WO2001014547A1 - Nouveau transporteur abc et ses utilisations - Google Patents

Nouveau transporteur abc et ses utilisations Download PDF

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Publication number
WO2001014547A1
WO2001014547A1 PCT/CA2000/000964 CA0000964W WO0114547A1 WO 2001014547 A1 WO2001014547 A1 WO 2001014547A1 CA 0000964 W CA0000964 W CA 0000964W WO 0114547 A1 WO0114547 A1 WO 0114547A1
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transporter
abcb
nucleic acid
polypeptide
protein
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PCT/CA2000/000964
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English (en)
Inventor
Stephane Le Bihan
Catriona Wilson
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Active Pass Pharmaceuticals, Inc.
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Priority to CA002383074A priority Critical patent/CA2383074A1/fr
Priority to JP2001518860A priority patent/JP2003520026A/ja
Priority to AU66773/00A priority patent/AU6677300A/en
Priority to EP00954221A priority patent/EP1210423A1/fr
Publication of WO2001014547A1 publication Critical patent/WO2001014547A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

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 alloste ⁇ cally 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 ABCB12 transporter nucleic acid and protein molecules (also human UMAT (after the rat homolog termed ubiquitously expressed mammalian ABC half-transporter (UMAT)).
  • ABCB12 transporter molecules of the present invention are useful as targets for developing modulating agents to regulate a va ⁇ ety of cellular processes, particularly the transport of neurotoxic molecules, e.g., ⁇ -amyloid peptide. across cell membranes or, e.g., the blood-brain banner (BBB).
  • BBB blood-brain banner
  • 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. (1995) Nature 373:523; and Suzuki et al. (1994) Science 264:1336).
  • Other neurological disease involving toxic polypeptides include, e.g., p ⁇ on diseases, Huntington's disease, Parkinson's disease, etc. (for a review see Hardy et al (1998) Science 282: 1075-1079.
  • modulation of amyloid- ⁇ protein export with a modulator of human ABCB12 transporter would be expected to modulate amyloid deposition and thus, Alzheimer's disease.
  • the ABCB12 transporter molecules of the invention are useful as targets for developing modulating agents of multidrug resistance.
  • the molecules of the present invention are useful as diagnostic and therapeutic tools.
  • this invention provides isolated nucleic acid molecules encoding ABCB12 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments suitable as pnmers or hyb ⁇ dization probes for the detection of ABCB 12-encod ⁇ ng nucleic acids.
  • an ABCB12 transporter nucleic acid molecule of the invention is at least 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 1-164 of SEQ ED NO. 1. In another embodiment, the nucleic acid molecule includes SEQ ID NO: 3 and nucleotides 2697- 2893 of SEQ ID NO: 1.
  • an ABCB12 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 ED NO: 2.
  • an ABCB12 transporter nucleic acid molecule includes a nucleotide sequence encoding a protein having an am o acid sequence at least 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 ABCB12 transporter having the amino acid sequence of SEQ ID NO. 2.
  • the nucleic acid molecule is at least 2696 nucleotides in length.
  • the nucleic acid molecule is at least 2574 nucleotides in length and encodes a protein having ABCB 12 transporter activity (as descnbed herein).
  • nucleic acid molecules preferably ABCB12 transporter nucleic acid molecules, which specifically detect ABCB12 transporter nucleic acid molecules relative to nucleic acid molecules encoding non-ABCB12 transporter proteins.
  • a nucleic acid molecule is at least 50, 60, 70, 80, 90, 100, 150, 200, 300, 400, 500, 500-1000, 1000-1500, 1500-2000, 2000-2500, or 2500- 3000 or more nucleotides in length and/or hyb ⁇ dizes under st ⁇ ngent conditions to a nucleic acid molecule compnsing the nucleotide sequence shown in SEQ ID NO: 1, or a complement thereof.
  • 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 hyb ⁇ dize under st ⁇ ngent conditions to nucleotides 165-2696 of SEQ ID NO: 1. In other prefened embodiments, the nucleic acid molecules compnse nucleotides 165-2696 of SEQ ID NO: 1.
  • the nucleic acid molecule encodes a naturally occurnng alle c vanant of a polypeptide compnsing the amino acid sequence of SEQ ED NO: 2, wherein the nucleic acid molecule hybndizes to a nucleic acid molecule compnsing SEQ ID NO: 1 or 3 under stnngent conditions.
  • Another embodiment of the invention provides an isolated nucleic acid molecule which is antisense to an ABCB12 transporter nucleic acid molecule, e.g., the coding strand of an ABCB12 transporter nucleic acid molecule.
  • Another aspect of the invention provides a vector compnsing an ABCB12 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 ABCB12 transporter protein, by cultunng 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 ABCB12 transporter protein, includes at least one transmembrane domain and has an am o acid sequence at least about 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.
  • the protein preferably an ABCB12 transporter protein
  • the protein includes at least one transmembrane domain and is encoded by a nucleic acid molecule having a nucleotide sequence which hyb ⁇ dizes under st ⁇ ngent hyb ⁇ dization conditions to a nucleic acid molecule compnsing 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 comp ⁇ ses at least 15 am o acids (e.g., contiguous ammo acids) of the amino acid sequence of SEQ ID NO: 2.
  • the protein preferably an ABCB12 transporter protein
  • the invention features an isolated protein, preferably an
  • ABCB12 transporter protein which is encoded by a nucleic acid molecule consisting of a nucleotide sequence at least 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 ABCB12 transporter protein, which is encoded by a nucleic acid molecule consisting of a nucleotide sequence which hyb ⁇ dizes under st ⁇ ngent hyb ⁇ dization conditions to a nucleic acid molecule compnsing 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-ABCB12 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 ABCB12 transporter proteins.
  • the ABCB12 transporter proteins, biologically active portions thereof, or expressible nucleic acids encoding the foregoing can be incorporated into pharmaceutical compositions, which optionally include pharmaceutically acceptable earners
  • the present invention provides a method for detecting the presence of an ABCB12 transporter nucleic acid molecule, protein or polypeptide in a biological sample by contacting the biological sample with an agent capable of detecting an ABCB 12 transporter nucleic acid molecule, protein or polypeptide such that the presence of an ABCB 12 transporter nucleic acid molecule, protein or polypeptide is detected in the biological sample
  • the present invention provides a method for detecting the presence of ABCB12 transporter activity in a biological sample by contacting the biological sample with an agent capable of detecting an indicator of ABCB12 transporter activity such that the presence of ABCB12 transporter activity is detected in the biological sample.
  • the invention provides a method for modulating ABCB12 transporter activity compnsing contacting a cell capable of expressing an ABCB12 transporter with an agent that modulates ABCB12 transporter activity such that ABCB12 transporter activity in the cell is modulated.
  • the agent inhibits ABCB 12 transporter activity.
  • the agent stimulates ABCB 12 transporter activity.
  • the agent is an antibody that specifically binds to an ABCB 12 transporter protein.
  • the agent modulates the ability of the ABCB 12 transporter to allostencally modify the function of other membrane proteins.
  • the agent modulates expression of ABCB 12 transporter by modulating transc ⁇ ption of an ABCB 12 transporter gene or translation of an ABCB 12 transporter mRNA.
  • the agent is a nucleic acid molecule having a nucleotide sequence that is antisense to the coding strand of an ABCB 12 transporter mRNA or an ABCB 12 transporter gene.
  • the methods of the present invention are used to treat a subject having a disorder characte ⁇ zed by abenant or unwanted ABCB 12 transporter protein or nucleic acid expression or activity by admimstenng an agent which is an ABCB 12 transporter modulator to the subject.
  • the ABCB 12 transporter modulator is an ABCB 12 transporter protein.
  • the ABCB 12 transporter modulator is an ABCB 12 transporter nucleic acid molecule.
  • the ABCB 12 transporter modulator is a peptide, peptidomimetic, or other small molecule, e.g., a molecule that is carbohydrate-based, hpid-based, nucleic-acid based, natural organic-based, or synthetically denved organic-based.
  • the present invention also provides a diagnostic assay for identifying the presence or absence of a genetic alteration characte ⁇ zed by at least one of (I) abenant modification or mutation of a gene encoding an ABCB 12 transporter protein; (n) mis-regulation of the gene; and (in) abenant post-translational modification of an ABCB 12 transporter protein, wherein a wild-type form of the gene encodes a protein with an ABCB12 transporter activity.
  • the invention provides a method for identifying a compound that binds to or modulates the activity of an ABCB 12 transporter protein, by providing an indicator composition compnsing an ABCB 12 transporter protein having ABCB 12 transporter activity, contacting the indicator composition with a test compound, and determining the effect of the test compound on ABCB 12 transporter activity in the indicator composition to identify a compound that modulates the activity of an ABCB 12 transporter protein (e.g., an ABCB 12 transporter protein associated with a membrane).
  • an indicator composition compnsing an ABCB 12 transporter protein having ABCB 12 transporter activity
  • contacting the indicator composition with a test compound and determining the effect of the test compound on ABCB 12 transporter activity in the indicator composition to identify a compound that modulates the activity of an ABCB 12 transporter protein (e.g., an ABCB 12 transporter protein associated with a membrane).
  • an ABCB 12 transporter protein e.g., an ABCB 12 transporter protein associated with a membrane
  • Figure 1 depicts the cDNA sequence and predicted amino acid sequence of a human ABCB 12 transporter.
  • the nucleotide sequence conesponds to nucleic acids 1 to 2893 of SEQ ID NO: 1.
  • the coding region without the 5 ' and 3' untranslated regions of the human ABCB 12 transporter gene is shown in SEQ ED NO: 3.
  • Figure 2 depicts the ammo acid sequence of the ABCB 12 transporter molecule conesponding to am o acids 1 to 843 of SEQ ID NO: 2.
  • Figure 3 depicts an amino acid sequence alignment of the human ABCB 12 transporter polypeptide and polypeptides found in vanous species.
  • ABC transporter family member
  • UMAT human UMAT
  • 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.
  • ABC transporters are associated with the transport of substrates across the blood-brain-barner.
  • the transport of substances in cells of the brain and substances across the blood-brain-bamer is, at lease in part, controlled by ABC transporter molecules.
  • 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 ABCB12 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-barner.
  • the ABCB 12 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 ABCB 12 transporter molecules descnbed herein can 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 barner (Schinkel A.H., et al, (1994) Cell, 11, 491) and therefore identification of the sequence of the human ABCB 12 transporter descnbed herein, affords the development of new strategies for alternativeng the function of the blood brain barner. 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 descnbed in, e.g., U.S. Patent Application No.
  • family when refer ⁇ ng 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 occur ⁇ ng and can be from either the same or different species.
  • a family can contain a first protein of human o ⁇ gin, as well as other, distinct proteins of human o ⁇ gin or alternatively, can contain homologues of non-human o ⁇ gin.
  • Members of a family may also have common functional characte ⁇ stics.
  • the family of ABC transporter proteins compnse 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 descnbed in, for example, Zaelles W.N. et al, (1996) Annual Rev. Neuronsci. 19: 235-63, the contents of which are inco ⁇ orated herein by reference.
  • Isolated proteins of the present invention preferably ABCB 12 transporter proteins, have an amino acid sequence sufficiently homologous to the amino acid sequence of SEQ ID 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 ammo acid or nucleotide sequence which contains a sufficient or minimum number of identical or equivalent (e.g., an ammo 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 am o 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.
  • an “ABCB 12 transporter activity”, “biological activity of ABCB 12 transporter” or “functional activity of ABCB 12 transporter” refers to an activity exerted by an ABCB 12 transporter protein, polypeptide or nucleic acid molecule on an ABCB 12 transporter responsive cell or on an ABCB 12 transporter protein substrate, as determined in vitro, or in vitro, according to standard techniques.
  • an ABCB 12 transporter activity has the ability to act as an energy-dependent (ATP) molecular pump.
  • an ABCB 12 activity is a direct activity, such as an association with membrane associated protein and/or the transport of an endogenous or exogenous substrate across a biological membrane.
  • the ABCB 12 activity is the ability of the polypeptide to allostencally modify the function of other membrane protein. For example, in some cells, modulation of p-glycoprotein by an ABCB 12 transporter modulator has been shown to alter the magnitude of volume-activated chlonde cunents (reviewed in Higgins, C. F Volume-activated chlonde cunents associated with the multidrug resistance P-glycoprotein, J Physwl 482:31S-36S (1995)).
  • p-glycoprotein and other ABC transporters have multiple functions, one of which is to allostencally modify the function of the other membrane proteins
  • the present invention is consistent with a model in which the alloste ⁇ c modification of other membrane proteins by e.g., an ABCB12 transporter, is responsible for a change in the transport of a substrate, e.g., ⁇ -amyloid, a cytotoxic drug, or other small molecule.
  • an ABCB12 activity is at least one or more of the following activities (I) activation of an ABCB12-dependent signal transduction pathway; ( ⁇ ) modulation of the transport of a substrate (e.g., cytotoxic drug, ⁇ -amyloid) across a membrane; (in) interaction of an ABCB12 protein with a non-ABC2 membrane associated molecule; (iv) modulation of the development or differentiation of an ABCB12-express ⁇ ng cell; (v) modulation of the development or differentiation of a non- ABCB12-express ⁇ ng cell; (vi) modulation of the homeostasis of an ABCB12-expressmg cell; and (vn) modulation of the homeostasis of a non- ABCB12-express ⁇ ng cell.
  • a substrate e.g., cytotoxic drug, ⁇ -amyloid
  • another embodiment of the invention features isolated ABCB 12 transporter proteins and polypeptides having an ABCB 12 transporter activity.
  • Prefened proteins are ABCB 12 transporter proteins having at least one transmembrane domain, preferably two transmembrane domains, and, preferably, an ABCB 12 transporter activity.
  • nucleotide sequence of the isolated human ABCB 12 transporter protein cDNA and the predicted ammo acid sequence of the human ABCB 12 transporter polypeptide are shown in Fig. 5 and in SEQ ED NOs: 1 and 2, respectively.
