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WO2002031126A2 - Regulation of human cyclophilin-type peptidyl-prolyl cis-trans isomerase - Google Patents

Regulation of human cyclophilin-type peptidyl-prolyl cis-trans isomerase Download PDF

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Publication number
WO2002031126A2
WO2002031126A2 PCT/EP2001/011704 EP0111704W WO0231126A2 WO 2002031126 A2 WO2002031126 A2 WO 2002031126A2 EP 0111704 W EP0111704 W EP 0111704W WO 0231126 A2 WO0231126 A2 WO 0231126A2
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cyclophilin
prolyl cis
polypeptide
type peptidyl
trans isomerase
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WO2002031126A3 (en
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Zhimin Zhu
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Bayer AG
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Bayer AG
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y502/00—Cis-trans-isomerases (5.2)
    • C12Y502/01—Cis-trans-Isomerases (5.2.1)
    • C12Y502/01008—Peptidylprolyl isomerase (5.2.1.8), i.e. cyclophilin
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/90—Isomerases (5.)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • This invention relates to nucleic acid and amino acid sequences of a cyclophilin-type peptidyl-prolyl cis-trans isomerase and to the use of these sequences in the diagnosis, treatment, and prevention of cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders.
  • isomerases Numerous essential biochemical reactions involve the isomerization of a substrate. Enzymes which catalyze such reactions are known as isomerases. U.S. Patent No. 6,030,825. A number of isomerases have been described catalyzing steps in a wide variety of biochemical pathways including protein folding, phototransduction, and various anabolic and catabolic pathways in organisms ranging from bacteria to humans.
  • PPIases peptidyl-prolyl cis-trans isomerases
  • FKBP FK506 binding proteins
  • CyPs cyclophilins
  • FKBPs bind the potent immunosuppressants. FK506 and rapamycin, thereby inhibiting signaling pathways in T-cells. Specifically, the PPIase activity of FKBPs is inhibited by binding of FK506 or rapamycin.
  • FKBP12 FKBP13
  • FKBP25 FKBP52
  • FKBP65 FKBP65
  • CyP was originally characterized as the receptor for the immunosuppressant drug cyclosporin, an inhibitor of T-cell activation.
  • the peptidyl-prolyl isomerase activity of CyP may be part of the signaling pathway that leads to T-cell activation.
  • CyP's isomerase activity is essential for correct protein folding and/or protein trafficking and may also be involved in assembly/disassembly of protein complexes and regulation of protein activity.
  • CyP NinaA is required for correct localization of rhodopsins
  • CyP a mammalian CyP (Cyp40) is part of the Hsp90/Hsc70 complex that binds steroid receptors.
  • the mammalian CypA has been shown to bind the gag protein from human immunodeficiency virus 1 (HIN-1), an interaction that can be inhibited by cyclosporin. Because cyclosporin has potent anti-HIN-1 activity, CypA may play an essential function in HIN-1 replication. Finally, Cyp40 has been shown to bind and inactivate the transcription factor c-Myb, an effect that is reversed by cyclosporin. This effect implicates CyPs in the regulation of transcription, transformation, and differentiation (Bergsma, D. J. et al (1991) J. Biol. Chem.
  • One embodiment of the invention is a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
  • Yet another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation.
  • a test compound is contacted with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
  • Binding between the test compound and the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is detected.
  • a test compound which binds to the cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide is thereby identified as a potential agent for decreasing extracellular matrix degradation.
  • the agent can work by decreasing the activity of the cyclophilin-type peptidyl-prolyl cis-trans isomerase.
  • Another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation.
  • a test compound is contacted with a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1 ; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
  • Binding of the test compound to the polynucleotide is detected.
  • a test compound which binds to the polynucleotide is identified as a potential agent for decreasing extracellular matrix degradation.
  • the agent can work by decreasing the amount of the cyclophilin-type peptidyl-prolyl cis-trans isomerase through interacting with the cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA.
  • Another embodiment of the invention is a method of screening for agents which regulate extracellular matrix degradation.
  • a test compound is contacted with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide is detected.
  • a test compound which increases cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide relative to cyclophilin-type peptidyl-prolyl cis- trans isomerase activity in the absence of the test compound is thereby identified as a potential agent for increasing extracellular matrix degradation.
  • a test compound which decreases cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide relative to cyclophilin-type peptidyl-prolyl cis-trans isomerase activity in the absence of the test compound is thereby identified as a potential agent for decreasing extracellular matrix degradation.
  • Even another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation.
  • a test compound is contacted with a cyclop lin-type peptidyl-prolyl cis-trans isomerase product of a polynucleotide which comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
  • Binding of the test compound to the cyclophilin-type peptidyl-prolyl cis-trans isomerase product is detected.
  • a test compound which binds to the cyclophilin-type peptidyl-prolyl cis-trans isomerase product is thereby identified as a potential agent for decreasing extracellular matrix degradation.
  • Still another embodiment of the invention is a method of reducing extracellular " matrix degradation.
  • a cell is contacted with a reagent which specifically binds to a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or the product encoded by the polynucleotide, wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1 ; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
  • Cyclophilin-type peptidyl-prolyl cis-trans isomerase activity in the cell is thereby decreased.
  • the invention thus provides a human cyclophilin-type peptidyl-prolyl cis-trans isomerase which can be used to identify test compounds which may act, for example, as activators or inhibitors at the enzyme's active site.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase and fragments thereof also are useful in raising specific antibodies which can block the enzyme and effectively reduce its activity.
  • Fig. 1 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:l).
  • Fig. 2 shows the amino acid sequence deduced from the DNA-sequence ofFigJ (SEQ ID NO:2).
  • Fig. 3 shows the amino acid sequence of the protein identified by trembl Accession
  • Fig. 4 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:4).
  • Fig. 5 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 5).
  • Fig. 6 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:6).
  • Fig. 4 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:4).
  • Fig. 5 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID
  • FIG. 7 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:7).
  • Fig. 8 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:8).
  • Fig. 9 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl eis- trans isomerase polypeptide (SEQ ID NO:9).
  • Fig. 10 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 10).
  • Fig. 11 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 11).
  • Fig. 12 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 12).
  • FIG. 13 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 13).
  • Fig. 14 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO : 14).
  • Fig. 15 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 15).
  • Fig. 16 shows the amino acid sequence deduced from the DNA-sequence of Fig. 15 (SEQ ID NO:16).
  • Fig. 17 shows the BLASTP alignment of human cyclophilin-type peptidyl-prolyl cis-trans isomerase (SEQ ID NO:2) with the protein identified with swiss
  • Fig. 18 shows the HMMPFAM alignment of SEQ ID NO:2 against pfam
  • Fig. 19 shows the BLASTP - alignment of SEQ ID NO:2 against pdb
  • Fig. 20 shows the Block results.
  • Fig. 21 shows the expression profiling of cyclophilin- type peptidyl-prolyl cis-trans isomerase rnRNA.
  • the invention relates to an isolated polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide and being selected from the group consisting of: a) a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16; b) a polynucleotide comprising the sequence of SEQ ID NO: 1 or 15; c) a polynucleotide which hybridizes under stringent conditions to a polynucleotide specified in (a) and (b);
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase comprises the amino acid sequence shown in SEQ ID NO:2 and 16.
  • a coding sequence for human cyclophilin-type peptidyl-prolyl cis-trans isomerase is shown in SEQ ID NO:l and 15.
  • ESTs are expressed in human fetal, kidney, colon carcinoma, germinal center B cell, multiple sclerosis lesions, prostate gland, testis, fetal lung, kidney, placenta, spleen, and cervix..
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase is 50% identical over 159 amino acids to the C. elegans protein identified with trembl Accession No. Z36949 (SEQ ID NO:3) and annotated as "PEPTIDYL-PROLYL CIS-TRANS
  • Human cyclophihn-type peptidyl-prolyl cis-trans isomerase of the invention is expected to be useful for the same purposes as previously identified cyclophilin-type peptidyl-prolyl cis-trans isomerase enzymes.
  • Human cyclophilin-type peptidyl- prolyl cis-trans isomerase is believed to be useful in therapeutic methods to treat disorders such as cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase also can be used to screen for human cyclophilin-type peptidyl-prolyl cis-trans isomerase activators and inhibitors.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides comprise at least 6, 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, or 645 contiguous amino acids selected from the amino acid sequence shown in SEQ ID NO:2 or 16 or a biologically active variant thereof, as defined below.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide of the invention therefore can be a portion of a cyclophilin-type peptidyl-prolyl cis-trans isomerase protein, a full-length cyclophilin-type peptidyl-prolyl cis-trans isomerase protein, or a fusion protein comprising all or a portion of a cyclophilin-type peptidyl-prolyl cis-frans isomerase protein.
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide variants have amino acid sequences which are at least about 51, 55, 60, 65, or 70, preferably about 75, 80, 85, 90, 96, 96, or 98% identical to the amino acid sequence shown in SEQ ID NO:2 or 16 or a fragment thereof. Percent identity between a putative cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide variant and an amino acid sequence of SEQ ID NO:2 or 16 or a fragment thereof. Percent identity between a putative cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide variant and an amino acid sequence of SEQ ID
  • NO:2 or 16 is determined using the Blast2 alignment program (Blosum62, Expect 10, standard genetic codes).
  • Variations in percent identity can be due, for example, to amino acid substitutions, insertions, or deletions.
  • Amino acid substitutions are defined as one for one amino acid replacements. They are conservative in nature when the substituted amino acid has similar structural and/or chemical properties. Examples of conservative replacements are substitution of a leucine with an isoleucine or valine, an aspartate with a glutamate, or a threonine with a serine.
  • a ino acid insertions or deletions are changes to or within an amino acid sequence. They typically fall in the range of about 1 to 5 amino acids. Guidance in determining which amino acid residues can be substituted, inserted, or deleted without abolishing biological or immunological activity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be found using computer programs well known in the art, such as DNASTAR software. Whether an amino acid change results in a biologically active cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can readily be determined by assaying for peptidyl-prolyl cis-trans isomerase activity, as described for example, in the specific examples, below.
  • Fusion proteins are useful for generating antibodies against cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide amino acid sequences and for use in various assay systems. For example, fusion proteins can be used to identify proteins which interact with portions of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. Protein affinity chromatography or library-based assays for protein- protein interactions, such as the yeast two-hybrid or phage display systems, can be used for this purpose. Such methods are well known in the art and also can be used as drug screens.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide fusion protein comprises two polypeptide segments fused together by means of a peptide bond.
  • the first polypeptide segment comprises at least 6, 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, or 645 contiguous amino acids of SEQ ID NO:2 or 16 or of a biologically active variant, such as those described above.
  • the first polypeptide segment also can comprise full-length cyclophilin-type peptidyl-prolyl cis-frans isomerase protein.
  • the second polypeptide segment can be a full-length protein or a protein fragment.
  • Proteins commonly used in fusion protein construction include ⁇ -galactosidase, ⁇ - glucuronidase, green fluorescent protein (GFP), autofluorescent proteins, including blue fluorescent protein (BFP), glutathione-S-fransferase (GST), luciferase, horseradish peroxidase (HRP), and chloramphenicol acetyltransferase (CAT).
  • epitope tags are used in fusion protein constructions, including histidine (His) tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV- G tags, and thioredoxin (Tix) tags.
  • fusion constructions can include maltose binding protein (MBP), S-tag, Lex a DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSN) BP16 protein fusions.
  • MBP maltose binding protein
  • S-tag S-tag
  • GAL4 DNA binding domain fusions GAL4 DNA binding domain fusions
  • HSN herpes simplex virus
  • a fusion protein also can be engineered to contain a cleavage site located between the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide-encoding sequence and the heterologous protein sequence, so that the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be cleaved and purified away from the heterologous moiety.
  • a fusion protein can be synthesized chemically, as is known in the art.
  • a fusion protein is produced by covalently linking two polypeptide segments or by standard procedures in the art of molecular biology.
  • Recombinant D ⁇ A methods can be used to prepare fusion proteins, for example, by making a D ⁇ A construct which comprises coding sequences selected from the complement of SEQ ID ⁇ OJ or 15 in proper reading frame with nucleotides encoding the second polypeptide segment and expressing the D ⁇ A construct in a host cell, as is known in the art.
  • kits for constructing fusion proteins are available from companies such as Promega Corporation (Madison, WI), Stratagene (La Jolla, CA), CLO ⁇ TECH (Mountain View, CA), Santa Cruz Biotechnology (Santa Cruz, CA), MBL International Corporation (MIC; Watertown, MA), and Quantum Biotechnologies
  • Species homologs of human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be obtained using cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide polynucleotides (described below) to make suitable probes or primers for screening cDNA expression libraries from other species, such as mice, monkeys, or yeast, identifying cDNAs which encode homologs of cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, and expressing the cDNAs as is known in the art.
  • Polynucleotides described below
  • a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be single- or double-stranded and comprises a coding sequence or the complement of a coding sequence for a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • a coding sequence for human cyclophilin-type peptidyl-prolyl cis-trans isomerase is shown in SEQ ID NO:l and 15 and is found on chromosome 5. The coding sequence is contained within a longer sequence shown in SEQ ID NO:4.
  • nucleotide sequences encoding human cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides, as well as homologous nucleotide sequences which are at least about 50, 55, 60, 65, 70, preferably about 75, 90, 96, or 98% identical to the nucleotide sequence shown in SEQ ID NOJ or 15 or its complement also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides.
  • Percent sequence identity between the sequences of two polynucleotides is determined using computer programs such as ALIGN which employ the FASTA algorithm, using an af ⁇ ine gap search with a gap open penalty of -12 and a gap extension penalty of -2.
  • cDNA Complementary DNA
  • species homologs, and variants of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides which encode biologically active cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides.
  • Variants and homologs of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides described above also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides.
  • homologous cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide sequences can be identified by hybridization of candidate polynucleotides to known cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides under stringent conditions, as is known in the art.
  • homologous sequences can be identified which contain at most about 25-30% basepair mismatches. More preferably, homologous nucleic acid strands contain 15-25% basepair mismatches, even more preferably 5-15% basepair mismatches.
  • Species homologs of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides disclosed herein also can be identified by making suitable probes or primers and screening cDNA expression libraries from other species, such as mice, monkeys, or yeast.
  • Human variants of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides can be identified, for example, by screening human cDNA expression libraries. It is well known that the T m of a double-stranded DNA decreases by 1-1.5 °C with every 1% decrease in homology (Bonner et al., J. Mol Biol. 81, 123 (1973).
  • Variants of human cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides or cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides of other species can therefore be identified by hybridizing a putative homologous cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide with a polynucleotide having a nucleotide sequence of SEQ ID NO:l or 15 or the complement thereof to form a test hybrid.
  • the melting temperature of the test hybrid is compared with the melting temperature of a hybrid comprising polynucleotides having perfectly complementary nucleotide sequences, and the number or percent of basepair mismatches within the test hybrid is calculated.
  • Nucleotide sequences which hybridize to cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides or their complements following stringent hybridization and/or wash conditions also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides.
  • Stringent wash conditions are well known and understood in the art and are disclosed, for example, in Sambrook et al, MOLECULAR CLONING: A LABORATORY MANUAL, 2d ed., 1989, at pages 9.50-9.51.
  • a combination of temperature and salt concentration should be chosen that is approximately 12-20 °C below the calculated T m of the hybrid under study.
  • Stringent wash conditions include, for example, 4X SSC at 65 °C, or 50% form- amide, 4X SSC at 42 °C, or 0.5X SSC, 0.1% SDS at 65 °C.
  • Highly stringent wash conditions include, for example, 0.2X SSC at 65 °C.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be isolated free of other cellular components such as membrane components, proteins, and lipids.
  • Polynucleotides can be made by a cell and isolated using standard nucleic acid purification techniques, or synthesized using an amplification technique, such as the polymerase chain reaction (PCR), or by using an automatic synthesizer. Methods for isolating polynucleotides are routine and are known in the art. Any such technique for obtaining a polynucleotide can be used to obtain isolated cyclophilin- type peptidyl-prolyl cis-trans isomerase polynucleotides.
  • restriction enzymes and probes can be used to isolate polynucleotide fragments which comprises cyclophilin-type peptidyl-prolyl cis-trans isomerase nucleotide sequences. Isolated polynucleotides are in preparations which are free or at least 70, 80, or 90% free of other molecules.
  • Human cyclophilin-type peptidyl-prolyl cis-frans isomerase cDNA molecules can be made with standard molecular biology techniques, using cyclophilin-type peptidyl- prolyl cis-frans isomerase mRNA as a template.
  • Human cyclophilin-type peptidyl- prolyl cis-frans isomerase cDNA molecules can thereafter be replicated using molecular biology techniques known in the art and disclosed in manuals such as Sambrook et al. (1989).
  • An amplification technique, such as PCR, can be used to obtain additional copies of polynucleotides of the invention, using either human genomic DNA or cDNA as a template.
  • synthetic chemistry techniques can be used to synthesizes cyclophilin- type peptidyl-prolyl cis-frans isomerase polynucleotides.
  • the degeneracy of the genetic code allows alternate nucleotide sequences to be synthesized which will encode a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide having, for example, an amino acid sequence shown in SEQ ID NO:2 or 16 or a biologically active variant thereof.
  • the partial sequence disclosed herein can be used to identify the corresponding full length gene from which it was derived.
  • the partial sequence can be nick-translated or end-labeled with 32 P using polynucleotide kinase using labeling methods known to those with skill in the art (BASIC METHODS IN MOLECULAR BIOLOGY, Davis et al., eds., Elsevier Press, N.Y., 1986).
  • a lambda library prepared from human tissue can be directly screened with the labeled sequences of interest or the library can be converted en masse to pBluescript (Sfratagene Cloning Systems, La Jolla, Calif.
  • Positive cDNA clones are analyzed to determine the amount of additional sequence they contain using PCR with one primer from the partial sequence and the other primer from the vector.
  • Clones with a larger vector-insert PCR product than the original partial sequence are analyzed by restriction digestion and DNA sequencing to determine whether they contain an insert of the same size or similar as the mRNA size determined from Northern blot Analysis.
  • the complete sequence of the clones can be determined, for example after exonuclease III digestion (McCombie et al., Methods 3, 33-40, 1991).
  • a series of deletion clones are generated, each of which is sequenced.
  • the resulting overlapping sequences are assembled into a single contiguous sequence of high redundancy (usually three to five overlapping sequences at each nucleotide position), resulting in a highly accurate final sequence.
  • PCR-based methods can be used to extend the nucleic acid sequences disclosed herein to detect upstream sequences such as promoters and regulatory elements.
  • restriction-site PCR uses universal primers to retrieve unknown sequence adjacent to a known locus (Sarkar, PCR Methods Applic. 2, 318-322, 1993). Genomic DNA is first amplified in the presence of a primer to a linker sequence and a primer specific to the known region. The amplified sequences are then subjected to a second round of PCR with the same linker primer and another specific primer internal to the first one. Products of each round of PCR are transcribed with an appropriate RNA polymerase and sequenced using reverse transcriptase.
  • Inverse PCR also can be used to amplify or extend sequences using divergent primers based on a known region (Triglia et al., Nucleic Acids Res. 16, 8186, 1988).
  • Primers can be designed using commercially available software, such as OLIGO 4.06 Primer Analysis software (National Biosciences Inc., Madison, Minn.), to be 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68-72 °C.
  • the method uses several restriction enzymes to generate a suitable fragment in the known region of a gene. The fragment is then circularized by intramolecular ligation and used as a PCR template.
  • capture PCR which involves PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA (Lagerstrom et al., PCR Methods Applic. 1, 111-119,
  • multiple restriction enzyme digestions and ligations also can be used to place an engineered double-stranded sequence into an unknown fragment of the DNA molecule before performing PCR.
  • PCR, nested primers, and PROMOTERFINDER libraries can be used to walk genomic DNA (CLONTECH, Palo Alto, Calif.). This process avoids the need to screen libraries and is useful in finding infron/exon junctions.
  • libraries that have been size-selected to include larger cDNAs Randomly-primed libraries are preferable, in that they will contain more sequences which contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA.
  • Genomic libraries can be useful for extension of sequence into 5' non-transcribed regulatory regions.
  • capillary electrophoresis systems can be used to analyze the size or confirm the nucleotide sequence of PCR or sequencing products.
  • capillary sequencing can employ flowable polymers for electrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and detection of the emitted wavelengths by a charge coupled device camera.
  • Output/light intensity can be converted to electrical signal using appropriate software (e.g. GENOTYPER and Sequence NAVIGATOR, Perkin Elmer), and the entire process from loading of samples to computer analysis and electronic data display can be computer controlled.
  • Capillary electrophoresis is especially preferable for the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be obtained, for example, by purification from human cells, by expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides, or by direct chemical synthesis.
  • Human cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides can be purified from any cell which expresses the enzyme, including host cells which have been transfected with cyclophilin-type peptidyl-prolyl cis-trans isomerase expression constructs.
  • a purified cyclophilin-type peptidyl-prolyl cis-trans isomerase poly- peptide is separated from other compoimds which normally associate with the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide in the cell, such as certain proteins, carbohydrates, or lipids, using methods well-known in the art.
  • Such methods include, but are not limited to, size exclusion chromatography, ammonium sulfate fractionation, ion exchange chromatography, affinity chromatography, and preparative gel electrophoresis.
  • a preparation of purified cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides is at least 80% pure; preferably, the preparations are 90%, 95%, or 99% pure. Purity of the preparations can be assessed by any means known in the art, such as SDS-polyacrylamide gel electrophoresis.
  • the polynucleotide can be inserted into an expression vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • Methods which are well known to those skilled in the art can be used to construct expression vectors containing sequences encoding cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides and appropriate franscriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook et al. (1989) and in Ausubel et al., CURRENT
  • a variety of expression vector/host systems can be utilized to contain and express sequences encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase poly- peptide.
  • microorganisms such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors, insect cell systems infected with virus expression vectors (e.g., baculovirus), plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids), or animal cell systems.
  • microorganisms such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with virus expression vectors (e.g., baculovirus), plant
  • control elements or regulatory sequences are those non-translated regions of the vector — enhancers, promoters, 5' and 3' unfranslated regions — which interact with host cellular proteins to carry out transcription and translation. Such elements can vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, can be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the
  • BLUESCRIPT phagemid (Stratagene, LaJolla, Calif.) or pSPORTl plasmid (Life Technologies) and the tike can be used.
  • the baculovirus polyhedrin promoter can be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO, and storage protein genes) or from plant viruses ( .g., viral promoters or leader sequences) can be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable.
  • vectors based on SV40 or EBV can be used with an appropriate selectable marker.
  • a number of expression vectors can be selected depending upon the use intended for the cyclophilin-type peptidyl-prolyl cis-trans isomerase poly- peptide. For example, when a large quantity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is needed for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified can be used. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRLPT (Stratagene).
  • a sequence encoding the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of ⁇ -galactosidase so that a hybrid protein is produced.
  • pIN vectors Van Heeke & Schuster, J. Biol. Chem. 264, 5503-5509, 1989
  • pGEX vectors Promega, Madison, Wis.
  • GST glutathione S-fransferase
  • fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • Proteins made in such systems can be designed to include heparin, thrombin, or factor Xa protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
  • yeast Saccharomyces cerevisiae a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH can be used.
  • constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH.
  • sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be driven by any of a number of promoters.
  • viral promoters such as the 35 S and 19S promoters of CaMV can be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6, 307-311, 1987).
  • plant promoters such as the small subunit of RUBISCO or heat shock promoters can be used (Coruzzi et al, EMBO J. 3, 1671-1680, 1984; Brogue et al, Science 224, 838-843, 1984; Winter et al, Results Probl.
  • constructs can be introduced into plant cells by direct DNA transformation or by pathogen-mediated fransfection. Such techniques are described in a number of generally available reviews (e.g., Hobbs or Murray, in MCGRAW HILL YEARBOOK OF SCIENCE AND TECHNOLOGY, McGraw Hill, New York, NX, pp. 191-196, 1992).
  • An insect system also can be used to express a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide.
  • Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae.
  • Sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter.
  • Successful insertion of cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein.
  • the recombinant viruses can then be used to infect S. frugiperda cells or Trichoplusia larvae in which cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be expressed (Engelhard et al, Proc. Nat. Acad. Sci. 91, 3224-3227, 1994).
