WO2006053125A2 - Gp201: procedes et compositions de traitement du cancer - Google Patents

Gp201: procedes et compositions de traitement du cancer Download PDF

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WO2006053125A2
WO2006053125A2 PCT/US2005/040738 US2005040738W WO2006053125A2 WO 2006053125 A2 WO2006053125 A2 WO 2006053125A2 US 2005040738 W US2005040738 W US 2005040738W WO 2006053125 A2 WO2006053125 A2 WO 2006053125A2
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mammal
expression
cancer
cell
tumor
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PCT/US2005/040738
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WO2006053125A3 (fr
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Maria I. Chiu
Murray Robinson
Ronan O'hagan
Karuppiah Kannan
David Bailey
Lorena Lerner
Ti Cai
Heidi Okamura
S. K. Wright
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Aveo Pharmaceuticals, Inc.
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Publication of WO2006053125A2 publication Critical patent/WO2006053125A2/fr
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    • 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
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • 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
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/01—Phosphotransferases with an alcohol group as acceptor (2.7.1)
    • C12Y207/01037—Protein kinase (2.7.1.37)
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/14—Type of nucleic acid interfering N.A.
    • 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
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/53—Physical structure partially self-complementary or closed

Definitions

  • the field of the invention is molecular biology and oncology. Background of the Invention
  • GP201 functionally complements the HER2 oncogene in an inducible, spontaneous, in vivo cancer model (mouse). It has also been discovered that interfering RNAs that target GP201 expression inhibit the growth of certain tumor cells in vitro.
  • the invention provides GP201 antagonists that inhibit GP201 gene expression or GP201 protein activity.
  • Antagonists that inhibit GP201 gene expression include an interfering RNA that inhibits the expression of GP201, a GP201 antisense nucleic acid, and an anti-GP201 ribozyme.
  • the sense strand sequences of four exemplary siRNAs of the invention are SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5 and SEQ ID NO: 6.
  • GP201 antagonists of the invention inhibit tumorigenesis, tumor development, tumor maintenance, tumor recurrence, tumor growth, or the growth of tumor cells in vitro.
  • the invention also provides methods of inducing apoptosis in a cell. The methods include contacting the cell with an effective amount of a GP201 antagonist.
  • the invention also provides methods of treating a hyperproliferative condition in a mammal, e.g., a human patient.
  • the method includes administering to the mammal an effective amount of a GP201 antagonist.
  • Cancer is an example of such a hyperproliferative condition.
  • Other examples of hyperproliferative conditions are uncontrolled angiogenesis, psoriasis, arteriosclerosis, arthritis and diabetic retinopathy.
  • the method of treating a hyperproliferative condition includes administering a second therapeutic agent.
  • the second therapeutic agent can be, for example, an anti-angio genie agent, anti-metastatic agent, agent that induces hypoxia, agent that induces apoptosis, or an agent that inhibits cell survival signals.
  • cancer therapeutics include farnesyl transferase inhibitors, tamoxifen, herceptin, taxol, STI571, cisplatin, fluorocil, Cytoxan, and ionizing radiation.
  • the invention also provides a host cell containing a recombinant DNA construct that includes a GP201 -encoding sequence operably linked to an expression control sequence, and a genetic mutation that causes the host cell to have a greater likelihood of becoming a cancer cell than a cell not comprising the genetic mutation.
  • a mutation can be, e.g., a mutation that deletes or inactivates a tumor suppressor gene, or a mutation that activates an oncogene.
  • tumor suppressor genes include INK4a, P53, Rb, PTEN, LATS, APAFl, Caspase 8, APC, DPC4, KLF6, GSTPl, ELAC2/HPC2 and NKX3.1.
  • oncogenes include K-RAS, H-RAS, N-RAS, EGFR, MDM2, TGF- ⁇ , RhoC, AKT family members, myc, ⁇ -catenin, PGDF, C-MET, PDK-CA, CDK4, cyclin B 1 , cyclin D 1 , estrogen receptor gene, progesterone receptor gene, HER2 (also known as neu or ErbB2), ErbBl, ErbB3, ErbB4, TGF ⁇ , ras-GAP, She, Nek, Src, Yes, Fyn, Wnt, and Bcl2.
  • the invention also provides a genetically modified non-human mammal, e.g., a mouse, at least some of whose cells contain a genome that includes: (a) a recombinant GP201 -encoding nucleic acid operably linked to an expression control sequence, and (b) a genetic mutation that causes the mammal to have a greater susceptibility to cancer than a mammal whose cells do not contain the genetic mutation.
  • the genetic mutation involves a tumor suppressor gene and renders the tumor suppressor gene non-functional.
  • the genetically modified nonhuman mammal can be a conventional transgenic mammal, all of whose cells contain the recombinant GP201 -encoding nucleic acid operably linked to an expression control sequence, and the genetic mutation that causes the mammal to have increased susceptibility to cancer.
  • the mammal is a chimeric mammal at least some of whose, but not all of whose, somatic cells contain the recombinant GP201 -encoding nucleic acid operably linked to an expression control sequence, and the genetic mutation that causes the mammal to have a increased susceptibility to cancer.
  • the percentage of somatic cells containing the recombinant GP201 -encoding nucleic acid operably linked to an expression control sequence, and a genetic mutation that causes the mammal to have a greater susceptibility to cancer is between 5% and 95%. Preferably it is between 15% and 85%.
  • the GP201 -encoding nucleic acid is operably linked to a tissue-specific expression system.
  • the invention also provides a genetically modified nonhuman mammal, wherein the genetic modification reduces or eliminates expression of one or both of the mammal's endogenous GP201 alleles.
  • a genetic modification reduces or eliminates expression of one or both of the mammal's endogenous GP201 alleles.
  • Such reduction or elimination of GP201 expression can be achieved, for example, when the genetic modification is addition of an RNAi expression construct targeting GP201 gene expression, or when the genetic modification is a knockout of one or both of the GP201 alleles.
  • Such a genetic modification can reduce or eliminate GP201 expression in a tissue- specific manner.
  • the genetically modified mammal is chimeric with respect to the genetic modification.
  • the invention also provides a screening method for identifying a compound useful for treating a hyperproliferative condition such as cancer.
  • the method includes: (a) identifying a biomarker whose level correlates with inhibition of GP201 activity; and (b) detecting a change in the level of the biomarker in the presence of a test compound relative to the level of the biomarker detected in the absence of the test compound.
  • the invention also provides a screening method for identifiying a compound useful in treatment of a hyperproliferative condition such as cancer.
  • the method includes: (a) providing an inhibitor of GP201 expression or activity; (b) identifying a negative control biomarker pattern formed by a plurality of biomarkers in a cancer cell wherein the cell is not contacted with the inhibitor of GP201 expression or activity; (c) identifying a positive control biomarker pattern formed by a plurality of biomarkers in the cancer cell wherein the cancer cell is contacted with the inhibitor of GP201 expression or activity; (d) identifying a test biomarker pattern formed by a plurality of biomarkers in the cancer cell wherein the cancer cell is contacted with a candidate compound but not contacted with the inhibitor of GP201 expression or activity; and (e) comparing the negative control biomarker pattern, positive control biomarker pattern and test biomarker pattern, and detecting a greater similarity between the positive control biomarker pattern and the test biomarker pattern than between the negative
  • the invention also provides a screening method for identifying a compound that inhibits GP201 activity.
  • the method includes the steps of: (a) providing a suitable reaction mixture containing a GP201 substrate and ATP; (b) adding to the preparation a test compound; (c) adding to the preparation a suitable amount of GP201 ; and (d) detecting a decrease in production of phosphorylated product in the presence of the test compound relative to production of phosphorylated product in the absence of the test compound.
  • the screening method involves a pyruvate kinase/lactate dehydrogenase coupled assay system. Casein is an example of a useful GP 201 substrate for such assay systems.
  • the invention also provides methods of diagnosing an abnormal hype ⁇ roliferative condition, e.g., cancer, in a subject. These methods involve detecting the expression level of a GP201 gene or the activity level of a GP201 protein.
  • An abnormally high level relative to control e.g., at least about 50%, 100%, 150%, 200%, 250%, or 300% higher, indicates an abnormal hyperproliferative condition.
  • all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. In case of conflict, the present specification, including definitions, will control. All publications, patents and other references mentioned herein are incorporated by reference in their entirety.
  • the word "comprise,” or variations such as “comprises” or “comprising” is intended to include the stated integer or group of integers, but not to exclude any other integer or group of integers.
  • GP201 Up-regulation of GP201 contributes to tumorigenesis and tumor maintenance.
  • GP201 was identified as a cancer therapeutic target using the Mammalian Second Site Suppression ("MaSS") screening system described below and in WO 02/079419.
