucleotide binding fold, specifying the human ABC2 polypeptide as a full-transporter (see Fig. 2 and SEQ ED NO: 2). Using standard art recognized bioinformatic software, the human ABC2 transporter was determined to have partial sequence identity with a polypeptide in the HUGE database (human unidentified gene-encoded large proteins) maintained by the Kazusa DNA Research Institute (see http://www.kazusa.or.jp/). The next greatest sequence homology between ABC2 and other gene products was observed with the human ABC transporter polypeptide termed "ABCl" (51% similarity). lesser homologies were noted between ABC2 (HsA2.2) and other transporters (see Table 2 and Fig. 3).
Table 2. Percentage of amino acid similarity and identity between human ABC2 protein and its closest protein orthologs (similarity/identity) according to Pairwise Global Alignment (MacVector 6.5) using standard parameter settings.
Figure imgf000069_0001
The human ABC2 transporter polypeptide was also analyzed with respect to potential membrane spanning segments. Hydropathy plots and 2D fold models obtained using publicly available bioinformatic tools (Heidelberg, Germany, http://dodo.cpmc.columbia.edu/predictprotein/) defined 12 putative transmembrane spanning regions (TMH). Six TMH are in the N-terminal sequence of the protein, five TMH are in the C-terminal sequence of the protein and one TMH (hinge) is in the middle region. All TMH have a helical 2D fold structure, which indicate that human ABC2 is a membrane anchored protein (see Figs. 4 and 5). Therefore, the human ABC2 transporter polypeptide exhibits the typical features conserved among ABC transporters. ABC transporter proteins structural organization represents variations on common themes. One common theme is the basic structure of those transporters with twelve hydrophobic transmembrane segments and two hydrophilic ATP binding sites, either present in a single polypeptide chain or assembled from half or quarter molecules.
Accordingly, the amino acid sequence of human ABC2 defines it as a novel full transporter. Art recognized bioinformatic modeling tools indicate that the N-terminal part is in an "outside conformation, while the ATP binding cassettes of the predicted ABC2 protein are in an "inside" conformation. Thus, it appears that human ABC2 transporter can be associated with an intracellular membrane structure or with a cytoplasmic membrane.
EXAMPLE 3 TISSUE DISTRIBUTION OF HUMAN ABC2 TRANSPORTER mRNA This example describes the tissue distribution of ABC2 transporter mRNA, as can be determined by Northern blot hybridization and in situ hybridization.
Northern blot hybridizations with the various RNA samples are performed under standard conditions and washed under stringent conditions, i.e., 0.2XSSC at 65°C. The DNA probe is radioactively labeled with ^P-dCIP using the Prime-It kit (Stratagene, La Jolla, CA) according to the instructions of the supplier. Filters containing human mRNA (MultiTissue Northern I and MultiTissue Northern II from Clontech, Palo Alto, CA) are probed in ExpressHyb hybridization solution (Clontech) and washed at high stringency according to manufacturer's recommendations.
For in situ analysis, various tissues obtained from brains, e.g. rat or mouse brains, are first frozen on dry ice. Ten-micrometer-thick coronal sections of the tissues are postfixed with 4% formaldehyde in DEPC treated IX phosphate- buffered saline at room temperature for 10 minutes before being rinsed twice in DEPC IX phosphate-buffered saline and once in 0.1 M triethanolamine-HCl (pH 8.0). Following incubation in 0.25% acetic anhydride-0.1 M triethanolamine-HCl for 10 minutes, sections are rinsed in DEPC 2X SSC (IX SSC is 0.15M NaCl plus 0.015M sodium citrate). Tissue is then dehydrated through a series of ethanol washes, incubated in 100% chloroform for 5 minutes, and then rinsed in 100% ethanol for 1 minute and 95% ethanol for 1 minute and allowed to air dry.
Hybridizations are performed with 35s-radiolabeled (5 x i()7 cpm/ml) cRNA probes. Probes are incubated in the presence of a solution containing 600 mM NaCl, 10 mM Tris (pH 7.5), 1 mM EDTA, 0.01% sheared salmon sperm DNA, 0.01% yeast tRNA, 0.05% yeast total RNA type XI, IX Denhardt's solution, 50% formamide, 10% dextran sulfate, 100 mM dithiothreitol, 0.1% sodium dodecyl sulfate (SDS), and 0.1% sodium thiosulfate for 18 hours at 55°C.