  • Mammalian Expression Systems A number of viral-based expression systems can be used to express cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides in mammalian host cells. For example, if an adenovirus is used as an expression vector, sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be ligated into an adenovirus transcription/translation complex comprising the late promoter and tripartite leader sequence.
  • Insertion in a non-essential El or E3 region of the viral genome can be used to obtain a viable virus which is capable of expressing a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide in infected host cells (Logan & Shenk, Proc. Natl Acad. Sci. 81, 3655-3659, 1984).
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer, can be used to increase expression in mammalian host cells.
  • RSV Rous sarcoma virus
  • HACs Human artificial chromosomes
  • HACs also can be used to deliver larger fragments of DNA than can be contained and expressed in a plasmid.
  • HACs of 6M to 10M are constructed and delivered to cells via conventional delivery methods (e.g., liposomes, polycationic amino polymers, or vesicles).
  • Specific initiation signals also can be used to achieve more efficient translation of sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides. Such signals include the ATG initiation codon and adjacent sequences.
  • a host cell strain can be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, Hpidation, and acylation.
  • Post-franslational processing which cleaves a "prepro" form of the polypeptide also can be used to facilitate correct insertion, folding and/or function.
  • Different host cells which have specific cellular machinery and characteristic mechanisms for post-franslational activities (e.g., CHO,
  • HeLa, MDCK, HEK293, and WI38 are available from the American Type Culture Collection (ATCC; 10801 University Boulevard, Manassas, VA 20110-2209) and can be chosen to ensure the correct modification and processing of the foreign protein. Stable expression is preferred for long-term, high-yield production of recombinant proteins.
  • cell lines which stably express cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides can be transformed using expression vectors which can contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector.
  • cells can be allowed to grow for 1-2 days in an enriched medium before they are switched to a selective medium.
  • the purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced cyclophilin-type peptidyl-prolyl cis-trans isomerase sequences.
  • Resistant clones of stably fransformed cells can be proliferated using tissue culture techniques appropriate to the cell type. See, for example, ANIMAL CELL CULTURE, R.I. Freshney, ed., 1986.
  • Any number of selection systems can be used to recover fransformed cell lines.
  • herpes simplex virus thymidine kinase (Wigler et al, Cell 11, 223-32, 1977) and adenine phosphoribosyltransferase (Lowy et al., Cell 22, 817-23, 1980) genes which can be employed in tkr or aprt cells, respectively.
  • antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection.
  • dhfr confers resistance to methofrexate (Wigler et al, Proc. Nail. Acad. Sci.
  • npt confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., J. Mol. Biol. 150, 1-14, 1981), and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murray, 1992, supra). Additional selectable genes have been described. For example, trpB allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. 85, 8047-51, 1988).
  • Visible markers such as anthocyanins, ⁇ -glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, can be used to identify transformants and to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes et al., Methods Mol Biol. 55, 121-131, 1995).
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide is also present, its presence and expression may need to be confirmed.
  • a sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is inserted within a marker gene sequence, transformed cells containing sequences which encode a cyclo- philin-type peptidyl-prolyl cis-trans isomerase polypeptide can be identified by the absence of marker gene function.
  • a marker gene can be placed in tandem with a sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
  • host cells which contain a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide and which express a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include membrane, solution, or chip-based technologies for the detection and/or quantification of nucleic acid or protein.
  • the presence of a polynucleotide sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be detected by DNA-DNA or DNA-RNA hybridization or amplification using probes or fragments or fragments of polynucleotides encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • Nucleic acid amplification-based assays involve the use of oligonucleotides selected from sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide to detect transformants which contain a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
  • a variety of protocols for detecting and measuring the expression of a cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide, using either polyclonal or monoclonal antibodies specific for the polypeptide, are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS).
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmunoassay
  • FACS fluorescence activated cell sorting
  • a two-site, monoclonal-based immunoassay using monoclonal antibodies reactive to two non-interfering epitopes on a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be used, or a competitive binding assay can be employed.
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides include oligolabeling, nick translation, end-labeling, or PCR amphfication using a labeled nucleotide.
  • sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be cloned into a vector for the production of an mRNA probe.
  • RNA probes are known in the art, are commercially available, and can be used to synthesize RNA probes in vitro by addition of labeled nucleotides and an appropriate RNA polymerase such as T7, T3, or SP6. These procedures can be conducted using a variety of commercially available kits
  • reporter molecules or labels which can be used for ease of detection include radionuclides, enzymes, and fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • Host cells transformed with nucleotide sequences encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
  • the poly- peptide produced by a transformed cell can be secreted or contained infracellularly depending on the sequence and/or the vector used.
  • expression vectors containing polynucleotides which encode cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be designed to contain signal sequences which direct secretion of soluble cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides through a prokaryotic or eukaryotic cell membrane or which direct the membrane insertion of membrane-bound cyclophilin- type peptidyl-prolyl cis-frans isomerase polypeptide.
  • purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized i nmunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.).
  • cleavable linker sequences such as those specific for Factor Xa or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide also can be used to facilitate purification.
  • One such expression vector provides for expression of a fusion protein containing a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide and 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site.
  • the histidine residues facilitate purification by IMAC (immobilized metal ion affinity chromatography, as described in Porath et al., Prot. Exp. Purifi 3, 263-281, 1992), while the enterokinase cleavage site provides a means for purifying the cyclophilin- type peptidyl-prolyl cis-frans isomerase polypeptide from the fusion protein.
  • Vectors which contain fusion proteins are disclosed in Kroll et ah, DNA Cell Biol. 12, 441-453, 1993.
  • Sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers et al., Nucl. Acids Res. Symp. Ser. 215-223, 1980; Horn et al. Nucl. Acids Res. Symp. Ser. 225-232, 1980).
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide itself can be produced using chemical methods to synthesize its amino acid sequence, such as by direct peptide synthesis using solid-phase techniques (Merrifield, J. Am. Chem. Soc.
  • Protein synthesis can be performed using manual techniques or by automation. Automated synthesis can be achieved, for example, using Applied Biosystems 431 A Peptide Synthesizer (Perkin Elmer).
  • fragments of cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be separately synthesized and combined using chemical methods to produce a full-length molecule.
  • the newly synthesized peptide can be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, PROTEINS: STRUCTURES AND MOLECULAR PRINCIPLES, WH Freeman and Co., New York, N.Y., 1983).
  • the composition of a synthetic cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure; see Creighton, supra).
  • any portion of the amino acid sequence of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins to produce a variant polypeptide or a fusion protein. Production of Altered Polypeptides
  • codons pre- ferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce an RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
  • nucleotide sequences disclosed herein can be engineered using methods generally known in the art to alter cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide-encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the polypeptide or mRNA product.
  • DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides can be used to engineer the nucleotide sequences.
  • site-directed mutagenesis can be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations, and so forth.
  • Antibody as used herein includes intact immunoglobulin molecules, as well as fragments thereof, such as Fab, F(ab') 2 , and Fv, which are capable of binding an epitope of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide.
  • an antibody which specifically binds to an epitope of a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide can be used therapeutically, as well as in immunochemical assays, such as Western blots, ELISAs, radioimmunoassays, i-mmunohistochemical assays, immunoprecipitations, or other immunochemical assays known in the art.
  • immunoassays can be used to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays are well known in the art. Such immunoassays typically involve the measurement of complex formation between an immunogen and an antibody which specifically binds to the immunogen.
  • an antibody which specifically binds to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide provides a detection signal at least 5-, 10-, or 20-fold higher than a detection signal provided with other proteins when used in an immunochemical assay.
  • antibodies which specifically bind to cyclo- philin-type peptidyl-prolyl cis-frans isomerase polypeptides do not detect other proteins in immunochemical assays and can immunoprecipitate a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide from solution.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be used to immunize a mammal, such as a mouse, rat, rabbit, guinea pig, monkey, or human, to produce polyclonal antibodies.
  • a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be conjugated to a carrier protein, such as bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin.
  • a carrier protein such as bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin.
  • various adjuvants can be used to increase the immunological response.
  • Such adjuvants include, but are not limited to, Freund's adjuvant, mineral gels (e.g., aluminum hydroxide), and surface active substances (e.g. lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol).
  • BCG Bacilli Calmette-Gueri ⁇
  • Corynebacterium parvum are especially useful.
  • Monoclonal antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These techniques include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kohler et al, Nature 256,
  • chimeric antibodies the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used (Morrison et al., Proc. Natl. Acad. Sci. 81, 6851-6855, 1984; Neuberger et al., Nature 312, 604-608, 1984; Takeda et al, Nature 314, 452-454, 1985).
  • Monoclonal and other antibodies also can be "humanized” to prevent a patient from mounting an immune response against the antibody when it is used therapeutically. Such antibodies may be sufficiently similar in sequence to human antibodies to be used directly in therapy or may require alteration of a few key residues.
  • rodent antibodies and human sequences can be minimized by replacing residues which differ from those in the human sequences by site directed mutagenesis of individual residues or by grating of entire complementarity determining regions.
  • humanized antibodies can be produced using recombinant methods, as described in GB2188638B.
  • Antibodies which specifically bind to a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide can contain antigen binding sites which are either partially or fully humanized, as disclosed in U.S. 5,565,332.
  • single chain antibodies can be adapted using methods known in the art to produce single chain antibodies which specifically bind to cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides.
  • Antibodies with related specificity, but of distinct idiot pic composition, can be generated by chain shuffling from random combinatorial immunoglobin libraries (Burton, Proc. Natl. Acad. Sci. 88, 11120-23, 1991).
  • Single-chain antibodies also can be constructed using a DNA amphfication method, such as PCR, using hybridoma cDNA as a template (Thirion et ah, 1996, Eur. J.
  • Single-chain antibodies can be mono- or bispecific, and can be bivalent or tefravalent. Construction of tefravalent, bispecific single-chain antibodies is taught, for example, in Coloma & Morrison, 1997, Nat. Biotechnol 15, 159-63. Construction of bivalent, bispecific single-chain antibodies is taught in Mallender & Noss, 1994, J. Biol. Chem. 269, 199-206.
  • a nucleotide sequence encoding a single-chain antibody can be constructed using manual or automated nucleotide synthesis, cloned into an expression construct using standard recombinant D ⁇ A methods, and introduced into a cell to express the coding sequence, as described below.
  • single-chain antibodies can be produced directly using, for example, filamentous phage technology (Verhaar et al., 1995, Int. J. Cancer 61, 497-501; ⁇ icholls et ah, 1993, J. Immunol. Meth. 165, 81-91).
  • Antibodies which specifically bind to cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides also can be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Orlandi et ah, Proc. Natl. Acad. Sci. 86, 3833-3837, 1989; Winter et ah, Nature 349, 293-299, 1991).
  • antibodies can be constructed and used therapeutically in methods of the invention.
  • chimeric antibodies can be constructed as disclosed in WO 93/03151.
  • Binding proteins which are derived from immunoglobulins and which are multivalent and multispecific, such as the "diabodies" described in WO 94/13804, also can be prepared.
  • Antibodies according to the invention can be purified by methods well known in the art. For example, antibodies can be affinity purified by passage over a column to which a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide is bound. The bound antibodies can then be eluted from the column using a buffer with a high salt concentration.
  • Antisense oligonucleotides are nucleotide sequences which are complementary to a specific DNA or RNA sequence. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form complexes and block either transcription or translation. Preferably, an antisense oligonucleotide is at least 11 nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides long. Longer sequences also can be used. Antisense oligonucleotide molecules can be provided in a DNA construct and introduced into a cell as described above to decrease the level of cyclophilin-type peptidyl-prolyl cis- trans isomerase gene products in the cell.
  • Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides, or a combination of both. Oligonucleotides can be synthesized manually or by an automated synthesizer, by covalently linking the 5' end of one nucleotide with the V end of another nucleotide with non-phosphodiester internucleotide linkages such alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonothioates, alkylphosphonates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxymethyl esters, carbonates, and phosphate triesters. See Brown, Meth. Mol.
  • Modifications of cyclophilin-type peptidyl-prolyl cis-frans isomerase gene expression can be obtained by designing antisense oligonucleotides which will form duplexes to the control, 5', or regulatory regions of the cyclophilin-type peptidyl- prolyl cis-trans isomerase gene. Oligonucleotides derived from the transcription initiation site, e.g., between positions -10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or chaperons.
  • An antisense oligo- nucleotide also can be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
  • Precise complementarity is not required for successful complex formation between an antisense oligonucleotide and the complementary sequence of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
  • Antisense oligonucleotides which comprise, for example, 2, 3, 4, or 5 or more stretches of contiguous nucleotides which are precisely complementary to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide, each separated by a stretch of contiguous nucleotides which are not complementary to adjacent cyclophilin-type peptidyl- prolyl cis-frans isomerase nucleotides, can provide sufficient targeting specificity for cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA.
  • each stretch of complementary contiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length.
  • Non-complementary intervening sequences are preferably 1, 2, 3, or 4 nucleotides in length.
  • One skilled in the art can easily use the calculated melting point of an antisense-sense pair to determine the degree of mismatching which will be tolerated between a particular antisense oligonucleotide and a particular cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide sequence.
  • Antisense oligonucleotides can be modified without affecting their ability to hybridize to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide. These modifications can be internal or at one or both ends of the antisense molecule.
  • intemucleoside phosphate linkages can be modified by adding cholesteryl or diamine moieties with varying numbers of carbon residues between the amino groups and terminal ribose.
  • Modified bases and or sugars such as arabinose instead of ribose, or a 3', 5' -substituted oligonucleotide in which the 3' hydroxyl group or the 5' phosphate group are substituted, also can be employed in a modified antisense oligonucleotide.
  • modified oligonucleotides can be prepared by methods well known in the art. See, e.g., Agrawal et ah, Trends Biotechnol 10,
  • Ribozymes are RNA molecules with catalytic activity. See, e.g., Cech, Science 236,
  • Ribozymes can be used to inhibit gene function by cleaving an RNA sequence, as is known in the art (e.g., Haseloff et ah, U.S. Patent 5,641,673).
  • the mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. Examples include engineered hammerhead motif ribozyme molecules that can specifically and efficiently catalyze endonucleolytic cleavage of specific nucleotide sequences.
  • the coding sequence of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be used to generate ribozymes which will specifically bind to mRNA transcribed from the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
  • Methods of designing and constructing ribozymes which can cleave other RNA molecules in trans in a highly sequence specific manner have been developed and described in the art (see Haseloff et a Nature 334, 585-591, 1988).
  • the cleavage activity of ribozymes can be targeted to specific RNAs by engineering a discrete "hybridization" region into the ribozyme.
  • the hybridization region contains a sequence complementary to the target RNA and thus specifically hybridizes with the target (see, for example, Gerlach et ah, EP 321 ,201 ).
  • ribozyme cleavage sites within a cyclophilin-type peptidyl-prolyl cis-trans isomerase RNA target can be identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target RNA containing the cleavage site can be evaluated for secondary structural features which may render the target inoperable.
  • RNA targets also can be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays. Longer complementary sequences can be used to increase the affinity of the hybridization sequence for the target.
  • the hybridizing and cleavage regions of the ribozyme can be integrally related such that upon hybridizing to the target RNA through the complementary regions, the catalytic region of the ribozyme can cleave the target.
  • Ribozymes can be introduced into cells as part of a DNA construct. Mechanical methods, such as microinjection, liposome-mediated fransfection, electroporation, or calcium phosphate precipitation, can be used to introduce a ribozyme-containing DNA construct into cells in which it is desired to decrease cyclophilin-type peptidyl- prolyl cis-trans isomerase expression. Alternatively, if it is desired that the cells stably retain the DNA construct, the construct can be supplied on a plasmid and maintained as a separate element or integrated into the genome of the cells, as is known in the art.
  • a ribozyme-encoding DNA construct can include transcriptional regulatory elements, such as a promoter element, an enhancer or UAS element, and a transcriptional terminator signal, for controlling transcription of ribozymes in the cells.
  • ribozymes can be engineered so that ribozyme expression will occur in response to factors which induce expression of a target gene. Ribozymes also can be engineered to provide an additional level of regulation, so that destruction of mRNA occurs only when both a ribozyme and a target gene are induced in the cells.
  • genes whose products interact with human cyclophilin-type peptidyl-prolyl cis-frans isomerase may represent genes which are differentially expressed in disorders including, but not limited to, cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders. Further, such genes may represent genes which are differentially regulated in response to manipulations relevant to the progression or treatment of such diseases. Additionally, such genes may have a temporally modulated expression, increased or decreased at different stages of tissue or organism development. A differentially expressed gene may also have its expression modulated under control versus experimental conditions. In addition, the human cyclophilin-type peptidyl- prolyl cis-trans isomerase gene or gene product may itself be tested for differential expression.
  • the degree to which expression differs in a normal versus a diseased state need only be large enough to be visualized via standard characterization techniques such as differential display techniques.
  • standard characterization techniques such as differential display techniques.
  • Other such standard characterization techniques by which expression differences may be visualized include but are not limited to, quantitative RT (reverse transcriptase), PCR, and Northern analysis.
  • RNA samples are obtained from tissues of experimental subjects and from corresponding tissues of control subjects. Any RNA isolation technique which does not select against the isolation of mRNA may be utilized for the purification of such RNA samples. See, for example, Ausubel et ah, ed. dislike CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, Inc. New York, 1987-1993. Large numbers of tissue samples may readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski, U.S. Patent 4,843,155.
  • Transcripts within the collected RNA samples which represent RNA produced by differentially expressed genes are identified by methods well known to those of skill in the art. They include, for example, differential screening (Tedder et ah, Proc. Natl. Acad. Sci. U.S.A. 85, 208-12, 1988), subtractive hybridization (Hedrick et ah, Nature 308, 149-53; Lee et ah, Proc. Natl. Acad. Sci. U.S.A. 88, 2825, 1984), and, preferably, differential display (Liang & Pardee, Science 257, 967-71, 1992; U.S. Patent 5,262,311).
  • the differential expression information may itself suggest relevant methods for the treatment of disorders involving the human cyclophilin-type peptidyl-prolyl cis-frans isomerase.
  • treatment may include a modulation of expression of the differentially expressed genes and or the gene encoding the human cyclophilin-type peptidyl-prolyl cis-frans isomerase.
  • the differential expression information may indicate whether the expression or activity of the differentially expressed gene or gene product or the human cyclophilin-type peptidyl-prolyl cis-trans isomerase gene or gene product are up-regulated or down-regulated.
  • the invention provides assays for screening test compounds which bind to or modulate the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase poly- peptide or a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
  • a test compound preferably binds to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or polynucleotide. More preferably, a test compound decreases or increases activity by at least about 10, preferably about 50, more preferably about 75, 90, or 100% relative to the absence of the test compound.
  • Test compounds can be pharmacologic agents already known in the art or can be compounds previously unknown to have any pharmacological activity.
  • the compounds can be naturally occurring or designed in the laboratory. They can be isolated from microorganisms, animals, or plants, and can be produced recombinantly, or synthesized by chemical methods known in the art. If desired, test compounds can be obtained using any of the numerous combinatorial library methods known in the art, including but not limited to, biological libraries, spatially addressable parallel solid phase or solution phase libraries, synthetic library methods requiring deconvolution, the "one-bead one-compound” library method, and synthetic library methods using affinity chromatography selection.
  • the biological library approach is limited to polypeptide libraries, while the other four approaches are applicable to polypeptide, non-peptide oligomer, or small molecule libraries of compounds. See Lam, Anticancer Drug Des. 12, 145, 1997.
  • Test compounds can be screened for the ability to bind to cyclophilin-type peptidyl- prolyl cis-frans isomerase polypeptides or polynucleotides or to affect cyclophilin- type peptidyl-prolyl cis-frans isomerase activity or cyclophilin-type peptidyl-prolyl cis-frans isomerase gene expression using high throughput screening.
  • high throughput screening many discrete compounds can be tested in parallel so that large numbers of test compounds can be quickly screened.
  • the most widely established techniques utilize 96-well microtiter plates. The wells of the microtiter plates typically require assay volumes that range from 50 to 500 ⁇ l.
  • many instruments, materials, pipettors, robotics, plate washers, and plate readers are commercially available to fit the 96-well format.
  • free format assays or assays that have no physical barrier between samples, can be used.
  • an assay using pigment cells (melanocytes) in a simple homogeneous assay for combinatorial peptide libraries is described by Jayawickreme et ah, Proc. Natl. Acad. Sci. U.S.A. 19, 1614-18 (1994).
  • the cells are placed under agarose in pefri dishes, then beads that carry combinatorial compounds are placed on the surface of the agarose.
  • the combinatorial compounds are partially released the compounds from the beads. Active compounds can be visualized as dark pigment areas because, as the compounds diffuse locally into the gel matrix, the active compounds cause the cells to change colors.
  • Chelsky placed a simple homogenous enzyme assay for carbonic anhydrase inside an agarose gel such that the enzyme in the gel would cause a color change throughout the gel. Thereafter, beads carrying combinatorial compounds via a photolinker were placed inside the gel and the compounds were partially released by UV-light. Compounds that inhibited the enzyme were observed as local zones of inhibition having less color change.
  • test samples are placed in a porous matrix.
  • One or more assay components are then placed within, on top of, or at the bottom of a matrix such as a gel, a plastic sheet, a filter, or other form of easily manipulated solid support.
  • a matrix such as a gel, a plastic sheet, a filter, or other form of easily manipulated solid support.
  • the test compound is preferably a small molecule which binds to and occupies, for example, the active site of the cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide, such that normal biological activity is prevented.
  • small molecules include, but are not limited to, small peptides or peptide-like molecules.
  • either the test compound or the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can comprise a detectable label, such as a fluorescent, radioisotopic, chemiluminescent, or enzymatic label, such as horseradish per- oxidase, alkaline phosphatase, or luciferase.
  • a detectable label such as a fluorescent, radioisotopic, chemiluminescent, or enzymatic label, such as horseradish per- oxidase, alkaline phosphatase, or luciferase.
  • Detection of a test compound which is bound to the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can then be accomplished, for example, by direct counting of radioemmission, by scintillation counting, or by determining conversion of an appropriate substrate to a detectable product.
  • binding of a test compound to a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be determined without labeling either of the interactants.
  • a microphysiometer can be used to detect binding of a test compound with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • a microphysiometer e.g., CytosensorTM
  • CytosensorTM is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS).
  • Changes in this acidification rate can be used as an indicator of the interaction between a test compound and a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide (McConnell et ah, Science 257, 1906-1912, 1992).
  • Determining the ability of a test compound to bind to a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide also can be accomplished using a technology such as real-time Bimolecular Interaction Analysis (BIA) (Sjolander & Urbaniczky, Anah Chem. 63, 2338-2345, 1991, and Szabo et ah, Curr. Opin. Struct. Biol. 5, 699-705, 1995).
  • BIA is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcoreTM). Changes in the optical phenomenon surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be used as a "bait protein" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent 5,283,317; Zervos et ah, Cell 72, 223-232, 1993; Madura et ah, J. Biol. Chem. 268,.
  • the two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains.
  • the assay utilizes two different DNA constructs.
  • polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be fused to a polynucleotide encoding the DNA binding domain of a known transcription factor (e.g., GAL-4).
  • a DNA sequence that encodes an unidentified protein (“prey" or "sample” can be fused to a polynucleotide that codes for the activation domain of the known transcription factor.
  • the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ), which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected, and cell colonies containing the functional transcription factor can be isolated and used to obtain the DNA sequence encoding the protein which interacts with the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • a reporter gene e.g., LacZ
  • either the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide (or polynucleotide) or the test compound can be bound to a solid support.
  • Suitable solid supports include, but are not limited to, glass or plastic slides, tissue culture plates, microtiter wells, tubes, silicon chips, or particles such as beads (including, but not limited to, latex, polystyrene, or glass beads).
  • Any method known in the art can be used to attach the enzyme polypeptide (or polynucleotide) or test compound to a solid support, including use of covalent and non-covalent linkages, passive absorption, or pairs of binding moieties attached respectively to the polypeptide (or polynucleotide) or test compound and the solid support.
  • Test compounds are preferably bound to the solid support in an array, so that the location of individual test compounds can be tracked. Binding of a test compound to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide (or polynucleotide) can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro- centrifuge tubes.
  • the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is a fusion protein comprising a domain that allows the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide to be bound to a solid support.
  • glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St.
  • a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or polynucleotide
  • a test compound can be immobilized utilizing conjugation of biotin and streptavidin.