  • the GP201 protein i.e., PLK3 (polo-like kinase 3), also known as CNK,
  • FNK, PRK, and l_44702099 is a putative serine/threonine kinase. It contains both a catalytic domain and a putative regulatory domain.
  • PLK3 is a member of the "polo" family of serine/threonine kinases, and is likely to play a role in cell cycle progression and tumorigenesis.
  • An exemplary human GP201 protein contains 646 amino acid residues and has the following amino acid sequence:
  • nucleotice sequence of one exemplary cDNA encoding this polypeptide is: CCTGGGCGCC AGCGCAGCGT AGCAAATCCA GGCAGCGCCA CGCGCGGCCG
  • AGGCTCTCCT CATGCTGTTT AGTGATGGCA CTGTCCAGGT GAACTTCTAC GGGGACCACA CCAAGCTGAT TCTCAGTGGC TGGGAGCCCC TCCTTGTGAC TTTTGTGGCC CGAAATCGTA GTGCTTGTAC TTACCTCGCT TCCCACCTTC GGCAGCTGGG CTGCTCTCCA GACCTGCGGC AGCGACTCCG CTATGCTCTG CGCCTGCTCC GGGACCGCAG CCCAGCCTAG GACCCAAGCC CTGAGGCCTG AGGCCTGTGC CTGTCAGGCT CTGGCCCTTG CCTT
  • the open reading frame of the above sequence is nucleotides 101-2041
  • GP201 sequences include those identified by GenBank accession numbers GL41872373; GI33872964; GI50487854; and GI41872374.
  • PLK3 transcripts are highly detected in placenta, lung, followed by skeletal muscle, heart, pancreas, ovaries and kidney and weakly detected in liver and brain.
  • the message apparently has a short half-life in cells of hematopoietic origin, and is strongly detected in terminally differentiated macrophages.
  • High expression of PLK3 is detected in cancers of the bladder, breast, colon, ovary, pancreas and lung.
  • PLK3 is also expressed in glioblastomas and specifically in breast cancer associated vascular endothelium.
  • the GP201 gene is likely to be involved in development (including maintenance, progression, angiogenesis, and/or metastasis) of cancers, e.g., cancers found in skin (e.g., melanoma), lung, prostate, breast, colorectal, liver, pancreatic, brain, testicular, ovarian, uterine, cervical, kidney, thyroid, bladder, esophageal, and hematological tissues.
  • cancers e.g., cancers found in skin (e.g., melanoma), lung, prostate, breast, colorectal, liver, pancreatic, brain, testicular, ovarian, uterine, cervical, kidney, thyroid, bladder, esophageal, and hematological tissues.
  • RNA interference RNA interference
  • nucleic acid sequences specifically provided herein are sequences of deoxyribonucleotides. However, the given sequences are to be interpreted as would be appropriate to the polynucleotide composition. For example, if the isolated nucleic acid is RNA, the given sequence intends ribonucleotides, with uridine substituted for thymidine.
  • differences from naturally occurring nucleic acids e.g., non-native bases, altered internucleoside linkages, and post-synthesis modification, can be present throughout the length of the GP201 nucleic acid or can be usefully localized to discrete portions thereof. For example, a chimeric nucleic acid can be synthesized with discrete DNA and RNA domains and demonstrated utility for targeted gene repair. See, e.g., U.S. Pat. Nos. 5,760,012 and 5,731,181.
  • SNPs single nucleotide polymorphisms
  • this invention provides not only isolated nucleic acids identical in sequence to those described with particularity herein, but also isolated nucleic acids that are allelic variants of those particularly described nucleic acid sequences. In some embodiments, such sequence variations result from human intervention, e.g., by random or directed mutagenesis.
  • the invention provides isolated nucleic acid molecules that encode the entirety or part (e.g., at least five, seven, or nine contiguous amino acid residues) of the GP201 protein, including allelic variants of this protein.
  • the genetic code is degenerate and codon choice for optimal expression varies from species to species.
  • the coding sequences of this invention include degenerate variants of the sequences described herein with particularity.
  • the isolated polynucleotide comprises a nucleotide sequence encoding SEQ ID NO: 1.
  • nucleic acids can be used, for example, to express the GP201 protein or specific portions of the protein, either alone or as elements of a fusion protein, e.g., to express epitopic or immunogenic fragments of the GP201 protein.
  • nucleic acids are used to produce non-human mammals of the invention.
  • nucleic acids also can be used as probes to hybridize to GP201 nucleic acids and related nucleic acid sequences.
  • This invention also relates to nucleic acids comprising sequences coding for polypeptides containing conservative amino acid substitutions or moderately conservative amino acid substitutions from those polypeptides described with particularity herein. These amino acid substitutions can be due to, e.g., allelic variations, naturally occurring mutations, or man-made mutations.
  • This invention also relates to isolated polynucleotides that hybridize to one or more of the above-described GP201 nucleic acids.
  • These cross-hybridizing nucleic acids can be used, e.g., as hybridization probes, primers, and/or for expression of proteins that are related to GP201 as isoforms and homo logs, e.g., paralogs, and orthologs.
  • the invention relates to an isolated nucleic acid comprising a sequence that hybridizes under high stringency conditions to a probe comprising a fragment of SEQ ID NO: 2 having at least 15, 16, 18, 20, 24, or 25 nucleotides.
  • high stringency conditions are defined for solution phase hybridization as aqueous hybridization (i.e., free of formamide) in 6X SSC (where 2OX SSC contains 3.0 M NaCl and 0.3 M sodium citrate), 1% SDS at 65°C for 8-12 hours, followed by two washes in 0.2X SSC, 0.1% SDS at 65°C for 20 minutes. It will be appreciated by the skilled worker that hybridization at 65 0 C will occur at different rates depending on a number of factors including the length and percent identity of the sequences which are hybridizing.
  • the hybridizing portion of a reference nucleic acid is typically at least 15 nucleotides in length, and often at least 17 , 20, 25, 30, 35, 40 or 50 nucleotides in length.
  • Cross-hybridizing nucleic acids that hybridize to a larger portion of the reference nucleic acid - for example, to a portion of at least 50, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more nucleotides, up to and including the entire length of the reference nucleic acid, are also useful.
  • nucleic Acid Fragments Fragments of the above-described nucleic acids also relate to this invention.
  • GP201 polypeptide fragment e.g., immunogenic fragment.
  • the nucleic acid probes may comprise a detectable label, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • a detectable label e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor.
  • Such probes can be used as a part of a diagnostic kit for identifying cells or tissues that (i) incorrectly express a GP201 protein, e.g., aberrant splicing, or abnormal mRNA levels, or (ii) harbor a mutation in the GP201 gene, such as a deletion, an insertion, or a point mutation.
  • diagnostic kits preferably include labeled reagents and instructional inserts for their use.
  • the nucleic acid primers can be used in PCR, primer extension and the like. They can be, e.g., at least 6 nucleotides (e.g., at least 7, 8, 9, or 10) in length.
  • the primers can hybridize to an exon sequence of a GP201 gene, e.g., for amplification of a GP201 mRNA or cDNA.
  • the primers can hybridize to an intron sequence or an upstream or downstream regulatory sequence of a GP201 gene, to utilize non-transcribed, e.g., regulatory portions of the genomic structure of a GP201 gene.
  • the nucleic acid primers also can be used, e.g., to prime single base extension (SBE) for SNP detection (see, e.g., U.S. Pat. No. 6,004,744).
  • SBE single base extension
  • Isothermal amplification approaches, such as rolling circle amplification, are also now well- described. See, e.g., Schweitzer et al., Curr. Opin. Biotechnol. 12(l):21-7 (2001); U.S. Patent Nos. 5,854,033 and 5,714,320 and PCT international patent publications WO 97/19193 and WO 00/15779.
  • Rolling circle amplification can be combined with other techniques to facilitate SNP detection.
  • nucleic acid fragments that encode 5 or more contiguous amino acids are useful in directing the synthesis of peptides that have utility in mapping the epitopes of the GP201 protein. See, e.g., Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1984); and U.S. Pat. Nos. 4,708,871 and 5,595,915. Such nucleic acid fragments are also useful in directing the synthesis of peptides that have utility as immunogens.
  • the invention further relates to single exon probes having portions of no more than one exon of the GP201 gene.
  • Such single exon probes have utility in identifying and characterizing splice variants.
  • these probes are useful for identifying and discriminating the expression of distinct isoforms of GP201.
  • Some embodiments of the invention relate to isolated nucleic acids that are antisense polynucleotides that specifically hybridize to GP201 sense polynucleotides.
  • the antisense nucleic acid molecule can be complementary to the entire coding or non-coding region of GP201, but more often is antisense to only a portion of the coding or non-coding region of GP201 mRNA.