  • the human ABCB 12 transporter gene which is approximately 2893 nucleotides in length, encodes a protein having a molecular weight of approximately 94 kDa and which is approximately 843 amino acid residues in length. Vanous aspects of the invention are descnbed in further detail in the following subsections:
  • nucleic acid molecules that encode ABCB 12 transporter proteins or biologically active portions thereof, as well as nucleic acid fragments sufficient for use as hyb ⁇ dization probes to identify ABCB12-encodmg nucleic acid molecules (e.g., ABCB 12 transporter mRNA) and fragments for use as PCR pnmers for the amplification or mutation of ABCB 12 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 s gle-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 de ⁇ ved.
  • the isolated ABCB 12 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 denved
  • an "isolated" nucleic acid molecule such as a cDNA molecule, can be substantially free of other cellular mate ⁇ al, 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 ID 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 ID NO: 1 or 3 as a hybndization probe, ABCB 12 transporter nucleic acid molecules can be isolated using standard hyb ⁇ dization and cloning techniques (e.g., as descnbed in Sambrook, J., Fntsh, E. F., and Maniatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed..
  • 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 pnmers designed based upon the sequence of SEQ ED NO: I or 3.
  • a nucleic acid of the invention can be amplified using cDNA, mRNA or alternatively, genomic DNA, as a template and appropnate oligonucleotide pnmers according to standard PCR amplification techniques.
  • the nucleic acid so amplified can be cloned into an appropnate vector and charactenzed by DNA sequence analysis.
  • oligonucleotides conesponding to ABCB 12 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 comp ⁇ ses the nucleotide sequence shown in SEQ ID NO: 1.
  • SEQ ID NO: 1 conesponds to the human ABCB 12 cDNA.
  • This cDNA comp ⁇ ses sequences encoding the human ABCB 12 protein (i.e., "the coding region", from nucleotides 165-2696), as well as 5' untranslated sequences (nucleotides 1-164) and 3' untranslated sequences (nucleotides 2697- 2893).
  • the nucleic acid molecule can compnse only the coding region of SEQ ID NO: 1 (e.g., nucleotides 165-2696, conesponding to SEQ ID NO: 3).
  • an isolated nucleic acid molecule of the invention compnses 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 hybndize 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 comp ⁇ ses a nucleotide sequence which is at least about 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 compnse 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 pnmer or a fragment encoding a portion of an ABCB 12 transporter protein, e.g., a biologically active portion of an ABCB 12 transporter protein.
  • the nucleotide sequence determined from the cloning of the ABCB 12 transporter gene allows for the generation of probes and pnmers designed for use m identifying and/or cloning other ABCB 12 transporter family members, as well as ABCB 12 transporter homologues from other species.
  • the probe/pnmer typically compnses substantially pu ⁇ fied oligonucleotide.
  • the oligonucleotide typically comp ⁇ ses a region of nucleotide sequence that hyb ⁇ dizes under st ⁇ ngent 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 ID NO: 1 or 3 of an anti- sense sequence of SEQ ID NO: 1 or 3, or of a naturally occurring alle c vanant or mutant of SEQ ED NO: 1 or 3.
  • a nucleic acid molecule of the present invention comp ⁇ ses 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 2500-3000, or more nucleotides in length and hyb ⁇ dizes under st ⁇ ngent hyb ⁇ dization conditions to a nucleic acid molecule of SEQ ID NO: 1 or 3.
  • Probes based on the ABCB 12 transporter nucleotide sequences can be used to detect transc ⁇ pts or genomic sequences encoding the same or homologous proteins.
  • the probe further comp ⁇ ses 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 ABCB 12 transporter protein, such as by measu ⁇ ng a level of an ABCB 12- encoding nucleic acid in a sample of cells from a subject e.g., detecting ABCB 12 transporter mRNA levels or determining whether a genomic ABCB 12 transporter gene has been mutated or deleted.
  • a nucleic acid fragment encoding a "biologically active portion of an ABCB 12 transporter protein” can be prepared by isolating a portion of the nucleotide sequence of SEQ ID NO: 1 or 3 which encodes a polypeptide having an ABCB 12 transporter biological activity (the biological activities of the ABCB12 transporter proteins are descnbed herein), expressing the encoded portion of the ABCB 12 transporter protein (e.g., by recombinant expression in vitro) and assessing the activity of the encoded portion of the ABCB 12 transporter protein
  • the invention further encompasses nucleic acid molecules that differ from the nucleotide sequence shown in SEQ ED NO.
  • 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 polymo ⁇ hisms that lead to changes in the amino acid sequences of the ABCB 12 transporter proteins may exist within a population (e.g., the human population)
  • Such genetic polymo ⁇ hism in the ABCB 12 transporter genes may exist among individuals within a population due to natural allelic vanation.
  • the terms "gene” and "recombinant gene” refer to nucleic acid molecules which include an open reading frame encoding an ABCB 12 transporter protein, preferably a mammalian ABCB 12 transporter protein, and can further include non-coding regulatory sequences, and introns.
  • Allelic va ⁇ ants of human ABCB 12 transporter include both functional and nonfunctional ABCB 12 transporter proteins.
  • Functional allelic vanants are naturally occur ⁇ ng amino acid sequence vanants of the human ABCB 12 transporter that maintain the ability to bind an ABCB 12 transporter ligand.
  • Functional allelic va ⁇ ants will typically contain only conservative substitution of one or more ammo acids of SEQ ID NO: 2 or substitution, deletion or insertion of non-c ⁇ tical residues in non-cntical regions of the protein.
  • Non-functional allelic va ⁇ ants are naturally occur ⁇ ng amino acid sequence va ⁇ ants of the human ABCB 12 transporter protein that do not have the ability to either bind an ABCB 12 transporter ligand.
  • Non-functional allelic va ⁇ ants will typically contain a non-conservative substitution, a deletion, or insertion or premature truncation of the am o acid sequence of SEQ ID NO. 2 or a substitution, insertion or deletion in c ⁇ tical residues or cntical regions.
  • the present invention further provides non-human orthologues of the human ABCB 12 transporter protein.
  • Orthologues of the human ABCB 12 transporter protein are proteins that are isolated from non-human organisms and possess the same ABCB 12 transporter activity of the human ABCB 12 transporter protein Orthologues of the human ABCB 12 protein can readily be identified as compnsing an amino acid sequence that is substantially homologous to SEQ ED NO: 2.
  • nucleic acid molecules encoding other ABC transporter family members and, thus, which have a nucleotide sequence which differs from the ABCB 12 transporter sequences of SEQ ID NO: 1 or 3 are intended to be within the scope of the invention.
  • another ABC transporter cDNA can be identified based on the nucleotide sequence of the human ABCB 12 transporter.
  • nucleic acid molecules encoding ABCB 12 transporter proteins from different species, e.g., mammals, and which, thus, have a nucleotide sequence which differs from the ABCB 12 transporter sequences of SEQ ID NO: 1 or 3 are intended to be within the scope of the invention.
  • a mouse ABCB 12 transporter cDNA can be identified based on the nucleotide sequence of the human ABCB 12 transporter.
  • Nucleic acid molecules conesponding to natural allelic vanants and homologues of the ABCB 12 transporter cDNAs of the invention can be isolated based on their homology to the ABCB 12 transporter nucleic acids disclosed herein using the cDNAs disclosed herein, or a portion thereof, as a hyb ⁇ dization probe according to standard hyb ⁇ dization techniques under st ⁇ ngent hyb ⁇ dization conditions.
  • Nucleic acid molecules conesponding to natural allelic va ⁇ ants and homologues of the ABCB 12 transporter cDNAs of the invention can further be isolated by mapping to the same chromosome or locus as the ABCB 12 transporter gene.
  • an isolated nucleic acid molecule of the invention is at least 15, 20, 25, 30 or more nucleotides in length and hyb ⁇ dizes under st ⁇ ngent conditions to the nucleic acid molecule compnsing 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.
  • the term "hyb ⁇ dizes under st ⁇ ngent conditions" is intended to descnbe conditions for hybndization and washing under which nucleotide sequences at least 75% homologous to each other typically remain hyb ⁇ dized 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 hyb ⁇ dized to each other.
  • st ⁇ ngent hyb ⁇ dization 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 prefened, non-limiting example of st ⁇ ngent hyb ⁇ dization conditions are hyb ⁇ dization in 6X sodium chlonde/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 sodium chlonde/sodium citrate
  • an isolated nucleic acid molecule of the invention that hyb ⁇ dizes under st ⁇ ngent conditions to the sequence of SEQ ID NO: 1 or 3 conesponds to a naturally-occur ⁇ ng nucleic acid molecule.
  • a "naturally- occurnng" 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 va ⁇ ants of the ABCB 12 transporter sequences that may exist in the population
  • changes can be introduced by mutation into the nucleotide sequences of SEQ ID NO: 1 or 3, thereby leading to changes in the amino acid sequence of the encoded ABCB 12 transporter proteins, without alte ⁇ ng the functional ability of the ABCB 12 transporter proteins.
  • nucleotide substitutions leading to amino acid substitutions at "non-essential" amino acid residues can be made in the sequence of SEQ ED NO: 1 or 3.
  • nucleic acid molecules encoding ABCB 12 transporter proteins that contain changes in amino acid residues that are not essential for activity.
  • Such ABCB 12 transporter proteins differ in amino acid sequence from SEQ ID NO: 2, yet retain biological activity.
  • the isolated nucleic acid molecule compnses a nucleotide sequence encoding a protein, wherein the protein compnses 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 ID NO. 2.
  • An isolated nucleic acid molecule encoding an ABCB 12 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 ammo acid substitutions, additions or deletions are introduced into the encoded protein. Mutations can be introduced into SEQ ID 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 am o acid residue is replaced with an amino acid residue having a similar side chain.
  • Families of am o acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysme, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, se ⁇ ne, threonine, tyrosme, cysteine), nonpolar side chains (e.g., alanine, va ne, leucine, isoleucine, proline, phenylalanme, methionine, tryptophan), beta-branched side chains (e.g., threonine, va ne, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanme, try
  • a predicted nonessenual amino acid residue in an ABCB 12 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 ABCB 12 transporter coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for ABCB 12 transporter biological activity to identify mutants that retain activity. Following mutagenesis of SEQ ID NO. 1 or 3 the encoded protein can be expressed recombinantly and the activity of the protein can be determined
  • a mutant ABCB 12 transporter protein can be assayed for the ability to interact with a non-ABCB12 transporter molecule, e.g., an ABCB 12 transporter ligand, e.g., a polypeptide or a small molecule.
  • a non-ABCB12 transporter molecule e.g., an ABCB 12 transporter ligand, e.g., a polypeptide or a small molecule.
  • an antisense nucleic acid compnses 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 ABCB 12 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 ABCB 12.
  • the term "coding region” refers to the region of the nucleotide sequence compnsing codons which are translated into amino acid residues (e.g., the coding region of human ABCB 12 conesponds to SEQ ID NO: 3).
  • the antisense nucleic acid molecule is antisense to a "noncoding region" of the coding strand of a nucleotide sequence encoding ABCB 12.
  • noncoding region refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also refened to as 5' and 3' untranslated regions). Given the coding strand sequences encoding ABCB 12 transporter disclosed herein
  • 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 e.g., an antisense oligonucleotide
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorourac ⁇ l, 5-bromourac ⁇ l, 5-chlorourac ⁇ l, 5- ⁇ odourac ⁇ l, hypoxanthine, xanthine, 4-acetylcytos ⁇ ne, 5- (carboxyhydroxylmethyl) uracil, 5-carboxymethylam ⁇ nomethyl-2-th ⁇ ou ⁇ d ⁇ ne, 5- carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine.
  • N6- lsopentenyladenme 1-methylguan ⁇ ne, 1-methyl ⁇ nos ⁇ ne, 2,2-d ⁇ methylguan ⁇ ne, 2-methyladen ⁇ ne, 2-methylguamne, 3-methylcytos ⁇ ne, 5-methylcytosme, N6-aden ⁇ ne, 7-methylguan ⁇ ne, 5- methylaminomethyluracil, 5-methoxyam ⁇ nomethyl-2-th ⁇ ourac ⁇ l, beta-D-mannosylqueosine, 5'- methoxycarboxymethyluracil, 5-methoxyurac ⁇ l, 2-methylth ⁇ o-N6- ⁇ sopentenyladen ⁇ ne, urac ⁇ l-5- oxyacetic acid (v), wybutoxosme, pseudouracil, queosine, 2-th ⁇ ocytos ⁇ ne, 5-methyl-2- thiouracil, 2-th ⁇ ourac ⁇ l, 4-th ⁇ ourac ⁇ l, 5-methylurac ⁇ l, urac ⁇ l-5-
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense o ⁇ entation (i.e., RNA transc ⁇ bed from the inserted nucleic acid will be of an antisense o ⁇ entation to a target nucleic acid of interest, descnbed 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 hybndize with or bind to cellular mRNA and/or genomic DNA encoding an ABCB 12 transporter protein to thereby inhibit expression of the protein, e.g., by inhibiting transc ⁇ ption and/or translation.
  • the hybndization can be by conventional nucleotide complementanty 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 descnbed herein.
  • the antisense nucleic acid molecule of the invention is an ⁇ - anomenc nucleic acid molecule
  • An ⁇ -anome ⁇ c nucleic acid molecule forms specific double- stranded hybnds 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 compnse a 2'-o-methylnbonucleot ⁇ de (Inoue et al (1987) Nucleic Acids Res. 15:6131-6148) or a chime ⁇ c RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215:327-330).
  • an antisense nucleic acid of the invention is a ⁇ bozyme.
  • Ribozymes are catalytic RNA molecules with nbonuclease activity which are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region
  • nbozymes e.g., hammerhead nbozymes (descnbed in Haselhoff and Gerlach (1988) Nature 334:585-591)
  • a nbozyme having specificity for an ABCB12-encod ⁇ ng nucleic acid can be designed based upon the nucleotide sequence of an ABCB 12 transporter cDNA disclosed herein (i.e., SEQ ID NO: 1).