  • Biotinylated cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides (or polynucleotides) or test compounds .can be prepared from biotin-NHS(N-hydroxysuccinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, 111.) and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical).
  • antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, polynucleotide, or a test compound, but which do not interfere with a desired binding site, such as the active site of the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, can be derivatized to the wells of the plate. Unbound target or protein can be trapped in the wells by antibody conjugation.
  • Methods for detecting such complexes include immunodetection of complexes using antibodies which specifically bind to the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or test compound, enzyme-linked assays which rely on detecting an activity of the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, and SDS gel electrophoresis under non-reducing conditions.
  • Any cell which comprises a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or polynucleotide can be used in a cell-based assay system.
  • a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Binding of the test compound to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide or polynucleotide is determined as described above.
  • Test compounds can be tested for the ability to increase or decrease the enzymatic activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • Enzymatic activity can be measured, for example, as described in the specific examples, below. Enzyme assays can be carried out after contacting either a purified cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, a cell membrane preparation, or an intact cell with a test compound.
  • a test compound which decreases an enzymatic activity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% is identified as a potential therapeutic agent for decreasing cyclophilin-type peptidyl- prolyl cis-trans isomerase activity.
  • a test compound which increases an enzymatic activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% is identified as a potential therapeutic agent for increasing human cyclophilin-type peptidyl-prolyl cis-trans isomerase activity.
  • test compounds which increase or decrease cyclophilin-type peptidyl-prolyl cis-trans isomerase gene expression are identified.
  • a cyclophilin- type peptidyl-prolyl cis-trans isomerase polynucleotide is contacted with a test compound, and the expression of an RNA or polypeptide product of the cyclophilin- type peptidyl-prolyl cis-frans isomerase polynucleotide is determined.
  • the level of expression of appropriate mRNA or polypeptide in the presence of the test compound is compared to the level of expression of mRNA or polypeptide in the absence of the test compound.
  • the test compound can then be identified as a modulator of expression based on this comparison.
  • test compound when expression of mRNA or polypeptide is greater in the presence of the test compound than in its absence, the test compound is identified as a stimulator or enhancer of the mRNA or polypeptide expression.
  • test compound when expression of the mRNA or polypeptide is less in the presence of the test compound than in its absence, the test compound is identified as an inhibitor of the mRNA or polypeptide expression.
  • the level of cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA or poly- peptide expression in the cells can be determined by methods well known in the art for detecting mRNA or polypeptide. Either qualitative or quantitative methods can be used.
  • the presence of polypeptide products of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be determined, for example, using a variety of techniques known in the art, including immunochemical methods such as radio- immunoassay, Western blotting, and immunohistochemistry.
  • polypeptide synthesis can be determined in vivo, in a cell culture, or in an in vitro translation system by detecting incorporation of labeled amino acids into a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide.
  • Such screening can be carried out either in a cell-free assay system or in an intact cell.
  • Any cell which expresses a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be used in a cell-based assay system.
  • the cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Either a primary culture or an established cell line, such as CHO or human embryonic kidney
  • 293 cells can be used.
  • compositions of the invention can comprise, for example, a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide, ribozymes or antisense oligonucleotides, antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, or mimetics, activators, inhibitors, or inhibitors of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide activity.
  • compositions can be administered alone or in combination with at least one other agent, such as stabilizing compound, which can be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose, and water.
  • agent such as stabilizing compound
  • the compositions can be administered to a patient alone, or in combination with other agents, drugs or hormones.
  • compositions of the invention can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, infra-arterial, inframedullary, infrathecal, infraventricular, transdermal, subcutaneous, infraperitoneal, intranasal, parenteral, topical, sublingual, or rectal means.
  • Pharmaceutical compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
  • compositions for oral use can be obtained through combination of active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores.
  • Suitable excipients are carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxy- propylmethyl-cellulose, or sodium carboxymethylcellulose; gums including arabic and fragacanth; and proteins such as gelatin and collagen.
  • disintegrating or solubilizing agents can be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.
  • Dragee cores can be used in conjunction with suitable coatings, such as concentrated sugar solutions, which also can contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • suitable coatings such as concentrated sugar solutions, which also can contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments can be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.
  • Push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol.
  • Push-fit capsules can contain active ingredients mixed with a filler or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers.
  • the active compounds can be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.
  • compositions suitable for parenteral administration can be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline.
  • Aqueous injection suspensions can contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dexfran.
  • suspensions of the active compounds can be prepared as appropriate oily injection suspensions.
  • Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes.
  • Non-lipid polycationic amino polymers also can be used for delivery.
  • the suspension also can contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.
  • penetrants appropriate to the particular barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
  • compositions of the present invention can be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • the pharmaceutical composition can be provided as a salt and can be formed with many acids, including but not limited to, hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents than are the corresponding free base forms.
  • the preferred preparation can be a lyophilized powder which can contain any or all of the following: 1-50 mM histidine, 0J%-2% sucrose, and 2-7% mannitol, at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
  • compositions can be placed in an appropriate container and labeled for treatment of an indicated condition.
  • labeling would include amount, frequency, and method of administration.
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase of the invention and cyclophilin-type peptidyl-prolyl cis-trans isomerase.
  • expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase is closely associated with cancerous or proliferating tissue, and with reproductive tissue. Therefore, cyclophilin-type peptidyl-prolyl cis-trans isomerase appears to be associated with cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders.
  • Cancer is a disease fundamentally caused by oncogenic cellular transformation. There are several hallmarks of transformed cells that distinguish them from their normal counterparts and underlie the pathophysiology of cancer. These include uncontrolled cellular proliferation, unresponsiveness to normal death-inducing signals (immortalization), increased cellular motility and invasiveness, increased ability to recruit blood supply through induction of new blood vessel formation (angiogenesis), genetic instability, and dysregulated gene expression. Various combinations of these aberrant physiologies, along with the acquisition of drug-resistance frequently lead to an intractable disease state in which organ failure and patient death ultimately ensue.
  • Genes or gene fragments identified through genomics can readily be expressed in one or more heterologous expression systems to produce functional recombinant proteins. These proteins are characterized in vitro for their biochemical properties and then used as tools in high-throughput molecular screening programs to identify chemical modulators of their biochemical activities. Activators and/or inhibitors of target protein activity can be identified in this manner and subsequently tested in cellular and in vivo disease models for anti-cancer activity. Optimization of lead compounds with iterative testing in biological models and detailed pharmacokinetic and toxicological analyses form the basis for drug development and subsequent testing in humans.
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclo- philin-type peptidyl-prolyl cis-trans isomerase.
  • disorders include a cancer, such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, cholecystitis, contact dermatitis, Crohn's disease, a cancer,
  • allergens typically elicit a specific IgE response and, although in most cases the allergens themselves have little or no intrinsic toxicity, they induce pathology when the IgE response in turn elicits an IgE-dependent or T cell-dependent hypersensitivity reaction.
  • Hypersensitivity reactions can be local or systemic and typically occur within minutes of allergen exposure in individuals who have previously been sensitized to an allergen.
  • the hypersensitivity reaction of allergy develops when the allergen is recognized by IgE antibodies bound to specific receptors on the surface of effector cells, such as mast cells, basophils, or eosinophils, which causes the activation of the effector cells and the release of mediators that produce the acute signs and symptoms of the reactions.
  • Allergic diseases include asthma, allergic rhinitis (hay fever), atopic dermatitis, and anaphylaxis.
  • Asthma is though to arise as a result of interactions between multiple genetic and environmental factors and is characterized by three major features: 1) intermittent and reversible airway obstruction caused by bronchoconsfriction, increased mucus production, and thickening of the walls of the airways that leads to a narrowing of the airways, 2) airway hyperresponsiveness caused by a decreased control of airway caliber, and 3) airway inflammation.
  • Certain cells are critical to the inflammatory reaction of asthma and they include T cells and antigen presenting cells, B cells that produce IgE, and mast cells, basophils, eosinophils, and other cells that bind IgE.
  • effector cells accumulate at the site of allergic reaction in the airways and release toxic products that contribute to the acute pathology and eventually to the tissue destruction related to the disorder.
  • Other resident cells such as smooth muscle cells, lung epithelial cells, mucus-producing cells, and nerve cells may also be abnormal in individuals with asthma and may contribute to the pathology. While the airway obstruction of asthma, presenting clinically as an intermittent wheeze and shortness of breath, is generally the most pressing symptom of the disease requiring immediate treatment, the inflammation and tissue destruction associated with the disease can lead to irreversible changes that eventually make asthma a chronic disabling disorder requiring long-term management.
  • Glycophorin A Cho and Sharom, Cell. Immunol. 145, 223-39, 1992
  • cyclosporin Alexander et ah, Lancet 339, 324-28, 1992
  • a nonapeptide fragment of IL-2 Zav'yalov et ah, Immunol. Lett. 31, 285-88, 1992
  • all inhibit interleukin-2 dependent T lymphocyte proliferation however, they are known to have many other effects.
  • cyclosporin is used as a immuno- suppressant after organ transplantation.
  • Cyclophilin-type peptidyl-prolyl cis-trans isomerase is a widely distributed, highly expressed molecule (Fig. 21), indicating that its function is fundamental to common activities of a wide variety of cell types. As a member of the cyclophilin family, this function is the folding, transport, and assembly of proteins.
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase Although the expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase is high in most tissues, its expression in the testis, skeletal muscle, uterus, and lung is somewhat higher than in other tissue. This indicates that the these tissues produce a comparatively large amount of specific protein types that require cyclophilin-type peptidyl-prolyl cis-trans isomerase activity to allow them to fold or combine with other molecules before assuming an active conformation.
  • a vector capable of expressing cyclophilin-type peptidyl-prolyl cis-frans isomerase or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those described above.
  • a pharmaceutical composition comprising a substantially purified cyclophilin-type peptidyl-prolyl cis-frans isomerase in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those provided above.
  • an activator which modulates the activity of cyclophilin-type peptidyl-prolyl cis-frans isomerase may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those listed above.
  • an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase.
  • disorders may include, but are not limited to, those discussed above.
  • an antibody which specifically binds cyclophilin-type peptidyl-prolyl cis-trans isomerase may be used directly as an inhibitor or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express cyclophilin-type peptidyl-prolyl cis-frans isomerase.
  • a vector expressing the complement of the polynucleotide encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase may be administered to a subject to freat or prevent a disorder associated with increased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those described above.
  • any of the proteins, inhibitors, antibodies, activators, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles.
  • the combination of therapeutic agents may act synergistically to effect the freatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.
  • An inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase may be produced using methods which are generally known in the art.
  • purified cyclophilin-type peptidyl-prolyl cis-frans isomerase may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind cyclophilin-type peptidyl-prolyl cis-trans isomerase.
  • Antibodies to cyclophilin-type peptidyl-prolyl cis-frans isomerase may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are especially preferred for therapeutic use.
  • This invention further pertains to the use of novel agents identified by the screening assays described above. Accordingly, it is within the scope of this invention to use a test compound identified as described herein in an appropriate animal model.
  • an agent identified as described herein e.g., a modulating agent, an antisense nucleic acid molecule, a specific antibody, ribozyme, or a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide binding molecule
  • an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent.
  • this invention pertains to uses of novel agents identified by the above- described screening assays for freatments as described herein.
  • a reagent which affects cyclophilin-type peptidyl-prolyl cis-trans isomerase activity can be administered to a human cell, either in vitro or in vivo, to reduce cyclophilin- type peptidyl-prolyl cis-trans isomerase activity.
  • the reagent preferably binds to an expression product of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase gene. If the expression product is a protein, the reagent is preferably an antibody.
  • an antibody can be added to a preparation of stem cells which have been removed from the body. The cells can then be replaced in the same or another human body, with or without clonal propagation, as is known in the art.
  • the reagent is delivered using a liposome.
  • the liposome is stable in the animal into which it has been administered for at least about 30 minutes, more preferably for at least about 1 hour, and even more preferably for at least about 24 hours.
  • a liposome comprises a lipid composition that is capable of targeting a reagent, particularly a polynucleotide, to a particular site in an animal, such as a human.
  • the lipid composition of the liposome is capable of targeting to a specific organ of an animal, such as the lung, liver, spleen, heart brain, lymph nodes, and skin.
  • a liposome useful in the present invention comprises a lipid composition that is capable of fusing with the plasma membrane of the targeted cell to deliver its contents to the cell.
  • the transfection efficiency of a liposome is about 0.5 ⁇ g of DNA per 16 nmole of liposome delivered to about 10 6 cells, more preferably about 1.0 ⁇ g of DNA per 16 nmole of liposome delivered to about 10 ⁇ cells, and even more preferably about 2.0 ⁇ g of DNA per 16 nmol of liposome delivered to about 10 6 cells.
  • a liposome is between about 100 and 500 nm, more preferably between about 150 and 450 nm, and even more preferably between about 200 and 400 nm in diameter.
  • Suitable liposomes for use in the present invention include those liposomes standardly used in, for example, gene delivery methods known to those of skill in the art. More preferred liposomes include liposomes having a polycationic lipid composition and/or liposomes having a cholesterol backbone conjugated to polyethylene glycol.
  • a liposome comprises a compound capable of targeting the liposome to a particular cell type, such as a cell-specific ligand exposed on the outer surface of the liposome. Complexing a liposome with a reagent such as an antisense oligonucleotide or ribozyme can be achieved using methods which are standard in the art (see, for example, U.S. Patent 5,705,151).
  • polynucleotide is combined with about 8 nmol of liposomes, more preferably from about 0.5 ⁇ g to about 5 ⁇ g of polynucleotides are combined with about 8 nmol liposomes, and even more preferably about 1.0 ⁇ g of polynucleotides is combined with about 8 nmol liposomes.
  • antibodies can be delivered to specific tissues in vivo using receptor-mediated targeted delivery.
  • Receptor-mediated DNA delivery techniques are taught in, for example, Findeis et al. Trends in Biotechnol 11, 202-05 (1993); Chiou et ah, GENE THERAPEUTICS: METHODS AND APPLICATIONS , OF DIRECT GENE TRANSFER (J.A. Wolff, ed.) (1994); Wu & Wu, J. Biol. Chem. 263, 621-24 (1988); Wu et ah, J. Biol. Chem. 269, 542-46 (1994); Zenke et ah, Proc. Natl. Acad. Sci.
  • a therapeutically effective dose refers to that amount of active ingredient which increases or decreases cyclophilin-type peptidyl-prolyl cis- trans isomerase activity relative to the cyclophilin-type peptidyl-prolyl cis-trans isomerase activity which occurs in the absence of the therapeutically effective dose.
  • the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models, usually mice, rabbits, dogs, or pigs.
  • the animal model also can be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • Therapeutic efficacy and toxicity e.g., ED 50 (the dose therapeutically effective in 50% of the population) and LD 50 (the dose lethal to 50% of the population), can be determined by standard pharmaceutical procedures in cell cultures or experimental animals.
  • the dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD 50 /ED 50 .
  • compositions which exhibit large therapeutic indices are preferred.
  • the data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use.
  • the dosage contained in such compositions is preferably within a range of circulating concenfrations that include the ED 50 with little or no toxicity.
  • the dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
  • Dosage and administration are adjusted to provide sufficient levels of the active ingredient or to maintain the desired effect.
  • Factors which can be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy.
  • Long-acting pharmaceutical compositions can be administered every 3 to 4 days, every week, or once every two weeks depending on the half-life and clearance rate of the particular formulation.
  • Normal dosage amounts can vary from 0J to 100,000 micrograms, up to a total dose of about 1 g, depending upon the route of administration.
  • Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.
  • polynucleotides encoding the antibody can be constructed and introduced into a cell either ex vivo or in vivo using well- established techniques including, but not limited to, fransferrin-polycation-mediated DNA transfer, fransfection with naked or encapsulated nucleic acids, liposome- mediated cellular fusion, intracellular transportation of DNA-coated latex beads, protoplast fusion, viral infection, elecfroporation, "gene gun,” and DEAE- or calcium phosphate-mediated fransfection.
  • Effective in vivo dosages of an antibody are in the range of about 5 ⁇ g to about 50 ⁇ g/kg, about 50 ⁇ g to about 5 mg kg, about 100 ⁇ g to about 500 ⁇ g/kg of patient body weight, and about 200 to about 250 ⁇ g/kg of patient body weight.
  • effective in vivo dosages are in the range of about 100 ng to about 200 ng, 500 ng to about 50 mg, about 1 ⁇ g to about 2 mg, about 5 ⁇ g to about 500 ⁇ g, and about 20 ⁇ g to about 100 ⁇ g of DNA.
  • the reagent is preferably an antisense oligonucleotide or a ribozyme.
  • Polynucleotides which express antisense oligo- nucleotides or ribozymes can be introduced into cells by a variety of methods, as described above.
  • a reagent reduces expression of a cyclophilin-type peptidyl-prolyl cis-frans isomerase gene or the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% relative to the absence of the reagent.
  • the effectiveness of the mechanism chosen to decrease the level of expression of a cyclophilin-type peptidyl- prolyl cis-frans isomerase gene or the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be assessed using methods well known in the art, such as hybridization of nucleotide probes to cyclophilin-type peptidyl-prolyl cis- trans isomerase-specific mRNA, quantitative RT-PCR, immunologic detection of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, or measurement of cyclophilin-type peptidyl-prolyl cis-trans isomerase activity.
  • any of the pharmaceutical compositions of the invention can be administered in combination with other appropriate therapeutic agents.
  • Selection of the appropriate agents for use in combination therapy can be made by one of ordinary skill in the art, according to conventional pharmaceutical principles.
  • the combination of therapeutic agents can act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.
  • any of the therapeutic methods described above can be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.
  • Human cyclophilin-type peptidyl-prolyl cis-frans isomerase also can be used in diagnostic assays for detecting diseases and abnormalities or susceptibility to diseases and abnormalities related to the presence of mutations in the nucleic acid sequences which encode the enzyme. For example, differences can be determined between the cDNA or genomic sequence encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase in individuals afflicted with a disease and in normal individuals. If a mutation is observed in some or all of the afflicted individuals but not in normal individuals, then the mutation is likely to be the causative agent of the disease.
  • Sequence differences between a reference gene and a gene having mutations can be revealed by the direct DNA sequencing method.
  • cloned DNA segments can be employed as probes to detect specific DNA segments.
  • the sensitivity of this method is greatly enhanced when combined with PCR.
  • a sequencing primer can be used with a double-stranded PCR product or a single-stranded template molecule generated by a modified PCR.
  • the sequence determination is performed by conventional procedures using radiolabeled nucleotides or by automatic sequencing procedures using fluorescent tags.
  • DNA sequence differences can be carried out by detection of alteration in electrophoretic mobility of DNA fragments in gels with or without denaturing agents. Small sequence deletions and insertions can be visualized, for example, by high resolution gel electrophoresis. DNA fragments of different sequences can be distinguished on denaturing formamide gradient gels in which the mobilities of different DNA fragments are retarded in the gel at different positions according to their specific melting or partial melting temperatures (see, e.g., Myers et ah, Science 230, 1242, 1985). Sequence changes at specific locations can also be revealed by nuclease protection assays, such as RNase and S 1 protection or the chemical cleavage method (e.g., Cotton et ah, Proc.
  • the detection of a specific DNA sequence can be performed by methods such as hybridization, RNase protection, chemical cleavage, direct DNA sequencing or the use of restriction enzymes and Southern blotting of genomic DNA.
  • direct methods such as gel-electrophoresis and DNA sequencing, mutations can also be detected by in situ analysis.
  • Altered levels of a cyclophilin-type peptidyl-prolyl cis-trans isomerase also can be detected in various tissues.
  • Assays used to detect levels of the receptor polypeptides in a body sample, such as blood or a tissue biopsy, derived from a host are well known to those of skill in the art and include radioimmunoassays, competitive binding assays, Western blot analysis, and ELISA assays. ,
  • the polynucleotide of SEQ ID NO: 1 is inserted into the expression vector pCEV4 and the expression vector pCEV4-cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide obtained is transfected into human embryonic kidney 293 cells. From these cells extracts are obtained and peptidyl prolyl cis/trans isomerase activity is assayed by as described by Rahfeld, J. U., et al. (1994; FEBS Lett. 352: 180-184). The assay is performed at 10 °C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and the cell extracts at a variety of concentrations.
  • the substrate Suc-Ala-Xaa-Pro-Phe-4-NA
  • the substrate is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation.
  • An aliquot (2 ⁇ l) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above.
  • the trans to cis conversion is measured by the hydrolysis of the cis conformer by chymotrypsin, producing 4-nitroanilide which is detected specfrophotometrically by absorbance at 390 nm.
  • 4-Nitroanilide appears in a time-dependent manner and is proportional to the amount of cyclophilin-type peptidyl-prolyl cis-trans isomerase in the assay. It is shown that the polypeptide of SEQ ID NO: 2 has a cyclophilin-type peptidyl-prolyl cis-frans isomerase activity.
  • the Pichia pastoris expression vector pPICZB (Invitrogen, San Diego, CA) is used to produce large quantities of recombinant human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides in yeast.
  • the cyclophilin-type peptidyl-prolyl cis- trans isomerase-encoding DNA sequence is derived from SEQ ID NO: 15. Before insertion into vector pPICZB, the DNA sequence is modified by well known methods in such a way that it contains at its 5 '-end an initiation codon and at its - OS ⁇
  • the yeast is cultivated under usual conditions in 5 liter shake flasks and the recombinantly produced protein isolated from the culture by affinity chromatography
  • Ni-NTA-Resin Ni-NTA-Resin
  • the bound polypeptide is eluted with buffer, pH 3.5, and duralized. Separation of the polypeptide from the His6 reporter tag is accomplished by site-specific proteolysis using enterokinase (Invifrogen, San Diego, CA) according to manufacturer's instructions. Purified human cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide is obtained.
  • Purified cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides comprising a glutathione-S-transferase protein and absorbed onto glutathione-derivatized wells of 96-well microtiter plates are contacted with test compounds from a small molecule library at pH 7.0 in a physiological buffer solution.
  • Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides comprise the amino acid sequence shown in SEQ ID NO: 16.
  • the test compounds comprise a fluorescent tag.
  • the samples are incubated for 5 minutes to one hour. Control samples are incubated in the absence of a test compound.
  • the buffer solution containing the test compounds is washed from the wells.
  • Binding of a test compound to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is detected by fluorescence measurements of the contents of the wells.
  • a test compound which increases the fluorescence in a well by at least 15% relative to fluorescence of a well in which a test compound is not incubated is identified as a compound which binds to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
  • test compound is administered to a culture of human cells transfected with a cyclophilin-type peptidyl-prolyl cis-trans isomerase expression construct and incubated at 37 °C for 10 to 45 minutes.
  • a culture of the same type of cells which have not been transfected is incubated for the same time without the test compound to provide a negative control.
  • RNA is isolated from the two cultures as described in Chirgwin et ah, Biochem. 18, 5294-99, 1979).
  • Northern blots are prepared using 20 to 30 ⁇ g total RNA and hybridized with a 32 P-labeled cyclophilin-type peptidyl-prolyl cis-trans isomerase- specific probe at 65 ° C in Express-hyb (CLONTECH).
  • the probe comprises at least 11 contiguous nucleotides selected from the complement of SEQ ID NO: 15.
  • test compound which decreases the cyclophilin-type peptidyl-prolyl cis-trans isomerase- specific signal relative to the signal obtained in the absence of the test compound is identified as an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase gene expression.
  • test compound is administered to a culture of human cells fransfected with a cyclophilin-type peptidyl-prolyl cis-frans isomerase expression construct and incubated at 37 °C for 10 to 45 minutes.
  • a culture of the same type of cells which have not been transfected is incubated for the same time without the test compound to provide a negative control.
  • Peptidyl prolyl cis/trans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J. U., et al. (1994; FEBS Lett. 352: 180-184).
  • the assay is performed at 10 °C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and CPCI at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation.
  • test compound which decreases the activity of the cyclophilin-type peptidyl-prolyl cis-frans isomerase relative to the activity in the absence of the test compound is identified as an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase activity.
  • Cyclophilin-type peptidyl-prolyl cis-trans isomerase function is assessed by expressing the sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase at physiologically elevated levels in mammalian cell culture systems.
  • cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression.
  • Vectors of choice include pCMV SPORT (Life Technologies) and pCR3J (Invitrogen, Carlsbad Calif), both of which contain the cytomegalovirus promoter.
  • recombinant vector 5-10 ⁇ g of recombinant vector are fransiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or elecfroporation.