  • the antisense oligonucleotide can be complementary to the region surrounding the translation start site of GP201 mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
  • the antisense nucleic acids of this invention may form a stable duplex with its target sequence, or, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix, hi other embodiments, the antisense nucleic acid molecule of the invention is an ⁇ -anomeric nucleic acid molecule.
  • An ⁇ -anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual ⁇ -units, the strands run parallel to each other (Gaultier et al. Nucl. Acids Res 15: 6625-6641 (1987)).
  • An antisense target sequence is a nucleotide sequence specific to GP201, and can be designed through use of a publicly available sequence database, and/or through use of commercially available sequence comparison programs.
  • Antisense nucleic acids of the invention can then be constructed using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been inserted in an antisense orientation, i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest.
  • the antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecule or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids.
  • phosphorothioate derivatives and acridine substituted nucleotides can be used.
  • Phosphorothioate and methylphosphonate antisense oligonucleotides are useful in practicing the invention.
  • the antisense nucleic acid molecule can also comprise a 2'-O-methylribonucleotide (Inoue et al, Nucl. Acids Res.
  • the antisense oligonucleotides may be further modified by adding poly-L-lysine, transferrin, poly lysine, or cholesterol moieties at their 5' end.
  • the antisense molecules will be tested for undesired non-specific effects such as the induction of ds-RNA stress response genes in the interferon pathway. Only those molecules that do not induce a significant non-specific response will be subsequently used.
  • Antisense molecules can be administered to a mammal or generated in situ via an expression vector, such that they bind to cellular RNA and/or genomic DNA encoding a GP201 protein, thereby inhibiting GP201 expression. Suppression of GP201 expression at either the transcriptional or translational level is useful to treat certain cancer conditions in patients or to generate cellular or animal models for cancer characterized by aberrant GP201 expression.
  • An antisense molecule can be administered by direct injection at a tissue site of a subject. Alternatively, an antisense molecule can be designed to target selected cells, e.g., cancer cells overexpressing GP201, and then administered systemically.
  • an antisense nucleic acid of the invention is part of a GP201 -specific ribozyme (or, as modified, a "nucleozyme”).
  • Ribozymes are catalytic RNA molecules with ribonuclease activity capable of cleaving a single- stranded nucleic acid, such as an mRNA, to which they have a complementary region.
  • ribozymes such as hammerhead, hairpin, and Group I intron ribozymes can cleave GP201 mRNA transcripts catalytically, thereby inhibiting translation of GP201 mRNA.
  • a ribozyme having specificity for a GP201- encoding nucleic acid can be designed based upon the nucleotide sequence of a GP201 polynucleotide disclosed herein (SEQ ID NO: 2). See, e.g., U.S. Patent Nos. 5,116,742; 5,334,711; 5,652,094; and 6,204,027.
  • SEQ ID NO: 2 a derivative of a Tetrahymena L- 19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a GP201 -encoding mRNA. See, e.g., Cech et al, U.S. Pat.
  • GP201 mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., Science 261:1411-1418 (1993).
  • the ribozymes and other antisense reagents of this invention include appended groups such as peptides. This is useful for targeting host cell receptors, facilitating transport across the cell membrane (Letsinger et al., Proc. Natl. Acad. Sci. USA 86:6553-6556 (1989); Lemaitre et al., Proc. Natl.
  • GP201 gene can be inhibited by targeting nucleotide sequences complementary to the regulatory region of the GP201, e.g., the GP201 promoter and/or enhancers, to form triple helical structures that prevent transcription of the GP201 gene in target cells.
  • nucleotide sequences complementary to the regulatory region of the GP201 e.g., the GP201 promoter and/or enhancers
  • triple helical structures that prevent transcription of the GP201 gene in target cells.
  • PNA Peptide Nucleic Acids
  • PNA peptide nucleic acids
  • the phosphodiester backbone of the nucleic acid is replaced with an amide-containing backbone, in particular by repeating N-(2-aminoethyl) glycine units linked by amide bonds.
  • Nucleobases are bound directly or indirectly to aza-nitrogen atoms of the amide portion of the backbone, typically by methylene carbonyl linkages.
  • PNA oligomers can be synthesized using conventional solid phase peptide synthesis as described in Hyrup et al., supra; and Perry-O'Keefe et al, Proc. Natl. Acad. Sci. USA 93:14670-675 (1996).
  • GP201-based PNAs can be used in therapeutic and diagnostic applications.
  • PNAs can be used as antisense or antigene agents for sequence- specific modulation of gene expression by, e.g., inducing transcription arrest, inducing translation arrest, or inhibiting replication.
  • GP201 -based PNAs also can be used in the analysis of single base pair mutations in a gene. This can be done by PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., Sl nucleases, or as probes or primers for DNA sequence and hybridization (Hyrup et al., supra; Perry-O'Keefe, supra).
  • PNAs of GP201 are modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art.
  • PNA-DNA chimeras of GP201 can be generated that may combine the advantageous properties of PNA and DNA.
  • Such chimeras allow DNA recognition enzymes, e.g., RNase H and DNA polymerases, to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity.
  • PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup et al., supra).
  • the synthesis of PNA-DNA chimeras can be performed as described in Hyrup, supra and Finn et al., Nucl. Acids Res. 24:3357-63 (1996).
  • RNAi RNA interference
  • dsRNA double-stranded RNA
  • RNAi results in degradation of mRNAs homologous in sequence to the dsRNA.
  • the mediators of the degradation are 21- to 23-nucleotide small interfering RNAs (siRNAs) generated by ribonuclease III cleavage from the longer dsRNAs.
  • Molecules of siRNA typically have 2- to 3-nucleotide 3' overhanging ends resembling the RNAse III processing products of long dsRNAs that normally initiate RNAi. When introduced into a cell, they assemble with an endonuclease complex (RNA-induced silencing complex), which then guides cleavage of the targeted mRNA. This results in a phenotype with suppressed expression of the protein encoded by the targeted mRNA.
  • RNA-induced silencing complex RNA-induced silencing complex
  • the small size of siRNAs avoids activation of the dsRNA-inducible interferon system in mammalian cells. This helps avoid the nonspecific phenotypes normally produced by dsRNA larger than 30 base pairs in somatic cells.
  • Small interfering RNA oligonucleotides can be designed using commercially available software programs, e.g., the OligoEngine siRNA design tool available at http://www.oligoengine.com, or purchased from commercial vendors, e.g., Dharmacon RNA Technologies, Lafayette, CO.
  • Preferred siRNAs of this invention range about 19-29 basepairs in length for the double-stranded portion.
  • the siRNAs are hairpin RNAs having an about 19- 29 bp stem and an about 4-34 nucleotide loop.
  • siRNAs are highly specific for a GP201 target region and may comprise any 19-29 bp fragment of a GP201 mRNA that has at least 1 (e.g., at least 2 or 3) bp mismatch with a non- GP201 -related sequence.
  • the GP201 siRNAs do not bind to RNAs having more than 3 mismatches.
  • the sense strand sequences of four exemplary siRNAs for GP201 are:
  • siRNAs may be used individually or pooled and used in combination. Small interfering RNAs that target an RNA region having 10 or more nucleotide overlap with an aforementioned exemplary target region are also useful.
  • Intracellular transcription of siRNAs can be achieved by cloning the siRNA templates into RNA polymerase III (Pol III) transcription units, which normally encode the small nuclear RNA U6 or the human RNAse P RNA Hl .
  • RNA polymerase III Poly III
  • Two approaches can be used for expressing siRNA: (1) sense and antisense strands constituting the siRNA duplex are transcribed by individual promoters; or (2) siRNAs are expressed as fold-back stem-loop structures that give rise to siRNAs after intracellular processing.
  • Inducible promoters can also be used to drive the expression of the siRNA.
  • the following short hairpin RNAs can be expressed by inserting the following sequences (minus the two terminal UU) after the U6 small RNA promoter.
  • the first base of the following sequences is the transcriptional start site of the U6 promoter.
  • the sequence can be used with a primer specific to the U6 small RNA promoter to form double-stranded DNA in a polymerase chain reaction, using a vector containing this U6 promoter as a template.
  • the PCR product can then be ligated into a vector.
  • sequences below can be added downstream to the U6 promoter by annealing two oligonucleotides, one containing the sense sequence (below) and the other containing the antisense sequence and containing appropriate overhang nucleotides to allow ligation into U6 promoter vector digested by a restriction enzyme.
  • the short hairpin sequence is followed by 4 or more Ts to allow termination of transcription. Expression of the insert leads to expression of a short hairpin RNA.
  • the hairpin structure displays inhibitory effects on GP201 expression.