  • SEQ ID NO: 1 the nucleotide sequence of an ABCB 12 transporter cDNA disclosed herein.
  • a denvative 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 ABCB12-encod ⁇ ng 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.
  • ABCB 12 transporter mRNA can be used to select a catalytic RNA having a specific ⁇ bonuclease activity from a pool of RNA molecules. See, e.g., Bartel, D. and Szostak, J.W. (1993) Science 261: 1411-1418.
  • ABCB 12 transporter gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the ABCB 12 transporter (e.g., the ABCB 12 transporter promoter and/or enhancers) to form t ⁇ ple helical structures that prevent transcnption of the ABCB12 transporter gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the ABCB 12 transporter e.g., the ABCB 12 transporter promoter and/or enhancers
  • the ABCB 12 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, hyb ⁇ dization, 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 deoxy ⁇ bose 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 hybndization 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 descnbed in Hyrup B. et al. ( 1996) supra, Pe ⁇ y-OKeefe et al. Proc. Natl. Acad. Sci. 93: 14670-675.
  • PNAs of ABCB 12 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 transcnption or translation anest or inhibiting replication.
  • PNAs of ABCB 12 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 restnction enzymes' when used in combination with other enzymes, (e.g., SI nucleases (Hyrup B. (1996) supra)); or as probes or pnmers for DNA sequencing or hybndization (Hyrup B.
  • PNAs of ABCB 12 transporter nucleic acid molecules can be modified, (e.g., to enhance their stability or cellular uptake), by attaching lipophi c 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 ABCB 12 transporter nucleic acid molecules can be generated which may combine the advantageous properties of PNA and DNA.
  • 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 appropnate lengths selected in terms of base stacking, number of bonds between the nucleobases, and onentation (Hyrup B. (1996) supra). The synthesis of PNA- DNA chimeras can be performed as descnbed 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-methoxyt ⁇ tyl)am ⁇ no-5'-deoxy-thym ⁇ d ⁇ ne 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 chime ⁇ c molecule with a 5' PNA segment and a 3' DNA segment (Finn P.J. et al. ( 1996) supra).
  • modified nucleoside analogs e.g., 5'-(4-methoxyt ⁇ tyl)am ⁇ no-5'-deoxy-thym ⁇ d ⁇ ne phosphoramidite
  • chime ⁇ c 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 vitro), 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 vitro
  • 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 hybndization-t ⁇ ggered 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, hyb ⁇ dization t ⁇ ggered cross-linking agent, transport agent, or hyb ⁇ dization-t ⁇ ggered cleavage agent).
  • ABCB 12 Transporter Proteins and Ant ⁇ -ABCB 12 Transporter Antibodies One aspect of the invention pertains to isolated ABCB 12 transporter proteins, and biologically active portions thereof, as well as polypeptide fragments suitable for use as immunogens to raise ant ⁇ -ABCB 12 transporter antibodies.
  • native ABCB 12 transporter proteins can be isolated from cells or tissue sources by an appropnate pu ⁇ fication scheme using standard protein punfication techniques.
  • ABCB 12 transporter protems are produced by recombinant DNA techniques.
  • an ABCB 12 transporter protein or polypeptide can be synthesized chemically using standard peptide synthesis techniques.
  • an “isolated” or “pu ⁇ fied” protein or biologically active portion thereof is substantially free of cellular matenal or other contaminating proteins from the cell or tissue source from which the ABCB 12 transporter protein is denved, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • the language “substantially free of cellular mate ⁇ al” includes preparations of ABCB 12 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 mate ⁇ al” includes preparations of ABCB 12 transporter protein having less than about 30% (by dry weight) of non-ABCB 12 transporter protein (also refened to herein as a "contaminating protein"), more preferably less than about 20% of non-ABCB 12 transporter protein, still more preferably less than about 10% of non-ABCB 12 transporter protein, and most preferably less than about 5% non-ABCB 12 transporter protein.
  • 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 ABCB 12 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 ABCB 12 transporter protein having less than about 30% (by dry weight) of chemical precursors or non-ABCB 12 transporter chemicals, more preferably less than about 20% chemical precursors or non-ABCB 12 transporter chemicals, still more preferably less than about 10% chemical precursors or non-ABCB 12 transporter chemicals, and most preferably less than about 5% chemical precursors or non-ABCB 12 transporter chemicals
  • a "biologically active portion" of an ABCB 12 transporter protein includes a fragment of an ABCB 12 transporter protein which participates in an interaction between an ABCB 12 transporter molecule and a non-ABCB 12 transporter molecule.
  • Biologically active portions of an ABCB 12 transporter protein include peptides compnsing amino acid sequences sufficiently homologous to or de ⁇ ved from the amino acid sequence of the ABCB 12 transporter protein, e.g., the amino acid sequence shown in SEQ ID NO. 2, which include less amino acids than the full length ABCB 12 transporter proteins, and exhibit at least one activity of an ABCB 12 transporter protein.
  • biologically active portions compnse a domain or motif with at least one activity of the ABCB 12 transporter protein.
  • a biologically active portion of an ABCB 12 transporter protein can be a polypeptide which is, for example, 10, 25, 50, 100, 200, 300, 400, 500, 600, 700.
  • Biologically active portions of an ABCB 12 transporter protein can be used as targets for developing agents which modulate an ABCB 12 transporter mediated activity.
  • a biologically active portion of an ABCB 12 transporter protein comp ⁇ ses at least one transmembrane domain. It is to be understood that a prefened biologically active portion of an ABCB 12 transporter protein of the present invention may contain at least one transmembrane domain. Another prefened biologically active portion of an ABCB 12 transporter protein may contain at least two transmembrane domains. One or more of these transmembrane domains may associate to form a membrane-spanning domain.
  • the biologically active portion of the ABCB 12 transporter protein may include multiple clusters of conserved residues that define an ATP binding domain.
  • the biologically active portion of the ABCB 12 transporter protein may compnse 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 descnbed 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 ABCB 12 transporter protein.
  • the ABCB 12 transporter protein has an amino acid sequence shown in SEQ ID NO. 2.
  • the ABCB 12 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 va ⁇ ation or mutagenesis, as descnbed in detail in subsection I above.
  • the ABCB 12 transporter protein is a protein which compnses 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 ED NO: 2.
  • the sequences are aligned for optimal compa ⁇ son pu ⁇ oses (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 companson pu ⁇ oses).
  • the length of a reference sequence aligned for compa ⁇ son pu ⁇ oses 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 ABCB 12 transporter amino acid sequence of SEQ TD NO: 2 having 843 amino acid residues, at least 253, preferably at least 337, more preferably at least 422, even more preferably at least 506, and even more preferably at least 590, 674, 759, or 843 amino acid residues are aligned).
  • the amino acid residues or nucleotides at conesponding 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 compa ⁇ son of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algonthm. In a prefened embodiment, the percent identity between two amino acid sequences is determined using standard art recognized compa ⁇ son software using standard parameter settings.
  • the Needleman and Wunsch (J. Mol. Biol. (48):444-453 (1970)) algonthm which has been inco ⁇ orated into the GAP program in the GCG software package can be employed using either a Blossum 62 matnx or a PAM250 matnx, 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 matnx and a gap weight of 40, 50, 60.
  • the percent identity between two ammo acid or nucleotide sequences is determined using the algonthm of E. Meyers and W. Miller (CABIOS, 4: 11-17 (1988)) which has been inco ⁇ orated 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 descnbed 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.
  • the invention also provides ABCB 12 transporter chimenc or fusion proteins.
  • an ABCB12 transporter "chimenc protein” or “fusion protein” comp ⁇ ses an ABCB12 transporter polypeptide operatively linked to a non-ABCB 12 transporter polypeptide.
  • ABCB 12 transporter polypeptide refers to a polypeptide having an am o acid sequence conesponding to ABCB 12
  • a non-ABCB 12 transporter polypeptide refers to a polypeptide having an ammo acid sequence conesponding to a protein which is not substantially homologous to the ABCB 12 transporter protein, e.g., a protein which is different from the ABCB 12 transporter protein and which is denved from the same or a different organism.
  • the ABCB 12 transporter polypeptide can conespond to all or a portion of an ABCB 12 transporter protein.
  • an ABCB 12 transporter fusion protein comp ⁇ ses at least one biologically active portion of an ABCB 12 transporter protein.
  • an ABCB 12 transporter fusion protein comp ⁇ ses at least two biologically active portions of an ABCB12 transporter protein.
  • the term "operatively linked" is intended to indicate that the ABCB12 transporter polypeptide and the non-ABCB 12 transporter polypeptide are fused m-frame to each other.
  • the non-ABCB 12 transporter polypeptide can be fused to the N-terminus or C-terminus of the ABCB 12 transporter polypeptide.
  • the fusion protein is a GST-ABCB12 transporter fusion protein in which the ABCB 12 transporter sequences are fused to the C-terminus of the GST sequences.
  • Such fusion proteins can facilitate the pu ⁇ fication of recombinant ABCB 12.
  • the fusion protein is an ABCB 12 transporter protein containing a heterologous signal sequence at its N-terminus.
  • expression and/or secretion of ABCB 12 transporter can be increased through use of a heterologous signal sequence.
  • the ABCB 12 transporter fusion proteins of the invention can be inco ⁇ orated into pharmaceutical compositions and administered to a subject in vitro
  • the ABCB 12 transporter fusion proteins can be used to affect the bioavailabi ty of an ABCB 12 transporter substrate
  • Use of ABCB 12 transporter fusion proteins may be useful therapeutically for the treatment of disorders caused by, for example, (1) abenant modification or mutation of a gene encoding an ABCB12 transporter protein; ( ⁇ ) mis-regulation of the ABCB12 transporter gene; and (in) abenant post-translational modification of an ABCB 12 transporter protein.
  • ABCB12-fus ⁇ on proteins of the invention can be used as immunogens to produce ant ⁇ -ABCB 12 transporter antibodies in a subject, to punfy ABCB12 transporter ligands and in screening assays to identify molecules which inhibit the interaction of an ABCB 12 transporter with an ABCB 12 transporter substrate.
  • an ABCB 12 transporter chimenc 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, restnction enzyme digestion to provide for appropnate termini, filling-in of cohesive ends as appropnate, 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 earned out using anchor pnmers which give ⁇ se to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and reamplified to generate a chime ⁇ c gene sequence (see, for example, Current Protocols in Molecular Biology, eds. Ausubel et al. John Wiley & Sons: 1992).
  • many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST polypeptide).
  • An ABCB 12 transporter-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the ABCB 12 transporter protein.
  • the present invention also pertains to va ⁇ ants of the ABCB 12 transporter proteins which function as either ABCB 12 transporter agonists or as ABCB 12 transporter antagonists.
  • Va ⁇ ants of the ABCB 12 transporter proteins can be generated by mutagenesis, e.g., discrete point mutation or truncation of an ABCB 12 transporter protein.
  • An agonist of the ABCB 12 transporter proteins can retain substantially the same, or a subset, of the biological activities of the naturally occumng form of an ABCB12 transporter protein
  • An antagonist of an ABCB 12 transporter protein can inhibit one or more of the activities of the naturally occur ⁇ ng form of the ABCB 12 transporter protein by, for example, competitively modulating an activity of an ABCB 12 transporter protein.
  • treatment of a subject with a va ⁇ ant having a subset of the biological activities of the naturally occumng form of the protein has fewer side effects in a subject relative to treatment with the naturally occur ⁇ ng form of the ABCB 12 transporter protein.
  • va ⁇ ants of an ABCB 12 transporter protein which function as either ABCB 12 transporter agonists (mimetics) or as ABCB 12 transporter antagonists can be identified by screening combinato ⁇ al branes of mutants, e.g., truncation mutants, of an ABCB 12 transporter protein
  • a va ⁇ egated library of ABCB 12 transporter vanants is generated by combinatonal mutagenesis at the nucleic acid level and is encoded by a va ⁇ egated gene library
  • a va ⁇ egated library of ABCB 12 transporter va ⁇ ants can be produced by, for example, enzymatically ligating a mixture of synthetic oligonucleotides into gene sequences such that a degenerate set of potential ABCB 12 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 ABCB 12 transporter sequences therein
  • There are a vanety of methods which can be used to produce hbranes of potential ABCB 12 transporter vanants 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 appropnate 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 ABCB 12 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 ⁇ /. (1984) Science 198:1056; Ike et al.
  • hbranes of fragments of an ABCB 12 transporter protein coding sequence can be used to generate a va ⁇ egated population of ABCB 12 transporter fragments for screening and subsequent selection of va ⁇ ants of an ABCB 12 transporter protein.
  • a library of coding sequence fragments can be generated by treating a double stranded PCR fragment of an ABCB 12 transporter coding sequence with a nuclease under conditions wherein nicking occurs only about once per molecule, denatu ⁇ ng the double stranded DNA, renatunng 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 de ⁇ ved which encodes N-terminal, C-terminal and internal fragments of vanous sizes of the ABCB 12 transporter protein.
  • Recursive ensemble mutagenesis (REM), a new technique which enhances the frequency of functional mutants in the hbranes, can be used in combination with the screening assays to identify ABCB 12 transporter va ⁇ ants (Arkin and Yourvan (1992) Proc. Natl. Acad. Sci. USA 59:781 1- 7815; Delgrave et al. (1993) Protein Engineering 6(3):327-331).
  • An isolated ABCB 12 transporter protein, or a portion or fragment thereof, can be used as an immunogen to generate antibodies that bind ABCB 12 transporter using standard techniques for polyclonal and monoclonal antibody preparation.
  • a full-length ABCB 12 transporter protein can be used or, alternatively, the invention provides antigenic peptide fragments of ABCB 12 transporter for use as immunogens.
  • Prefened epitopes encompassed by the antigenic peptide are regions of ABCB 12 transporter that are located on the surface of the protein, e.g., hydrophilic regions, as well as regions with high antigenicity.