  • a marker protein e.g., Green Fluorescent Protein (GFP; Clontech), CD64, or a CD64-GFP fusion protein.
  • FCM Flow cytometry
  • cyclophilin-type peptidyl-prolyl cis-trans isomerase The influence of cyclophilin-type peptidyl-prolyl cis-trans isomerase on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase and either CD64 or CD64-GFP.
  • CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG).
  • Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success N.Y.).
  • mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding cyclophilin-type peptidyl- prolyl cis-trans isomerase and other genes of interest can be analyzed by Northern analysis or microarray techniques
  • Expression profiling is based on a quantitative polymerase chain reaction (PCR) analysis, also called kinetic analysis, first described in Higuchi et al., 1992 and Higuchi et al., 1993.
  • PCR polymerase chain reaction
  • the principle is that at any given cycle within the exponential phase of PCR, the amount of product is proportional to the initial number of template copies.
  • mRNA messenger RNA
  • cDNA DNA copy
  • quantitative RT-PCR quantitative reverse transcription-polymerase chain reaction
  • RNA from different human tissues was used as a template to synthsize first-strand cDNA using the SUPERSCRIPTTM First-Strand Synthesis System for RT-PCR (Life Technologies, Rockville , MD, USA).
  • First-strand cDNA synthesis was carried out according to the manufacturer's protocol using oligo (dT) to hybridize to the 3' poly A tails of mRNA and prime the synthesis reaction. 10 ng of the first-strand cDNA was then used as template in a polymerase chain reaction.
  • the polymerase chain reaction was performed in a LightCycler (Roche Molecular Biochemicals, Indianapolis, IN, USA), in the presence of the DNA-binding fluorescent dye SYBR Green I which binds to the minor groove of the DNA double helix, produced only when double-stranded DNA is successfully synthesized in the reaction (Morrison et al., 1998).
  • SYBR Green I the DNA-binding fluorescent dye which binds to the minor groove of the DNA double helix
  • Green I emits light that can be quantitatively measured by the LightCycler machine.
  • the polymerase chain reaction was carried out using oligonucleotide primers cyclophilin-type peptidyl-prolyl cis-trans isomerase_DNA-L2
  • G3PDH glyceraldehyde-3- ⁇ hosphatase
  • HPRT hypoxanthine guanine phophoribosyl transferase
  • beta-actin beta-actin
  • PBGD porphobilinogen deaminase
  • the level of housekeeping gene expression is considered to be relatively constant for all tissues (Adams et al., 1993, Adams et al., 1995, Liew et al., 1994) and therefore can be used as a gauge to approximate relative numbers of cells per .mu.g of total RNA used in the cDNA synthesis step. Except for the use of a slightly different set of housekeeping genes and the use of the LightCycler system to measure expression levels, the normalization procedure was similar to that described in the RNA Master Blot User Manual, Apendix C (1997, Clontech Laboratories, Palo Alto, CA, USA).
  • RNAs used for the cDNA synthesis along with their supplier and catalog numbers are shown in Table 1.
  • oligonucleotides comprising at least 11 contiguous nucleotides selected from the complement of SEQ ID NO:l or 15 is performed on a Pharmacia Gene Assembler series synthesizer using the phosphoroamidite procedure (Uhlmann et ah, Chem. Rev. 90, 534-83, 1990). Following assembly and deprotection, oligonucleotides are ethanol-precipitated twice, dried, and suspended in phosphate-buffered saline (PBS) at the desired concentration.
  • PBS phosphate-buffered saline
  • oligonucleotide Purity of these oligonucleotides is tested by capillary gel electrophoreses and ion exchange HPLC. Endotoxin levels in the oligonucleotide preparation are determined using the Limulus Amebocyte Assay (Bang, Biol Bull. (Woods Hole, Mass.) 105, 361 -362, 1953).
  • An aqueous composition containing the antisense oligonucleotides is administered to the patient by inhalation.
  • Severity of asthma is monitored over a period of days or weeks by noting changes in patients' asthmatic symptoms, measuring lung function, or measuring changes in markers of lung inflammation such as numbers of inflammatory cells or concentrations of inflammatory mediators in fluid sampled from patients' lungs by bronchoalveolar lavage. Asthma severity is reduced due to decreased cyclophilin- type peptidyl-prolyl cis-trans isomerase activity.
  • Tests for activity of T cells are used to evaluate agents that modulate the expression or activity of costimulatory molecules-cytokines, cytokine receptors, signalling molecules, or other molecules involved in T cell activation
  • BALB/c mice are injected with a single intravenous injection of 10 ⁇ g of 145- 2C11 (purified hamster anti-mouse CD3 monoclonal antibodies, PHARMINGEN). Compound is administered intraperitoneally 60 min prior to the anti-CD3 mAb injection. Blood is collected 90 min after the antibody injection. Serum is obtained by centrifugation at 3000 r.p.m. for 10 min. Serum levels of cytokines, such as IL-2 and IL-4, or other secreted molecules are determined by an ELISA. Proteins which regulate the CD3 downstream signaling can be evaluated in this model.
  • Tests for activity of B cells are used to evaluate agents that modulate the expression or activity of the B cell receptor, signaling molecules, or other molecules involved in B cell activation/immunoglobulin class switching
  • BALB/c mice are injected intravenously with 0.8 mg of purified goat anti- mouse IgD antibody or PBS (defined as day 0). Compound is administered intraperitoneally from day 0 to day 6. On day 7 blood is collected and serum is obtained by centrifugation at 3000 r.p.m. for 10 min. Serum levels of total IgE are determined by YAMASA's ELISA kit and other Ig subtypes are measured by an Ig ELISA KIT (Rougier Bio-tech's, Montreal, Canada). Proteins that regulate IgD downsfream signaling and Ig class switching can be evaluated. 3. Tests for activity of monocytes/macrophages are used to evaluate agents that modulate the expression or activity of signalling molecules, transcription factors.
  • Compound is administered to BALB/c mice by infraperitoneal injection and one hour later the mice given LPS (200 ⁇ g/mouse) by infraperitoneal injection. Blood is collected 90 minutes after the LPS injection and plasma is obtained. TNF- ⁇ concentration in the sample is determined using an ELISA kit. Proteins that regulate downstream effects of LPS stimulation, such as NF- ⁇ B activation, can be evaluated.
  • Tests for activity of eosinophils are used to evaluate agents that modulate the expression or activity of the eotaxin receptor, signaling molecules, cyto- skeletal molecules, or adhesion molecules.
  • mice are injected infradermally with a 2.5 ml of air on days -6 and —
  • Differential cell counts in the exudate are performed by staining with May- Grunwald Gimsa solution. Proteins that regulate signaling by the eotaxin receptor or regulate eosinophil trafficking can be evaluated.
  • PC A Passive cutaneous anaphylaxis test in rats 6 Weeks old male Wistar rats are sensitized intradermally (i.d.) on their shaved backs with 50 ⁇ l of 0J ⁇ g/ml mouse anti-DNP IgE monoclonal antibody (SPE-7) under a light anesthesia. After 24 hours, the rats are challenged intravenously with 1 ml of saline containing 0.6 mg DNP-BSA (30) (LSL CO., LTD) and 0.005 g of Evans blue. Compounds are injected intraperitoneally (i.p.) 0.5 hr prior to antigen injection.
  • Rats without the sensitization, challenge, and compound treatment are used as a control and rats with sensitization, challenge and vehicle treatment are used to determine the value without inhibition. Thirty minutes after the challenge, the rats are sacrificed, and the skin of the back is removed. Evans blue dye in the skin is extracted in formamide overnight at 63°C. Absorbance at 620 nm is then measured to obtain the optical density of the leaked dye.
  • % inhibition ⁇ (mean vehicle value - sample value)/(mean vehicle value mean control value) ⁇ x 100
  • Proteins that regulate mast cell degranulation, vascular permeability, or receptor antagonists against histamine receptors, serotonin receptors, or cysteinyl leukofriene receptors can be evaluated.
  • Proteins that regulate mast cell degranulation, vascular permeability or receptor antagonists against histamine receptors, serotonin receptors, or cysteinyl leukofriene receptors can be evaluated. Proteins that regulate the contraction of smooth muscle can be also evaluated.
  • T cells A purified population of T cells is prepared by ficoll density cenfrifugation followed by separation on a nylon wool column, rosetting with sheep red blood cells, or using magnetic beads coated with antibodies.
  • the T cells are activated with mitogen for 36 to 42 hours and labeled with 3 H-thymidine during the last 16 hours of the activation.
  • Airway smooth muscle cells or bronchial microvascular endothelial cells are obtained from lung transplant tissue, from bronchus resections from cancer patients, from cadavers, or as cell lines from commercial sources. If fresh tissue is used as the source of cells, the smooth muscle cells and endothelial cells can be isolated from tissue by dissection followed by digestion for 30-60 minutes in a solution containing
  • adherent cells are lysed by adding 300 ⁇ l 1% Triton-X 100 in PBS to each well and quantitating the radioactivity in a scintillation counter. The percent binding is calculated as counts recovered from adherent cells/total input counts x 100%

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Abstract

Reagents which regulate human cyclophilin-type peptidyl-prolyl cis-trans isomerase and reagents which bind to human cyclophilin-type peptidyl-prolyl cis-trans isomerase gene products can play a role in preventing, ameliorating, or correcting dysfunctions or diseases including, but not limited to, cancer, autoimmune/inflammatory disorders, and reproductive disorders.

Description

REGULATION OF HUMAN CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
This application claims the benefit of and incorporates by reference co-pending provisional applications Serial No. 60/239,104 filed October 11, 2000 and Serial No. 60/313,820 filed August 22, 2001.
TECHNICAL FIELD OF THE INVENTION
This invention relates to nucleic acid and amino acid sequences of a cyclophilin-type peptidyl-prolyl cis-trans isomerase and to the use of these sequences in the diagnosis, treatment, and prevention of cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders.
BACKGROUND OF THE INVENTION
Numerous essential biochemical reactions involve the isomerization of a substrate. Enzymes which catalyze such reactions are known as isomerases. U.S. Patent No. 6,030,825. A number of isomerases have been described catalyzing steps in a wide variety of biochemical pathways including protein folding, phototransduction, and various anabolic and catabolic pathways in organisms ranging from bacteria to humans.
One class of isomerases is known as peptidyl-prolyl cis-trans isomerases (PPIases).
PPIases catalyze the cis to trans isomerization of .certain proline imidic bonds in proteins. Two families of PPIases are the FK506 binding proteins (FKBP), and cyclophilins (CyPs). FKBPs bind the potent immunosuppressants. FK506 and rapamycin, thereby inhibiting signaling pathways in T-cells. Specifically, the PPIase activity of FKBPs is inhibited by binding of FK506 or rapamycin. There are five members of the FKBP family which are named according to their calculated molecular masses (FKBP12, FKBP13, FKBP25, FKBP52, and FKBP65) and localized to different regions of the cell where they associate with different protein complexes (Coss, M. et al. (1995) J. Biol. Chem. 270:29336-29341; Schreiber, S. L. (1991) Science 251:283-287).
CyP was originally characterized as the receptor for the immunosuppressant drug cyclosporin, an inhibitor of T-cell activation. Thus, the peptidyl-prolyl isomerase activity of CyP may be part of the signaling pathway that leads to T-cell activation. Subsequent work demonstrated that CyP's isomerase activity is essential for correct protein folding and/or protein trafficking and may also be involved in assembly/disassembly of protein complexes and regulation of protein activity. For example, in Drosophila, the CyP NinaA is required for correct localization of rhodopsins, while a mammalian CyP (Cyp40) is part of the Hsp90/Hsc70 complex that binds steroid receptors. The mammalian CypA has been shown to bind the gag protein from human immunodeficiency virus 1 (HIN-1), an interaction that can be inhibited by cyclosporin. Because cyclosporin has potent anti-HIN-1 activity, CypA may play an essential function in HIN-1 replication. Finally, Cyp40 has been shown to bind and inactivate the transcription factor c-Myb, an effect that is reversed by cyclosporin. This effect implicates CyPs in the regulation of transcription, transformation, and differentiation (Bergsma, D. J. et al (1991) J. Biol. Chem.
266:23204-23214; Hunter, T. (1998) Cell 92: 141-143; and Leverson, J. D. andΝess, S. A. (1998) Mol. Cell. 1:203-211).
The discovery of a new cyclophilin-type peptidyl-prolyl cis/trans isomerase and the polynucleotides encoding it satisfies a need in the art by providing new compositions which are useful in the diagnosis, prevention, and treatment of cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders. SUMMARY OF THE INVENTION
It is an object of the invention to provide reagents and methods of regulating a human cyclophilin-type peptidyl-prolyl cis-trans isomerase. This and other objects of the invention are provided by one or more of the embodiments described below.
One embodiment of the invention is a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
Yet another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation. A test compound is contacted with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
Binding between the test compound and the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is detected. A test compound which binds to the cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide is thereby identified as a potential agent for decreasing extracellular matrix degradation. The agent can work by decreasing the activity of the cyclophilin-type peptidyl-prolyl cis-trans isomerase.
Another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation. A test compound is contacted with a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1 ; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
Binding of the test compound to the polynucleotide is detected. A test compound which binds to the polynucleotide is identified as a potential agent for decreasing extracellular matrix degradation. The agent can work by decreasing the amount of the cyclophilin-type peptidyl-prolyl cis-trans isomerase through interacting with the cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA.
Another embodiment of the invention is a method of screening for agents which regulate extracellular matrix degradation. A test compound is contacted with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16.
A cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide is detected. A test compound which increases cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide relative to cyclophilin-type peptidyl-prolyl cis- trans isomerase activity in the absence of the test compound is thereby identified as a potential agent for increasing extracellular matrix degradation. A test compound which decreases cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide relative to cyclophilin-type peptidyl-prolyl cis-trans isomerase activity in the absence of the test compound is thereby identified as a potential agent for decreasing extracellular matrix degradation.
Even another embodiment of the invention is a method of screening for agents which decrease extracellular matrix degradation. A test compound is contacted with a cyclop lin-type peptidyl-prolyl cis-trans isomerase product of a polynucleotide which comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
Binding of the test compound to the cyclophilin-type peptidyl-prolyl cis-trans isomerase product is detected. A test compound which binds to the cyclophilin-type peptidyl-prolyl cis-trans isomerase product is thereby identified as a potential agent for decreasing extracellular matrix degradation.
Still another embodiment of the invention is a method of reducing extracellular " matrix degradation. A cell is contacted with a reagent which specifically binds to a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or the product encoded by the polynucleotide, wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 1 ; the nucleotide sequence shown in SEQ ID NO: 1; nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO: 15; and the nucleotide sequence shown in SEQ ID NO: 15.
Cyclophilin-type peptidyl-prolyl cis-trans isomerase activity in the cell is thereby decreased.
The invention thus provides a human cyclophilin-type peptidyl-prolyl cis-trans isomerase which can be used to identify test compounds which may act, for example, as activators or inhibitors at the enzyme's active site. Human cyclophilin-type peptidyl-prolyl cis-trans isomerase and fragments thereof also are useful in raising specific antibodies which can block the enzyme and effectively reduce its activity.
BRIEF DESCRIPTION OF THE DRAWINGS
Fig. 1 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:l). Fig. 2 shows the amino acid sequence deduced from the DNA-sequence ofFigJ (SEQ ID NO:2). Fig. 3 shows the amino acid sequence of the protein identified by trembl Accession
No. Z36949 (SEQ ID NO:3). Fig. 4 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:4). Fig. 5 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 5). Fig. 6 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:6). Fig. 7 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:7). Fig. 8 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO:8). Fig. 9 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl eis- trans isomerase polypeptide (SEQ ID NO:9).
Fig. 10 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 10). Fig. 11 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 11). Fig. 12 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 12). Fig. 13 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 13). Fig. 14 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO : 14).
Fig. 15 shows the DNA-sequence encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide (SEQ ID NO: 15). Fig. 16 shows the amino acid sequence deduced from the DNA-sequence of Fig. 15 (SEQ ID NO:16). Fig. 17 shows the BLASTP alignment of human cyclophilin-type peptidyl-prolyl cis-trans isomerase (SEQ ID NO:2) with the protein identified with swiss|P52012|CYP4_CAEEL (SEQ ID NO:3). Fig. 18 shows the HMMPFAM alignment of SEQ ID NO:2 against pfam|hmm|pro_isomerase. Fig. 19 shows the BLASTP - alignment of SEQ ID NO:2 against pdb|lA33|lA33. Fig. 20 shows the Block results.
Fig. 21 shows the expression profiling of cyclophilin- type peptidyl-prolyl cis-trans isomerase rnRNA.
DETAILED DESCRIPTION OF THE INVENTION
The invention relates to an isolated polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide and being selected from the group consisting of: a) a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide comprising an amino acid sequence selected from the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16; b) a polynucleotide comprising the sequence of SEQ ID NO: 1 or 15; c) a polynucleotide which hybridizes under stringent conditions to a polynucleotide specified in (a) and (b); d) a polynucleotide the sequence of which deviates from the polynucleotide sequences specified in (a) to (c) due to the degeneration of the genetic code; and e) a polynucleotide which represents a fragment, derivative or allelic variation of a polynucleotide sequence specified in (a) to (d).
Furthermore, it has been discovered by the present applicant that a novel cyclophilin-type peptidyl-prolyl cis-trans isomerase, particularly a human cyclophilin-type peptidyl-prolyl cis-trans isomerase, is a discovery of the present invention. Human cyclophilin-type peptidyl-prolyl cis-trans isomerase comprises the amino acid sequence shown in SEQ ID NO:2 and 16. A coding sequence for human cyclophilin-type peptidyl-prolyl cis-trans isomerase is shown in SEQ ID NO:l and 15. Related ESTs (SEQ ID NOS:5-14) are expressed in human fetal, kidney, colon carcinoma, germinal center B cell, multiple sclerosis lesions, prostate gland, testis, fetal lung, kidney, placenta, spleen, and cervix..
Human cyclophilin-type peptidyl-prolyl cis-trans isomerase is 50% identical over 159 amino acids to the C. elegans protein identified with trembl Accession No. Z36949 (SEQ ID NO:3) and annotated as "PEPTIDYL-PROLYL CIS-TRANS
ISOMERASE 4 (EC 5.2J.8) (PPIASE) (ROTAMAS (CYCLOPHILIN-4)" (Fig. 17). Alignments of SEQ ID NO: 16 with known isomerase sequences are shown in Figs. 17-19.
Human cyclophihn-type peptidyl-prolyl cis-trans isomerase of the invention is expected to be useful for the same purposes as previously identified cyclophilin-type peptidyl-prolyl cis-trans isomerase enzymes. Human cyclophilin-type peptidyl- prolyl cis-trans isomerase is believed to be useful in therapeutic methods to treat disorders such as cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders. Human cyclophilin-type peptidyl-prolyl cis-trans isomerase also can be used to screen for human cyclophilin-type peptidyl-prolyl cis-trans isomerase activators and inhibitors.
Polypeptides Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides according to the invention comprise at least 6, 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, or 645 contiguous amino acids selected from the amino acid sequence shown in SEQ ID NO:2 or 16 or a biologically active variant thereof, as defined below. A cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide of the invention therefore can be a portion of a cyclophilin-type peptidyl-prolyl cis-trans isomerase protein, a full-length cyclophilin-type peptidyl-prolyl cis-trans isomerase protein, or a fusion protein comprising all or a portion of a cyclophilin-type peptidyl-prolyl cis- frans isomerase protein.
Biologically Active Variants
Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide variants which are biologically active, e.g., retain a cyclophilin-type peptidyl-prolyl cis-trans isomerase activity, also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides. Preferably, naturally or non-naturally occurring cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide variants have amino acid sequences which are at least about 51, 55, 60, 65, or 70, preferably about 75, 80, 85, 90, 96, 96, or 98% identical to the amino acid sequence shown in SEQ ID NO:2 or 16 or a fragment thereof. Percent identity between a putative cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide variant and an amino acid sequence of SEQ ID
NO:2 or 16 is determined using the Blast2 alignment program (Blosum62, Expect 10, standard genetic codes).
Variations in percent identity can be due, for example, to amino acid substitutions, insertions, or deletions. Amino acid substitutions are defined as one for one amino acid replacements. They are conservative in nature when the substituted amino acid has similar structural and/or chemical properties. Examples of conservative replacements are substitution of a leucine with an isoleucine or valine, an aspartate with a glutamate, or a threonine with a serine.
A ino acid insertions or deletions are changes to or within an amino acid sequence. They typically fall in the range of about 1 to 5 amino acids. Guidance in determining which amino acid residues can be substituted, inserted, or deleted without abolishing biological or immunological activity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be found using computer programs well known in the art, such as DNASTAR software. Whether an amino acid change results in a biologically active cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can readily be determined by assaying for peptidyl-prolyl cis-trans isomerase activity, as described for example, in the specific examples, below.
Fusion Proteins
Fusion proteins are useful for generating antibodies against cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide amino acid sequences and for use in various assay systems. For example, fusion proteins can be used to identify proteins which interact with portions of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. Protein affinity chromatography or library-based assays for protein- protein interactions, such as the yeast two-hybrid or phage display systems, can be used for this purpose. Such methods are well known in the art and also can be used as drug screens.
A cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide fusion protein comprises two polypeptide segments fused together by means of a peptide bond. The first polypeptide segment comprises at least 6, 10, 15, 20, 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575, 600, 625, or 645 contiguous amino acids of SEQ ID NO:2 or 16 or of a biologically active variant, such as those described above. The first polypeptide segment also can comprise full-length cyclophilin-type peptidyl-prolyl cis-frans isomerase protein.
The second polypeptide segment can be a full-length protein or a protein fragment. Proteins commonly used in fusion protein construction include β-galactosidase, β- glucuronidase, green fluorescent protein (GFP), autofluorescent proteins, including blue fluorescent protein (BFP), glutathione-S-fransferase (GST), luciferase, horseradish peroxidase (HRP), and chloramphenicol acetyltransferase (CAT). Additionally, epitope tags are used in fusion protein constructions, including histidine (His) tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV- G tags, and thioredoxin (Tix) tags. Other fusion constructions can include maltose binding protein (MBP), S-tag, Lex a DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSN) BP16 protein fusions. A fusion protein also can be engineered to contain a cleavage site located between the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide-encoding sequence and the heterologous protein sequence, so that the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be cleaved and purified away from the heterologous moiety.
A fusion protein can be synthesized chemically, as is known in the art. Preferably, a fusion protein is produced by covalently linking two polypeptide segments or by standard procedures in the art of molecular biology. Recombinant DΝA methods can be used to prepare fusion proteins, for example, by making a DΝA construct which comprises coding sequences selected from the complement of SEQ ID ΝOJ or 15 in proper reading frame with nucleotides encoding the second polypeptide segment and expressing the DΝA construct in a host cell, as is known in the art. Many kits for constructing fusion proteins are available from companies such as Promega Corporation (Madison, WI), Stratagene (La Jolla, CA), CLOΝTECH (Mountain View, CA), Santa Cruz Biotechnology (Santa Cruz, CA), MBL International Corporation (MIC; Watertown, MA), and Quantum Biotechnologies
(Montreal, Canada; 1-888-DΝA-KITS).
Identification of Species Homologs
Species homologs of human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be obtained using cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide polynucleotides (described below) to make suitable probes or primers for screening cDNA expression libraries from other species, such as mice, monkeys, or yeast, identifying cDNAs which encode homologs of cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, and expressing the cDNAs as is known in the art. Polynucleotides
A cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be single- or double-stranded and comprises a coding sequence or the complement of a coding sequence for a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. A coding sequence for human cyclophilin-type peptidyl-prolyl cis-trans isomerase is shown in SEQ ID NO:l and 15 and is found on chromosome 5. The coding sequence is contained within a longer sequence shown in SEQ ID NO:4.
Degenerate nucleotide sequences encoding human cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides, as well as homologous nucleotide sequences which are at least about 50, 55, 60, 65, 70, preferably about 75, 90, 96, or 98% identical to the nucleotide sequence shown in SEQ ID NOJ or 15 or its complement also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides. Percent sequence identity between the sequences of two polynucleotides is determined using computer programs such as ALIGN which employ the FASTA algorithm, using an afϊine gap search with a gap open penalty of -12 and a gap extension penalty of -2. Complementary DNA (cDNA) molecules, species homologs, and variants of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides which encode biologically active cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides.