  • siRNA oligonucleotide or its coding sequence can be delivered into a target cell via a variety of methods, including but not limited to, liposome fusion (transposomes), routine nucleic acid transfection methods such as electroporation, calcium phosphate precipitation, or microinjection, and infection by viral vectors.
  • liposome fusion transposomes
  • routine nucleic acid transfection methods such as electroporation, calcium phosphate precipitation, or microinjection
  • infection by viral vectors including but not limited to, liposome fusion (transposomes), routine nucleic acid transfection methods such as electroporation, calcium phosphate precipitation, or microinjection, and infection by viral vectors.
  • the above-described isolated nucleic acids can be used as hybridization probes to characterize GP201 nucleic acids in both genomic and transcript-derived nucleic acid samples.
  • the probes can be used to detect gross alterations in the GP201 genomic locus, such as deletions, insertions, translocations, and duplications of the GP201 genomic locus.
  • Methods of detection include fluorescence in situ hybridization (FISH) to chromosome spreads, comparative genomic hybridization (CGH), array CGH (e.g., on microarrays containing GP201 -coding sequences or BAC comprising GP201- coding sequences), and spectral karyotyping (SKY).
  • FISH fluorescence in situ hybridization
  • CGH comparative genomic hybridization
  • array CGH e.g., on microarrays containing GP201 -coding sequences or BAC comprising GP201- coding sequences
  • SKY spectral karyotyping
  • the probes also can be used to assess smaller genomic alterations using, e.g., Southern blot detection of restriction fragment length polymorphisms.
  • the nucleic acid probes can be also used to isolate genomic clones that include the nucleic acids of the present invention, which thereafter can be restriction mapped and sequenced to identify deletions, insertions, amplifications, translocations, and substitutions (e.g., SNPs) at the sequence level.
  • the nucleic acid probes can also be used to isolate GP201 nucleic acids from cDNA libraries, permitting sequence level characterization of GP201 RNA messages, including identification of deletions, insertions, truncations (including deletions, insertions, and truncations of exons in alternatively spliced forms) and single nucleotide polymorphisms. Some of the nucleic acids also can be used as amplification primers for real time PCR to detect the above-described genomic alterations. Such genomic alterations of the GP201 gene often play a role in tumor genesis, maintenance and development, and thus can be used as markers for diagnosis and prognosis of GP201 -mediated cancers.
  • the nucleic acid probes can be used to measure the representation of GP201 clones in a cDNA library, used as primers for quantitative real time PCR, or otherwise used to measure expression level of the GP201 gene. Measurement of GP201 expression has particular utility in diagnostic assays for cancer-related conditions associated with abnormal GP201 expression. Moreover, differences in the expression levels of the gene before and after a cancer event (e.g., cancer genesis, maintenance, regression, and metastasis) are useful in determining the effect of a candidate cancer drug, identifying cancer types, designing diagnostics and prognostics, and predicting likely outcome of a cancer therapy.
  • a cancer event e.g., cancer genesis, maintenance, regression, and metastasis
  • the nucleic acids also can be used to introduce mutations (e.g., null mutations, dominant negative mutations, dominant acting mutations) into a GP201 locus of an animal via homologous recombination.
  • mutations e.g., null mutations, dominant negative mutations, dominant acting mutations
  • Such animals e.g., knock out mice
  • homologous recombination can be used to replace the endogenous regulatory elements with heterologous regulatory elements, i.e., elements not natively associated with the gene in the same manner. This can alter the expression of GP201, both for production of GP201 protein, and for gene therapy. See, e.g., U.S. Pat. Nos. 5,981,214; 6,048,524 and 5,272,071.
  • Fragments of the above-described polynucleotides smaller than those typically used for homologous recombination can also be used for targeted gene correction or alteration, possibly by cellular mechanisms different from those engaged during homologous recombination. See, e.g., U.S. Pat. Nos. 5,945,339; 5,888,983; 5,871,984; 5,795,972; 5,780,296; 5,760,012; 5,756,325; 5,731,181; and Culver et al., Nature Biotechnol. 17:989-93 (1999); Gamper et al., Nucl. Acids Res. 28:4332-9 (2000). II. VECTORS AND HOST CELLS A. General Consideration
  • This invention relates to nucleic acid constructs containing one or more of the isolated nucleic acid molecules encoding all or part of GP201.
  • the vectors can be used to propagate the new nucleic acid molecules in host cells, to shuttle the molecules between host cells derived from disparate organisms, to insert the molecules into host genomes, to express sense or antisense RNA transcripts or interfering RNAs, and/or to express GP201 polypeptides.
  • the vectors are derived from virus, plasmid, prokaryotic or eukaryotic chromosomal elements, or some combination thereof, and may optionally include at least one origin of replication, at least one site for insertion of heterologous nucleic acid, and at least one selectable marker.
  • This invention relates to host cells, which can be either prokaryotic (bacteria) or eukaryotic (e.g., yeast, insect, plant and animal cells).
  • a host cell strain may be chosen for its ability to process the expressed protein in the desired fashion.
  • post-translational modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, hydroxylation, sulfation, lipidation, and acylation.
  • Some embodiments of the invention may involve GP201 proteins with such post-translational modifications.
  • Exemplary prokaryotic host cells are E. coli, Caulobacter crescentus, Streptomyces species, and Salmonella typhimurium cells. Vectors useable in these cells include, without limitation, those related to pBR322 and the pUC plasmids.
  • Exemplary yeast host cells are Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia pastoris, and Pichia methanolica. Any suitable vector can be used, e.g., YIp vectors, replicating episomal YEp vectors containing centromere sequences CEN and autonomously replicating sequences ARS.
  • Insect cells may be advantageous, e.g., for high efficiency protein expression.
  • Exemplary insect host cells are those from Spodoptera frugiperda, e.g., Sf9 and SGl cell lines, and EXPRESSFTM cells (Protein Sciences Corp., Meriden, CT, USA), Drosophila S2 cells, and Trichoplusia ni HIGH FIVE ® Cells (Invitrogen, Carlsbad, CA, USA). Where the host cells are Spodoptera frugiperda cells, the vector replicative strategy is typically based upon the baculovirus life cycle.
  • Exemplary mammalian host cells are COSl and C0S7 cells, NSO cells, Chinese hamster ovary (CHO) cells, NIH 3T3 cells, 293 cells, HEPG2 cells, HeLa cells, L cells, MDCK, HEK293, WI38, murine ES cell lines (e.g., from strains
  • 129/SV C57/BL6, DBA-I, 129/SVJ
  • K562 Jurkat cells
  • BW5147 any other commercially available human cancer cell lines.
  • Cells with elevated Her2 expression such as human cancer lines BT474 and SKO V3, can also be used.
  • Other useful mammalian cell lines are well known and are available from the American Type Culture Collection (ATCC ® ) (Manassas, VA, USA) and the National Institute of General medical Sciences (NIGMS) Human Genetic Cell Repository at the Coriell Cell Repositories (Camden, NJ, USA).
  • Vectors intended for autonomous extrachromosomal replication in mammalian cells typically include a viral origin, such as the SV40 origin (for replication in cell lines expressing the large T-antigen, such as COSl and C0S7 cells), the papillomavirus origin, or the EBV origin for long term episomal replication (for use in, e.g., 293-EBNA cells, which constitutively express the EBV EBNA-I gene product and adenovirus ElA).
  • Vectors intended for integration, and thus replication as part of the mammalian chromosome optionally include an origin of replication functional in mammalian cells, e.g., the SV40 origin.
  • Useful vectors also include vectors based on viruses such as lentiviruses, adenovirus, adeno- associated virus, vaccinia virus, parvoviruses, herpesviruses, poxviruses, Semliki Forest viruses, and retroviruses.
  • viruses such as lentiviruses, adenovirus, adeno- associated virus, vaccinia virus, parvoviruses, herpesviruses, poxviruses, Semliki Forest viruses, and retroviruses.
  • Plant cells also can be used for expression, with the vector replicon typically derived from a plant virus (e.g., cauliflower mosaic virus; tobacco mosaic virus) and selectable markers chosen for suitability in plants.
  • a plant virus e.g., cauliflower mosaic virus; tobacco mosaic virus
  • the invention relates to artificial chromosomes, e.g., bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs), mammalian artificial chromosomes (MACs), and human artificial chromosomes (HACs), that contain the GP201 nucleic acid of interest.
  • Vectors often include elements that permit in vitro transcription of RNA from the inserted heterologous nucleic acid.
  • Such vectors typically include a phage promoter, such as that from T7, T3, or SP6, flanking the nucleic acid insert. Often two different such promoters flank the inserted nucleic acid, permitting separate in vitro production of both sense and antisense strands.
  • BACs bacterial artificial chromosomes
  • YACs yeast artificial chromosomes
  • MACs mammalian artificial chromosomes
  • HACs human artificial chromosomes
  • Expression vectors often include a variety of other genetic elements operatively linked to the protein-encoding heterologous nucleic acid insert.