  • An ABCB 12 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 appropnate lmmunogenic preparation can contain, for example, recombinantly expressed ABCB 12 transporter protein or a chemically synthesized ABCB 12 transporter polypeptide.
  • the preparation can further include an adjuvant, such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent.
  • an adjuvant such as Freund's complete or incomplete adjuvant, or similar immunostimulatory agent. Immunization of a suitable subject with an lmmunogenic ABCB 12 transporter preparation induces a polyclonal ant ⁇ -ABCB12 transporter antibody response.
  • antibody refers to immunoglobu n molecules and immunologically active portions of immunoglobuhn molecules, i.e., molecules that contain an antigen binding site which specifically binds (immunoreacts with) an antigen, such as ABCB12 transporter.
  • immunologically active portions of immunoglobuhn 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 ABCB 12 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 lmmunoreacting with a particular epitope of ABCB 12 transporter.
  • a monoclonal antibody composition thus typically displays a single binding affinity for a particular ABCB 12 transporter protein with which it immunoreacts.
  • Polyclonal ant ⁇ -ABCB12 transporter antibodies can be prepared as descnbed above by immunizing a suitable subject with an ABCB 12 transporter immunogen.
  • the ant ⁇ -ABCB 12 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 ABCB 12 transporter.
  • ELISA enzyme linked immunosorbent assay
  • the antibody molecules directed against ABCB 12 transporter can be isolated from the mammal (e.g., from the blood) and further punfied 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 hybndoma technique onginally descnbed 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.
  • an immortal cell line typically a myeloma
  • lymphocytes typically splenocytes
  • the culture supematants of the resulting hybndoma cells are screened to identify a hybndoma producing a monoclonal antibody that binds ABCB 12 transporter.
  • the immortal cell line (e.g., a myeloma cell line) is de ⁇ ved from the same mammalian species as the lymphocytes.
  • mu ⁇ ne hyb ⁇ domas can be made by fusing lymphocytes from a mouse immunized with an lmmunogenic preparation of the present invention with an immortalized mouse cell line.
  • Prefened immortal cell lines are mouse myeloma cell lines that are sensitive to culture medium containing hypoxanthine, aminopte ⁇ n 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.
  • HAT-sensitive mouse myeloma cells are fused to mouse splenocytes using polyethylene glycol ("PEG").
  • Hybndoma 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).
  • Hybndoma cells producing a monoclonal antibody of the invention are detected by screening the hybndoma culture supematants for antibodies that bind ABCB 12, e.g., using a standard ELISA assay.
  • a monoclonal anti- ABCB12 transporter antibody can be identified and isolated by screening a recombinant combinatonal immunoglobuhn library (e.g., an antibody phage display library) with ABCB12 transporter to thereby isolate immunoglobuhn library members that bind ABCB 12.
  • Kits for generating and screening phage display hbranes are commercially available (e.g., the Pharmacia Recombinant Phage Antibody System, Catalog No. 27-9400-01; and the Stratagene SurfZAPTM Phage Displav Kit, Catalog No. 240612).
  • examples of methods and reagents particularly amenable for use in generating and screening antibody display library can be found in, for example, Ladner et al. U.S. Patent No. 5,223,409; Kang et al. PCT
  • recombinant ant ⁇ -ABCB 12 transporter antibodies such as chime ⁇ c and humanized monoclonal antibodies, compnsing both human and non-human portions, which can be made using standard recombinant DNA techniques, are within the scope of the invention.
  • chime ⁇ c and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods descnbed in Robinson et al.
  • An ant ⁇ -ABCB12 transporter antibody (e.g., monoclonal antibody) can be used to isolate ABCB 12 transporter by standard techniques, such as affinity chromatography or immunoprecipitation.
  • An ant ⁇ -ABCB 12 transporter antibody can facilitate the pu ⁇ fication of natural ABCB 12 transporter from cells and of recombinantly produced ABCB 12 transporter expressed in host cells.
  • an ant ⁇ -ABCB12 transporter antibody can be used to detect ABCB 12 transporter protein (e.g., in a cellular lysate or cell supernatant) in order to evaluate the abundance and pattern of expression of the ABCB 12 transporter protein.
  • Ant ⁇ -ABCB 12 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 vanous enzymes, prosthetic groups, fluorescent mate ⁇ als, luminescent mate ⁇ als, bioluminescent matenals, and radioactive matenals.
  • suitable enzymes include horseradish peroxidase, alkaline phosphatase, -galactosidase, or acetylchohnesterase;
  • suitable prosthetic group complexes include streptavidin/biotin and avidm/biotin;
  • suitable fluorescent mate ⁇ als include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorot ⁇ azinylamine fluorescein, dansyl chlonde or phycoerythnn;
  • an example of a luminescent mate ⁇ al includes lummol;
  • bioluminescent mate ⁇ als include luciferase, lucifenn, and aequo ⁇ n, and examples of suitable radioactive mate ⁇ al include 125 I, 131 1, 35 S, 33 P, 32 P, or 3 H.
  • vectors preferably expression vectors, containing a nucleic acid encoding an ABCB 12 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.
  • 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.
  • vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bactenal vectors having a bacte ⁇ al on gin of replication and episomal mammalian vectors).
  • Other vectors e.g., non-episomal mammalian vectors
  • certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are refened 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.
  • viral vectors e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses
  • the recombinant expression vectors of the invention compnse 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 transcnption/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 descnbed, 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 descnbed herein (e.g., ABCB 12 transporter proteins, mutant forms of ABCB 12 transporter proteins, fusion proteins, and the like).
  • proteins or peptides including fusion proteins or peptides, encoded by nucleic acids as descnbed herein (e.g., ABCB 12 transporter proteins, mutant forms of ABCB 12 transporter proteins, fusion proteins, and the like).
  • the recombinant expression vectors of the invention can be designed for expression of ABCB 12 transporter proteins in prokaryotic or eukaryotic cells.
  • ABCB 12 transporter proteins can be expressed in bacte ⁇ al 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 Enzvmology 185, Academic Press, San Diego, CA (1990).
  • the recombinant expression vector can be transcnbed and translated in vitro, for example using T7 promoter regulatory sequences and T7 polymerase. Expression of proteins in prokaryotes is most often earned 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 pu ⁇ oses: 1) to increase expression of recombinant protein; 2) to increase the solubility of the recombinant protein; and 3) to aid in the punfication of the recombinant protein by acting as a ligand in affinity punfication.
  • 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 punfication 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.
  • Punfied fusion proteins can be utilized in ABCB12 transporter activity assays, (e.g., direct assays or competitive assays descnbed in detail below), or to generate antibodies specific for ABCB 12 transporter proteins, for example.
  • an ABCB 12 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 inadiated recipients. The pathology of the subject recipient is then examined after sufficient time has passed (e.g., six (6) weeks).
  • suitable inducible non-fusion E. coli expression vectors include pTrc
  • Target gene expression from the pTrc vector relies on host RNA polymerase transcnption from a hybnd t ⁇ -lac fusion promoter.
  • Target gene expression from the pET 1 Id vector relies on transcnption 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 harbonng a T7 gnl gene under the transc ⁇ ptional control of the lacUV 5 promoter.
  • One strategy to maximize recombinant protein expression in E. coli is to express the protein in a host bactena 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 ammo 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 earned out by standard DNA synthesis techniques.
  • the ABCB 12 transporter expression vector is a yeast expression vector.
  • yeast expression vectors for expression in yeast S. cerevisiae include pYepSecl (Baldan, 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 Co ⁇ oration, San Diego, CA), and picZ (InVitrogen Co ⁇ , San Diego, CA).
  • ABCB 12 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 se ⁇ es (Smith et al. ( 1983) Mol. Cell Biol 3:2156-2165) and the pVL se ⁇ es (Lucklow and Summers (1989) Virologv 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 de ⁇ ved from polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40.
  • suitable expression systems for both prokaryotic and eukaryotic cells see chapters 16 and 17 of Sambrook, J., Fntsh, E. F., and Mamatis, T. Molecular Cloning: A Laboratory Manual. 2nd, ed.. Cold Spring Harbor Laboratory, Cold Sp ⁇ ng Harbor Laboratory Press, Cold Sp ⁇ ng Harbor, NY, 1989.
  • the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid).
  • tissue-specific regulatory elements are known in the art.
  • suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert et al. (1987) Genes Dev. 1:268-277), lymphoid-specific promoters (Calame and Eaton (1988) Adv. Immunol. 43:235-275), in particular promoters of T cell receptors (Winoto and Baltimore (1989) EMBO J.
  • promoters are also encompassed, for example the munne 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 compnsing a DNA molecule of the invention cloned into the expression vector in an antisense o ⁇ entation. That is, the DNA molecule is operatively linked to a regulatory sequence in a manner which allows for expression (by transcnption of the DNA molecule) of an RNA molecule which is antisense to ABCB 12 transporter mRNA.
  • Regulatory sequences operatively linked to a nucleic acid cloned in the antisense o ⁇ entation can be chosen which direct the continuous expression of the antisense RNA molecule in a va ⁇ ety 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.
  • Another aspect of the invention pertains to host cells mto which an ABCB12 transporter nucleic acid molecule of the invention is introduced, e.g., an ABCB 12 transporter nucleic acid molecule within a recombinant expression vector or an ABCB 12 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 ABCB12 transporter protein can be expressed in bacte ⁇ al cells such as E. coli, insect cells, yeast or mammalian cells (such as Chinese hamster ovary cells (CHO) or COS cells).
  • bacte ⁇ al 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.
  • transformation and transfection are intended to refer to a va ⁇ ety of art-recognized techniques for introducing foreign nucleic acid (e.g., DNA) into a host cell, including calcium phosphate or calcium chlonde co-precipitation, DEAE-dextran-mediated transfection, hpofection, 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 Sp ⁇ ng Harbor Laboratory Press, Cold Sp ⁇ ng 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
  • ABCB 12 transporter protein 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 inco ⁇ orated 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 ABCB12 transporter protein.
  • the invention further provides methods for producing an ABCB 12 transporter protein using the host cells of the invention.
  • the method comp ⁇ ses cultu ⁇ ng the host cell of the invention (into which a recombinant expression vector encoding an ABCB 12 transporter protein has been introduced) in a suitable medium such that an ABCB 12 transporter protein is produced.
  • the method further comp ⁇ ses isolating an ABCB 12 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.
  • a host cell of the invention is a fertilized oocyte or an embryonic stem cell into which ABCB12-codmg sequences have been introduced.
  • Such host cells can then be used to create non-human transgenic animals in which exogenous ABCB 12 transporter sequences have been introduced into their genome or homologous recombinant animals in which endogenous ABCB 12 transporter sequences have been altered.
  • Such animals are useful for studying the function and or activity of an ABCB 12 transporter and for identifying and/or evaluating modulators of ABCB 12 transporter activity.
  • a "transgenic animal” is a non-human animal, preferably a mammal, more preferably a rodent such as a rat or mouse, in which one or more of the cells of the animal includes a transgene.
  • Other examples of transgenic animals include non-human p ⁇ mates, 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 ABCB 12 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, p ⁇ or to development of the animal.
  • a transgenic animal of the invention can be created by introducing an ABCB 12- 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 ABCB 12 transporter cDNA sequence of SEQ ID NO: 1 can be introduced as a transgene into the genome of a non-human animal Alternatively, a nonhuman homologue of a human ABCB 12 transporter gene, such as a mouse or rat ABCB 12 transporter gene, can be used as a transgene. Alternatively, an ABCB 12 transporter gene homologue, such as another ABCB 12 transporter family member, can be isolated based on hybndization to the ABCB12 transporter cDNA sequences of SEQ ID NO: 1 or 3 (descnbed further in subsection I above) and used as a transgene. Intromc 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 ABCB 12 transporter transgene to direct expression of an ABCB 12 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 descnbed, 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 Spnng Harbor Laboratory Press, Cold Sp ⁇ ng 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 ABCB 12 transporter transgene in its genome and/or expression of ABCB 12 transporter mRNA in tissues or cells of the animals. A transgenic founder animal can then be used to breed additional animals canymg the transgene. Moreover, transgenic animals canying a transgene encoding an ABCB 12 transporter protein can further be bred to other transgenic animals cany g other transgenes, for example, animals canying a transgene encoding a neurotoxic polypeptide such as ⁇ -amyloid.
  • a vector is prepared which contains at least a portion of an ABCB 12 transporter gene into which a deletion, addition or substitution has been introduced to thereby alter, e.g., functionally disrupt, the ABCB 12 transporter gene.
  • the ABCB 12 transporter gene can be a human gene (e.g., the cDNA of SEQ ID NO: 3), but more preferably, is a non-human homologue of a human ABCB 12 transporter gene (e.g., a cDNA isolated by st ⁇ ngent hyb ⁇ dization with the nucleotide sequence of SEQ ED NO: 1)
  • a mouse ABCB 12 transporter gene can be used to construct a homologous recombination nucleic acid molecule, e.g., a vector, suitable for alternativeng an endogenous
  • the homologous recombination nucleic acid molecule is designed such that, upon homologous recombination, the endogenous ABCB 12 transporter gene is functionally disrupted (i.e., no longer encodes a functional protein; also refened to as a "knock out" vector).
  • the homologous recombination nucleic acid molecule can be designed such that, upon homologous recombination, the endogenous ABCB 12 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 ABCB 12 transporter protein).
  • the altered portion of the ABCB 12 transporter gene is flanked at its 5' and 3 ' ends by additional nucleic acid sequence of the ABCB 12 transporter gene to allow for homologous recombination to occur between the exogenous ABCB 12 transporter gene earned by the homologous recombination nucleic acid molecule and an endogenous ABCB 12 transporter gene in a cell, e.g., an embryonic stem cell.
  • the additional flanking ABCB 12 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 descnption 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 ABCB 12 transporter gene has homologously recombined with the endogenous ABCB 12 transporter gene are selected (see e.g., Li, E.