Identification of Polynucleotide Variants and Homologs
Variants and homologs of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides described above also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides. Typically, homologous cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide sequences can be identified by hybridization of candidate polynucleotides to known cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides under stringent conditions, as is known in the art. For example, using the following wash conditions-2X SSC (0.3 M NaCl, 0.03 M sodium cifrate, pH 7.0), 0.1% SDS, room temperature twice, 30 minutes each; then 2X SSC, 0.1% SDS, 50 °C once, 30 minutes; then 2X SSC, room temperature twice, 10 minutes each— homologous sequences can be identified which contain at most about 25-30% basepair mismatches. More preferably, homologous nucleic acid strands contain 15-25% basepair mismatches, even more preferably 5-15% basepair mismatches.
Species homologs of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides disclosed herein also can be identified by making suitable probes or primers and screening cDNA expression libraries from other species, such as mice, monkeys, or yeast. Human variants of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides can be identified, for example, by screening human cDNA expression libraries. It is well known that the Tm of a double-stranded DNA decreases by 1-1.5 °C with every 1% decrease in homology (Bonner et al., J. Mol Biol. 81, 123 (1973). Variants of human cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides or cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides of other species can therefore be identified by hybridizing a putative homologous cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide with a polynucleotide having a nucleotide sequence of SEQ ID NO:l or 15 or the complement thereof to form a test hybrid. The melting temperature of the test hybrid is compared with the melting temperature of a hybrid comprising polynucleotides having perfectly complementary nucleotide sequences, and the number or percent of basepair mismatches within the test hybrid is calculated.
Nucleotide sequences which hybridize to cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides or their complements following stringent hybridization and/or wash conditions also are cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides. Stringent wash conditions are well known and understood in the art and are disclosed, for example, in Sambrook et al, MOLECULAR CLONING: A LABORATORY MANUAL, 2d ed., 1989, at pages 9.50-9.51. Typically, for stringent hybridization conditions a combination of temperature and salt concentration should be chosen that is approximately 12-20 °C below the calculated Tm of the hybrid under study. The Tra of a hybrid between a cyclophilin- type peptidyl-prolyl cis-trans isomerase polynucleotide having a nucleotide sequence shown in SEQ ID NO:l or 15 or the complement thereof and a polynucleotide sequence which is at least about 50, preferably about 75, 90, 96, or 98% identical to one of those nucleotide sequences can be calculated, for example, using the equation of Bolton and McCarthy, Proc. Natl Acad. Set U.S.A. 48, 1390 (1962): Tm = 81.5 °C - 16.6(log10[Na+]) + 0.41 (%G + C) - 0.63(%formamide) - 600/1), where /
= the length of the hybrid in basepairs.
Stringent wash conditions include, for example, 4X SSC at 65 °C, or 50% form- amide, 4X SSC at 42 °C, or 0.5X SSC, 0.1% SDS at 65 °C. Highly stringent wash conditions include, for example, 0.2X SSC at 65 °C.
Preparation of Polynucleotides
A cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be isolated free of other cellular components such as membrane components, proteins, and lipids. Polynucleotides can be made by a cell and isolated using standard nucleic acid purification techniques, or synthesized using an amplification technique, such as the polymerase chain reaction (PCR), or by using an automatic synthesizer. Methods for isolating polynucleotides are routine and are known in the art. Any such technique for obtaining a polynucleotide can be used to obtain isolated cyclophilin- type peptidyl-prolyl cis-trans isomerase polynucleotides. For example, restriction enzymes and probes can be used to isolate polynucleotide fragments which comprises cyclophilin-type peptidyl-prolyl cis-trans isomerase nucleotide sequences. Isolated polynucleotides are in preparations which are free or at least 70, 80, or 90% free of other molecules. Human cyclophilin-type peptidyl-prolyl cis-frans isomerase cDNA molecules can be made with standard molecular biology techniques, using cyclophilin-type peptidyl- prolyl cis-frans isomerase mRNA as a template. Human cyclophilin-type peptidyl- prolyl cis-frans isomerase cDNA molecules can thereafter be replicated using molecular biology techniques known in the art and disclosed in manuals such as Sambrook et al. (1989). An amplification technique, such as PCR, can be used to obtain additional copies of polynucleotides of the invention, using either human genomic DNA or cDNA as a template.
Alternatively, synthetic chemistry techniques can be used to synthesizes cyclophilin- type peptidyl-prolyl cis-frans isomerase polynucleotides. The degeneracy of the genetic code allows alternate nucleotide sequences to be synthesized which will encode a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide having, for example, an amino acid sequence shown in SEQ ID NO:2 or 16 or a biologically active variant thereof.
Extending Polynucleotides
The partial sequence disclosed herein can be used to identify the corresponding full length gene from which it was derived. The partial sequence can be nick-translated or end-labeled with 32P using polynucleotide kinase using labeling methods known to those with skill in the art (BASIC METHODS IN MOLECULAR BIOLOGY, Davis et al., eds., Elsevier Press, N.Y., 1986). A lambda library prepared from human tissue can be directly screened with the labeled sequences of interest or the library can be converted en masse to pBluescript (Sfratagene Cloning Systems, La Jolla, Calif.
92037) to facilitate bacterial colony screening (see Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, Cold Spring Harbor Laboratory Press (1989, pg. 1.20). Both methods are well known in the art. Briefly, filters with bacterial colonies containing the library in pBluescript or bacterial lawns containing lambda plaques are denatured, and the DNA is fixed to the filters. The filters are hybridized with the labeled probe using hybridization conditions described by Davis et al., 1986. The partial sequences, cloned into lambda or pBluescript, can be used as positive controls to assess background binding and to adjust the hybridization and washing stringencies necessary for accurate clone identification. The resulting autoradio- grams are compared to duplicate plates of colonies or plaques; each exposed spot corresponds to a positive colony or plaque. The colonies or plaques are selected, expanded and the DNA is isolated from the colonies for further analysis and sequencing.
Positive cDNA clones are analyzed to determine the amount of additional sequence they contain using PCR with one primer from the partial sequence and the other primer from the vector. Clones with a larger vector-insert PCR product than the original partial sequence are analyzed by restriction digestion and DNA sequencing to determine whether they contain an insert of the same size or similar as the mRNA size determined from Northern blot Analysis.
Once one or more overlapping cDNA clones are identified, the complete sequence of the clones can be determined, for example after exonuclease III digestion (McCombie et al., Methods 3, 33-40, 1991). A series of deletion clones are generated, each of which is sequenced. The resulting overlapping sequences are assembled into a single contiguous sequence of high redundancy (usually three to five overlapping sequences at each nucleotide position), resulting in a highly accurate final sequence.
Various PCR-based methods can be used to extend the nucleic acid sequences disclosed herein to detect upstream sequences such as promoters and regulatory elements. For example, restriction-site PCR uses universal primers to retrieve unknown sequence adjacent to a known locus (Sarkar, PCR Methods Applic. 2, 318-322, 1993). Genomic DNA is first amplified in the presence of a primer to a linker sequence and a primer specific to the known region. The amplified sequences are then subjected to a second round of PCR with the same linker primer and another specific primer internal to the first one. Products of each round of PCR are transcribed with an appropriate RNA polymerase and sequenced using reverse transcriptase.
Inverse PCR also can be used to amplify or extend sequences using divergent primers based on a known region (Triglia et al., Nucleic Acids Res. 16, 8186, 1988). Primers can be designed using commercially available software, such as OLIGO 4.06 Primer Analysis software (National Biosciences Inc., Plymouth, Minn.), to be 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68-72 °C. The method uses several restriction enzymes to generate a suitable fragment in the known region of a gene. The fragment is then circularized by intramolecular ligation and used as a PCR template.
Another method which can be used is capture PCR, which involves PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA (Lagerstrom et al., PCR Methods Applic. 1, 111-119,
1991). In this method, multiple restriction enzyme digestions and ligations also can be used to place an engineered double-stranded sequence into an unknown fragment of the DNA molecule before performing PCR.
Another method which can be used to retrieve unknown sequences is that of Parker et al, Nucleic Acids Res. 19, 3055-3060, 1991). Additionally, PCR, nested primers, and PROMOTERFINDER libraries (CLONTECH, Palo Alto, Calif.) can be used to walk genomic DNA (CLONTECH, Palo Alto, Calif.). This process avoids the need to screen libraries and is useful in finding infron/exon junctions. When screening for full-length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. Randomly-primed libraries are preferable, in that they will contain more sequences which contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries can be useful for extension of sequence into 5' non-transcribed regulatory regions.
Commercially available capillary electrophoresis systems can be used to analyze the size or confirm the nucleotide sequence of PCR or sequencing products. For example, capillary sequencing can employ flowable polymers for electrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and detection of the emitted wavelengths by a charge coupled device camera. Output/light intensity can be converted to electrical signal using appropriate software (e.g. GENOTYPER and Sequence NAVIGATOR, Perkin Elmer), and the entire process from loading of samples to computer analysis and electronic data display can be computer controlled. Capillary electrophoresis is especially preferable for the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample.
Obtaining Polypeptides
Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be obtained, for example, by purification from human cells, by expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotides, or by direct chemical synthesis.
Protein Purification
Human cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides can be purified from any cell which expresses the enzyme, including host cells which have been transfected with cyclophilin-type peptidyl-prolyl cis-trans isomerase expression constructs. A purified cyclophilin-type peptidyl-prolyl cis-trans isomerase poly- peptide is separated from other compoimds which normally associate with the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide in the cell, such as certain proteins, carbohydrates, or lipids, using methods well-known in the art. Such methods include, but are not limited to, size exclusion chromatography, ammonium sulfate fractionation, ion exchange chromatography, affinity chromatography, and preparative gel electrophoresis. A preparation of purified cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides is at least 80% pure; preferably, the preparations are 90%, 95%, or 99% pure. Purity of the preparations can be assessed by any means known in the art, such as SDS-polyacrylamide gel electrophoresis.
Expression of Polynucleotides
To express a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide, the polynucleotide can be inserted into an expression vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art can be used to construct expression vectors containing sequences encoding cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides and appropriate franscriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook et al. (1989) and in Ausubel et al., CURRENT
PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N. Y., 1989.
A variety of expression vector/host systems can be utilized to contain and express sequences encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase poly- peptide. These include, but are not limited to, microorganisms, such as bacteria fransformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors, insect cell systems infected with virus expression vectors (e.g., baculovirus), plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids), or animal cell systems.
The control elements or regulatory sequences are those non-translated regions of the vector — enhancers, promoters, 5' and 3' unfranslated regions — which interact with host cellular proteins to carry out transcription and translation. Such elements can vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, can be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the
BLUESCRIPT phagemid (Stratagene, LaJolla, Calif.) or pSPORTl plasmid (Life Technologies) and the tike can be used. The baculovirus polyhedrin promoter can be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO, and storage protein genes) or from plant viruses ( .g., viral promoters or leader sequences) can be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell tine that contains multiple copies of a nucleotide sequence encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, vectors based on SV40 or EBV can be used with an appropriate selectable marker.
Bacterial and Yeast Expression Systems
In bacterial systems, a number of expression vectors can be selected depending upon the use intended for the cyclophilin-type peptidyl-prolyl cis-trans isomerase poly- peptide. For example, when a large quantity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is needed for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified can be used. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRLPT (Stratagene). In a BLUESCRIPT vector, a sequence encoding the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of β-galactosidase so that a hybrid protein is produced. pIN vectors (Van Heeke & Schuster, J. Biol. Chem. 264, 5503-5509, 1989) or pGEX vectors (Promega, Madison, Wis.) also can be used to express foreign polypeptides as fusion proteins with glutathione S-fransferase (GST).
In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems can be designed to include heparin, thrombin, or factor Xa protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
In the yeast Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH can be used. For reviews, see Ausubel et al. (1989) and Grant et al., Methods En∑ymol 153, 516-544, 1987.
Plant and Insect Expression Systems
If plant expression vectors are used, the expression of sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be driven by any of a number of promoters. For example, viral promoters such as the 35 S and 19S promoters of CaMV can be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6, 307-311, 1987). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters can be used (Coruzzi et al, EMBO J. 3, 1671-1680, 1984; Brogue et al, Science 224, 838-843, 1984; Winter et al, Results Probl. Cell Differ. 17, 85-105, 1991). These constructs can be introduced into plant cells by direct DNA transformation or by pathogen-mediated fransfection. Such techniques are described in a number of generally available reviews (e.g., Hobbs or Murray, in MCGRAW HILL YEARBOOK OF SCIENCE AND TECHNOLOGY, McGraw Hill, New York, NX, pp. 191-196, 1992). An insect system also can be used to express a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide. For example, in one such system Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. Sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses can then be used to infect S. frugiperda cells or Trichoplusia larvae in which cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be expressed (Engelhard et al, Proc. Nat. Acad. Sci. 91, 3224-3227, 1994).
Mammalian Expression Systems A number of viral-based expression systems can be used to express cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides in mammalian host cells. For example, if an adenovirus is used as an expression vector, sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be ligated into an adenovirus transcription/translation complex comprising the late promoter and tripartite leader sequence. Insertion in a non-essential El or E3 region of the viral genome can be used to obtain a viable virus which is capable of expressing a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide in infected host cells (Logan & Shenk, Proc. Natl Acad. Sci. 81, 3655-3659, 1984). If desired, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, can be used to increase expression in mammalian host cells.
Human artificial chromosomes (HACs) also can be used to deliver larger fragments of DNA than can be contained and expressed in a plasmid. HACs of 6M to 10M are constructed and delivered to cells via conventional delivery methods (e.g., liposomes, polycationic amino polymers, or vesicles). Specific initiation signals also can be used to achieve more efficient translation of sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or franslational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals (including the ATG initiation codon) should be provided. The initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used (see Scharf et al., Results Probl. Cell Differ. 20, 125-162, 1994).
Host Cells
A host cell strain can be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, Hpidation, and acylation. Post-franslational processing which cleaves a "prepro" form of the polypeptide also can be used to facilitate correct insertion, folding and/or function. Different host cells which have specific cellular machinery and characteristic mechanisms for post-franslational activities (e.g., CHO,
HeLa, MDCK, HEK293, and WI38), are available from the American Type Culture Collection (ATCC; 10801 University Boulevard, Manassas, VA 20110-2209) and can be chosen to ensure the correct modification and processing of the foreign protein. Stable expression is preferred for long-term, high-yield production of recombinant proteins. For example, cell lines which stably express cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides can be transformed using expression vectors which can contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells can be allowed to grow for 1-2 days in an enriched medium before they are switched to a selective medium. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced cyclophilin-type peptidyl-prolyl cis-trans isomerase sequences. Resistant clones of stably fransformed cells can be proliferated using tissue culture techniques appropriate to the cell type. See, for example, ANIMAL CELL CULTURE, R.I. Freshney, ed., 1986.
Any number of selection systems can be used to recover fransformed cell lines.
These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al, Cell 11, 223-32, 1977) and adenine phosphoribosyltransferase (Lowy et al., Cell 22, 817-23, 1980) genes which can be employed in tkr or aprt cells, respectively. Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methofrexate (Wigler et al, Proc. Nail. Acad. Sci. 77, 3567-70, 1980), npt confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., J. Mol. Biol. 150, 1-14, 1981), and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murray, 1992, supra). Additional selectable genes have been described. For example, trpB allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. 85, 8047-51, 1988). Visible markers such as anthocyanins, β-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, can be used to identify transformants and to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes et al., Methods Mol Biol. 55, 121-131, 1995).
Detecting Expression Although the presence of marker gene expression suggests that the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide is also present, its presence and expression may need to be confirmed. For example, if a sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is inserted within a marker gene sequence, transformed cells containing sequences which encode a cyclo- philin-type peptidyl-prolyl cis-trans isomerase polypeptide can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
Alternatively, host cells which contain a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide and which express a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include membrane, solution, or chip-based technologies for the detection and/or quantification of nucleic acid or protein. For example, the presence of a polynucleotide sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be detected by DNA-DNA or DNA-RNA hybridization or amplification using probes or fragments or fragments of polynucleotides encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. Nucleic acid amplification-based assays involve the use of oligonucleotides selected from sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide to detect transformants which contain a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide.
A variety of protocols for detecting and measuring the expression of a cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide, using either polyclonal or monoclonal antibodies specific for the polypeptide, are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay using monoclonal antibodies reactive to two non-interfering epitopes on a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be used, or a competitive binding assay can be employed. These and other assays are described in Hampton et al., SEROLOGICAL METHODS: A LABORATORY MANUAL, APS Press, St. Paul, Minn., 1990) and Maddo et /., J. Exp. Med. 158, 1211-1216, 1983).
A wide variety of labels and conjugation techniques are known by those skilled in the art and can be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides include oligolabeling, nick translation, end-labeling, or PCR amphfication using a labeled nucleotide. Alternatively, sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and can be used to synthesize RNA probes in vitro by addition of labeled nucleotides and an appropriate RNA polymerase such as T7, T3, or SP6. These procedures can be conducted using a variety of commercially available kits
(Amersham Pharmacia Biotech, Promega, and US Biochemical). Suitable reporter molecules or labels which can be used for ease of detection include radionuclides, enzymes, and fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like. Expression and Purification of Polypeptides
Host cells transformed with nucleotide sequences encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The poly- peptide produced by a transformed cell can be secreted or contained infracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be designed to contain signal sequences which direct secretion of soluble cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptides through a prokaryotic or eukaryotic cell membrane or which direct the membrane insertion of membrane-bound cyclophilin- type peptidyl-prolyl cis-frans isomerase polypeptide.
As discussed above, other constructions can be used to join a sequence encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide to a nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized i nmunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.). Inclusion of cleavable linker sequences such as those specific for Factor Xa or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide also can be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide and 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification by IMAC (immobilized metal ion affinity chromatography, as described in Porath et al., Prot. Exp. Purifi 3, 263-281, 1992), while the enterokinase cleavage site provides a means for purifying the cyclophilin- type peptidyl-prolyl cis-frans isomerase polypeptide from the fusion protein. Vectors which contain fusion proteins are disclosed in Kroll et ah, DNA Cell Biol. 12, 441-453, 1993.
Chemical Synthesis
Sequences encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers et al., Nucl. Acids Res. Symp. Ser. 215-223, 1980; Horn et al. Nucl. Acids Res. Symp. Ser. 225-232, 1980). Alternatively, a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide itself can be produced using chemical methods to synthesize its amino acid sequence, such as by direct peptide synthesis using solid-phase techniques (Merrifield, J. Am. Chem. Soc. 85, 2149-2154, 1963; Roberge et al., Science 269, 202-204, 1995). Protein synthesis can be performed using manual techniques or by automation. Automated synthesis can be achieved, for example, using Applied Biosystems 431 A Peptide Synthesizer (Perkin Elmer).
Optionally, fragments of cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be separately synthesized and combined using chemical methods to produce a full-length molecule.
The newly synthesized peptide can be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, PROTEINS: STRUCTURES AND MOLECULAR PRINCIPLES, WH Freeman and Co., New York, N.Y., 1983). The composition of a synthetic cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure; see Creighton, supra). Additionally, any portion of the amino acid sequence of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins to produce a variant polypeptide or a fusion protein. Production of Altered Polypeptides
As will be understood by those of skill in the art, it may be advantageous to produce cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons pre- ferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce an RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
The nucleotide sequences disclosed herein can be engineered using methods generally known in the art to alter cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide-encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the polypeptide or mRNA product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides can be used to engineer the nucleotide sequences. For example, site-directed mutagenesis can be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations, and so forth.
Antibodies
Any type of antibody known in the art can be generated to bind specifically to an epitope of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. "Antibody" as used herein includes intact immunoglobulin molecules, as well as fragments thereof, such as Fab, F(ab')2, and Fv, which are capable of binding an epitope of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide.
Typically, at least 6, 8, 10, or 12 contiguous amino acids are required to form an epitope. However, epitopes which involve non-contiguous amino acids may require more, e.g., at least 15, 25, or 50 amino acids. An antibody which specifically binds to an epitope of a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide can be used therapeutically, as well as in immunochemical assays, such as Western blots, ELISAs, radioimmunoassays, i-mmunohistochemical assays, immunoprecipitations, or other immunochemical assays known in the art. Various immunoassays can be used to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays are well known in the art. Such immunoassays typically involve the measurement of complex formation between an immunogen and an antibody which specifically binds to the immunogen.
Typically, an antibody which specifically binds to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide provides a detection signal at least 5-, 10-, or 20-fold higher than a detection signal provided with other proteins when used in an immunochemical assay. Preferably, antibodies which specifically bind to cyclo- philin-type peptidyl-prolyl cis-frans isomerase polypeptides do not detect other proteins in immunochemical assays and can immunoprecipitate a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide from solution.
Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides can be used to immunize a mammal, such as a mouse, rat, rabbit, guinea pig, monkey, or human, to produce polyclonal antibodies. If desired, a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be conjugated to a carrier protein, such as bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin. Depending on the host species, various adjuvants can be used to increase the immunological response. Such adjuvants include, but are not limited to, Freund's adjuvant, mineral gels (e.g., aluminum hydroxide), and surface active substances (e.g. lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol). Among adjuvants used in humans, BCG (bacilli Calmette-Gueriή) and Corynebacterium parvum are especially useful. Monoclonal antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These techniques include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kohler et al, Nature 256,
495-497, 1985; Kozbor et al, J. Immunol. Methods 81, 31-42, 1985; Cote et al, Proc. Natl Acad. Sci. 80, 2026-2030, 1983; Cole et al., Mol Cell Biol. 62, 109-120, 1984).
In addition, techniques developed for the production of "chimeric antibodies," the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used (Morrison et al., Proc. Natl. Acad. Sci. 81, 6851-6855, 1984; Neuberger et al., Nature 312, 604-608, 1984; Takeda et al, Nature 314, 452-454, 1985). Monoclonal and other antibodies also can be "humanized" to prevent a patient from mounting an immune response against the antibody when it is used therapeutically. Such antibodies may be sufficiently similar in sequence to human antibodies to be used directly in therapy or may require alteration of a few key residues. Sequence differences between rodent antibodies and human sequences can be minimized by replacing residues which differ from those in the human sequences by site directed mutagenesis of individual residues or by grating of entire complementarity determining regions. Alternatively, humanized antibodies can be produced using recombinant methods, as described in GB2188638B. Antibodies which specifically bind to a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide can contain antigen binding sites which are either partially or fully humanized, as disclosed in U.S. 5,565,332.
Alternatively, techniques described for the production of single chain antibodies can be adapted using methods known in the art to produce single chain antibodies which specifically bind to cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides. Antibodies with related specificity, but of distinct idiot pic composition, can be generated by chain shuffling from random combinatorial immunoglobin libraries (Burton, Proc. Natl. Acad. Sci. 88, 11120-23, 1991).
Single-chain antibodies also can be constructed using a DNA amphfication method, such as PCR, using hybridoma cDNA as a template (Thirion et ah, 1996, Eur. J.
Cancer Prev. 5, 507-11). Single-chain antibodies can be mono- or bispecific, and can be bivalent or tefravalent. Construction of tefravalent, bispecific single-chain antibodies is taught, for example, in Coloma & Morrison, 1997, Nat. Biotechnol 15, 159-63. Construction of bivalent, bispecific single-chain antibodies is taught in Mallender & Noss, 1994, J. Biol. Chem. 269, 199-206.
A nucleotide sequence encoding a single-chain antibody can be constructed using manual or automated nucleotide synthesis, cloned into an expression construct using standard recombinant DΝA methods, and introduced into a cell to express the coding sequence, as described below. Alternatively, single-chain antibodies can be produced directly using, for example, filamentous phage technology (Verhaar et al., 1995, Int. J. Cancer 61, 497-501; Νicholls et ah, 1993, J. Immunol. Meth. 165, 81-91).
Antibodies which specifically bind to cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides also can be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Orlandi et ah, Proc. Natl. Acad. Sci. 86, 3833-3837, 1989; Winter et ah, Nature 349, 293-299, 1991).
Other types of antibodies can be constructed and used therapeutically in methods of the invention. For example, chimeric antibodies can be constructed as disclosed in WO 93/03151. Binding proteins which are derived from immunoglobulins and which are multivalent and multispecific, such as the "diabodies" described in WO 94/13804, also can be prepared. Antibodies according to the invention can be purified by methods well known in the art. For example, antibodies can be affinity purified by passage over a column to which a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide is bound. The bound antibodies can then be eluted from the column using a buffer with a high salt concentration.