  • examples of other such genetic elements are promoters and enhancer elements.
  • Other elements are those that facilitate RNA processing, e.g., transcription termination signals, splicing signals and polyadenylation signals.
  • Other elements are those that facilitate translation, e.g., ribosomal consensus sequences.
  • Examples of other transcription control sequences are operators and silencers. Use of such expression control elements, including those that confer constitutive or inducible expression, and developmental or tissue-regulated expression are known in the art.
  • Constitutively active promoters include, without limitation, a CMV promoter, EF l ⁇ , retroviral LTRs, and SV40 early region.
  • Inducible promoters useful in this invention include, without limitation, a tetracycline-inducible promoter, a metallothionine promoter, the IPTG/lacI promoter system, the ecdysone promoter system, and the "lox stop lox" system for irreversibly deleting inhibitory sequences for translation or transcription.
  • a GP201 gene is placed between lox sites,. Upon expression of the ere enzyme, the GP201 gene is deleted from the genome so that the GP201 activity is permanently eliminated.
  • the activity of a GP201 protein also can be inducibly switched on or off by fusing the GP201 protein to, e.g., an estrogen receptor polypeptide sequence, where administration of estrogen or an estrogen analog (e.g., hydroxytamoxifen) will allow the correct folding of the GP201 polypeptide into a functional protein.
  • an estrogen receptor polypeptide sequence e.g., an estrogen receptor polypeptide sequence
  • an estrogen analog e.g., hydroxytamoxifen
  • Tissue-specific promoters that can be used in driving expression of GP201 in animal models include, without limitation: a tyrosinase promoter or a TRP2 promoter in the case of melanoma cells and melanocytes; an MMTV or WAP promoter in the case of breast cells and/or cancers; a Villin or FABP promoter in the case of intestinal cells and/or cancers; a PJP promoter in the case of pancreatic beta cells; a Keratin promoter in the case of keratinocytes; a Probasin promoter in the case of prostatic epithelium; a Nestin or GFAP promoter in the case of CNS cells and/or cancers; a Tyrosine Hydroxylase, SlOO promoter or neurofilament promoter in the case of neurons; the pancreas-specific promoter described in Edlund et al., Science 230:912-916 (1985); a Clara cell secretory protein promoter in the case of
  • promoters include, without limitation, the murine hox promoters (Kessel and Gruss, Science 249:374- 379 (1990)) and the ⁇ -fetoprotein promoter (Campes and Tilghman, Genes Dev. 3:537-546 (1989)).
  • murine hox promoters Kessel and Gruss, Science 249:374- 379 (1990)
  • ⁇ -fetoprotein promoter Campes and Tilghman, Genes Dev. 3:537-546 (1989).
  • Expression vectors can be designed to fuse the expressed polypeptide to small protein tags that facilitate purification and/or visualization. Many such tags are known and available. Expression vectors can also be designed to fuse proteins encoded by the heterologous nucleic acid insert to polypeptides larger than purification and/or identification tags. Useful protein fusions include those that permit display of the encoded protein on the surface of a phage or cell, fusions to intrinsically fluorescent proteins, such as luciferase or those that have a green fluorescent protein (GFP)-like chromophore, and fusions for use in two hybrid selection systems.
  • GFP green fluorescent protein
  • vectors For secretion of expressed proteins, a wide variety of vectors are available which include appropriate sequences that encode secretion signals, such as leader peptides.
  • Vectors designed for phage display, yeast display, and mammalian display for example, target recombinant proteins using an N-terminal cell surface targeting signal and a C-terminal transmembrane anchoring domain.
  • Stable expression is readily achieved by integration into the host cell genome of vectors (preferably having selectable markers), followed by selection for integrants.
  • the present invention relates to GP201 proteins and various fragments suitable for use, e.g., as antigens, biomarkers for diseases, and in therapeutic compositions.
  • the invention also relates to fusions of GP201 polypeptides to heterologous polypeptides or other moieties.
  • the invention relates to an isolated GP201 polypeptide (SEQ ID NO: 1), optionally containing one or more conservative amino acid substitutions.
  • the invention also relates to fragments of the GP201 polypeptide, particularly fragments having at least 5, 6, 8, or 15 amino acids of SEQ ID NO: 1. Larger fragments of at least 20, 25, 30, 35, 50, 75, 100, 150 or more amino acids are also useful, and at times preferred.
  • the GP201 fragments of the invention may be continuous portions of the native GP201 protein. However, it will be appreciated that knowledge of the GP201 gene and protein sequences permits recombining of various domains that are not contiguous in the native GP201 protein.
  • This invention also relates to fusions of GP201 polypeptides to heterologous polypeptides.
  • fusion means that the GP201 polypeptide is linearly contiguous to the heterologous polypeptide in a peptide- bonded polymer of amino acids or amino acid analogues.
  • heterologous polypeptide means a polypeptide that does not naturally occur in contiguity with the GP201 fusion partner.
  • the fusion polypeptide can consist entirely of a plurality of fragments of the GP201 protein in altered arrangement, hi such a case, any of the GP201 fragments can be considered heterologous to the other GP201 fragments in the fusion protein.
  • the heterologous polypeptide included within the fusion protein is at least 6 amino acids in length, often at least 8 amino acids in length, and preferably, at least 15, 20, and 25 amino acids in length.
  • the heterologous sequences can target the GP201 polypeptide to a selected cell by binding to a cell surface receptor, prolong the serum life of the GP201 polypeptide (e.g., an IgG Fc region), make the GP201 polypeptide detectable (e.g., a luciferase or a green fluorescent protein), facilitate purification (e.g., His tag, FLAG, etc.), facilitate secretion of recombinantly expressed proteins (e.g., into the periplasmic space or extracellular milieu for prokaryotic hosts, into the culture medium for eukaryotic cells, through incorporation of secretion signals and/or leader sequences).
  • fusions include fusions that permit use of the protein of the present invention as bait in a yeast two-hybrid system, fusions that display the encoded protein on the surface of a phage or cell, and fusions to intrinsically detectable proteins, such as fluorescent or light-emitting proteins.
  • proteins and protein fragments also can be fused to protein toxins, such as Pseudomonas exotoxin A, diphtheria toxin, shiga toxin A, anthrax toxin lethal factor, ricin, or other toxic moieties in order to effect specific ablation of cells that bind or take up the proteins.
  • protein toxins such as Pseudomonas exotoxin A, diphtheria toxin, shiga toxin A, anthrax toxin lethal factor, ricin, or other toxic moieties in order to effect specific ablation of cells that bind or take up the proteins.
  • the polypeptides can be composed of natural amino acids linked by native peptide bonds, or can contain any or all of nonnatural amino acid analogues, normative bonds, and post-synthetic (post-translational) modifications, either throughout the length of the polypeptide or localized to one or more portions thereof.
  • nonnatural amino acid analogues normative bonds
  • post-synthetic (post-translational) modifications either throughout the length of the polypeptide or localized to one or more portions thereof.
  • the range of such nonnatural analogues, normative inter-residue bonds, or post-synthesis modifications will be limited to those that do not interfere with the biological function of the polypeptide.
  • D-enantiomers of natural amino acids can readily be incorporated during chemical peptide synthesis: peptides assembled from D-amino acids are more resistant to proteolytic attack; incorporation of D-enantiomers can also be used to confer specific three dimensional conformations on the peptide.
  • amino acid analogues commonly added during chemical synthesis include ornithine, norleucine, phosphorylated amino acids (typically phosphoserine, phosphothreonine, phosphotyrosine), L-malonyltyrosine, a non-hydrolyzable analog of phosphotyrosine (KoIe et al., Biochem. Biophys. Res. Com. 209:817-821 (1995)), and various halogenated phenylalanine derivatives.
  • the isolated GP201 polypeptides can also include non-native inter-residue bonds, including bonds that lead to circular and branched forms.
  • the isolated GP201 polypeptides can also include post-translational and post-synthetic modifications, either throughout the length of the protein or localized to one or more portions thereof.
  • the isolated polypeptide when produced by recombinant expression in eukaryotic cells, can include N-linked and/or O-linked glycosylation, the pattern of which will reflect both the availability of glycosylation sites on the protein sequence and the identity of the host cell. Further modification of glycosylation pattern can be performed enzymatically.
  • recombinant polypeptides of the invention may also include an initial modified methionine residue, in some cases resulting from host-mediated processes.
  • Amino acid analogues having detectable labels are also usefully incorporated during synthesis to provide a labeled polypeptide (e.g., biotin, various chromophores, or fluorophores).
  • the GP201 polypeptides of this invention can also usefully be conjugated to polyethylene glycol (PEG). PEGylation increases the serum half life of proteins administered intravenously for replacement therapy.