  • Progeny harbo ⁇ ng 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 germhne transmission of the transgene.
  • Methods for constructing homologous recombination nucleic acid molecules, e.g., vectors, or homologous recombinant animals are descnbed further in Bradley, A.
  • transgenic non-human animals can be produced which contain selected systems which allow for regulated expression of the transgene.
  • cre/loxP recombinase system of bacte ⁇ ophage PL for a descnption of the cre ⁇ oxP recombinase system, see, e.g., Lakso et al (1992) Proc. Natl. Acad. Sci. USA 89:6232-6236.
  • 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.
  • 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 stenle diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glyce ⁇ ne, propylene glycol or other synthetic solvents; antibactenal 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 chlonde or dextrose. pH can be adjusted with acids or bases, such as hydrochlonc acid or sodium hydroxide.
  • a stenle diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glyce ⁇ ne, propylene glycol or other synthetic solvents
  • antibactenal agents such as benzyl
  • compositions suitable for injectable use include stenle aqueous solutions (where water soluble) or dispersions and stenle powders for the extemporaneous preparation of stenle injectable solutions or dispersion.
  • suitable earners include physiological saline, bacte ⁇ ostatic water, Cremophor ELTM (BASF, Parsippany, NJ) or phosphate buffered saline (PBS). In all cases, the composition must be stenle and should be fluid to the extent that easy synngabihty exists.
  • the earner 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
  • vanous antibactenal 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 chlonde
  • Prolonged abso ⁇ tion of the injectable compositions can be brought about by including in the composition an agent which delays abso ⁇ tion, for example, aluminum monostearate and gelatin.
  • Stenle injectable solutions can be prepared by inco ⁇ orating the active compound (e.g., a fragment of an ABCB 12 transporter protein or an ant ⁇ -ABCB 12 transporter antibody) in the required amount in an appropnate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sten zation.
  • the active compound e.g., a fragment of an ABCB 12 transporter protein or an ant ⁇ -ABCB 12 transporter antibody
  • dispersions are prepared by inco ⁇ orating the active compound into a stenle vehicle which contains a basic ABCB 12 transporter dispersion medium and the required other ingredients from those enumerated above.
  • the prefened 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 stenle-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible earner. They can be enclosed in gelatin capsules or compressed into tablets. For the pu ⁇ ose of oral therapeutic administration, the active compound can be inco ⁇ orated with excipients and used in the form of tablets, troches, or capsules, oral compositions can also be prepared using a fluid earner for use as a mouthwash, wherein the compound in the fluid earner is applied orally and swished and expectorated or swallowed. Pharmaceutically compatible binding agents, and/or adjuvant matenals 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, P ⁇ mogel, or com starch; a lubncant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide: a sweetening agent such as sucrose or saccha ⁇ n; or a flavonng agent such as peppermint, methyl sa cylate, or orange flavonng.
  • a binder such as microcrystalline cellulose, gum tragacanth or gelatin
  • an excipient such as starch or lactose, a disintegrating agent such as alginic acid, P ⁇ mogel, or com starch
  • a lubncant such as magnesium stearate or Sterotes
  • the compounds are delivered in the form of an aerosol spray from pressured container or dispenser which contains a suitable propellant, e.g., gas such as carbon dioxide, or a nebulizer.
  • a suitable propellant e.g., gas such as carbon dioxide, or a nebulizer.
  • Systemic administration can also be by transmucosal or transdermal means.
  • penetrants appropnate to the barner 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 de ⁇ vatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays or suppositones.
  • 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 suppositones (e.g., with conventional suppository bases such as cocoa butter and other glycendes) or retention enemas for rectal delivery.
  • the active compounds are prepared with earners 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, polyanhyd ⁇ des, polyglyco c acid, collagen, polyorthoesters, and polylactic acid. Methods for preparation of such formulations will be apparent to those skilled in the art.
  • the mate ⁇ als can also be obtained commercially from Alza Co ⁇ oration and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to infected cells with monoclonal antibodies to viral antigens) can also be used as pharmaceutically acceptable earners.
  • 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 earner
  • the specification for the dosage unit forms of the invention are dictated by and directly dependent on the unique charactenstics 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 expenmental 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 prefened. 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 compnse a slow release matnx 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 descnbed herein can be used in one or more of the following methods: a) screening assays; b) predictive medicine (e.g., diagnostic assays, prognostic assays, monitonng clinical t ⁇ als, 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 ABCB12 transporter protein (e.g., via a recombinant expression vector in a host cell in gene therapy applications), to detect ABCB 12 transporter mRNA (e.g., in a biological sample) or a genetic alteration in an ABCB 12 transporter gene, and to modulate ABCB 12 transporter activity, as descnbed further below.
  • the ABCB 12 transporter proteins can be used to treat disorders charactenzed by insufficient or excessive production of an ABCB 12 transporter substrate or production of ABCB 12 transporter inhibitors.
  • ABCB 12 transporter proteins can be used to screen for naturally occur ⁇ ng ABCB 12 transporter substrates, to screen for drugs or compounds which modulate ABCB 12 transporter activity, as well as to treat disorders charactenzed by insufficient or excessive production of ABCB 12 transporter protein or production of ABCB 12 transporter protein forms which have decreased, abenant or unwanted activity compared to ABCB 12 transporter wild type protein.
  • anti- ABCB12 transporter antibodies of the invention can be used to detect and isolate ABCB12 transporter proteins, regulate the bioavailabihty of ABCB 12 transporter proteins, and modulate ABCB 12 transporter activity.
  • the invention provides a method (also refened to herein as a "screening assay") for identifying modulators, i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to ABCB 12 transporter proteins, have a stimulatory or inhibitory effect on, for example, ABCB 12 transporter expression or ABCB 12 transporter activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of ABCB 12 transporter substrate.
  • modulators i.e., candidate or test compounds or agents (e.g., peptides, peptidomimetics, small molecules or other drugs) which bind to ABCB 12 transporter proteins, have a stimulatory or inhibitory effect on, for example, ABCB 12 transporter expression or ABCB 12 transporter activity, or have a stimulatory or inhibitory effect on, for example, the expression or activity of ABCB 12 transporter substrate.
  • the invention provides assays for screening candidate or test compounds which are substrates of an ABCB 12 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 ABCB 12 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 combinatonal library methods known in the art, including: biological hbranes; spatially addressable parallel solid phase or solution phase hbranes; synthetic library methods requmng deconvolution; the 'one-bead one-compound' library method; and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to peptide hbranes, while the other four approaches are applicable to peptide, non-peptide ohgomer or small molecule hbranes of compounds (Lam, K.S. (1997) Anticancer Drug Des. 12.145)
  • an assay is a cell-based assay in which a cell which expresses an
  • ABCB 12 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to modulate ABCB 12 transporter activity is determined. Determining the ability of the test compound to modulate ABCB 12 transporter activity can be accomplished by momtonng, for example, cellular transport of organic anions, organic cations, cytotoxic anti-cancer drugs, intracellular calcium, potassium, phosphatidylchohne, sodium concentration, neuronal membrane depola ⁇ zation, a neurotoxic polypeptide (e.g., ⁇ -amyloid), or the activity of an ABCB 12 transporter-regulated transcnption factor.
  • the cell for example, can be of mammalian ong , e.g., a neuronal cell.
  • the ability of the test compound to modulate ABCB 12 transporter binding to a substrate or to bind to ABCB 12 transporter can also be determined. Determining the ability of the test compound to modulate ABCB 12 transporter binding to a substrate can be accomplished, for example, by coupling the ABCB 12 transporter substrate with a radioisotope or enzymatic label such that binding of the ABCB 12 transporter substrate to ABCB 12 transporter can be determined by detecting the labeled ABCB 12 transporter substrate in a complex.
  • Determining the ability of the test compound to bind ABCB 12 transporter can be accomplished, for example, by coupling the compound with a radioisotope or enzymatic label such that binding of the compound to ABCB 12 transporter can be determined by detecting the labeled ABCB 12 transporter compound in a complex.
  • compounds e.g., ABCB12 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 appropnate substrate to product.
  • suitable compounds include, but are not limited to, verapamil, desmethoxyverapamil, chloroquine, quinine, chinchonidme, p ⁇ maquine, tamoxifen, dihydrocyclospo ⁇ n, yohimbine, corynanthine, rese ⁇ ine, physostigmine, acndine, ac ⁇ dine orange, quinacnne, t ⁇ fluoroperazine chlo ⁇ romazine, propanolol, atropine, tryptamine, forsko n, 1,9-d ⁇ deoxyforskohn, cyclosponn, (US Patent 4,117,118 (1978)), PSC-833 (cyclosponn D, 6-[(2S, 4R, 6E)-4-methyl-2-(methylam ⁇ no)-3-oxo-6-octeno ⁇ c ac ⁇ d]-(9CI)), [US Patent 5,525,590]
  • a compound e.g., an ABCB 12 transporter substrate
  • a microphysiometer can be used to detect the interaction of a compound with ABCB 12 transporter without the labeling of either the compound or the ABCB12. McConnell, H. M. et al. (1992) Science 257: 1906-1912.
  • an assay is a cell-based assay compnsing contacting a cell expressing an ABCB 12 transporter target molecule (e.g., an ABCB 12 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 ABCB 12 transporter target molecule. Determining the ability of the test compound to modulate the activity of an ABCB 12 transporter target molecule can be accomplished, for example, by determining the ability of the ABCB 12 transporter protein to bind to or interact with the ABCB 12 transporter target molecule
  • Determining the ability of the ABCB 12 transporter protein or a biologically active fragment thereof, to bind to or interact with an ABCB 12 transporter target molecule can be accomplished by one of the methods descnbed above for determining direct binding
  • determining the ability of the ABCB 12 transporter protein to bind to or interact with an ABCB 12 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 appropnate substrate, detecting the induction of a reporter gene (compnsing 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 cellular second messenger of the target i.e., intracellular Ca2+, diacylglycerol, IP3, and the like
  • detecting catalytic/enzymatic activity of the target an appropnate substrate detecting the induction of a reporter gene (compns
  • an assay of the present invention is a cell-free assay in which an ABCB 12 transporter protein or biologically active portion thereof is contacted with a test compound and the ability of the test compound to bind to the ABCB 12 transporter protein or biologically active portion thereof is determined
  • Prefened biologically active portions of the ABCB 12 transporter proteins to be used in assays of the present invention include fragments which participate in interactions with non-ABCB 12 transporter molecules, e.g , fragments with high surface probability scores (see, for example, Figure 2). Binding of the test compound to the ABCB 12 transporter protein can be determined either directly or indirectly as descnbed above.
  • the assay includes contacting the ABCB 12 transporter protein or biologically active portion thereof with a known compound which binds ABCB 12 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 ABCB 12 transporter protein, wherein determining the ability of the test compound to interact with an ABCB 12 transporter protein compnses determining the ability of the test compound to preferentially bind to ABCB 12 transporter or biologically active portion thereof as compared to the known compound
  • the assay is a cell-free assay in which an ABCB 12 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 ABCB12 transporter protein or biologically active portion thereof is determined.
  • Determining the ability of the test compound to modulate the activity of an ABCB 12 transporter protein can be accomplished, for example, by determining the ability of the ABCB 12 transporter protein to bind to an ABCB 12 transporter target molecule by one of the methods descnbed above for determining direct binding. Alternatively, for example, ATP binding can be measured.
  • Determining the ability of the ABCB 12 transporter protein to bind to an ABCB 12 transporter target molecule can also be accomplished using a technology such as real-time Biomolecular Interaction Analysis (BIA).
  • BIOA Biomolecular Interaction Analysis
  • BIOA 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.
  • SPR surface plasmon resonance
  • determining the ability of the test compound to modulate the activity of an ABCB 12 transporter protein can be accomplished by determining the ability of the ABCB 12 transporter protein to further modulate the activity of a downstream effector of an ABCB 12 transporter target molecule.
  • the activity of the effector molecule on an appropnate target can be determined or the binding of the effector to an appropnate target can be determined as previously descnbed.
  • the cell-free assay involves contacting an ABCB 12 transporter protein or biologically active portion thereof with a known compound which binds the ABCB 12 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 ABCB 12 transporter protein, wherein determining the ability of the test compound to interact with the ABCB 12 transporter protein compnses determining the ability of the ABCB 12 transporter protein to preferentially bind to or modulate the activity of an ABCB 12 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., ABCB 12 transporter proteins or biologically active portions thereof ).
  • isolated proteins e.g., ABCB 12 transporter proteins or biologically active portions thereof.
  • binding of a test compound to an ABCB 12 transporter protein, or interaction of an ABCB 12 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-cent ⁇ fuge tubes.
  • a fusion protein can be provided which adds a domain that allows one or both of the proteins to be bound to a matnx.
  • glutath ⁇ one-S-transferase/ABCB12 transporter fusion proteins or glutathione-S- transferase/target fusion proteins can be adsorbed onto glutathione Sepharose beads (Sigma Chemical, St. Louis, MO) or glutathione denvatized microtiter plates, which are then combined with the test compound or the test compound and either the non-adsorbed target protein or
  • ABCB 12 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 matnx immobilized in the case of beads, complex determined either directly or indirectly, for example, as descnbed above. Alternatively, the complexes can be dissociated from the matnx, and the level of ABCB 12 transporter binding or activity determined using standard techniques
  • an ABCB 12 transporter protein or an ABCB12 transporter target molecule can be immobilized utilizing conjugation of biotin and streptavidin
  • Biotinylated ABCB 12 transporter protein or target molecules can be prepared from biotin-NHS (N-hydroxy-succinimide) using techniques known in the art (e.g., biotmylation kit, Pierce Chemicals, Rockford, IL), and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical)
  • antibodies reactive with ABCB 12 transporter protein or target molecules but which do not interfere with binding of the ABCB 12 transporter protein to its target molecule can be denvatized to the wells of the plate, and unbound target or ABCB 12 transporter protein trapped in the wells by antibody conjugation Methods for detecting such complexes, in addition to those descnbed above for the GST-immobihzed complexes
  • modulators of ABCB 12 transporter expression are identified in a method wherein a cell is contacted with a candidate compound and the expression of ABCB 12 transporter mRNA or protein in the cell is determined.