Antisense Oligonucleotides
Antisense oligonucleotides are nucleotide sequences which are complementary to a specific DNA or RNA sequence. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form complexes and block either transcription or translation. Preferably, an antisense oligonucleotide is at least 11 nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides long. Longer sequences also can be used. Antisense oligonucleotide molecules can be provided in a DNA construct and introduced into a cell as described above to decrease the level of cyclophilin-type peptidyl-prolyl cis- trans isomerase gene products in the cell.
Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides, or a combination of both. Oligonucleotides can be synthesized manually or by an automated synthesizer, by covalently linking the 5' end of one nucleotide with the V end of another nucleotide with non-phosphodiester internucleotide linkages such alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonothioates, alkylphosphonates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxymethyl esters, carbonates, and phosphate triesters. See Brown, Meth. Mol.
Biol. 20, 1-8, 1994; Sonveaux, Meth. Mol. Biol 26, 1-72, 1994; Uhlmann et ah, Chem. Rev. 90, 543-583, 1990.
Modifications of cyclophilin-type peptidyl-prolyl cis-frans isomerase gene expression can be obtained by designing antisense oligonucleotides which will form duplexes to the control, 5', or regulatory regions of the cyclophilin-type peptidyl- prolyl cis-trans isomerase gene. Oligonucleotides derived from the transcription initiation site, e.g., between positions -10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or chaperons. Therapeutic advances using triplex DNA have been described in the literature (e.g., Gee et ah, in Huber & Carr, MOLECULAR AND IMMUNOLOGIC APPROACHES, Futura Publishing Co., Mt. Kisco, N.Y., 1994). An antisense oligo- nucleotide also can be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
Precise complementarity is not required for successful complex formation between an antisense oligonucleotide and the complementary sequence of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide. Antisense oligonucleotides which comprise, for example, 2, 3, 4, or 5 or more stretches of contiguous nucleotides which are precisely complementary to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide, each separated by a stretch of contiguous nucleotides which are not complementary to adjacent cyclophilin-type peptidyl- prolyl cis-frans isomerase nucleotides, can provide sufficient targeting specificity for cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA. Preferably, each stretch of complementary contiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length. Non-complementary intervening sequences are preferably 1, 2, 3, or 4 nucleotides in length. One skilled in the art can easily use the calculated melting point of an antisense-sense pair to determine the degree of mismatching which will be tolerated between a particular antisense oligonucleotide and a particular cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide sequence. Antisense oligonucleotides can be modified without affecting their ability to hybridize to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide. These modifications can be internal or at one or both ends of the antisense molecule. For example, intemucleoside phosphate linkages can be modified by adding cholesteryl or diamine moieties with varying numbers of carbon residues between the amino groups and terminal ribose. Modified bases and or sugars, such as arabinose instead of ribose, or a 3', 5' -substituted oligonucleotide in which the 3' hydroxyl group or the 5' phosphate group are substituted, also can be employed in a modified antisense oligonucleotide. These modified oligonucleotides can be prepared by methods well known in the art. See, e.g., Agrawal et ah, Trends Biotechnol 10,
152-158, 1992; Uhlmaim et al, Chem. Rev. 90, 543-584, 1990; Uhhnann et ah, Tetrahedron. Lett. 215, 3539-3542, 1987.
Ribozymes Ribozymes are RNA molecules with catalytic activity. See, e.g., Cech, Science 236,
1532-1539; 1987; Cech, Ann. Rev. Biochem. 59, 543-568; 1990, Cech, Curr. Opin. Struct. Biol. 2, 605-609; 1992, Couture & Stinchcomb, Trends Genet. 12, 510-515, 1996. Ribozymes can be used to inhibit gene function by cleaving an RNA sequence, as is known in the art (e.g., Haseloff et ah, U.S. Patent 5,641,673). The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. Examples include engineered hammerhead motif ribozyme molecules that can specifically and efficiently catalyze endonucleolytic cleavage of specific nucleotide sequences.
The coding sequence of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be used to generate ribozymes which will specifically bind to mRNA transcribed from the cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide. Methods of designing and constructing ribozymes which can cleave other RNA molecules in trans in a highly sequence specific manner have been developed and described in the art (see Haseloff et a Nature 334, 585-591, 1988). For example, the cleavage activity of ribozymes can be targeted to specific RNAs by engineering a discrete "hybridization" region into the ribozyme. The hybridization region contains a sequence complementary to the target RNA and thus specifically hybridizes with the target (see, for example, Gerlach et ah, EP 321 ,201 ).
Specific ribozyme cleavage sites within a cyclophilin-type peptidyl-prolyl cis-trans isomerase RNA target can be identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target RNA containing the cleavage site can be evaluated for secondary structural features which may render the target inoperable. Suitability of candidate cyclophilin-type peptidyl-prolyl cis-trans isomerase RNA targets also can be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays. Longer complementary sequences can be used to increase the affinity of the hybridization sequence for the target. The hybridizing and cleavage regions of the ribozyme can be integrally related such that upon hybridizing to the target RNA through the complementary regions, the catalytic region of the ribozyme can cleave the target.
Ribozymes can be introduced into cells as part of a DNA construct. Mechanical methods, such as microinjection, liposome-mediated fransfection, electroporation, or calcium phosphate precipitation, can be used to introduce a ribozyme-containing DNA construct into cells in which it is desired to decrease cyclophilin-type peptidyl- prolyl cis-trans isomerase expression. Alternatively, if it is desired that the cells stably retain the DNA construct, the construct can be supplied on a plasmid and maintained as a separate element or integrated into the genome of the cells, as is known in the art. A ribozyme-encoding DNA construct can include transcriptional regulatory elements, such as a promoter element, an enhancer or UAS element, and a transcriptional terminator signal, for controlling transcription of ribozymes in the cells.
As taught in Haseloff et ah, U.S. Patent 5,641,673, ribozymes can be engineered so that ribozyme expression will occur in response to factors which induce expression of a target gene. Ribozymes also can be engineered to provide an additional level of regulation, so that destruction of mRNA occurs only when both a ribozyme and a target gene are induced in the cells.
Differentially Expressed Genes
Described herein are methods for the identification of genes whose products interact with human cyclophilin-type peptidyl-prolyl cis-frans isomerase. Such genes may represent genes which are differentially expressed in disorders including, but not limited to, cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders. Further, such genes may represent genes which are differentially regulated in response to manipulations relevant to the progression or treatment of such diseases. Additionally, such genes may have a temporally modulated expression, increased or decreased at different stages of tissue or organism development. A differentially expressed gene may also have its expression modulated under control versus experimental conditions. In addition, the human cyclophilin-type peptidyl- prolyl cis-trans isomerase gene or gene product may itself be tested for differential expression.
The degree to which expression differs in a normal versus a diseased state need only be large enough to be visualized via standard characterization techniques such as differential display techniques. Other such standard characterization techniques by which expression differences may be visualized include but are not limited to, quantitative RT (reverse transcriptase), PCR, and Northern analysis.
Identification of Differentially Expressed Genes To identify differentially expressed genes total RNA or, preferably, mRNA is isolated from tissues of interest. For example, RNA samples are obtained from tissues of experimental subjects and from corresponding tissues of control subjects. Any RNA isolation technique which does not select against the isolation of mRNA may be utilized for the purification of such RNA samples. See, for example, Ausubel et ah, ed.„ CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, Inc. New York, 1987-1993. Large numbers of tissue samples may readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski, U.S. Patent 4,843,155.
Transcripts within the collected RNA samples which represent RNA produced by differentially expressed genes are identified by methods well known to those of skill in the art. They include, for example, differential screening (Tedder et ah, Proc. Natl. Acad. Sci. U.S.A. 85, 208-12, 1988), subtractive hybridization (Hedrick et ah, Nature 308, 149-53; Lee et ah, Proc. Natl. Acad. Sci. U.S.A. 88, 2825, 1984), and, preferably, differential display (Liang & Pardee, Science 257, 967-71, 1992; U.S. Patent 5,262,311).
The differential expression information may itself suggest relevant methods for the treatment of disorders involving the human cyclophilin-type peptidyl-prolyl cis-frans isomerase. For example, treatment may include a modulation of expression of the differentially expressed genes and or the gene encoding the human cyclophilin-type peptidyl-prolyl cis-frans isomerase. The differential expression information may indicate whether the expression or activity of the differentially expressed gene or gene product or the human cyclophilin-type peptidyl-prolyl cis-trans isomerase gene or gene product are up-regulated or down-regulated.
Screening Methods
The invention provides assays for screening test compounds which bind to or modulate the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase poly- peptide or a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide. A test compound preferably binds to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or polynucleotide. More preferably, a test compound decreases or increases activity by at least about 10, preferably about 50, more preferably about 75, 90, or 100% relative to the absence of the test compound.
Test Compounds
Test compounds can be pharmacologic agents already known in the art or can be compounds previously unknown to have any pharmacological activity. The compounds can be naturally occurring or designed in the laboratory. They can be isolated from microorganisms, animals, or plants, and can be produced recombinantly, or synthesized by chemical methods known in the art. If desired, test compounds can be obtained using any of the numerous combinatorial library methods known in the art, including but not limited to, biological libraries, spatially addressable parallel solid phase or solution phase libraries, synthetic library methods requiring deconvolution, the "one-bead one-compound" library method, and synthetic library methods using affinity chromatography selection. The biological library approach is limited to polypeptide libraries, while the other four approaches are applicable to polypeptide, non-peptide oligomer, or small molecule libraries of compounds. See Lam, Anticancer Drug Des. 12, 145, 1997.
Methods for the synthesis of molecular libraries are well known i the art (see, for example, DeWitt et ah, Proc. Natl. Acad. Sci. U.S.A. 90, 6909, 1993; Erb et al. Proc. Nat Acad. Sci. U.S.A. 91, 11422, 1994; Zuckermann etah, J. Med. Chem. 37, 2678, 1994; Cho et ah, Science 261, 1303, 1993; Carell et ah, Angew. Chem. Int. Ed. Engh
33, 2059, 1994; Carell et ah, Angew. Chem. Int. Ed. Engl 33, 2061; Gallop et ah, J. Med. Chem. 37, 1233, 1994). Libraries of compounds can be presented in solution (see, e.g., Houghten, BioTechniques 13, 412-421, 1992), or on beads (Lam, Nature 354, 82-84, 1991), chips (Fodor, Nature 364, 555-556, 1993), bacteria or spores (Ladner, U.S. Patent 5,223,409), plasmids (Cull et ah, Proc. Natl. Acad. Sci. U.S.A. 89, 1865-1869, 1992), or phage (Scott & Smith, Science 249, 386-390, 1990; Devlin, Science 249, 404-406, 1990); Cwirla et ah, Proc. Natl. Acad. Sci. 97, 6378-6382, 1990; Felici, J. Mol. Biol. 222, 301-310, 1991; and Ladner, U.S. Patent 5,223,409).
High Throughput Screening
Test compounds can be screened for the ability to bind to cyclophilin-type peptidyl- prolyl cis-frans isomerase polypeptides or polynucleotides or to affect cyclophilin- type peptidyl-prolyl cis-frans isomerase activity or cyclophilin-type peptidyl-prolyl cis-frans isomerase gene expression using high throughput screening. Using high throughput screening, many discrete compounds can be tested in parallel so that large numbers of test compounds can be quickly screened. The most widely established techniques utilize 96-well microtiter plates. The wells of the microtiter plates typically require assay volumes that range from 50 to 500 μl. In addition to the plates, many instruments, materials, pipettors, robotics, plate washers, and plate readers are commercially available to fit the 96-well format.
Alternatively, "free format assays," or assays that have no physical barrier between samples, can be used. For example, an assay using pigment cells (melanocytes) in a simple homogeneous assay for combinatorial peptide libraries is described by Jayawickreme et ah, Proc. Natl. Acad. Sci. U.S.A. 19, 1614-18 (1994). The cells are placed under agarose in pefri dishes, then beads that carry combinatorial compounds are placed on the surface of the agarose. The combinatorial compounds are partially released the compounds from the beads. Active compounds can be visualized as dark pigment areas because, as the compounds diffuse locally into the gel matrix, the active compounds cause the cells to change colors.
Another example of a free format assay is described by Chelsky, "Strategies for
Screening Combinatorial Libraries: Novel and Traditional Approaches," reported at the First Annual Conference of The Society for Biomolecular Screening in Philadelphia, Pa. (Nov. 7-10, 1995). Chelsky placed a simple homogenous enzyme assay for carbonic anhydrase inside an agarose gel such that the enzyme in the gel would cause a color change throughout the gel. Thereafter, beads carrying combinatorial compounds via a photolinker were placed inside the gel and the compounds were partially released by UV-light. Compounds that inhibited the enzyme were observed as local zones of inhibition having less color change.
Yet another example is described by Salmon et ah, Molecular Diversity 2, 57-63 (1996). In this example, combinatorial libraries were screened for compounds that had cytotoxic effects on cancer cells growing in agar.
Another high throughput screening method is described in Beutel et ah, U.S. Patent 5,976,813. In this method, test samples are placed in a porous matrix. One or more assay components are then placed within, on top of, or at the bottom of a matrix such as a gel, a plastic sheet, a filter, or other form of easily manipulated solid support. When samples are introduced to the porous matrix they diffuse sufficiently slowly, such that the assays can be performed without the test samples running together.
Binding Assays
For binding assays, the test compound is preferably a small molecule which binds to and occupies, for example, the active site of the cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide, such that normal biological activity is prevented. Examples of such small molecules include, but are not limited to, small peptides or peptide-like molecules.
In binding assays, either the test compound or the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can comprise a detectable label, such as a fluorescent, radioisotopic, chemiluminescent, or enzymatic label, such as horseradish per- oxidase, alkaline phosphatase, or luciferase. Detection of a test compound which is bound to the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can then be accomplished, for example, by direct counting of radioemmission, by scintillation counting, or by determining conversion of an appropriate substrate to a detectable product.
Alternatively, binding of a test compound to a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide can be determined without labeling either of the interactants. For example, a microphysiometer can be used to detect binding of a test compound with a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide. A microphysiometer (e.g., Cytosensor™) is an analytical instrument that measures the rate at which a cell acidifies its environment using a light-addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between a test compound and a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide (McConnell et ah, Science 257, 1906-1912, 1992).
Determining the ability of a test compound to bind to a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide also can be accomplished using a technology such as real-time Bimolecular Interaction Analysis (BIA) (Sjolander & Urbaniczky, Anah Chem. 63, 2338-2345, 1991, and Szabo et ah, Curr. Opin. Struct. Biol. 5, 699-705, 1995). BIA is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore™). Changes in the optical phenomenon surface plasmon resonance (SPR) can be used as an indication of real-time reactions between biological molecules.
In yet another aspect of the invention, a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide can be used as a "bait protein" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent 5,283,317; Zervos et ah, Cell 72, 223-232, 1993; Madura et ah, J. Biol. Chem. 268,. 12046-12054, 1993; Bartel et ah, BioTechniques 14, 920-924, 1993; Iwabuchi et ah, Oncogene 8, 1693-1696, 1993; and Brent W094/ 10300), to identify other proteins which bind to or interact with the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide and modulate its activity.
The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. For example, in one construct, polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be fused to a polynucleotide encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct a DNA sequence that encodes an unidentified protein ("prey" or "sample") can be fused to a polynucleotide that codes for the activation domain of the known transcription factor. If the "bait" and the "prey" proteins are able to interact in vivo to form an protein-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ), which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected, and cell colonies containing the functional transcription factor can be isolated and used to obtain the DNA sequence encoding the protein which interacts with the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
It may be desirable to immobilize either the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide (or polynucleotide) or the test compound to facilitate separation of bound from unbound forms of one or both of the interactants, as well as to accommodate automation of the assay. Thus, either the cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide (or polynucleotide) or the test compound can be bound to a solid support. Suitable solid supports include, but are not limited to, glass or plastic slides, tissue culture plates, microtiter wells, tubes, silicon chips, or particles such as beads (including, but not limited to, latex, polystyrene, or glass beads). Any method known in the art can be used to attach the enzyme polypeptide (or polynucleotide) or test compound to a solid support, including use of covalent and non-covalent linkages, passive absorption, or pairs of binding moieties attached respectively to the polypeptide (or polynucleotide) or test compound and the solid support. Test compounds are preferably bound to the solid support in an array, so that the location of individual test compounds can be tracked. Binding of a test compound to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide (or polynucleotide) can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and micro- centrifuge tubes.
In one embodiment, the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is a fusion protein comprising a domain that allows the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide to be bound to a solid support. For example, glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo.) or glutathione derivatized micro- titer plates, which are then combined with the test compound or the test compound and the non-adsorbed cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide; the mixture is then 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. Binding of the interactants can be determined either directly or indirectly, as described above. Alternatively, the complexes can be dissociated from the solid support before binding is determined.
Other techniques for immobilizing proteins or polynucleotides on a solid support also can be used in the screening assays of the invention. For example, either a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide (or polynucleotide) or a test compound can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides (or polynucleotides) or test compounds .can be prepared from biotin-NHS(N-hydroxysuccinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, 111.) and immobilized in the wells of streptavidin-coated 96 well plates (Pierce Chemical). Alternatively, antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, polynucleotide, or a test compound, but which do not interfere with a desired binding site, such as the active site of the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, can be derivatized to the wells of the plate. Unbound target or protein can be trapped in the wells by antibody conjugation.
Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies which specifically bind to the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or test compound, enzyme-linked assays which rely on detecting an activity of the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, and SDS gel electrophoresis under non-reducing conditions.
Screening for test compounds which bind to a cyclophilin-type peptidyl-prolyl cis- frans isomerase polypeptide or polynucleotide also can be carried out in an intact cell. Any cell which comprises a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide or polynucleotide can be used in a cell-based assay system. A cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Binding of the test compound to a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide or polynucleotide is determined as described above.
Enzyme Assays
Test compounds can be tested for the ability to increase or decrease the enzymatic activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
Enzymatic activity can be measured, for example, as described in the specific examples, below. Enzyme assays can be carried out after contacting either a purified cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, a cell membrane preparation, or an intact cell with a test compound. A test compound which decreases an enzymatic activity of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% is identified as a potential therapeutic agent for decreasing cyclophilin-type peptidyl- prolyl cis-trans isomerase activity. A test compound which increases an enzymatic activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% is identified as a potential therapeutic agent for increasing human cyclophilin-type peptidyl-prolyl cis-trans isomerase activity.
Gene Expression
In another embodiment, test compounds which increase or decrease cyclophilin-type peptidyl-prolyl cis-trans isomerase gene expression are identified. A cyclophilin- type peptidyl-prolyl cis-trans isomerase polynucleotide is contacted with a test compound, and the expression of an RNA or polypeptide product of the cyclophilin- type peptidyl-prolyl cis-frans isomerase polynucleotide is determined. The level of expression of appropriate mRNA or polypeptide in the presence of the test compound is compared to the level of expression of mRNA or polypeptide in the absence of the test compound. The test compound can then be identified as a modulator of expression based on this comparison. For example, when expression of mRNA or polypeptide is greater in the presence of the test compound than in its absence, the test compound is identified as a stimulator or enhancer of the mRNA or polypeptide expression. Alternatively, when expression of the mRNA or polypeptide is less in the presence of the test compound than in its absence, the test compound is identified as an inhibitor of the mRNA or polypeptide expression.
The level of cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA or poly- peptide expression in the cells can be determined by methods well known in the art for detecting mRNA or polypeptide. Either qualitative or quantitative methods can be used. The presence of polypeptide products of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be determined, for example, using a variety of techniques known in the art, including immunochemical methods such as radio- immunoassay, Western blotting, and immunohistochemistry. Alternatively, polypeptide synthesis can be determined in vivo, in a cell culture, or in an in vitro translation system by detecting incorporation of labeled amino acids into a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide.
Such screening can be carried out either in a cell-free assay system or in an intact cell. Any cell which expresses a cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide can be used in a cell-based assay system. The cyclophilin-type peptidyl-prolyl cis-frans isomerase polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Either a primary culture or an established cell line, such as CHO or human embryonic kidney
293 cells, can be used.
Pharmaceutical Compositions
The invention also provides pharmaceutical compositions which can be administered to a patient to achieve a therapeutic effect. Pharmaceutical compositions of the invention can comprise, for example, a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, cyclophilin-type peptidyl-prolyl cis-trans isomerase polynucleotide, ribozymes or antisense oligonucleotides, antibodies which specifically bind to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, or mimetics, activators, inhibitors, or inhibitors of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide activity. The compositions can be administered alone or in combination with at least one other agent, such as stabilizing compound, which can be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose, and water. The compositions can be administered to a patient alone, or in combination with other agents, drugs or hormones.
In addition to the active ingredients, these pharmaceutical compositions can contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Pharmaceutical compositions of the invention can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, infra-arterial, inframedullary, infrathecal, infraventricular, transdermal, subcutaneous, infraperitoneal, intranasal, parenteral, topical, sublingual, or rectal means. Pharmaceutical compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
Pharmaceutical preparations for oral use can be obtained through combination of active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxy- propylmethyl-cellulose, or sodium carboxymethylcellulose; gums including arabic and fragacanth; and proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents can be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.
Dragee cores can be used in conjunction with suitable coatings, such as concentrated sugar solutions, which also can contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments can be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.
Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol. Push-fit capsules can contain active ingredients mixed with a filler or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the active compounds can be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.
Pharmaceutical formulations suitable for parenteral administration can be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions can contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dexfran. Additionally, suspensions of the active compounds can be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Non-lipid polycationic amino polymers also can be used for delivery. Optionally, the suspension also can contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. For topical or nasal administration, penetrants appropriate to the particular barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.
The pharmaceutical compositions of the present invention can be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. The pharmaceutical composition can be provided as a salt and can be formed with many acids, including but not limited to, hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents than are the corresponding free base forms. In other cases, the preferred preparation can be a lyophilized powder which can contain any or all of the following: 1-50 mM histidine, 0J%-2% sucrose, and 2-7% mannitol, at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
Further details on techniques for formulation and administration can be found in the latest edition of REMINGTON'S PHARMACEUTICAL SCIENCES (Maack Publishing Co.,
Easton, Pa.). After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. Such labeling would include amount, frequency, and method of administration.
Therapeutic Indications and Methods
Chemical and structural similarity, e.g., in the context of sequences and motifs, exists between regions of the cyclophilin-type peptidyl-prolyl cis-trans isomerase of the invention and cyclophilin-type peptidyl-prolyl cis-trans isomerase. In addition, the expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase is closely associated with cancerous or proliferating tissue, and with reproductive tissue. Therefore, cyclophilin-type peptidyl-prolyl cis-trans isomerase appears to be associated with cancer, asthma, autoimmune/inflammatory disorders, and reproductive disorders.
Cancer: Cancer is a disease fundamentally caused by oncogenic cellular transformation. There are several hallmarks of transformed cells that distinguish them from their normal counterparts and underlie the pathophysiology of cancer. These include uncontrolled cellular proliferation, unresponsiveness to normal death-inducing signals (immortalization), increased cellular motility and invasiveness, increased ability to recruit blood supply through induction of new blood vessel formation (angiogenesis), genetic instability, and dysregulated gene expression. Various combinations of these aberrant physiologies, along with the acquisition of drug-resistance frequently lead to an intractable disease state in which organ failure and patient death ultimately ensue.
Most standard cancer therapies target cellular proliferation and rely on the differential proliferative capacities between transformed and normal cells for their efficacy. This approach is hindered by the facts that several important normal cell types are also highly proliferative and that cancer cells frequently become resistant to these agents. Thus, the therapeutic indices for traditional anti-cancer therapies rarely exceed 2.0.
The advent of genomics-driven molecular target identification has opened up the possibility of identifying new cancer-specific targets for therapeutic intervention that will provide safer, more effective treatments for cancer patients. Thus, newly discovered tumor-associated genes and their products can be tested for their role(s) in disease and used as tools to discover and develop innovative therapies. Genes playing important roles in any of the physiological processes outlined above can be characterized as cancer targets.
Genes or gene fragments identified through genomics can readily be expressed in one or more heterologous expression systems to produce functional recombinant proteins. These proteins are characterized in vitro for their biochemical properties and then used as tools in high-throughput molecular screening programs to identify chemical modulators of their biochemical activities. Activators and/or inhibitors of target protein activity can be identified in this manner and subsequently tested in cellular and in vivo disease models for anti-cancer activity. Optimization of lead compounds with iterative testing in biological models and detailed pharmacokinetic and toxicological analyses form the basis for drug development and subsequent testing in humans.