  • Production of the isolated polypeptides optionally can be followed by purification from the producing cells.
  • Producing cells include, without limitation, recombinant cells overexpressing the polypeptides, naturally occurring cells (e.g., cancer cells) overxpressing the polypeptides, or established cancer cell lines overexpressing the polypeptides. If purification tags have been fused through use of an expression vector that appends such tags, purification can be effected, at least in part, by means appropriate to the tags, such as use of immobilized metal affinity chromatography for polyhistidine tags.
  • the isolated GP201 proteins maybe in pure or substantially pure form.
  • a purified protein is an isolated protein that is present at a concentration of at least 95%, as measured on a mass basis (w/w) with respect to total protein in a composition. Such purities can often be obtained during chemical synthesis without further purification, as, e.g., by HPLC. Purified proteins can be present at a concentration (measured on a mass basis with respect to total protein in a composition) of 96%, 97%, 98%, and even 99%. The proteins of the present invention can even be present at levels of 99.5%, 99.6%, and even 99.7%, 99.8%, or even 99.9% following purification.
  • substantially purified protein means a protein present at a concentration of at least 70%, measured on a mass basis with respect to total protein in a composition.
  • substantially purified protein is present at a concentration, measured on a mass basis with respect to total protein in a composition, of at least 75%, 80%, or even at least 85%, 90%, 91%, 92%, 93%, 94%, 94.5% or even at least 94.9%.
  • the purified and substantially purified proteins are in compositions that lack detectable ampholytes, acrylamide monomers, bis- acrylamide monomers, and polyacrylamide.
  • Certain fragments of at least 8, 9, 10 or 12 contiguous amino acids are also useful as competitive inhibitors of binding of the entire protein, or a portion thereof, to its ligand. Thus, such fragments can be used as anti-cancer agents to reduce the activity of GP201.
  • Fragments of at least six contiguous amino acids are useful in mapping B cell and T cell epitopes of the reference protein. See, e.g., Geysen et al., "Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid," Proc. Natl. Acad. Sci. USA 81:3998-4002 (1984) and U.S. Pat. Nos. 4,708,871 and 5,595,915. Because the fragment need not itself be immunogenic, part of an immunodominant epitope, nor even recognized by native antibody, to be useful in such epitope mapping, all fragments of at least six amino acids of the proteins of the present invention have utility in such a study.
  • Fragments of at least eight contiguous amino acids, often fifteen to thirty contiguous amino acids, have utility as immunogens for raising antibodies that recognize GP201 proteins or as vaccines for GP201 -mediated diseases such as cancers.
  • the GP201 proteins, fragments, and fusions of the present invention can usefully be attached to a substrate. When bound to a substrate, the polypeptides can be used to detect and quantify antibodies, e.g., in serum, that bind specifically to the immobilized protein. IV. ANTIBODIES AND APTAMERS A.
  • the invention relates to antibodies that bind specifically to the GP201 polypeptides.
  • the antibodies can be specific for linear epitopes, discontinuous epitopes, or conformational epitopes of such polypeptides, either as present on the polypeptide in its native conformation or as present on the polypeptides when denatured, e.g., by solubilization in SDS.
  • the antibodies both polyclonal and monoclonal, bind specifically to a polypeptide having an amino acid sequence presented in SEQ ID NO: 1.
  • an “antibody” means a full antibody, e.g., an antibody comprising two heavy chains and two light chains, or to an antigen-binding fragment of a full antibody.
  • Such fragments include, but are not limited to, those produced by digestion with various proteases, those produced by chemical cleavage and/or chemical dissociation, and those produced recombinantly, so long as the fragment remains capable of specific binding to an antigen.
  • fragments include Fab, Fab', F(ab') 2 and single chain Fv (scFv) fragments.
  • An antibody can be a murine or hamster antibody or a homolog thereof, or a fully human antibody.
  • An antibody also can be a humanized antibody, a chimeric antibody, an antibody fusion, a diabody, an intrabody, or a single-chained antibody.
  • An antibody can be of any isotype and subtype, for example, IgA (e.g., IgAl and IgA2), IgG (e.g., IgGl, IgG2, IgG3 and IgG4), IgE, IgD, IgM, wherein the light chains of the immunoglobulin may be of type kappa or lambda. While the useful antibodies are generally monoclonal, polyclonal antibodies from mice, rabbits, turkeys, or sheep may also be used.
  • the affinity or avidity of an antibody will be at least 1 x 10 "6 molar (M), preferably at least 5 x 10 ⁇ 7 M, more preferably at least 1 x 10 "7 M, with affinities and avidities of at least about 1 x 10 "8 M, 5 x 10 "9 M, or 1 x 10 "10 M being especially useful.
  • the antibodies are useful in a variety of in vitro immunoassays, such as western blotting and ELISA, in isolating and purifying GP201 proteins (e.g., by immunoprecipitation, immunoaffmity chromatography, or magnetic bead-mediated purification).
  • the antibodies are also useful as modulators (i.e., antagonists or agonists) of a GP201 protein in vivo to modulate the protein's interaction with its natural ligand.
  • the antibodies can also be used to conjugate to cytotoxic reagents for site-specific delivery.
  • the new antibodies can be variously associated with moieties appropriate for their uses.
  • the moieties can be an enzyme that catalyzes production and local deposition of a detectable product.
  • Exemplary enzymes are alkaline phosphatase, ⁇ -galactosidase, glucose oxidase, horseradish peroxidase (HRP), and urease.
  • the antibodies also can be labeled using colloidal gold. When the antibodies are used for flow cytometric detection and scanning laser cytometric detection, they can be labeled with fluorophores.
  • the antibodies of the present invention can usefully be labeled with biotin.
  • the antibodies of the present invention can usefully be labeled with radioisotopes.
  • the antibodies can be rendered detectable by conjugation to MRI contrast agents, such as radioisotopic labeling or gadolinium diethylenetriaminepentaacetic acid (DTPA).
  • DTPA gadolinium diethylenetriaminepentaacetic acid
  • the antibodies also can be conjugated to toxic agents so as to direct the agents to a tumor site.
  • the antibody is conjugated to Pseudomonas exotoxin A, diphtheria toxin, shiga toxin A, anthrax toxin lethal factor, or ricin.
  • Pseudomonas exotoxin A diphtheria toxin
  • shiga toxin A anthrax toxin lethal factor
  • ricin a complex regional antigen-derived ribulose-1 (IL-12), adasenofidasenofidasenofidasenofid
  • Small molecule toxins such as calicheamycin or chemotherapeutic agents can also be delivered via chemical conjugation to the antibodies.
  • the antibodies may also be used to deliver DNA to the tumor site as gene therapy to inhibit or otherwise modify the behavior of the tumor, e.g., to deliver an antisense reagent to the GP201 gene.
  • the antibodies can be bound to a substrate through a linker moiety.
  • the antibodies can be conjugated to filtration media, such as NHS-activated Sepharose or CNBr-activated Sepharose for immunoaffmity chromatography.
  • the antibodies also can be attached to paramagnetic microspheres, by, e.g., biotin-streptavidin interaction. The microsphere then can be used for isolation of cells that express or display the above-described proteins.
  • the antibodies also can be attached to the surface of a microtiter plate for ELISA.
  • Aptamers for GP201 are DNA-based or RNA-based molecules that bind to GP201 proteins with high affinity and specificity. Large libraries of nucleic acid compounds can be screened to identify specific molecules that e.g., bind GP201 polypeptides, or inhibit GP201 enzymatic activity. Like antibodies and small molecules, they can be used as research tools or therapeutic agents. For a review, see “Nucleic acid aptamers as tools and drugs: recent developments" by Rimrnele, Chembiochem 4:963-71 (2003)).
  • GP201 is a suitable therapeutic target for treating neoplasia, hyperplasia, malignant cancers, or any other hyperproliferative conditions.
  • the GP201 gene can be a target in cancers of the breast, skin, lung, prostate, colorectal tissue, liver, pancreas, brain, testis, ovary, uterus, cervix, kidney, thyroid, bladder, esophagus, and blood.
  • the invention relates to pharmaceutical compositions comprising GP201 nucleic acids, proteins, and antibodies, as well as mimetics, agonists, antagonists, or modulators of GP201 activity, and methods of using them to prevent or treat (i.e., ameliorate, mitigate, alleviate, slow, or inhibit) tumor growth, angiogenesis, metastasis or any other inappropriate cell proliferation.
  • Inhibitors of GP201 also can be administered in combination with one or more other therapeutic agents, for improved cancer treatment.
  • Other therapeutic agents suitable for co-administration with a GP201 inhibitor include, for example, an anti-angiogenic agent, an anti-metastatic agent, or an agent that creates a hypoxic environment.