  • the level of expression of ABCB 12 transporter mRNA or protein in the presence of the candidate compound is compared to the level of expression of ABCB 12 transporter mRNA or protein in the absence of the candidate compound.
  • the candidate compound can then be identified as a modulator of ABCB 12 transporter expression based on this compa ⁇ son. For example, when expression of ABCB 12 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 ABCB 12 transporter mRNA or protein expression.
  • the candidate compound when expression of ABCB 12 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 ABCB 12 transporter mRNA or protein expression.
  • the level of ABCB 12 transporter mRNA or protein expression in the cells can be determined by methods descnbed herein for detecting ABCB 12 transporter mRNA or protein.
  • the ABCB 12 transporter proteins can be used as "bait proteins" in a two-hyb ⁇ d assay or three-hyb ⁇ d 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.
  • ABCB12-b ⁇ nd ⁇ ng proteins bind to or interact with ABCB 12 transporter
  • ABCB 12 transporter proteins bind to or interact with ABCB 12 transporter
  • Such ABCB12-b ⁇ nd ⁇ ng proteins are also likely to be involved in the propagation of signals by the ABCB 12 transporter proteins or ABCB 12 transporter targets as, for example, downstream elements of an ABCB 12-med ⁇ ated signaling pathway.
  • ABCB 12-b ⁇ nd ⁇ ng proteins are likely to be ABCB 12 transporter inhibitors.
  • the two-hybnd system is based on the modular nature of most transcnption factors, which consist of separable DNA-bindmg and activation domains.
  • the assay utilizes two different DNA constructs.
  • the gene that codes for an ABCB 12 transporter protein is fused to a gene encoding the DNA binding domain of a known transcnption 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 transcnption factor.
  • the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcnption of a reporter gene (e.g., LacZ) which is operably linked to a transcnptional regulatory site responsive to the transcnption factor. Expression of the reporter gene can be detected and cell colonies containing the functional transcnption factor can be isolated and used to obtain the cloned gene which encodes the protein which interacts with the ABCB 12 transporter protein.
  • a reporter gene e.g., LacZ
  • the invention pertains to a combination of two or more of the assays descnbed 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 ABCB 12 transporter protein can be confirmed in vitro, e.g., in an animal.
  • This invention further pertains to novel agents identified by the above-desc ⁇ bed screening assays. Accordingly, it is within the scope of this invention to further use an agent identified as descnbed herein in an appropnate animal model.
  • an agent identified as descnbed herein e.g., an ABCB 12 transporter modulating agent, an antisense ABCB 12 transporter nucleic acid molecule, an ABCB12-spec ⁇ f ⁇ c antibody, or an ABCB12-b ⁇ nd ⁇ ng partner
  • an agent identified as descnbed 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-descnbed screening assays for treatments as descnbed herein.
  • Portions or fragments of the cDNA sequences identified herein (and the conesponding 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; (u) identify an individual from a minute biological sample (tissue typing); and (in) aid in forensic identification of a biological sample.
  • 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 ABCB 12 transporter nucleotide sequences, descnbed herein, can be used to map the location of the ABCB12 transporter genes on a chromosome.
  • the mapping of the ABCB 12 transporter sequences to chromosomes is an important first step in conelating these sequences with genes associated with disease.
  • ABCB 12 transporter genes can be mapped to chromosomes by prepa ⁇ ng PCR pnmers (preferably 15-25 bp in length) from the ABCB12 transporter nucleotide sequences.
  • Computer analysis of the ABCB 12 transporter sequences can be used to predict pnmers that do not span more than one exon in the genomic DNA, thus complicating the amplification process.
  • These pnmers can then be used for PCR screening of somatic cell hybnds containing individual human chromosomes. Only those hybnds containing the human gene conesponding to the ABCB 12 transporter sequences will yield an amplified fragment.
  • Somatic cell hyb ⁇ ds are prepared by fusing somatic cells from different mammals (e.g., human and mouse cells). As hyb ⁇ ds 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 vanous media, panels of hybnd 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.
  • Somatic cell hyb ⁇ ds containing only fragments of human chromosomes can also be produced by using human chromosomes with translocations and deletions.
  • PCR mapping of somatic cell hybnds 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 ABCB 12 transporter nucleotide sequences to design oligonucleotide pnmers, subloca zation can be achieved with panels of fragments from specific chromosomes. Other mapping strategies which can similarly be used to map an
  • ABCB 12 transporter sequence to its chromosome include in situ hyb ⁇ dization (descnbed 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 hybndization to chromosome specific cDNA hbranes.
  • Fluorescence in situ hybndization (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 bnefly 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.
  • clones larger than 1,000 bases have a higher likelihood of binding to a unique chromosomal location with sufficient signal intensity for simple detection.
  • 1,000 bases, and more preferably 2,000 bases will suffice to get good results at a reasonable amount of time.
  • 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.
  • Coding sequences are more likely to be conserved within gene families, thus increasing the chance of cross hyb ⁇ dizations du ⁇ ng chromosomal mapping.
  • differences in the DNA sequences between individuals affected and unaffected with a disease associated with the ABCB 12 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.
  • Compa ⁇ son 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.
  • complete sequencing of genes from several individuals can be performed to confirm the presence of a mutation and to distinguish mutations from polymo ⁇ hisms.
  • the ABCB 12 transporter sequences of the present invention can also be used to identify individuals from minute biological samples
  • RFLP rest ⁇ ction fragment length polymo ⁇ hism
  • an individual's genomic DNA is digested with one or more restnction enzymes, and probed on a Southern blot to yield unique bands for identification
  • This method does not suffer from the cunent 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 (descnbed 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 ABCB 12 transporter nucleotide sequences descnbed herein can be used to prepare two PCR pnmers from the 5' and 3' ends of the sequences. These pnmers can then be used to amplify an individual's DNA and subsequently sequence it.
  • Panels of conesponding 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 ABCB 12 transporter nucleotide sequences of the invention uniquely represent portions of the human genome. Allelic vanation 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 vanation between individual humans occurs with a frequency of about once per each 500 bases.
  • Each of the sequences descnbed herein can, to some degree, be used as a standard against which DNA from an individual can be compared for identification pu ⁇ oses.
  • SEQ ID NO 1 can comfortably provide positive individual identification with a panel of perhaps 10 to 1,000 pnmers 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 appropnate number of pnmers for positive individual identification would be 500-2,000.
  • a panel of reagents from ABCB 12 transporter nucleotide sequences descnbed 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 c ⁇ me scene as a means for positively identifying, for example, a pe ⁇ etrator of a c ⁇ me.
  • 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 cnme scene. The amplified sequence can then be compared to a standard, thereby allowing identification of the o ⁇ gin of the biological sample.
  • sequences of the present invention can be used to provide polynucleotide reagents, e.g., PCR pnmers, 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
  • actual base sequence information can be used for identification as an accurate alternative to patterns formed by rest ⁇ ction enzyme generated fragments.
  • Sequences targeted to noncoding regions of SEQ ED NO: 1 are particularly appropnate 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 ABCB12 transporter nucleotide sequences or portions thereof, e.g., fragments de ⁇ ved from the noncoding regions of SEQ ID NO: 1 having a length of at least 20 bases, preferably at least 30 bases.
  • the ABCB 12 transporter nucleotide sequences descnbed 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 hyb ⁇ dization 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 o ⁇ gin. Panels of such ABCB 12 transporter probes can be used to identify tissue by species and/or by organ type.
  • polynucleotide reagents e.g., labeled or labelable probes which can be used in, for example, an in situ hyb ⁇ dization 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 o ⁇ gin. Panels of such ABCB 12 transporter probes can be used to identify tissue by species and
  • these reagents e.g., ABCB 12 transporter pnmers 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 monito ⁇ ng clinical t ⁇ als are used for prognostic
  • one aspect of the present invention relates to diagnostic assays for determining ABCB 12 transporter protein and/or nucleic acid expression as well as ABCB 12 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 ⁇ sk of developing a disorder, associated with abenant or unwanted ABCB 12 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 ⁇ sk of developing a disorder associated with ABCB 12 transporter protein, nucleic acid expression or activity.
  • mutations in an ABCB 12 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 pnor to the onset of a disorder characte ⁇ zed by or associated with ABCB 12 transporter protein, nucleic acid expression or activity
  • Another aspect of the invention pertains to monito ⁇ ng the influence of agents (e.g., drugs, compounds) on the expression or activity of ABCB 12 transporter in clinical t ⁇ als
  • agents e.g., drugs, compounds
  • ABCB 12 transporter in clinical t ⁇ als
  • An exemplary method for detecting the presence or absence of ABCB 12 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 ABCB 12 transporter protein or nucleic acid (e.g., mRNA, genomic DNA) that encodes
  • a prefened agent for detecting ABCB 12 transporter mRNA or genomic DNA is a labeled nucleic acid probe capable of hybndizing to ABCB 12 transporter mRNA or genomic DNA.
  • the nucleic acid probe can be, for example, a full-length ABCB 12 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 hyb ⁇ dize under stnngent conditions to ABCB 12 transporter mRNA or genomic DNA.
  • a prefened agent for detecting ABCB 12 transporter protein is an antibody capable of binding to ABCB 12 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 p ⁇ mary 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 withm a subject. That is, the detection method of the invention can be used to detect ABCB 12 transporter mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vitro.
  • in vitro techniques for detection of ABCB 12 transporter mRNA include Northern hyb ⁇ dizations and in situ hybndizations.
  • In vitro techniques for detection of ABCB 12 transporter protein include enzyme linked immunosorbent assays
  • In vitro techniques for detection of ABCB 12 transporter genomic DNA include Southern hyb ⁇ dizations.
  • in vitro techniques for detection of ABCB 12 transporter protein include introducing into a subject a labeled ant ⁇ -ABCB12 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 sub j ect or genomic DNA molecules from the test subject.
  • a prefened 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 ABCB 12 transporter protein, mRNA, or genomic DNA, such that the presence of ABCB 12 transporter protein, mRNA or genomic DNA is detected in the biological sample, and compa ⁇ ng the presence of ABCB 12 transporter protein, mRNA or genomic DNA in the control sample with the presence of ABCB 12 transporter protein, mRNA or genomic DNA in the test sample.
  • kits for detecting the presence of ABCB 12 transporter in a biological sample can compnse a labeled compound or agent capable of detecting ABCB 12 transporter protein or mRNA in a biological sample; means for determining the amount of ABCB 12 transporter in the sample, and means for compa ⁇ ng the amount of ABCB 12 transporter in the sample with a standard.
  • the compound or agent can be packaged in a suitable container.
  • the kit can further compnse instructions for using the kit to detect an ABCB 12 transporter protein or nucleic acid.
  • the diagnostic methods descnbed herein can furthermore be utilized to identify subjects having or at nsk of developing a disease or disorder associated with abenant or unwanted ABCB 12 transporter expression or activity
  • the term "abenant” includes an ABCB 12 transporter expression or activity which deviates from the wild type ABCB 12 transporter expression or activity
  • Abenant 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.
  • abenant ABCB 12 transporter expression or activity is intended to include the cases in which a mutation in the ABCB 12 transporter gene causes the ABCB 12 transporter gene to be under-expressed or over-expressed and situations in which such mutations result in a nonfunctional ABCB 12 transporter protein or a protein which does not function in a wild-type fashion, e.g., a protein which does not interact with an ABCB 12 transporter ligand or one which interacts with a non-ABCB 12 transporter ligand.
  • the term "unwanted” includes an unwanted phenomenon involved in a biological response.
  • unwanted includes an ABCB 12 transporter expression or activity which is undesirable in a subject.
  • the assays descnbed herein can be utilized to identify a subject having or at nsk of developing a disorder associated with a misregulation in ABCB 12 transporter protein activity or nucleic acid expression.
  • the prognostic assays can be utilized to identify a subject having or at nsk for developmg a disorder associated with a misregulation in ABCB 12 transporter protein activity or nucleic acid expression.
  • the present invention provides a method for identifying a disease or disorder associated with abenant or unwanted ABCB 12 transporter expression or activity in which a test sample is obtained from a subject and ABCB 12 transporter protein or nucleic acid (e.g., mRNA or genomic DNA) is detected, wherein the presence of ABCB 12 transporter protein or nucleic acid is diagnostic for a subject having or at nsk of developing a disease or disorder associated with abenant or unwanted ABCB 12 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 descnbed herein can be used to determine whether a subject can be administered an agent (e.g., an agonist, antagonist, peptidomimetic, protein, peptide, nucleic acid, small molecule, or other drug candidate) to treat a disease or disorder associated with abenant or unwanted ABCB 12 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
  • a disease or disorder associated with abenant or unwanted ABCB 12 transporter expression or activity e.g., a cancer where the cells of the cancer have developed multidrug resistance.
  • the present invention provides methods for determining whether a subject can be effectively treated with an agent for a disorder associated with abenant or unwanted ABCB 12 transporter expression or activity in which a test sample is obtained and ABCB 12 transporter protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of ABCB 12 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 abenant or unwanted ABCB 12 transporter expression or activity).
  • the methods of the invention can also be used to detect genetic alterations in an
  • the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characte ⁇ zed by at least one of an alteration affecting the integ ⁇ ty of a gene encoding an ABCB 12-prote ⁇ n, or the mis-expression of the ABCB 12 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 ABCB 12 transporter gene; 2) an addition of one or more nucleotides to an ABCB 12 transporter gene; 3) a substitution of one or more nucleotides of an ABCB 12 transporter gene, 4) a chromosomal reanangement of an ABCB 12 transporter gene; 5) an alteration in the level of a messenger RNA transcnpt of an ABCB 12 transporter gene, 6) abenant modification of an ABCB 12 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 transcnpt of an ABCB 12 transporter gene, 8) a non-wild type level of an ABCB12-prote ⁇ n, 9) allelic loss of an ABCB 12 transporter gene, and 10) inappropnate post-translational modification of an ABCB12
  • detection of the alteration involves the use of a probe/pnmer m 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 ABCB12-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 pnmers which specifically hyb ⁇ dize to an ABCB 12 transporter gene under conditions such that hyb ⁇ dization and amplification of the ABCB12-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and compa ⁇ ng the length to a control sample.