In the treatment of cancer, autoimmune/inflammatory disorders, and reproductive disorders associated with increased cyclophilin-type peptidyl-prolyl cis-trans isomerase activity, it is desirable to decrease the expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase. In the treatment of the above conditions associated with decreased cyclophilin-type peptidyl-prolyl cis-frans isomerase activity, it is desirable to provide the protein or to increase the expression of cyclophilin-type peptidyl-prolyl cis-frans isomerase.
Therefore, in one embodiment, cyclophilin-type peptidyl-prolyl cis-trans isomerase or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclo- philin-type peptidyl-prolyl cis-trans isomerase. Examples of such disorders include a cancer, such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; an autoimmune/inflammatory disorder such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scieroderma, Sjogren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and exfracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma.; or a reproductive disorder such as disorders of prolactin production; infertility, including tubal disease, ovulatory defects, and endomefriosis; disruptions of the estrous cycle, disruptions of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, endometrial and ovarian tumors, uterine fibroids, autoimmune disorders, ectopic pregnancies, and teratogenesis; cancer of the breast, fibrocystic breast disease, and galactorrhea; disruptions of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, carcinoma of the male breast, and gynecomastia.
Allergy, anaphylaxis, asthma and inflammation. Allergy is a complex process in which environmental antigens induce clinically adverse reactions. The inducing antigens, called allergens, typically elicit a specific IgE response and, although in most cases the allergens themselves have little or no intrinsic toxicity, they induce pathology when the IgE response in turn elicits an IgE-dependent or T cell-dependent hypersensitivity reaction. Hypersensitivity reactions can be local or systemic and typically occur within minutes of allergen exposure in individuals who have previously been sensitized to an allergen. The hypersensitivity reaction of allergy develops when the allergen is recognized by IgE antibodies bound to specific receptors on the surface of effector cells, such as mast cells, basophils, or eosinophils, which causes the activation of the effector cells and the release of mediators that produce the acute signs and symptoms of the reactions. Allergic diseases include asthma, allergic rhinitis (hay fever), atopic dermatitis, and anaphylaxis. Asthma is though to arise as a result of interactions between multiple genetic and environmental factors and is characterized by three major features: 1) intermittent and reversible airway obstruction caused by bronchoconsfriction, increased mucus production, and thickening of the walls of the airways that leads to a narrowing of the airways, 2) airway hyperresponsiveness caused by a decreased control of airway caliber, and 3) airway inflammation. Certain cells are critical to the inflammatory reaction of asthma and they include T cells and antigen presenting cells, B cells that produce IgE, and mast cells, basophils, eosinophils, and other cells that bind IgE. These effector cells accumulate at the site of allergic reaction in the airways and release toxic products that contribute to the acute pathology and eventually to the tissue destruction related to the disorder. Other resident cells, such as smooth muscle cells, lung epithelial cells, mucus-producing cells, and nerve cells may also be abnormal in individuals with asthma and may contribute to the pathology. While the airway obstruction of asthma, presenting clinically as an intermittent wheeze and shortness of breath, is generally the most pressing symptom of the disease requiring immediate treatment, the inflammation and tissue destruction associated with the disease can lead to irreversible changes that eventually make asthma a chronic disabling disorder requiring long-term management.
Despite recent important advances in our understanding of the pathophysiology of asthma, the disease appears to be increasing in prevalence and severity (Gergen and Weiss, Am. Rev. Respir. Dis. 146, 823-24, 1992). It is estimated that 30-40% of the population suffer with atopic allergy, and 15% of children and 5% of adults in the population suffer from asthma (Gergen and Weiss, 1992). Thus, an enormous burden is placed on our health care resources. However, both diagnosis and freatment of asthma are difficult. The severity of lung tissue inflammation is not easy to measure and the symptoms of the disease are often indistinguishable from those of respiratory infections, chronic respiratory inflammatory disorders, allergic rhinitis, or other respiratory disorders. Often, the inciting allergen cannot be determined, making removal of the causative environmental agent difficult. Current pharmacological treatments suffer their own set of disadvantages. Commonly used therapeutic agents, such as beta agonists, can act as symptom relievers to transiently improve pulmonary function, but do not affect the underlying inflammation. Agents that can reduce the underlying inflammation, such as anti-inflammatory steroids, can have major drawbacks that range from immunosuppression to bone loss (Goodman and Gilman's
THE PHARMACOLOGIC BASIS OF THERAPEUTICS, Seventh Edition, MacMillan Publishing Company, NY, USA, 1985). In addition, many of the present therapies, such as inhaled corticosteroids, are short-lasting, inconvenient to use, and must be used often on a regular basis, in some cases for life, making failure of patients to comply with the freatment a major problem and thereby reducing their effectiveness as a treatment.
Because of the problems associated with conventional therapies, alternative treatment strategies have been evaluated. Glycophorin A (Chu and Sharom, Cell. Immunol. 145, 223-39, 1992), cyclosporin (Alexander et ah, Lancet 339, 324-28, 1992), and a nonapeptide fragment of IL-2 (Zav'yalov et ah, Immunol. Lett. 31, 285-88, 1992) all inhibit interleukin-2 dependent T lymphocyte proliferation; however, they are known to have many other effects. For example, cyclosporin is used as a immuno- suppressant after organ transplantation. While these agents may represent alterna- tives to steroids in the treatment of asthmatics, they inhibit interleukin-2 dependent T lymphocyte proliferation and potentially critical immune functions associated with homeostasis. Other freatments that block the release or activity of mediators of bronchochonstriction, such as cromones or anti-leukotrienes, have recently been introduced for the treatment of mild asthma, but they are expensive and not effective in all patients and it is unclear whether they have any effect on the chronic changes associated with asthmatic inflammation. What is needed in the art is the identification of a freatment that can act in pathways critical to the development of asthma_that both blocks the episodic attacks of the disorder and preferentially dampens the hyperactive allergic immune response without immunocompromising the patient. Cyclophilin-type peptidyl-prolyl cis-trans isomerase is a widely distributed, highly expressed molecule (Fig. 21), indicating that its function is fundamental to common activities of a wide variety of cell types. As a member of the cyclophilin family, this function is the folding, transport, and assembly of proteins.
Although the expression of cyclophilin-type peptidyl-prolyl cis-trans isomerase is high in most tissues, its expression in the testis, skeletal muscle, uterus, and lung is somewhat higher than in other tissue. This indicates that the these tissues produce a comparatively large amount of specific protein types that require cyclophilin-type peptidyl-prolyl cis-trans isomerase activity to allow them to fold or combine with other molecules before assuming an active conformation. Regulating the activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase in cells or tissues that produce cyclophilin-type peptidyl-prolyl cis-trans isomerase -activity-dependent proteins, therefore, potentially can be applied as freatment in pathogenic states where overproduction or underproduction of active protein leads to disease.
In another embodiment, a vector capable of expressing cyclophilin-type peptidyl-prolyl cis-frans isomerase or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those described above.
In a further embodiment, a pharmaceutical composition comprising a substantially purified cyclophilin-type peptidyl-prolyl cis-frans isomerase in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those provided above. In still another embodiment, an activator which modulates the activity of cyclophilin-type peptidyl-prolyl cis-frans isomerase may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those listed above.
In a further embodiment, an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase. Such disorders may include, but are not limited to, those discussed above. In one aspect, an antibody which specifically binds cyclophilin-type peptidyl-prolyl cis-trans isomerase may be used directly as an inhibitor or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express cyclophilin-type peptidyl-prolyl cis-frans isomerase.
In an additional embodiment, a vector expressing the complement of the polynucleotide encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase may be administered to a subject to freat or prevent a disorder associated with increased expression or activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase including, but not limited to, those described above.
In other embodiments, any of the proteins, inhibitors, antibodies, activators, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to effect the freatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects. An inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase may be produced using methods which are generally known in the art. In particular, purified cyclophilin-type peptidyl-prolyl cis-frans isomerase may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind cyclophilin-type peptidyl-prolyl cis-trans isomerase. Antibodies to cyclophilin-type peptidyl-prolyl cis-frans isomerase may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are especially preferred for therapeutic use.
This invention further pertains to the use of novel agents identified by the screening assays described above. Accordingly, it is within the scope of this invention to use a test compound identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., a modulating agent, an antisense nucleic acid molecule, a specific antibody, ribozyme, or a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide binding molecule) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above- described screening assays for freatments as described herein.
A reagent which affects cyclophilin-type peptidyl-prolyl cis-trans isomerase activity can be administered to a human cell, either in vitro or in vivo, to reduce cyclophilin- type peptidyl-prolyl cis-trans isomerase activity. The reagent preferably binds to an expression product of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase gene. If the expression product is a protein, the reagent is preferably an antibody. For treatment of human cells ex vivo, an antibody can be added to a preparation of stem cells which have been removed from the body. The cells can then be replaced in the same or another human body, with or without clonal propagation, as is known in the art.
In one embodiment, the reagent is delivered using a liposome. Preferably, the liposome is stable in the animal into which it has been administered for at least about 30 minutes, more preferably for at least about 1 hour, and even more preferably for at least about 24 hours. A liposome comprises a lipid composition that is capable of targeting a reagent, particularly a polynucleotide, to a particular site in an animal, such as a human. Preferably, the lipid composition of the liposome is capable of targeting to a specific organ of an animal, such as the lung, liver, spleen, heart brain, lymph nodes, and skin.
A liposome useful in the present invention comprises a lipid composition that is capable of fusing with the plasma membrane of the targeted cell to deliver its contents to the cell. Preferably, the transfection efficiency of a liposome is about 0.5 μg of DNA per 16 nmole of liposome delivered to about 106 cells, more preferably about 1.0 μg of DNA per 16 nmole of liposome delivered to about 10δ cells, and even more preferably about 2.0 μg of DNA per 16 nmol of liposome delivered to about 106 cells. Preferably, a liposome is between about 100 and 500 nm, more preferably between about 150 and 450 nm, and even more preferably between about 200 and 400 nm in diameter.
Suitable liposomes for use in the present invention include those liposomes standardly used in, for example, gene delivery methods known to those of skill in the art. More preferred liposomes include liposomes having a polycationic lipid composition and/or liposomes having a cholesterol backbone conjugated to polyethylene glycol. Optionally, a liposome comprises a compound capable of targeting the liposome to a particular cell type, such as a cell-specific ligand exposed on the outer surface of the liposome. Complexing a liposome with a reagent such as an antisense oligonucleotide or ribozyme can be achieved using methods which are standard in the art (see, for example, U.S. Patent 5,705,151). Preferably, from about 0J μg to about 10 μg of polynucleotide is combined with about 8 nmol of liposomes, more preferably from about 0.5 μg to about 5 μg of polynucleotides are combined with about 8 nmol liposomes, and even more preferably about 1.0 μg of polynucleotides is combined with about 8 nmol liposomes.
In another embodiment, antibodies can be delivered to specific tissues in vivo using receptor-mediated targeted delivery. Receptor-mediated DNA delivery techniques are taught in, for example, Findeis et al. Trends in Biotechnol 11, 202-05 (1993); Chiou et ah, GENE THERAPEUTICS: METHODS AND APPLICATIONS, OF DIRECT GENE TRANSFER (J.A. Wolff, ed.) (1994); Wu & Wu, J. Biol. Chem. 263, 621-24 (1988); Wu et ah, J. Biol. Chem. 269, 542-46 (1994); Zenke et ah, Proc. Natl. Acad. Sci.
USA. 87, 3655-59 (1990); Wu et ah, J. Biol. Chem. 266, 338-42 (1991).
Determination of a Therapeutically Effective Dose
The determination of a therapeutically effective dose is well within the capability of those skilled in the art. A therapeutically effective dose refers to that amount of active ingredient which increases or decreases cyclophilin-type peptidyl-prolyl cis- trans isomerase activity relative to the cyclophilin-type peptidyl-prolyl cis-trans isomerase activity which occurs in the absence of the therapeutically effective dose.
For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models, usually mice, rabbits, dogs, or pigs. The animal model also can be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans. Therapeutic efficacy and toxicity, e.g., ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population), can be determined by standard pharmaceutical procedures in cell cultures or experimental animals. The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50.
Pharmaceutical compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concenfrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
The exact dosage will be determined by the practitioner, in light of factors related to the subject that requires treatment. Dosage and administration are adjusted to provide sufficient levels of the active ingredient or to maintain the desired effect.
Factors which can be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long-acting pharmaceutical compositions can be administered every 3 to 4 days, every week, or once every two weeks depending on the half-life and clearance rate of the particular formulation.
Normal dosage amounts can vary from 0J to 100,000 micrograms, up to a total dose of about 1 g, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc. If the reagent is a single-chain antibody, polynucleotides encoding the antibody can be constructed and introduced into a cell either ex vivo or in vivo using well- established techniques including, but not limited to, fransferrin-polycation-mediated DNA transfer, fransfection with naked or encapsulated nucleic acids, liposome- mediated cellular fusion, intracellular transportation of DNA-coated latex beads, protoplast fusion, viral infection, elecfroporation, "gene gun," and DEAE- or calcium phosphate-mediated fransfection.
Effective in vivo dosages of an antibody are in the range of about 5 μg to about 50 μg/kg, about 50 μg to about 5 mg kg, about 100 μg to about 500 μg/kg of patient body weight, and about 200 to about 250 μg/kg of patient body weight. For administration of polynucleotides encoding single-chain antibodies, effective in vivo dosages are in the range of about 100 ng to about 200 ng, 500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg to about 100 μg of DNA.
If the expression product is mRNA, the reagent is preferably an antisense oligonucleotide or a ribozyme. Polynucleotides which express antisense oligo- nucleotides or ribozymes can be introduced into cells by a variety of methods, as described above.
Preferably, a reagent reduces expression of a cyclophilin-type peptidyl-prolyl cis- frans isomerase gene or the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% relative to the absence of the reagent. The effectiveness of the mechanism chosen to decrease the level of expression of a cyclophilin-type peptidyl- prolyl cis-frans isomerase gene or the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide can be assessed using methods well known in the art, such as hybridization of nucleotide probes to cyclophilin-type peptidyl-prolyl cis- trans isomerase-specific mRNA, quantitative RT-PCR, immunologic detection of a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, or measurement of cyclophilin-type peptidyl-prolyl cis-trans isomerase activity.
In any of the embodiments described above, any of the pharmaceutical compositions of the invention can be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy can be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents can act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.
Any of the therapeutic methods described above can be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.
Diagnostic Methods
Human cyclophilin-type peptidyl-prolyl cis-frans isomerase also can be used in diagnostic assays for detecting diseases and abnormalities or susceptibility to diseases and abnormalities related to the presence of mutations in the nucleic acid sequences which encode the enzyme. For example, differences can be determined between the cDNA or genomic sequence encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase in individuals afflicted with a disease and in normal individuals. If a mutation is observed in some or all of the afflicted individuals but not in normal individuals, then the mutation is likely to be the causative agent of the disease.
Sequence differences between a reference gene and a gene having mutations can be revealed by the direct DNA sequencing method. In addition, cloned DNA segments can be employed as probes to detect specific DNA segments. The sensitivity of this method is greatly enhanced when combined with PCR. For example, a sequencing primer can be used with a double-stranded PCR product or a single-stranded template molecule generated by a modified PCR. The sequence determination is performed by conventional procedures using radiolabeled nucleotides or by automatic sequencing procedures using fluorescent tags.
Genetic testing based on DNA sequence differences can be carried out by detection of alteration in electrophoretic mobility of DNA fragments in gels with or without denaturing agents. Small sequence deletions and insertions can be visualized, for example, by high resolution gel electrophoresis. DNA fragments of different sequences can be distinguished on denaturing formamide gradient gels in which the mobilities of different DNA fragments are retarded in the gel at different positions according to their specific melting or partial melting temperatures (see, e.g., Myers et ah, Science 230, 1242, 1985). Sequence changes at specific locations can also be revealed by nuclease protection assays, such as RNase and S 1 protection or the chemical cleavage method (e.g., Cotton et ah, Proc. Natl. Acad. Sci. USA 85, 4397-4401, 1985). Thus, the detection of a specific DNA sequence can be performed by methods such as hybridization, RNase protection, chemical cleavage, direct DNA sequencing or the use of restriction enzymes and Southern blotting of genomic DNA. In addition to direct methods such as gel-electrophoresis and DNA sequencing, mutations can also be detected by in situ analysis.
Altered levels of a cyclophilin-type peptidyl-prolyl cis-trans isomerase also can be detected in various tissues. Assays used to detect levels of the receptor polypeptides in a body sample, such as blood or a tissue biopsy, derived from a host are well known to those of skill in the art and include radioimmunoassays, competitive binding assays, Western blot analysis, and ELISA assays.,
All patents and patent applications cited in this disclosure are expressly incorporated herein by reference. The above disclosure generally describes the present invention. A more complete understanding can be obtained by reference to the following specific examples which are provided for purposes of illustration only and are not intended to limit the scope of the invention.
EXAMPLE 1
Detection of cyclophilin-type peptidyl-prolyl cis-trans isomerase activity
The polynucleotide of SEQ ID NO: 1 is inserted into the expression vector pCEV4 and the expression vector pCEV4-cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide obtained is transfected into human embryonic kidney 293 cells. From these cells extracts are obtained and peptidyl prolyl cis/trans isomerase activity is assayed by as described by Rahfeld, J. U., et al. (1994; FEBS Lett. 352: 180-184). The assay is performed at 10 °C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and the cell extracts at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 μl) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above. The trans to cis conversion is measured by the hydrolysis of the cis conformer by chymotrypsin, producing 4-nitroanilide which is detected specfrophotometrically by absorbance at 390 nm. 4-Nitroanilide appears in a time-dependent manner and is proportional to the amount of cyclophilin-type peptidyl-prolyl cis-trans isomerase in the assay. It is shown that the polypeptide of SEQ ID NO: 2 has a cyclophilin-type peptidyl-prolyl cis-frans isomerase activity.
EXAMPLE 2
Expression of recombinant human cyclophilin-type peptidyl-prolyl cis-trans isomerase
The Pichia pastoris expression vector pPICZB (Invitrogen, San Diego, CA) is used to produce large quantities of recombinant human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides in yeast. The cyclophilin-type peptidyl-prolyl cis- trans isomerase-encoding DNA sequence is derived from SEQ ID NO: 15. Before insertion into vector pPICZB, the DNA sequence is modified by well known methods in such a way that it contains at its 5 '-end an initiation codon and at its - OS ¬
S' -end an enterokinase cleavage site, a His6 reporter tag and a termination codon. Moreover, at both termini recognition sequences for restriction endonucleases are added and after digestion of the multiple cloning site of pPICZ B with the corresponding restriction enzymes the modified DNA sequence is ligated into pPICZB. This expression vector is designed for inducible expression in Pichia pastoris, driven by a yeast promoter. The resulting pPICZ/md-His6 vector is used to transform the yeast.
The yeast is cultivated under usual conditions in 5 liter shake flasks and the recombinantly produced protein isolated from the culture by affinity chromatography
(Ni-NTA-Resin) in the presence of 8 M urea. The bound polypeptide is eluted with buffer, pH 3.5, and neufralized. Separation of the polypeptide from the His6 reporter tag is accomplished by site-specific proteolysis using enterokinase (Invifrogen, San Diego, CA) according to manufacturer's instructions. Purified human cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide is obtained.
EXAMPLE 3
Identification of test compounds that bind to cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptides
Purified cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptides comprising a glutathione-S-transferase protein and absorbed onto glutathione-derivatized wells of 96-well microtiter plates are contacted with test compounds from a small molecule library at pH 7.0 in a physiological buffer solution. Human cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptides comprise the amino acid sequence shown in SEQ ID NO: 16. The test compounds comprise a fluorescent tag. The samples are incubated for 5 minutes to one hour. Control samples are incubated in the absence of a test compound. The buffer solution containing the test compounds is washed from the wells. Binding of a test compound to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide is detected by fluorescence measurements of the contents of the wells. A test compound which increases the fluorescence in a well by at least 15% relative to fluorescence of a well in which a test compound is not incubated is identified as a compound which binds to a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide.
EXAMPLE 4 Identification of a test compound which decreases cyclophilin-type peptidyl-prolyl cis-trans isomerase gene expression
A test compound is administered to a culture of human cells transfected with a cyclophilin-type peptidyl-prolyl cis-trans isomerase expression construct and incubated at 37 °C for 10 to 45 minutes. A culture of the same type of cells which have not been transfected is incubated for the same time without the test compound to provide a negative control.
RNA is isolated from the two cultures as described in Chirgwin et ah, Biochem. 18, 5294-99, 1979). Northern blots are prepared using 20 to 30 μg total RNA and hybridized with a 32P-labeled cyclophilin-type peptidyl-prolyl cis-trans isomerase- specific probe at 65 ° C in Express-hyb (CLONTECH). The probe comprises at least 11 contiguous nucleotides selected from the complement of SEQ ID NO: 15. A test compound which decreases the cyclophilin-type peptidyl-prolyl cis-trans isomerase- specific signal relative to the signal obtained in the absence of the test compound is identified as an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase gene expression. EXAMPLE 5
Identification of a test compound which decreases cyclophilin-type peptidyl-prolyl cis-trans isomerase activity
A test compound is administered to a culture of human cells fransfected with a cyclophilin-type peptidyl-prolyl cis-frans isomerase expression construct and incubated at 37 °C for 10 to 45 minutes. A culture of the same type of cells which have not been transfected is incubated for the same time without the test compound to provide a negative control.
Peptidyl prolyl cis/trans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J. U., et al. (1994; FEBS Lett. 352: 180-184). The assay is performed at 10 °C. in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and CPCI at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa-Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 μl) of the substrate dissolved in dimethyl sulf oxide (10 mg/ml) is added to the reaction mixture described above. The trans to cis conversion is measured by the hydrolysis of the cis conformer by chymotrypsin, producing 4-nitroanilide which is detected spectro- photometrically by absorbance at 390 nm. 4-Nifroanilide appears in a time-dependent manner and is proportional to the amount of cyclophilin-type peptidyl-prolyl cis- trans isomerase in the assay.
A test compound which decreases the activity of the cyclophilin-type peptidyl-prolyl cis-frans isomerase relative to the activity in the absence of the test compound is identified as an inhibitor of cyclophilin-type peptidyl-prolyl cis-trans isomerase activity. EXAMPLE 6
Functional Assays
Cyclophilin-type peptidyl-prolyl cis-trans isomerase function is assessed by expressing the sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include pCMV SPORT (Life Technologies) and pCR3J (Invitrogen, Carlsbad Calif), both of which contain the cytomegalovirus promoter. 5-10 μg of recombinant vector are fransiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or elecfroporation. One to two μg of an additional plasmid containing sequences encoding a marker protein are co-transfected. Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated, laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP, and to evaluate cellular properties, for example, their apoptotic state. FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994) Flow Cytometry, Oxford, New York N. Y. The influence of cyclophilin-type peptidyl-prolyl cis-trans isomerase on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding cyclophilin-type peptidyl-prolyl cis-trans isomerase and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success N.Y.). mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding cyclophilin-type peptidyl- prolyl cis-trans isomerase and other genes of interest can be analyzed by Northern analysis or microarray techniques.
EXAMPLE 7 Quantitative Expression Profiling
Expression profiling is based on a quantitative polymerase chain reaction (PCR) analysis, also called kinetic analysis, first described in Higuchi et al., 1992 and Higuchi et al., 1993. The principle is that at any given cycle within the exponential phase of PCR, the amount of product is proportional to the initial number of template copies. Using this technique, the expression levels of particular genes, which are transcribed from the chromosomes as messenger RNA (mRNA), are measured by first making a DNA copy (cDNA) of the mRNA, and then performing quantitative PCR on the cDNA, a method called quantitative reverse transcription-polymerase chain reaction (quantitative RT-PCR).
Quantitative RT-PCR analysis of RNA from different human tissues was performed to investigate the tissue distribution of cyclophilin-type peptidyl-prolyl cis-trans isomerase mRNA. 25 .mu.g of total RNA from various tissues (Human Total RNA Panel I-V, Clontech Laboratories, Palo Alto, CA, USA) was used as a template to synthsize first-strand cDNA using the SUPERSCRIPT™ First-Strand Synthesis System for RT-PCR (Life Technologies, Rockville , MD, USA). First-strand cDNA synthesis was carried out according to the manufacturer's protocol using oligo (dT) to hybridize to the 3' poly A tails of mRNA and prime the synthesis reaction. 10 ng of the first-strand cDNA was then used as template in a polymerase chain reaction.