  • Chemotherapeutic agents that can be co-administered with inhibitors of GP201 include folate antagonists, pyrimidine and purine antimetabolites, alkylating agents, platinum antitumor compounds, DNA interchelators, other agents that induce DNA damage, microtubule targeting products, small molecule inhibitors of protein kinases and biological inhibitors of growth factor receptors.
  • the GP201 inhibitor and additional therapeutic agent(s) may be used concurrently or sequentially, hi some embodiments, the subject is pre-treated with one or more agents, followed by treatment with a GP201 inhibitor.
  • the ability of tumor cells to detach from the primary site and produce metastases in a distant organ is due to the survival and growth of a unique subpopulation of cells with metastatic properties. Tumor growth and metastasis are angiogenesis-dependent. Inhibition of angiogenesis will generate a hypoxic environment in the tumor, forcing tumor cells to become more dependent upon the glycolytic pathway for energy generation. Accordingly, preventing angiogenesis in combination with inhibiting GP201 is a promising therapeutic strategy.
  • Angiogenesis inhibitors e.g. angiostatin, endostatin, Avastm or Regeneron's VEGF trap technology
  • GP201 inhibitors can be used in combination with GP201 inhibitors as an effective anti-cancer therapy.
  • Such a combination can be expected to have a synergistic effect.
  • This may also allow the use of a lower dose of GP201 inhibitor or anti-angiogenic agent or both in chemotherapy. This is desirable because it is likely to cause less toxicity in patients.
  • the use of combinations of therapeutic agents may circumvent drug resistance problems.
  • GP201 inhibitors can also be used in combination with agents that create a hypoxic environment to enhance the effect of GP201 inhibitor.
  • Hypoxia i.e., lack of oxygen
  • mammalian cells activate and express multiple genes. Tumor cells may respond to hypoxia by diminishing their proliferative rates, thereby leaving the cells viable but nonproliferating. Some transformed cell lines can also undergo apoptosis in extreme hypoxia and an acidic environment. Similar to inhibitors of angiogenesis, other agents that induce a hypoxic environment may sensitize tumor cells to inhibition of GP201 and use of hypoxia inducing agents in combination with inhibiting GP201 is therefore another promising therapeutic strategy.
  • TRAIL Tumor necrosis factor-related apoptosis- inducing ligand
  • FAM focal adhesion kinase
  • PB 'K phosphinositol 3' kinase
  • PKA protein kinase B
  • a composition of the invention typically contains from about 0.1 to 90% by weight (such as 1 to 20% or 1 to 10%) of a therapeutic agent of the invention in a pharmaceutically accepted carrier.
  • Solid formulations of the compositions for oral administration can contain suitable carriers or excipients, such as com starch, gelatin, lactose, acacia, sucrose, microcrystalline cellulose, kaolin, mannitol, dicalcium phosphate, calcium carbonate, sodium chloride, or alginic acid.
  • suitable carriers or excipients such as com starch, gelatin, lactose, acacia, sucrose, microcrystalline cellulose, kaolin, mannitol, dicalcium phosphate, calcium carbonate, sodium chloride, or alginic acid.
  • Disintegrators that can be used include, without limitation, microcrystalline cellulose, corn starch, sodium starch glycolate, and alginic acid.
  • Tablet binders that can be used include acacia, methylcellulose, sodium carboxymethylcellulose, polyvinylpyrrolidone (Povidone ), hydroxypropyl methylcellulose, sucrose, starch, and ethylcellulose.
  • Lubricants that can be used include magnesium stearates, stearic acid, silicone fluid, talc, waxes, oils, and colloidal silica.
  • Liquid formulations of the compositions for oral administration prepared in water or other aqueous vehicles can contain various suspending agents such as methylcellulose, alginates, tragacanth, pectin, kelgin, carrageenan, acacia, polyvinylpyrrolidone, and polyvinyl alcohol.
  • the liquid formulations can also include solutions, emulsions, syrups and elixirs containing, together with the active compound(s), wetting agents, sweeteners, and coloring and flavoring agents.
  • Various liquid and powder formulations can be prepared by conventional methods for inhalation into the lungs of the mammal to be treated.
  • Injectable formulations of the compositions can contain various carriers such as vegetable oils, dimethylacetamide, dimethylformamide, ethyl lactate, ethyl carbonate, isopropyl myristate, ethanol, polyols (glycerol, propylene glycol, liquid polyethylene glycol, and the like).
  • Physiologically acceptable excipients can include, for example, 5% dextrose, 0.9% saline, Ringer's solution or other suitable excipients.
  • Intramuscular preparations e.g., a sterile formulation of a suitable soluble salt form of the compounds, can be dissolved and administered in a pharmaceutical excipient such as Water-for-Injection, 0.9% saline, or 5% glucose solution.
  • a suitable insoluble form of the compound can be prepared and administered as a suspension in an aqueous base or a pharmaceutically acceptable oil base, such as an ester of a long chain fatty acid (e.g., ethyl oleate).
  • a topical semi-solid ointment formulation typically contains a concentration of the active ingredient from about 1 to 20%, e.g., 5 to 10%, in a carrier such as a pharmaceutical cream base.
  • Various formulations for topical use include drops, tinctures, lotions, creams, solutions, and ointments containing the active ingredient and various supports and vehicles.
  • the optimal percentage of the therapeutic agent in each pharmaceutical formulation varies according to the formulation itself and the therapeutic effect desired in the specific pathologies and correlated therapeutic regimens.
  • the pharmaceutical formulation will be administered to the patient by applying to the skin of the patient a transdermal patch containing the pharmaceutical formulation, and leaving the patch in contact with the patient's skin (generally for 1 to 5 hours per patch).
  • Other transdermal routes of administration e.g., through use of a topically applied cream, ointment, or the like
  • the pharmaceutical formulation(s) can also be administered via other conventional routes (e.g., parenteral, subcutaneous, intrapulmonary, transmucosal, intraperitoneal, intrauterine, sublingual, intrathecal, or intramuscular routes) by using standard methods.
  • the pharmaceutical formulations can be administered to the patient via injectable depot routes of administration such as by using 1-, 3-, or 6-month depot injectable or biodegradable materials and methods.
  • the therapeutic protein or antibody agent typically is administered at a daily dosage of 0.01 mg to 30 mg/kg of body weight of the patient (e.g., lmg/kg to 5 mg/kg).
  • the pharmaceutical formulation can be administered in multiple doses per day, if desired, to achieve the total desired daily dose.
  • the effectiveness of the method of treatment can be assessed by monitoring the patient for known signs or symptoms of a disorder.
  • compositions of the invention may be included in a container, package or dispenser alone or as part of a kit with labels and instructions for administration. These compositions can also be used in combination with other cancer therapies involving, e.g., radiation, photosensitizing compounds, anti ⁇ neoplastic agents and immunotoxics.
  • cancer therapies involving, e.g., radiation, photosensitizing compounds, anti ⁇ neoplastic agents and immunotoxics.
  • This invention provides genetically modified non-human mammals at least some of whose somatic cells and germ cells contain one of the above-described GP201 -coding nucleic acid of this invention (including both heterozygotes and homozygotes). Such mammals can be used to study the effect of the GP201 gene on tumorigenicity and tumor development, to study the role of GP201 on normal tissue development and differentiation, to identify via array CGH regions of the genome whose amplification or deletion is correlated with GP201 status, and to screen for and establish toxicity profiles of anti-cancer drugs.
  • This invention also provides genetically modified non-human mammals with targeted disruption of one or both copies of the endogenous GP201 gene.
  • Animal models according to the invention can be conventional germline transgenic animals or chimeric animals.
  • the inducible cancer model is a mouse whose genome has been modified to include: (a) an expression construct comprising a GP201 gene linked operably to an inducible promoter, and (b) a genetic mutation that causes the mouse to have greater susceptibility to cancer than a mouse not comprising said genetic mutation. Expression of the GP201 gene leads to formation of cancer in the mouse. The cancer regresses when expression of the GP201 gene is reduced.
  • Mutations that render the mammal more susceptible to cancer include disabling mutations in a tumor suppressor gene (e.g., INK4a), disabling mutations in a DNA repair gene (e.g., MSH2), and activating mutations in an oncogene (e.g., Her2, myc and ras).
  • a tumor suppressor gene e.g., INK4a
  • a DNA repair gene e.g., MSH2
  • an oncogene e.g., Her2, myc and ras.
  • Such testing also can be carried out in cells (e.g., human cells) that are engineered to contain an inducible oncogene and endowed with tumorigenic capacity by the presence of an appropriate combination of oncogenes, tumor suppressor genes, and/or telomerase.