After hybridization, slides are washed with 2X SSC. Sections are then sequentially incubated at 37°C in TNE (a solution containing 10 mM Tris-HCl (pH 7.6), 500 mM NaCl, and 1 mM EDTA), for 10 minutes, in TNE with 10 μg of RNase A per ml for 30 minutes, and finally in TNE for 10 minutes. Slides are then rinsed with 2X SSC at room temperature, washed with 2X SSC at 50°C for 1 hour, washed with 0.2X SSC at 55°C for 1 hour, and 0.2X SSC at 60°C for 1 hour. Sections are then dehydrated rapidly through serial ethanol-0.3 M sodium acetate concentrations before being air dried and exposed to Kodak Biomax MR scientific imaging film for 24 hours and subsequently dipped in NB-2 photoemulsion and exposed at 4°C for 7 days before being developed and counter stained. Electronic Northern analysis has indicated that the ABC2 transporter mRNA are fairly neuron-specific.
EXAMPLE 4 EXPRESSION OF A RECOMBINANT HUMAN ABC2 TRANSPORTER
POLYPEPTIDE IN BACTERIAL CELLS
In this example, the human ABC2 transporter is expressed as a recombinant glutathione-S-transferase (GST) fusion polypeptide in E. coli and the fusion polypeptide is isolated and characterized. Specifically, the human ABC2 transporter is fused to GST and this fusion polypeptide is expressed in E. coli, e.g., strain PEB199. As the human ABC2 transporter polypeptide is predicted to be approximately 223 kDa and GST is predicted to be 26 kDa, the fusion polypeptide is predicted to be approximately 249 kDa in molecular weight. Expression of the GST-ABC2 transporter fusion protein in PEB199 is induced with EPTG. The recombinant fusion polypeptide is purified from crude bacterial lysates of the induced PEB199 strain by affinity chromatography on glutathione beads. Using polyacrylamide gel electrophoretic analysis of the polypeptide purified from the bacterial lysates, the molecular weight of the resultant fusion polypeptide is determined. If desired, the polypeptide may be prepared in association with a membrane, such as, e.g., a micelle or membrane vesicle using art recognized techniques.
EXAMPLE 5 EXPRESSION OF RECOMBINANT HUMAN ABC2 TRANSPORTER POLYPEPTIDE
IN MAMMALIAN CELLS
To express the ABC2 transporter gene in a mammalian cell, e.g., COS cells, the pcDNA/Amp vector by Invitrogen Coφoration (San Diego, CA) is used. This vector contains an SV40 origin of replication, an ampicillin resistance gene, an E. coli replication origin, a CMV promoter followed by a polylinker region, and an SV40 intron and polyadenylation site. A DNA fragment encoding the entire ABC2 transporter protein and an HA tag (Wilson et al. (1984) Cell 37:767) or a FLAG tag fused in-frame to its 3' end of the fragment is cloned into the polylinker region of the vector, thereby placing the expression of the recombinant protein under the control of the CMV promoter. To construct the plasmid, the ABC2 transporter DNA sequence (see, e.g., SEQ ID NO:
3) is amplified by PCR using two primers. The 5' primer contains the restriction site of interest followed by approximately twenty nucleotides of the ABC2 transporter coding sequence starting from the initiation codon; the 3' end sequence contains complementary sequences to the other restriction site of interest, a translation stop codon, the HA tag or FLAG tag and the last 20 nucleotides of the ABC2 transporter coding sequence. The PCR amplified fragment and the pCDNA/Amp vector are digested with the appropriate restriction enzymes and the vector is dephosphorylated using the CIAP enzyme (New England Biolabs, Beverly, MA). Preferably the two restriction sites chosen are different so that the ABC2 transporter gene is inserted in the correct orientation. The ligation mixture is transformed into E. coli cells (strains HB101, DH5α, SURE, available from Stratagene Cloning Systems, La Jolla, CA, can be used), the transformed culture is plated on ampicillin media plates, and resistant colonies are selected. Plasmid DNA is isolated from transformants and examined by restriction analysis for the presence of the correct fragment.