The polymerase chain reaction was performed in a LightCycler (Roche Molecular Biochemicals, Indianapolis, IN, USA), in the presence of the DNA-binding fluorescent dye SYBR Green I which binds to the minor groove of the DNA double helix, produced only when double-stranded DNA is successfully synthesized in the reaction (Morrison et al., 1998). Upon binding to double-stranded DNA, SYBR
Green I emits light that can be quantitatively measured by the LightCycler machine. The polymerase chain reaction was carried out using oligonucleotide primers cyclophilin-type peptidyl-prolyl cis-trans isomerase_DNA-L2
(CAAAAAGCATCGTGCTGCAACT) and cyclophilin-type peptidyl-prolyl cis-trans isomerase_DNA-Rl (AATGGCACTGTCCGAAACTCGT) and measurements of the intensity of emitted light were taken following each cycle of the reaction when the reaction had reached a temperature of 81 degrees C. Intensities of emitted light were converted into copy numbers of the gene transcript per nanogram of template cDNA by comparison with simultaneously reacted standards of known concentration.
To correct for differences in mRNA transcription levels per cell in the various tissue types, a normalization procedure was performed using similarly calculated expression levels in the various tissues of five different housekeeping genes: glyceraldehyde-3-ρhosphatase (G3PDH), hypoxanthine guanine phophoribosyl transferase (HPRT), beta-actin, porphobilinogen deaminase (PBGD), and beta-2- microglobulin. The level of housekeeping gene expression is considered to be relatively constant for all tissues (Adams et al., 1993, Adams et al., 1995, Liew et al., 1994) and therefore can be used as a gauge to approximate relative numbers of cells per .mu.g of total RNA used in the cDNA synthesis step. Except for the use of a slightly different set of housekeeping genes and the use of the LightCycler system to measure expression levels, the normalization procedure was similar to that described in the RNA Master Blot User Manual, Apendix C (1997, Clontech Laboratories, Palo Alto, CA, USA). In brief, expression levels of the five housekeeping genes in all tissue samples were measured in three independent reactions per gene using the LightCycler and a constant amount (25 .mu.g) of starting RNA. The calculated copy numbers for each gene, derived from comparison with simultaneously reacted standards of known concentrations, were recorded and the mean number of copies of each gene in all tissue samples was determined. Then for each tissue sample, the expression of each housekeeping gene relative to the mean was calculated, and the average of these values over the five housekeeping genes was found. A normalization factor for each tissue was then calculated by dividing the final value for one of the tissues arbitrarily selected as a standard by the corresponding value for each of the tissues. To normalize an experimentally obtained value for the expression of a particular gene in a tissue sample, the obtained value was multiplied by the normalization factor for the tissue tested.
Results are given in Fig. 21, showing the experimentally obtained copy numbers of mRNA per 10 ng of first-strand cDNA on the left and the normalized values on the right. RNAs used for the cDNA synthesis, along with their supplier and catalog numbers are shown in Table 1.
References
Higuchi, R., Dollinger, G., Walsh, P.S. and Griffith, R. (1992) Simultaneous amplification and detection of specific DNA sequences. BioTechnology 10:413-417.
Higuchi, R., Fodder, C, Dollinger, G. and Watson, R. (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. BioTechnology 11:1026-1030. T.B. Morrison, J.J. Weis & C.T. Wittwer .(1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification.
Biotechniques 24:954-962. Adams, M. D., Keriavage, A. R., Fields, C. & Venter, C. (1993) 3,400 new expressed sequence tags identify diversity of transcripts in human brain. Nature Genet.
4:256-265. Adams, M. D., et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence.
Nature 311 supp:3-174. Liew, C. C, Hwang, D. M., Fung, Y. W., Laurenson, C, Cukerman, E., Tsui, S. &
Lee, C. Y. (1994) A catalog of genes in the cardiovascular system as identified by expressed sequence tags. Proc. Natl. Acad. Sci. USA 91:10145-10649
Table 1. Whole-body-screen tissues
Figure imgf000077_0001
EXAMPLE 8
Treatment of asthma with a reagent that specifically binds to a cyclophilin-type peptidyl-prolyl cis-trans isomerase gene product
Synthesis of antisense cyclophilin-type peptidyl-prolyl cis-frans isomerase oligonucleotides comprising at least 11 contiguous nucleotides selected from the complement of SEQ ID NO:l or 15 is performed on a Pharmacia Gene Assembler series synthesizer using the phosphoroamidite procedure (Uhlmann et ah, Chem. Rev. 90, 534-83, 1990). Following assembly and deprotection, oligonucleotides are ethanol-precipitated twice, dried, and suspended in phosphate-buffered saline (PBS) at the desired concentration. Purity of these oligonucleotides is tested by capillary gel electrophoreses and ion exchange HPLC. Endotoxin levels in the oligonucleotide preparation are determined using the Limulus Amebocyte Assay (Bang, Biol Bull. (Woods Hole, Mass.) 105, 361 -362, 1953).
An aqueous composition containing the antisense oligonucleotides is administered to the patient by inhalation.
Severity of asthma is monitored over a period of days or weeks by noting changes in patients' asthmatic symptoms, measuring lung function, or measuring changes in markers of lung inflammation such as numbers of inflammatory cells or concentrations of inflammatory mediators in fluid sampled from patients' lungs by bronchoalveolar lavage. Asthma severity is reduced due to decreased cyclophilin- type peptidyl-prolyl cis-trans isomerase activity.
EXAMPLE 9
In vivo validation of novel compounds 1. Tests for activity of T cells are used to evaluate agents that modulate the expression or activity of costimulatory molecules-cytokines, cytokine receptors, signalling molecules, or other molecules involved in T cell activation
Mouse anti-CD3-induced cytokine production model:
BALB/c mice are injected with a single intravenous injection of 10 μg of 145- 2C11 (purified hamster anti-mouse CD3 monoclonal antibodies, PHARMINGEN). Compound is administered intraperitoneally 60 min prior to the anti-CD3 mAb injection. Blood is collected 90 min after the antibody injection. Serum is obtained by centrifugation at 3000 r.p.m. for 10 min. Serum levels of cytokines, such as IL-2 and IL-4, or other secreted molecules are determined by an ELISA. Proteins which regulate the CD3 downstream signaling can be evaluated in this model.
2. Tests for activity of B cells are used to evaluate agents that modulate the expression or activity of the B cell receptor, signaling molecules, or other molecules involved in B cell activation/immunoglobulin class switching
Mouse anti-IgD induced IgE production model:
BALB/c mice are injected intravenously with 0.8 mg of purified goat anti- mouse IgD antibody or PBS (defined as day 0). Compound is administered intraperitoneally from day 0 to day 6. On day 7 blood is collected and serum is obtained by centrifugation at 3000 r.p.m. for 10 min. Serum levels of total IgE are determined by YAMASA's ELISA kit and other Ig subtypes are measured by an Ig ELISA KIT (Rougier Bio-tech's, Montreal, Canada). Proteins that regulate IgD downsfream signaling and Ig class switching can be evaluated. 3. Tests for activity of monocytes/macrophages are used to evaluate agents that modulate the expression or activity of signalling molecules, transcription factors.
Mouse LPS-induced TNF- a production model:
Compound is administered to BALB/c mice by infraperitoneal injection and one hour later the mice given LPS (200 μg/mouse) by infraperitoneal injection. Blood is collected 90 minutes after the LPS injection and plasma is obtained. TNF-α concentration in the sample is determined using an ELISA kit. Proteins that regulate downstream effects of LPS stimulation, such as NF-κB activation, can be evaluated.
4. Tests for activity of eosinophils are used to evaluate agents that modulate the expression or activity of the eotaxin receptor, signaling molecules, cyto- skeletal molecules, or adhesion molecules.
Mouse eotaxin-induced eosinophilia model:
BALB/c mice are injected infradermally with a 2.5 ml of air on days -6 and —
3 to prepare an airpouch. On day 0, compound is administered intraperitoneally, and 30 minutes later, IL-5 (300 ng/mouse) is injected intravenously. After an additional 30 minutes, eotaxin is injected (3 μg/mouse, i.d.). Four hours after the eotaxin injection, leukocytes in the airpouch exudate are collected and the number of total cells is counted.
Differential cell counts in the exudate are performed by staining with May- Grunwald Gimsa solution. Proteins that regulate signaling by the eotaxin receptor or regulate eosinophil trafficking can be evaluated.
5. Passive cutaneous anaphylaxis (PC A) test in rats 6 Weeks old male Wistar rats are sensitized intradermally (i.d.) on their shaved backs with 50 μl of 0J μg/ml mouse anti-DNP IgE monoclonal antibody (SPE-7) under a light anesthesia. After 24 hours, the rats are challenged intravenously with 1 ml of saline containing 0.6 mg DNP-BSA (30) (LSL CO., LTD) and 0.005 g of Evans blue. Compounds are injected intraperitoneally (i.p.) 0.5 hr prior to antigen injection. Rats without the sensitization, challenge, and compound treatment are used as a control and rats with sensitization, challenge and vehicle treatment are used to determine the value without inhibition. Thirty minutes after the challenge, the rats are sacrificed, and the skin of the back is removed. Evans blue dye in the skin is extracted in formamide overnight at 63°C. Absorbance at 620 nm is then measured to obtain the optical density of the leaked dye.
Percent inhibition of PC A with a compound is calculated as follows:
% inhibition = {(mean vehicle value - sample value)/(mean vehicle value mean control value)} x 100
Proteins that regulate mast cell degranulation, vascular permeability, or receptor antagonists against histamine receptors, serotonin receptors, or cysteinyl leukofriene receptors can be evaluated.
6. Anaphylactic bronchoconsfriction in rats
6 Weeks old male Wistar rats are sensitized intravenously (i.v.) with 10 μg mouse anti-DNP IgE, SPE-7, and 1 days later, the rats are challenged intravenously with 0.3 ml of saline containing 1.5 mg DNP-BSA (30) under anesthesia with urethane (1000 mg/kg, i.p.) and gallamine (50 mg/kg, i.v.). The trachea is cannulated for artifical respiration (2 ml/stroke, 70 strokes/min). Pulmonary inflation pressure (PIP) is recorded thruogh a side-arm of the cannula connected to a pressure transducer. Changes in PIP reflect a change of both resistance and compliance of the lungs. To evaluate a compound, the compound is given i.v. 5 min before challenge.
Proteins that regulate mast cell degranulation, vascular permeability or receptor antagonists against histamine receptors, serotonin receptors, or cysteinyl leukofriene receptors can be evaluated. Proteins that regulate the contraction of smooth muscle can be also evaluated.
7. T cell adhesion to smooth muscle cells or endothelial cells
A purified population of T cells is prepared by ficoll density cenfrifugation followed by separation on a nylon wool column, rosetting with sheep red blood cells, or using magnetic beads coated with antibodies. The T cells are activated with mitogen for 36 to 42 hours and labeled with 3H-thymidine during the last 16 hours of the activation.
Airway smooth muscle cells or bronchial microvascular endothelial cells are obtained from lung transplant tissue, from bronchus resections from cancer patients, from cadavers, or as cell lines from commercial sources. If fresh tissue is used as the source of cells, the smooth muscle cells and endothelial cells can be isolated from tissue by dissection followed by digestion for 30-60 minutes in a solution containing
1.7 mM ethyleneglycol-bis-(beta-aminoethylether)-N,N,N',N'-tetraacetic acid, 640 U/ml collagenase, 10 mg/ml soybean trypsin inhibitor, and 10 U/ml elastase. The smooth muscle cells or endothelial cells are grown in 24-well tissue culture dishes until confluent and then treated with a test compound and inflammatory mediators, such as TNF- for 24 hours. To measure adhesion, 6 x 105 T cells are added per well and allowed to adhere for one hour at 37°C. Nonadherent cells are removed by washing six times gently with medium. Finally, the remaining adherent cells are lysed by adding 300 μl 1% Triton-X 100 in PBS to each well and quantitating the radioactivity in a scintillation counter. The percent binding is calculated as counts recovered from adherent cells/total input counts x 100%

Claims

1. An isolated polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide and being selected from the group consisting of: a) a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide comprising an amino acid sequence selected form the group consisting of: amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 2; the amino acid sequence shown in SEQ ID NO: 2; amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO: 16; and the amino acid sequence shown in SEQ ID NO: 16. b) a polynucleotide comprising the sequence of SEQ ID NO: 1 or 15; c) a polynucleotide which hybridizes under stringent conditions to a polynucleotide specified in (a) and (b); d) a polynucleotide the sequence of which deviates from the polynucleotide sequences specified in (a) to (c) due to the degeneration of the genetic code; and e) a polynucleotide which represents a fragment, derivative or allelic variation of a polynucleotide sequence specified in (a to (d).
2. An expression vector containing any polynucleotide of claim 1.
3. A host cell containing the expression vector of claim 2.
4. A substantially purified cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide encoded by a polynucleotide of claim 1.
5. A method for producing a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide, wherein the method comprises the following steps: a) culturing the host cell of claim 3 under conditions suitable for the expression of the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide; and b) recovering the cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide from the host cell culture.
6. A method for detection of a polynucleotide encoding a cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide in a biological sample comprising the following steps: a) hybridizing any polynucleotide of claim 1 to a nucleic acid material of a biological sample, thereby forming a hybridization complex; and b) detecting said hybridization complex.
7. The method of claim 6, wherein before hybridization, the nucleic acid material of the biological sample is amplified.
8. A method for the detection of a polynucleotide of claim 1 or a cyclophilin- type peptidyl-prolyl cis-trans isomerase polypeptide of claim 4 comprising the steps of: contacting a biological sample with a reagent which specifically interacts with the polynucleotide or the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide.
9. A diagnostic kit for conducting the method of any one of claims 6 to 8.
10. A method of screening for agents which decrease the activity of a cyclophilin- type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a test compound with any cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide encoded by any polynucleotide of claim 1; detecting binding of the test compound to the cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide, wherein a test compound which binds to the polypeptide is identified as a potential therapeutic agent for decreasing the activity of a cyclophilin-type peptidyl-prolyl cis-frans isomerase.
11. A method of screening for agents which regulate the activity of a cyclophilin- type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a test compound with a cyclophilin-type peptidyl-prolyl cis-frans isomerase polypeptide encoded by any polynucleotide of claim 1; and detecting a cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide, wherein a test compound which increases the cyclophilin-type peptidyl-prolyl cis-trans isomerase activity is identified as a potential therapeutic agent for increasing the activity of the cyclophilin-type peptidyl- prolyl cis-frans isomerase, and wherein a test compound which decreases the cyclophilin-type peptidyl-prolyl cis-trans isomerase activity of the polypeptide is identified as a potential therapeutic agent for decreasing the activity of the cyclophilin-type peptidyl-prolyl cis-trans isomerase.
12. A method of screening for agents which decrease the activity of a cyclophilin- type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a test compound with any polynucleotide of claim 1 and detecting binding of the test compound to the polynucleotide, wherein a test compound which binds to the polynucleotide is identified as a potential therapeutic agent for decreasing the activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase.
13. A method of reducing the activity of cyclophilin-type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a cell with a reagent which specifically binds to any polynucleotide of claim 1 or any cyclophilin-type peptidyl-prolyl cis-trans isomerase polypeptide of claim 4, whereby the activity of cyclophilin-type peptidyl-prolyl cis-frans isomerase is reduced.
14. A reagent that modulates the activity of a cyclophilin-type peptidyl-prolyl cis- trans isomerase polypeptide or a polynucleotide wherein said reagent is identified by the method of any of the claim 10 to 12.
15. A pharmaceutical composition, comprising: the expression vector of claim 2 or the reagent of claim 14 and a pharmaceutically acceptable carrier.
16. Use of the expression vector of claim 2 or the reagent of claim 14 to produce a medicament for modulating the activity of a cyclophilin-type peptidyl- prolyl cis-trans isomerase polypeptide in a disease.
17. Use of claim 16 wherein the disease is cancer, asthma, an autoimmune/inflammatory disorder, or a reproductive disorder.
18. A cDNA encoding a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16.
19. The cDNA of claim 18 which comprises SEQ ID NO: 1 or 15.
20. The cDNA of claim 18 which consists of SEQ ID NO: 1 or 15.
21. An expression vector comprising a polynucleotide which encodes a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16.
22. The expression vector of claim 21 wherein the polynucleotide consists of SEQ ID NOJ or l5.
23. A host cell comprising an expression vector which encodes a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16.
24. The host cell of claim 23 wherein the polynucleotide consists of SEQ ID NO:l or 15.
25. A purified polypeptide comprising the amino acid sequence shown in SEQ ID
NO:2 or 16.
26. The purified polypeptide of claim 25 which consists of the amino acid sequence shown in SEQ ID NO: 2 or 16.
27. A fusion protein comprising a polypeptide having the amino acid sequence shown in SEQ ID NO:2 or 16.
28. A method of producing a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16, comprising the steps of: culturing a host cell comprising an expression vector which encodes the polypeptide under conditions whereby the polypeptide is expressed; and isolating the polypeptide.
29. The method of claim 28 wherein the expression vector comprises SEQ ID
NO:l or 15.
30. A method of detecting a coding sequence for a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16, comprising the steps of: hybridizing a polynucleotide comprising 11 contiguous nucleotides of SEQ ID NO:l or 15 to nucleic acid material of a biological sample, thereby forming a hybridization complex; and detecting the hybridization complex.
31. The method of claim 30 further comprising the step of amplifying the nucleic acid material before the step of hybridizing.
32. A kit for detecting a coding sequence for a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16, comprising: a polynucleotide comprising 11 contiguous nucleotides of SEQ ID NO:l or
15; and instructions for the method of claim 30.
33. A method of detecting a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16, comprising the steps of: contacting a biological sample with a reagent that specifically binds to the polypeptide to form a reagent-polypeptide complex; and detecting the reagent-polypeptide complex.
34. The method of claim 33 wherein the reagent is an antibody.
35. A kit for detecting a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16, comprising: an antibody which specifically binds to the polypeptide; and instructions for the method of claim 33.
36. A method of screening for agents which can modulate the activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a test compound with a polypeptide comprising an amino acid sequence selected from the group consisting of: (1) amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO:2 or 16 and (2) the amino acid sequence shown in SEQ ID NO:2 or 16; and detecting binding of the test compound to the polypeptide, wherein a test compound which binds to the polypeptide is identified as a potential agent for regulating activity of the human cyclophilin-type peptidyl-prolyl cis-frans isomerase.
37. The method of claim 36 wherein the step of contacting is in a cell.
38. The method of claim 36 wherein the cell is in vitro.
39. The method of claim 36 wherein the step of contacting is in a cell-free system.
40. The method of claim 36 wherein the polypeptide comprises a detectable label.
41. The method of claim 36 wherein the test compound comprises a detectable label.
42. The method of claim 36 wherein the test compound displaces a labeled ligand which is bound to the polypeptide.
43. The method of claim 36 wherein the polypeptide is bound to a solid support.
44. The method of claim 36 wherein the test compound is bound to a solid support.
45. A method of screening for agents which modulate an activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase, comprising the steps of: contacting a test compound with a polypeptide comprising an amino acid sequence selected from the group consisting of: (1) amino acid sequences which are at least about 51% identical to the amino acid sequence shown in SEQ ID NO:2 or 16 and (2) the amino acid sequence shown in SEQ ID NO:2 or 16; and detecting an activity of the polypeptide, wherein a test compound which increases the activity of the polypeptide is identified as a potential agent for increasing the activity of the human cyclophilin-type peptidyl-prolyl cis-trans isomerase, and wherein a test compound which decreases the activity of the polypeptide is identified as a potential agent for decreasing the activity of the
' human cyclophilin-type peptidyl-prolyl cis-trans isomerase.
46. The method of claim 45 wherein the step of contacting is in a cell.
47. The method of claim 45 wherein the cell is in vitro.
48. The method of claim 45 wherein the step of contacting is in a cell-free system.
49. A method of screening for agents which modulate an activity of a human cyclophilin-type peptidyl-prolyl cis-frans isomerase, comprising the steps of: contacting a test compound with a product encoded by a polynucleotide which comprises the nucleotide sequence shown in SEQ ID NOJ or 15; and detecting binding of the test compound to the product, wherein a test compound which binds to the product is identified as a potential agent for regulating the activity of the human cyclophilin-type peptidyl-prolyl cis-trans isomerase.
50. The method of claim 49 wherein the product is a polypeptide.
51. The method of claim 49 wherein the product is RNA.
52. A method of reducing activity of a human cyclophilin-type peptidyl-prolyl cis-frans isomerase, comprising the step of: contacting a cell with a reagent which specifically binds to a product encoded by a polynucleotide comprising the nucleotide sequence shown in SEQ ID NO:l or 15, whereby the activity of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase is reduced.
53. The method of claim 52 wherein the product is a polypeptide.
54. The method of claim 53 wherein the reagent is an antibody.
55. The method of claim 52 wherein the product is RNA.
56. The method of claim 55 wherein the reagent is an antisense oligonucleotide.
57. The method of claim 56 wherein the reagent is a ribozyme.
58. The method of claim 52 wherein the cell is in vitro.
59. The method of claim 52 wherein the cell is in vivo.
60. A pharmaceutical composition, comprising: a reagent which specifically binds to a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16; and a pharmaceutically acceptable carrier.
61. The pharmaceutical composition of claim 60 wherein the reagent is an antibody.
62. A pharmaceutical composition, comprising: a reagent which specifically binds to a product of a polynucleotide comprising the nucleotide sequence shown in SEQ ID NO:l or 15; and a pharmaceutically acceptable carrier.
63. The pharmaceutical composition of claim 62 wherein the reagent is a ribozyme.
64. The pharmaceutical composition of claim 62 wherein the reagent is an antisense oligonucleotide.
65. The pharmaceutical composition of claim 62 wherein the reagent is an antibody.
66. A pharmaceutical composition, comprising: an expression vector encoding a polypeptide comprising the amino acid sequence shown in SEQ ID NO:2 or 16; and a pharmaceutically acceptable carrier.
67. The pharmaceutical composition of claim 66 wherein the expression vector comprises SEQ ID NO.J or 15.
68. A method of treating a cyclophilin-type peptidyl-prolyl cis-trans isomerase dysfunction related disease, wherein the disease is selected from cancer, asthma, an autoimmune/inflammatory disorder, or a reproductive disorder comprising the step of: administering to a patient in need thereof a therapeutically effective dose of a reagent that modulates a function of a human cyclophilin-type peptidyl-prolyl cis-trans isomerase, whereby symptoms of the cyclophilin-type peptidyl- prolyl cis-frans isomerase dysfunction related disease are ameliorated.
69. The method of claim 68 wherein the reagent is identified by the method of claim 36.
70. The method of claim 68 wherein the reagent is identified by the method of claim 45.
71. The method of claim 68 wherein the reagent is identified by the method of claim 49.
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EP1932919A1 (en) * 2006-12-13 2008-06-18 Novartis AG Yeast-based screening method for the identification of compounds inhibiting a human peptidyl-prolyl cis/trans isomerase of the parvulin family
WO2023277640A1 (en) * 2021-07-02 2023-01-05 연세대학교 산학협력단 Pharmaceutical composition for treating cancer

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US5968802A (en) * 1995-06-07 1999-10-19 Wang; Bruce Nuclear cyclophilin
US6030825A (en) * 1998-08-19 2000-02-29 Incyte Pharmaceuticals, Inc. Cyclophilin-type peptidyl-prolyl cis/trans isomerase
AU2001241415A1 (en) * 2000-01-31 2001-08-07 Human Genome Sciences, Inc. Nucleic acids, proteins, and antibodies
AU2001234944A1 (en) * 2000-02-03 2001-08-14 Hyseq, Inc. Novel nucleic acids and polypeptides
JP2001245671A (en) * 2000-03-07 2001-09-11 Chiba Prefecture Novel genes and novel gene fragments cloned in human neuroblastoma

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1932919A1 (en) * 2006-12-13 2008-06-18 Novartis AG Yeast-based screening method for the identification of compounds inhibiting a human peptidyl-prolyl cis/trans isomerase of the parvulin family
WO2023277640A1 (en) * 2021-07-02 2023-01-05 연세대학교 산학협력단 Pharmaceutical composition for treating cancer

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