  • nucleic acid e.g., genomic, mRNA or both
  • 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 descnbed herein.
  • Alternative amplification methods include: self sustained sequence replication (Guatelh, J.C. et al, (1990) Proc. Natl. Acad. Sci. USA 87.1874-1878), transc ⁇ ptional amplification system (Kwoh, D.Y. et al, ( 1989) Proc. Natl Acad. Sci. USA 86: 1173-1 177), Q- Beta Rep case (Lizardi, P.M.
  • mutations in an ABCB 12 transporter gene from a sample cell can be identified by alterations in restnction enzyme cleavage patterns.
  • sample and control DNA is isolated, amplified (optionally), digested with one or more restnction 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 nbozymes 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 nbozyme cleavage site.
  • genetic mutations in ABCB 12 transporter can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density anays 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 ABCB 12 transporter can be identified in two dimensional anays containing light-generated DNA probes as described in Cronin, M.T. et al. supra.
  • a first hybridization anay 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 anays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization anay that allows the charactenzation of specific mutations by using smaller, specialized probe anays complementary to all variants or mutations detected.
  • Each mutation anay is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
  • any of a va ⁇ ety of sequencing reactions known in the art can be used to directly sequence the ABCB 12 transporter gene and detect mutations by companng the sequence of the sample ABCB12 transporter with the conesponding 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).
  • any of a va ⁇ ety 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 Intemationai Publication No. WO 94/16101 ; Cohen et al. (1996) Adv. Chromatogr. 36: 127- 162; and Griffin et al. (1993) Appl. Bioc em. Biotechnol. 38: 147-159).
  • Other methods for detecting mutations in the ABCB 12 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 hyb ⁇ dizing (labeled) RNA or DNA containing the wild-type ABCB 12 transporter sequence with potentially mutant RNA or DNA obtained from a tissue sample.
  • the double-stranded duplexes are treated with an agent which cleaves smgle-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 denatunng 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 ABCB 12 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 ABCB 12 transporter sequence e.g., a wild- type ABCB 12 transporter sequence
  • 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 ABCB 12 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. (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 ABCB 12 transporter nucleic acids will be denatured and allowed to renature.
  • the secondary structure of s gle-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 denatu ⁇ ng gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495).
  • DGGE denatu ⁇ ng 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-nch DNA by PCR.
  • a temperature gradient is used in place of a denatunng gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner ( 1987) Biophys Chem 265: 12753).
  • oligonucleotide pnmers may be prepared in which the known mutation is placed centrally and then hyb ⁇ dized to target DNA under conditions which permit hybndization 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 hybndized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hyb ⁇ dizing membrane and hyb ⁇ dized with labeled target DNA.
  • Oligonucleotides used as pnmers for specific amplification may cany the mutation of interest in the center of the molecule (so that amplification depends on differential hybndization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3' end of one pn er where, under appropnate 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 descnbed herein may be performed, for example, by utilizing prepackaged diagnostic kits compnsing at least one probe nucleic acid or antibody reagent descnbed 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 ABCB 12 transporter gene
  • any cell type or tissue which ABCB 12 transporter is expressed may be utilized in the prognostic assays descnbed herein
  • ABCB 12 transporter protein can be applied not only in ABCB 12 transporter drug screening, but also in clinical t ⁇ als.
  • the effectiveness of an agent determined by a screening assay as descnbed herein to increase ABCB 12 transporter gene expression, protein levels, or upregulate ABCB 12 transporter activity can be monitored in clinical t ⁇ als of subjects exhibiting decreased ABCB 12 transporter gene expression, protein levels, or downregulated ABCB 12 transporter activity
  • the effectiveness of an agent determined by a screening assay to decrease ABCB 12 transporter gene expression, protein levels, or downregulate ABCB 12 transporter activity can be monitored in clinical t ⁇ als of subjects exhibiting increased ABCB 12 transporter gene expression, protein levels, or upregulated ABCB 12 transporter activity.
  • an ABCB 12 transporter gene and preferably, other genes that have been implicated in, for example, an ABCB12-assoc ⁇ ated disorder can be used as a "read out" or markers of the phenotype of a particular cell.
  • genes, including ABCB 12, that are modulated in cells by treatment with an agent (e.g., compound, drug or small molecule) which modulates ABCB 12 transporter activity can be identified.
  • an agent e.g., compound, drug or small molecule
  • a screening assay as descnbed herein e.g., identified in a screening assay as descnbed herein.
  • cells can be isolated and RNA prepared and analyzed for the levels of expression of ABCB 12 transporter and other genes implicated in the ABCB 12- associated disorder, respectively.
  • the levels of gene expression can be quantified by northern blot analysis or RT-PCR, as descnbed herein, or alternatively by measunng the amount of protein produced, by one of the methods as descnbed herein, or by measunng the levels of activity of ABCB 12 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 vanous points du ⁇ ng treatment of the individual with the agent.
  • the present invention provides a method for monito ⁇ ng 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 descnbed herein) including the steps of (0 obtaining a pre- administration sample from a subject pnor to administration of the agent; (n) detecting the level of expression of an ABCB 12 transporter protein, mRNA, or genomic DNA in the preadministration sample; (in) obtaining one or more post-administration samples from the subject; (iv) detecting the level of expression or activity of the ABCB 12 transporter protein, mRNA, or genomic DNA in the post-administration samples; (v) compa ⁇ ng the level of expression or activity of the ABCB 12 transporter protein, mRNA, or genomic DNA in the pre- administration sample with the ABCB 12 transporter protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi)
  • increased administration of the agent may be desirable to increase the expression or activity of ABCB 12 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 ABCB 12 transporter to lower levels than detected, i.e. to decrease the effectiveness of the agent.
  • ABCB 12 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 ⁇ sk of (or susceptible to) a disorder or having a disorder associated with abenant or unwanted ABCB 12 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”.)
  • a drug e.g., a patient's "drug response phenotype", or "drug response genotype”.
  • another aspect of the invention provides methods for tailo ⁇ ng an individual's prophylactic or therapeutic treatment with either the ABCB12 transporter molecules of the present invention or ABCB 12 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 expe ⁇ ence toxic drug-related side effects.
  • the invention provides a method for preventing in a subject, a disease or condition associated with an abenant or unwanted ABCB 12 transporter expression or activity, by admimstenng to the subject an ABCB 12 transporter or an agent which modulates ABCB 12 transporter expression or at least one ABCB 12 transporter activity.
  • Subjects at nsk for a disease which is caused or cont ⁇ aded to by abenant or unwanted ABCB 12 transporter expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as descnbed herein.
  • Administration of a prophylactic agent can occur pnor to the manifestation of symptoms charactenstic of the ABCB 12 transporter abenancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
  • an ABCB12, ABCB12 transporter agonist or ABCB 12 transporter antagonist agent can be used for treating the subject.
  • the appropnate agent can be determined based on screening assays descnbed herein.
  • the modulatory method of the invention involves contacting a cell with an ABCB 1 transporter or agent that modulates one or more of the activities of ABCB 12 transporter protein activity associated with the cell.
  • An agent that modulates ABCB 12 transporter protein activity can be an agent as descnbed herein, such as a nucleic acid or a protein, a naturally-occur ⁇ ng target molecule of an ABCB 12 transporter protein (e.g., an ABCB 12 transporter substrate), an agent as descnbed herein, such as a nucleic acid or a protein, a naturally-occur ⁇ ng target molecule of an ABCB 12 transporter protein (e.g., an ABCB 12 transporter substrate), an agent as descnbed herein, such as a nucleic acid or a protein, a naturally-occur ⁇ ng target molecule of an ABCB 12 transporter protein (e.g., an ABCB 12 transporter substrate), an agent as descnbed herein, such as a nucleic acid or a protein, a naturally
  • the agent stimulates one or more ABCB 12 transporter activities.
  • stimulatory agents include active ABCB12 transporter protein and a nucleic acid molecule encoding ABCB 12 transporter that has been introduced into the cell.
  • the agent inhibits one or more ABCB 12 transporter activities. Examples of such inhibitory agents include antisense ABCB12 transporter nucleic acid molecules, ant ⁇ -ABCB12 transporter antibodies, and ABCB 12 transporter inhibitors.
  • modulatory methods can be performed in vitro (e.g., by cultu ⁇ ng the cell with the agent) or, alternatively, in vitro (e.g., by admimstenng the agent to a subject).
  • the present invention provides methods of treating an individual afflicted with a disease or disorder charactenzed by abenant or unwanted expression or activity of an ABCB 12 transporter protein or nucleic acid molecule.
  • the method involves admimstenng an agent (e.g., an agent identified by a screening assay descnbed herein), or combination of agents that modulates (e.g., upregulates or downregulates) ABCB12 transporter expression or activity.
  • the method involves admi stenng an ABCB 12 transporter protein or nucleic acid molecule as therapy to compensate for reduced, abenant, or unwanted ABCB 12 transporter expression or activity.
  • Stimulation of ABCB12 transporter activity is desirable in situations in which ABCB12 transporter is abnormally downregulated and or in which increased ABCB 12 transporter activity is likely to have a beneficial effect.
  • stimulation of ABCB 12 transporter activity is desirable in situations in which an ABCB 12 transporter is downregulated and or in which increased ABCB 12 transporter activity is likely to have a beneficial effect.
  • inhibition of ABCB 12 transporter activity is desirable in situations in which ABCB 12 transporter is abnormally upregulated and/or in which decreased ABCB 12 transporter activity is likely to have a beneficial effect.
  • an agent found to inhibit ABCB 12 transporter activity is used in combination with another therapy such that the targeting of that therapy across the blood-brain- barner is achieved.
  • ABCB 12 transporter molecules of the present invention as well as agents, or modulators which have a stimulatory or inhibitory effect on ABCB12 transporter activity (e.g., ABCB 12 transporter gene expression) as identified by a screening assay descnbed herein can be administered to individuals to treat (prophylactically or therapeutically) ABCB12-assoc ⁇ ated disorders associated with abenant or unwanted ABCB 12 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 alte ⁇ ng 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 ABCB 12 transporter molecule or ABCB 12 transporter modulator as well as tailo ⁇ ng the dosage and/or therapeutic regimen of treatment with an ABCB 12 transporter molecule or ABCB 12 transporter modulator.
  • Pharmacogenomics deals with clinically significant hereditary vanations 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. Physwl. 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.
  • G6PD glucose-6-phosphate dehydrogenase deficiency
  • a genome-wide association relies p ⁇ manly on a high-resolution map of the human genome consisting of already known gene-related markers (e.g., a "bi-allehc" gene marker map which consists of 60,000-100,000 polymo ⁇ hic or va ⁇ able sites on the human genome, each of which has two vanants.)
  • gene-related markers e.g., a "bi-allehc” gene marker map which consists of 60,000-100,000 polymo ⁇ hic or va ⁇ able sites on the human genome, each of which has two vanants.
  • 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 t ⁇ al 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- milhon 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 m a disease process, however, the vast majonty may not be disease-associated.
  • individuals Given a genetic map based on the occunence of such SNPs, individuals can be grouped into genetic categones 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.
  • 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 ABCB 12 transporter protein of the present invention
  • all common va ⁇ ants 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.
  • drug metabolizing enzymes e.g., N-acetyltransferase 2 (NAT 2) and cytochrome P450 enzymes CYP2D6 and CYP2C19
  • NAT 2 N-acetyltransferase 2
  • CYP2D6 and CYP2C19 cytochrome P450 enzymes
  • the gene coding for CYP2D6 is highly polymo ⁇ hic and several mutations have been identified in PM, which all lead to the absence of functional CYP2D6 Poor metabo zers of CYP2D6 and CYP2C19 quite frequently expe ⁇ ence 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 metabohzers 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 ABCB 12 transporter molecule or ABCB 12 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 appropnate 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 ABCB 12 transporter molecule or ABCB 12 transporter modulator, such as a modulator identified by one of the exemplary screening assays descnbed herein.
  • the human ABCB 12 transporter cDNA was isolated using polymerase chain reaction (PCR) and pnmers designed (descnbed below) from a rat nucleotide sequence (Genbank
  • PCR polymerase chain reaction
  • the cycling parameters were: denaturation at 94° C for 1 min; denaturation at 94° C for 30 sec, annealing at 60° C (PI and P2) or 70° C (P3 and an adaptor specific pnmer) for 30 sec, elongation at 70° C for 2 mm for 30 cycles; a final elongation step at 70° C for 5 mm.
  • Table 1 Oligonucleotide primers used for isolating the human ABCB12 transporter.
  • a second senes of PCR reactions were earned out to isolate the 5' untranslated region (UTR) of the human ABCB 12 transporter cDNA using the following methodology. Bnefly. a PCR reaction was earned out in a 25 ⁇ l final volume using 5 ⁇ l (maste ⁇ late) or 1 ⁇ l (subplate) of a human brain cDNA library (Ongene Technologies, Order No.
  • the first cDNA fragment (hsA14.2), obtained by polymerase chain reaction (PCR) from a human brain double- strand (ds) cDNA library using pnmers PI and P2, was determined to be 1964 base pairs (bp)
  • a second cDNA fragment (hsA 14.1) was obtained using rapid amplification of cDNA 3'-ends (3' RACE) using PCR, the human brain ds cDNA library, and pnmers P3 and an oligonucleotide specific to the adaptor linked to the 5 " and 3' ends of the cDNA library, and the resultant fragment was determined to be 1725 bp.