Eukaryotic cells, e.g., COS cells are subsequently transfected with the ABC2 transporter-pcDNA/Amp plasmid DNA using the calcium phosphate or calcium chloride co- precipitation methods, DEAE-dextran-mediated transfection, lipofection, or electroporation. Other suitable methods for transfecting host cells can be found in Sambrook, J., Fritsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1989. The expression of the ABC2 transporter polypeptide is detected by radiolabelling (35s-methionine or 35s-cysteine available from NEN, Boston, MA, can be used) and immunoprecipitation (Harlow, E. and Lane, D. Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1988) using an HA specific monoclonal antibody. Briefly, the cells are labeled for 8 hours with 35s-methionine (or 35s-cysteine). The culture media are then collected and the cells are lysed using detergents (RIPA buffer, 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM Tris, pH 7.5). Both the cell lysate and the culture media are precipitated with an HA specific monoclonal antibody. Precipitated polypeptides are then analyzed by SDS-PAGE.
Alternatively, DNA containing the ABC2 transporter coding sequence is cloned directly into the polylinker of the pCDNA/Amp vector using the appropriate restriction sites. The resulting plasmid is transfected into COS cells in the manner described above, and the expression of the ABC2 transporter polypeptide is detected by radiolabelling and immunoprecipitation using an ABC2 transporter specific monoclonal antibody.
EXAMPLE 6 IN VITRO AND IN VIVO SCREENING ASSAYS FOR MODULATORS OF A HUMAN
ABC2 TRANSPORTER
In this example, in vitro and in vivo assays for screening modulators of the human ABC2 transporter molecule are described.
Briefly, the ABC2 transporter is expressed in a mammalian cell line as described above and a base line for the cellular transport of a reference molecule, e.g., β-amyloid or other small molecule, is established. Cells are then incubated with a test compound and a change in the level of the cellular transport of the reference molecule is determined using standards techniques. A test compound that changes the transport of the detectable reference molecule is then identified as a candidate compound that alters ABC2 transporter activity. Lead compounds may then be tested on, e.g., cells of neuronal origin or, alternatively, on brain tissue from a test animal. Methods for conducting such an assay are known in the art. Preferably, lead test compounds that inhibit ABC2-mediated transport of, e.g., β-amyloid are further tested in vivo. Mouse models for various neurological diseases, e.g., amyloid disease, are also known in the art (see, e.g., Hardy et al, (1998) Science 282:1075-1079; Goate, et al, (1991) Nαtwre 349: 704; Games, et al, (1995) Nature 373: 523; and Suzuki, et al, (1994) Science 264: 1336).
Alternatively, a transgenic mouse model overexpressing an ABC2 transporter polypeptide, e.g., the human ABC2 transporter polypeptide or corresponding murine polypeptide is generated using the techniques described herein. This animal may then be tested directly or used as a cell or tissue source, e.g., brain tissue source, for testing modulators of the human ABC2 transporter polypeptide. Preferably, the animal is directly tested with a test compound and monitored for a physiological result, e.g., presence of β-amyloid in the cerebral spinal fluid (CSF). In a related extension of this in vivo assay, the animal may be breed with an animal overexpressing a undesired polypeptide, e.g., an amyloid polypeptide, and a change in the transport of the polypeptide is measured (e.g., in the CSF) as compared to a control.
Ideally, these test animals are further monitored in the presence or absence of a modulator of the ABC2 transporter.
In a modification of the assay, the activity of the ABC2 transporter is determined regarding the ability of a detectable reference molecule to cross the blood-brain barrier. In yet another modification of the assay, the animal is examined for the prevalence of multidrug resistant cells or tissues, and/or the sensitivity of the animal to cytotoxic drugs suitable for treating a neoplasm. Accordingly, these animals represent in vivo assay systems in which to test the ability of an ABC2 transporter and/or ABC2 transporter modulator to prevent, treat, or delay the onset of disease.
EQUIVALENTS
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

Claims

What is claimed:
1. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule comprising the nucleotide sequence set forth in
SEQ ID NO: 1, or a complement thereof; and b) a nucleic acid molecule comprising the nucleotide sequence set forth in SEQ ED NO: 3, or a complement thereof.
2. An isolated nucleic acid molecule which encodes a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 2.
3. An isolated nucleic acid molecule which encodes a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence set forth in SEQ ED NO: 2.