  • Each of the above cDNA fragments were subcloned and their nucleotide sequences were obtained using a automated DNA sequencing engine (LICOR).
  • the nucleic acid sequence of the isolated fragments was predicted to encode the human ortholog of the rat ubiquitously expressed mammalian ABC half-transporter termed UMAT.
  • the hsA14.1 and hsA14.2 fragments were determined to encode the 3' and 5' ends of the gene, respectively Together, the above fragments allowed for the isolation of a 2893 bp clone (hsA14.3) which contained the entire human ABCB 12 transporter gene coding sequence in addition to 5' and the 3' untranslated regions (UTR).
  • the nucleotide sequence encoding the human ABCB 12 transporter protein is shown in Figure 1 and is set forth as SEQ ED NO: 1.
  • the longest open reading frame of the human ABCB 12 transporter begins with the sequence GCCATGG which matches the consensus eukaryotic translation initiation motif at nucleotide position 165 (ATG) and ends with a TGA termination signal at position 2694.
  • the coding region (open reading frame) of SEQ TD NO: 1 is set forth as SEQ ID NO: 3.
  • a putative polyadenylation signal (AATAAA) is located in the 3' untranslated region at nucleotide position 2844 (Fig. 1). Starting from the first in-frame ATG, the open reading frame is predicted to encode a polypeptide of 843 ammo acids with a molecular weight of 94 kDa.
  • the am o 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 ABCB 12 transporter polypeptide was compared to amino acid sequences of known polypeptides and vanous motifs were identified.
  • the isolated clone was determined to encode a novel human ABC transporter polypeptide (ABCB12) with homology (85% at the amino acid level (BLASTp program against non-redundant SwissProt sequences), 86% at the nucleotide level (BLASTn program against non-redundant GenBank + EMBL + DDBJ + PDB sequences)) to the rat ubiquitously expressed mammalian ABC half- transporter (UMAT) polypeptide (Accession No. AJ003004; Hirsch-Emst et al, 1998, Biochem. Bwphys. Res. Comm. 249: 151-155). Accordingly, the novel human ABC transporter molecule of the invention (ABCB 12) is also refened to herein as the human UMAT polypeptide.
  • ABSB 12 novel human ABC transporter molecule of the invention
  • the closest human homolog is ABC7 (BLASTp program against non- redundant SwissProt sequences). Applying the Pairwise Global Clustal W Alignment reveals a 34% identity between the amino acid sequences of ABCB 12 and ABC7.
  • the ABCB 12 transporter polypeptide was also analyzed with respect to potential membrane spanning segments. Hydropathy plots and 2D fold models obtained using biomformatic tools (PredictProtein server, Heidelberg, Germany, see, http://dodo.cpmc.columbia.edu/predictprotein/) defined ten putative membrane spanning regions in the N-terminal sequence of the polypeptide, six of them having a helical 2-D fold structure, which suggests that the human ABCB 12 transporter is a membrane anchored protein.
  • the N-terminal part of the protein (am o acids 1-550) represents a non-conserved feature of ABCB12; amino acids 1-550 exhibit only 13% identity with ABC7, the closest human homolog to ABCB 12.
  • the C-terminal sequence of ABCB 12 (amino acids 601-843) contains multiple clusters of conserved residues which define an ATP binding domain (see, e.g., Figs. 2 and 3).
  • HTM1 Schpo 45/30 49/34 42/25 42/26 100/100
  • human ABCB 12 transporter can be associated with an intracellular membrane structure.
  • This example desc ⁇ bes the tissue dist ⁇ bution of ABCB 12 transporter mRNA, as can be determined by Northern blot hybndization and in situ hyb ⁇ dization.
  • Northern blot hyb ⁇ dizations with the vanous RNA samples are performed under standard conditions and washed under st ⁇ ngent conditions, i.e., 0.2XSSC at 65°C.
  • the DNA probe is radioactively labeled with ⁇ P-d TP using the Pnme-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
  • vanous 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 salme at room temperature for 10 minutes before being ⁇ nsed twice in DEPC IX phosphate-buffered saline and once in 0.1 M tnethanolamine-HCl (pH 8.0).
  • sections are ⁇ nsed in DEPC 2X SSC (IX SSC is 0.15M NaCl plus 0.015M sodium citrate).
  • Tissue is then dehydrated through a se ⁇ es of ethanol washes, incubated in 100% chloroform for 5 minutes, and then nnsed in 100% ethanol for 1 minute and 95% ethanol for 1 minute and allowed to air dry.
  • Hyb ⁇ dizations are performed with 35s-rad ⁇ olabeled (5 X 10 ⁇ cpm/ml) cRNA probes Probes are incubated in the presence of a solution containing 600 mM NaCl, 10 mM Tns (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 Tns-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 ⁇ nsed 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 Tns-HCl (pH 7.6), 500 mM NaCl, and 1 mM EDTA
  • Sections are then dehydrated rapidly through senal ethanol-0.3 M sodium acetate concentrations before being air d ⁇ ed 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 ABCB 12 transporter mRNA is fairly neuron-specific.
  • human ABCB 12 transporter is expressed as a recombinant glutathione- S-transferase (GST) fusion polypeptide in E. coli and the fusion polypeptide is isolated and characte ⁇ zed.
  • GST glutathione- S-transferase
  • the human ABCB 12 transporter is fused to GST and this fusion polypeptide is expressed in E. coli, e.g., strain PEB199.
  • the human ABCB 12 transporter polypeptide is predicted to be approximately 94 kDa and GST is predicted to be 26 kDa
  • the fusion polypeptide is predicted to be approximately 120 kDa in molecular weight. Expression of the GST-ABCB12 transporter fusion protein in PEB 199 is induced with IPTG.
  • the recombinant fusion polypeptide is pu ⁇ fied from crude bacte ⁇ al lysates of the induced PEB 199 strain by affinity chromatography on glutathione beads. Using polyacrylamide gel electrophoretic analysis of the polypeptide punfied from the bactenal 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 o ⁇ gin of replication, an ampicillin resistance gene, an E.
  • coli replication o ⁇ gin a CMV promoter followed by a polylinker region, and an SV40 intron and polyadenylation site
  • a DNA fragment encoding the entire ABCB 12 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.
  • the ABCB12 transporter DNA sequence (see, e.g., SEQ ID NO: 3) is amplified by PCR using two pnmers.
  • the 5' pnmer contains the restnction site of interest followed by approximately twenty nucleotides of the ABCB 12 transporter coding sequence starting from the initiation codon; the 3' end sequence contains complementary sequences to the other restnction site of interest, a translation stop codon, the HA tag or FLAG tag and the last 20 nucleotides of the ABCB 12 transporter coding sequence.
  • the PCR amplified fragment and the pCDNA/Amp vector are digested with the appropnate restnction enzymes and the vector is dephosphorylated using the CIAP enzyme (New England Biolabs, Beverly, MA).
  • the two restnction sites chosen are different so that the ABCB 12 transporter gene is inserted in the conect onentation.
  • 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 restnction analysis for the presence of the conect fragment.
  • Eukaryotic cells e.g., COS cells are subsequently transfected with the ABCB 12 transporter-pcDNA/Amp plasmid DNA using the calcium phosphate or calcium chlonde co- precipitation methods, DEAE-dextran-mediated transfection, hpofection, or electroporation
  • suitable methods for transfecting host cells can be found in Sambrook, J., F ⁇ tsh, E. F., and Maniatis, T. Molecular Cloning- A Laboratory Manual.
  • 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 Tns, 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.
  • detergents 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM Tns, pH 7.5.
  • DNA containing the ABCB 12 transporter coding sequence is cloned directly into the polylinker of the pCDNA/Amp vector using the appropnate restnction sites
  • the resulting plasmid is transfected into COS cells in the manner descnbed above, and the expression of the ABCB 12 transporter polypeptide is detected by radiolabelhng and immunoprecipitation using an ABCB 12 transporter specific monoclonal antibody.
  • in vitro and in vitro assays for screening modulators of the human ABCB 12 transporter molecule are descnbed.
  • the ABCB 12 transporter is expressed in a mammalian cell line as descnbed above and a base line for the cellular transport of a reference molecule, e.g., ⁇ -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 ABCB 12 transporter activity.
  • Lead compounds may then be tested on eukaryotic cells, e.g., cells of neuronal o ⁇ gin 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 ABCB12-med ⁇ ated transport of, e.g., ⁇ -amyloid are further tested in vitro.
  • a transgenic mouse model overexpressing an ABCB 12 transporter polypeptide e.g., the human ABCB 12 transporter polypeptide or conesponding mu ⁇ ne polypeptide is generated using the techniques descnbed 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 ABCB12 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 change in the transport of the polypeptide is measured (e.g., in the CSF) as compared to a control.
  • these test animals are further monitored in the presence or absence of a modulator of the ABCB 12 transporter.
  • the activity of the ABCB 12 transporter is determined regarding the ability of a detectable reference molecule to cross the blood-brain bamer.
  • 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.

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Abstract

L'invention concerne des molécules d'acide nucléique isolées désignées molécules d'acide nucléique du transporteur ABCB12, codant de nouveaux membres de la famille du transporteur ABC. Elle concerne également des molécules d'acide nucléique antisens, des vecteurs d'expression recombinants contenant des molécules d'acide nucléique du transporteur ABCB12, des cellules hôtes dans lesquelles on a introduit ces vecteurs d'expression et des animaux transgéniques non humains dans lesquels on a introduit ou interrompu le gène du transporteur ABCB12. Elle concerne encore des protéines de transport ABCB12 isolées, des protéines de fusion, des peptides antigéniques, des anticorps anti-transporteur ABCB12 et des méthodes de criblage servant à rechercher des modulateurs du transporteur ABCB12. Elle concerne, de plus, des procédés diagnostiques et thérapeutiques mettant en application des compositions décrites par l'invention.
PCT/CA2000/000964 1999-08-20 2000-08-18 Nouveau transporteur abc et ses utilisations WO2001014547A1 (fr)

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CA002383074A CA2383074A1 (fr) 1999-08-20 2000-08-18 Nouveau transporteur abc et ses utilisations
JP2001518860A JP2003520026A (ja) 1999-08-20 2000-08-18 新規なａｂｃ輸送体及びその利用
AU66773/00A AU6677300A (en) 1999-08-20 2000-08-18 Novel abc transporter and uses thereof
EP00954221A EP1210423A1 (fr) 1999-08-20 2000-08-18 Nouveau transporteur abc et ses utilisations

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Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001066732A1 (fr) * 2000-03-06 2001-09-13 Merck Patent Gmbh Transporteur abc humain s'exprimant dans le foie, atil
WO2001092304A2 (fr) * 2000-05-26 2001-12-06 Incyte Genomics, Inc. Transporteurs et canaux ioniques
WO2002070692A2 (fr) * 2001-03-05 2002-09-12 Active Pass Pharmaceuticals, Inc. Nouveaux transporteurs abca9 et leurs applications
WO2002094378A2 (fr) * 2001-05-22 2002-11-28 Active Pass Pharmaceuticals, Inc. Protection contre la perte des neurones a dopamine liee a la maladie de parkinson par la stimulation de l'activite fonctionnelle et/ou de l'expression des transporteurs d'abc

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Title
ALLIKMETS R ET AL: "Characterization of the human ABC superfamily: isolation and mapping of 21 new genes using the Expressed Sequence Tags Database", HUMAN MOLECULAR GENETICS,GB,OXFORD UNIVERSITY PRESS, SURREY, vol. 5, no. 10, 1996, pages 1649 - 1655, XP002120400, ISSN: 0964-6906 *
DATABASE EMBL 11 July 2000 (2000-07-11), HIRSCH-ERNST,K.I ET AL.: "Subcellular localization of the ABC transporter umat", XP002151663 *
DATABASE EMBL 5 August 1998 (1998-08-05), "Homo sapiens clone 24410 ABC transporter mRNA, partial cds", XP002151662 *
HIRSCH-ERNST K I ET AL: "Molecular cDNA cloning and tissue distribution of mRNA encoding a novel ATP-binding cassette (ABC) half-transporter", BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS,US,ACADEMIC PRESS INC. ORLANDO, FL, vol. 249, no. 1, 10 August 1998 (1998-08-10), pages 151 - 155, XP002120401, ISSN: 0006-291X *
MITSUHASHI N, MIKI T, SENBONGI H, YOKOI N, YANO H, MIYAZAKI M, NAKAJIMA N ET AL.: "MTABC3, a novel mitochondrial ATP-binding cassette protein involved in iron homeostasis", J. BIOL. CHEM., vol. 275, no. 23, 9 June 2000 (2000-06-09), pages 17536 - 17540, XP002151661 *

Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001066732A1 (fr) * 2000-03-06 2001-09-13 Merck Patent Gmbh Transporteur abc humain s'exprimant dans le foie, atil
WO2001092304A2 (fr) * 2000-05-26 2001-12-06 Incyte Genomics, Inc. Transporteurs et canaux ioniques
WO2001092304A3 (fr) * 2000-05-26 2003-03-06 Incyte Genomics Inc Transporteurs et canaux ioniques
WO2002070692A2 (fr) * 2001-03-05 2002-09-12 Active Pass Pharmaceuticals, Inc. Nouveaux transporteurs abca9 et leurs applications
WO2002070692A3 (fr) * 2001-03-05 2003-04-10 Active Pass Pharmaceuticals In Nouveaux transporteurs abca9 et leurs applications
WO2002094378A2 (fr) * 2001-05-22 2002-11-28 Active Pass Pharmaceuticals, Inc. Protection contre la perte des neurones a dopamine liee a la maladie de parkinson par la stimulation de l'activite fonctionnelle et/ou de l'expression des transporteurs d'abc
WO2002094378A3 (fr) * 2001-05-22 2004-02-05 Active Pass Pharmaceuticals In Protection contre la perte des neurones a dopamine liee a la maladie de parkinson par la stimulation de l'activite fonctionnelle et/ou de l'expression des transporteurs d'abc

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