4. An isolated nucleic acid molecule selected from the group consisting of: a) a nucleic acid molecule comprising a nucleotide sequence which is at least 86% homologous to the nucleotide sequence of SEQ ED NO: 1 or 3, or a complement thereof; b) a nucleic acid molecule comprising a fragment of at least 150 nucleotides of a nucleic acid comprising the nucleotide sequence of SEQ ED NO: 1 or 3, or a complement thereof; c) a nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence at least about 93% homologous to the amino acid sequence of SEQ ED NO: 2; and d) a nucleic acid molecule which encodes a fragment of a polypeptide comprising the amino acid sequence of SEQ ED NO: 2, wherein the fragment comprises at least 50 contiguous amino acid residues of the amino acid sequence of SEQ ID NO: 2.
5. An isolated nucleic acid molecule which hybridizes to the nucleic acid molecule of any one of claims 1, 2, 3, or 4 under stringent conditions.
6. An isolated nucleic acid molecule comprising a nucleotide sequence which is complementary to the nucleotide sequence of the nucleic acid molecule of any one of claims 1, 2, 3, or 4.
7. An isolated nucleic acid molecule comprising the nucleic acid molecule of any one of claims 1, 2, 3, or 4, and a nucleotide sequence encoding a heterologous polypeptide.
8. A vector comprising the nucleic acid molecule of any one of claims 1, 2, 3, or 4.
9. The vector of claim 8, which is an expression vector.
10. A host cell transfected with the expression vector of claim 9.
11. A method of producing a polypeptide comprising culturing the host cell of claim
10 in an appropriate culture medium to, thereby, produce the polypeptide.
12. An isolated polypeptide selected from the group consisting of: a) a fragment of a polypeptide comprising the amino acid sequence of SEQ ED NO: 2, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ED NO:
2; b) a naturally occurring allelic variant of a polypeptide comprising the amino acid sequence of SEQ ID NO: 2, wherein the polypeptide is encoded by a nucleic acid molecule which hybridizes to a nucleic acid molecule consisting of SEQ ED NO: 1 or 3 under stringent conditions; c) a polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence which is at least 50% homologous to a nucleic acid comprising the nucleotide sequence of SEQ ED NO: 1 or 3; d) a polypeptide comprising an amino acid sequence which is at least 50% homologous to the amino acid sequence of SEQ ED NO: 2.
13. The isolated polypeptide of claim 12 comprising the amino acid sequence of SEQ ID NO: 2.
14. The polypeptide of claim 12, further comprising heterologous amino acid sequences.
15. An antibody which selectively binds to a polypeptide of claim 12.
16. A method for detecting the presence of a polypeptide of claim 12 in a sample comprising: a) contacting the sample with a compound which selectively binds to the polypeptide; and b) determining whether the compound binds to the polypeptide in the sample to thereby detect the presence of a polypeptide of claim 12 in the sample.
17. The method of claim 16, wherein the compound which binds to the polypeptide is an antibody.
18. A kit comprising a compound which selectively binds to a polypeptide of claim 12 and instructions for use.
19. A method for detecting the presence of a nucleic acid molecule of any one of claims 1, 2, 3, or 4 in a sample comprising: a) contacting the sample with a nucleic acid probe or primer which selectively hybridizes to the nucleic acid molecule; and b) determining whether the nucleic acid probe or primer binds to a nucleic acid molecule in the sample to thereby detect the presence of a nucleic acid molecule of any one of claims 1, 2, 3, or 4 in the sample.
20. The method of claim 19, wherein the sample comprises mRNA molecules and is contacted with a nucleic acid probe.
21. A kit comprising a compound which selectively hybridizes to a nucleic acid molecule of any one of claims 1, 2, 3, or 4 and instructions for use.
22. A method for identifying a compound which binds to a polypeptide of claim 12 comprising: a) contacting the polypeptide, or a cell expressing the polypeptide with a test compound; and b) determining whether the polypeptide binds to the test compound.
23. The method of claim 22, wherein the binding of the test compound to the polypeptide is detected by a method selected from the group consisting of: a) detection of binding by direct detection of test compound/polypeptide binding; b) detection of binding using a competition binding assay; and c) detection of binding using an assay for ABC2 transporter activity.
24. A method for modulating the activity of a polypeptide of claim 12 comprising contacting the polypeptide or a cell expressing the polypeptide with a compound which binds to the polypeptide in a sufficient concentration to modulate the activity of the polypeptide.
25. A method for identifying a compound which modulates the activity of a polypeptide of claim 12 comprising: a) contacting a polypeptide of claim 12 with a test compound; and b) determining the effect of the test compound on the activity of the polypeptide to thereby identify a compound which modulates the activity of the polypeptide.
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