  • the mammal's genome comprises (i) a first expression construct containing a gene encoding a reverse tetracycline transactivator operably linked to a promoter, such as any tissue or cell type-specific promoter or any general promoter, and (ii) a second expression construct containing the GP201 gene operably linked to a promoter that is regulated by the reverse tetracycline transactivator and tetracycline (or a tetracycline analogue, for example, doxycycline).
  • a promoter such as any tissue or cell type-specific promoter or any general promoter
  • a second expression construct containing the GP201 gene operably linked to a promoter that is regulated by the reverse tetracycline transactivator and tetracycline (or a tetracycline analogue, for example, doxycycline).
  • tetracycline or analogue thereof
  • Other inducible systems such as those described above also can be employed.
  • This animal model can be used to determine the efficacy of a candidate compound in preventing or treating cancer.
  • This method involves administering to the mammal a candidate compound and observing the effect of the compound on tumor development, maintenance, angiogenesis and/or progression in the mammal. Regression and/or reduction of tumor size in the presence of the compound indicates effectiveness of the compound.
  • the effect of a candidate compound on the level of GP201 mRNA, protein, or activity in the mammal or cell lines derived from the mammal (or cell lines transfected with the gene) can be used to identify the candidate as an agonist or antagonist.
  • the ability to compare the effect of a test compound to that of genetically switching off the inducible oncogene in this system allows the identification of surrogate markers that are predictive of the clinical response to the compound.
  • the inducible model can be used to determine whether a compound can eradicate minimal residual tumor. Normally in the inducible model, a tumor regresses when the GP201 gene is switched from “on” to "off via the inducible promoter. But if a compound can eradicate minimal residual tumor, switching the gene back on after administration of the compound will not bring back the tumor.
  • the animal model also can be used to identify other cancer-related elements.
  • a detailed expression profile of gene expression in tumors undergoing regression or regrowth due to the inactivation or activation of the GP201 transgene is established.
  • Techniques used to establish the profile include the use of suppression subtraction (in cell culture), differential display, proteomic analysis, serial analysis of gene expression (SAGE), and expression/transcription profiling using cDNA and/or oligonucleotide microarrays. Then, comparisons of expression profiles at different stages of cancer development can be performed to identify genes whose expression patterns are altered.
  • This animal model can also be used to identify molecular surrogates of GP201 in another manner.
  • the expression of GP201 gene is turned off (by removal of the inducer), and another round of MaSS screening is performed using retroviral integration, cDNA complementation, or the genetic suppressor elements (GSE) method.
  • GSE genetic suppressor elements
  • the animal model also can be used to identify surrogate biomarkers for diagnosis or for following disease progression in patients.
  • the biomarkers can be identified based on the differences between the expression profiles of the "on" and “off states in the animal model. Blood or urine samples from the animal can be tested with ELISAs or other assays to determine which biomarkers are released from the tumor into circulation during tumor genesis, maintenance, or regression (when GP201 is turned off). These biomarkers are particularly useful clinically in following disease progression post anti-GP201 therapy.
  • GP201 activity is up-regulated in tumor cells
  • the above-described nucleic acid probes or antibodies are used to quantify the expression level of GP201 in a tissue sample.
  • An increase in that level relative to control indicates cancerous, neoplastic, or hyperplastic pathology of the tissue sample.
  • This type of test can be performed using conventional techniques such as RT-PCR, ribonuclease protection assays, in situ hybridization, Northern blot analysis, FISH, CGH, array CGH, SKY, and immunohistochemistry.
  • a GP201 protein or GP201 protein fragments may be found to be elevated in a tissue sample (e.g., blood or urine) of cancer patients relative to that of normal individuals. This elevation can be detected by, e.g., specific ELISAs, radioimmunoassays, or protein chip assays. Such tests may not only be useful for diagnosis of GP201 -related diseases such as cancers, but also for monitoring the progress of therapy using GP201 inhibitors.
  • Mo-MuLV producer cell line TMJ (NIH3T3 based cell line) was plated to the required number of plates (100 mm). These cells were cultured and maintained in RPMI media with 10% FBS. For viral production, TMJ cells were fed with 4-5 ml of fresh culture media, and culture supernatant was harvested 8-12 hours later. The supernatant was filtered through a 0.45 ⁇ M filter.
  • Cells for MaSS screen Material for MaSS screen was prepared from the spontaneous, oncogene-induced tumors derived from the animal model of choice.
  • HER2-induced mammary tumors arising from the breast HER2 model (BH) were dissociated by protease digestion and cultured in vitro for limited passages to produce individual culture lines such as BH3, BHl-I, BH 1-2, BH1-3, BH8 and BH15. These culture lines retain the in vivo tumorigenic potential of their parent tumor material, in a doxycycline-dependent manner.
  • Doxycycline-dependent, HER2-induced mammary tumor cells such as BHl-I, BH1-2, BH1-3 or BH3 cells were maintained in RPMI media with 10% fetal bovine serum and 10 nM ⁇ -estradiol in the presence of doxycycline (2 ⁇ g/ml).
  • BH cells were seeded at 30 percent confluence.
  • filtered Mo-MuLV viral supernatant was added to the BH cells in the presence of polybrene (6-8 ⁇ g/ml), ⁇ -estradiol (10 nM) and doxycycline (2 ⁇ g/ml).
  • infected BH cells were trypsinized, rinsed and resuspended in Hanks' Balanced Salt Solution. Cell suspensions were kept on ice and the handling time after trypsinization was kept to a minimum. About I X lO 6 Mo-MLV infected cells were injected onto the flank of SCID mice. Subsequent to injection, the recipient SCID mice were fed with water without doxycycline. The animals were observed for tumor development. Positive control animals were injected with I X lO 6 BH uninfected cells, but the recipient mice were fed with water containing doxycycline. Negative control animals were similarly injected with I X lO 6 uninfected BH cells.
  • Mo-MuLV-derived tumors typically developed after approximately 20-120 days, depending on the culture cells used. Tumors were harvested and tumor tissue processed for various uses, such as genomic DNA preparation, mRNA preparation, histological staining, and cryopreservation.
  • b. Recovery of integration sites by ligation-mediated PCR This recovery protocol involved a restriction endonuclease digestion of the genomic DNA from each Mo-MuLV derived tumor, followed by linker ligation, two PCR-amplification steps, and final cloning of the products into destination plasmids.
  • restriction enzymes can be used, including, but not limited to, BstYI and Tsp 5091. In the examples below, linkers and primers used for the BstYI and the Tsp 5091 protocols are given.
  • Genomic DNA was isolated from tumor tissues using the PureGene DNA isolation kit (Gentra Systems, Minneapolis, MN). Genomic DNA (1 ⁇ g) was digested to completion with either BstYI or Tsp509I and the reaction was terminated by either incubation at 65 0 C for 20 minutes or phenol/chloroform extraction. The digested samples were ligated with an annealed linker (BstYI linkers or Tsp509I linkers) in the molar ratio 1:10 (genomic fragment : linker) using NEB Quick Ligation kit (New England BioLabs , Beverly, MA).
  • Ligation mediated-PCR was performed with one primer specific to the LTR (5' or 3' LTR primer 1) and the other primer to the linker (Linker primer 1) with the following conditions: pre-incubation at 94°C for 10 min, then 28 cycles of (95°C for 15 sec, 55 0 C for 30 sec and 72 0 C for 2 min), and a final extension step at 72 0 C for 10 min.
  • the PCR products were diluted 1 :100 and nested PCR was performed under the following conditions: pre-incubation at 94°C for 10 min, then 28 cycles of (95°C for 15 sec, 58 0 C for 30 sec and 72 0 C for 2 min), a final extension step at 72 0 C for 10 min.
  • the second pair of primers have attB sites at the ends, and are designed to bind to the LTR and the linker region (5' or 3' LTR primer 2 and Linker primer 2).
  • the resulting nested PCR products were cleaned with Millipore
  • Mapping integration sites The precise site and orientation of retroviral integration into the mouse genome was mapped for the recovered sequences as follows. Retroviral leader sequences were trimmed from the recovered sequences, and homology searches for the trimmed sequences were performed in the NCBI MGSCV3 database by using the BLAST software program. Unique BLAST hits were analyzed and mapped to the mouse genome, and recurrent sites of integration in multiple mouse tumors were identified. NCBI Map View was used to identify the site of each recurrent retroviral integration onto the mouse genome.
  • Recurrence was defined as 2 or more integrations within a specified region, for example, 20 kb. Genes either containing the integration sites or immediately neighboring the sites were identified by using the MGS C V3 Gene map. Published literature shows that Mo-MuLV favors integration events near transcribed genes, frequently resulting in alterations in expression of the latter. Integration events within a gene implicates that particular gene as the best candidate target for the biological effects of said integrations. Using these criteria, a set of candidate genes involved in cancer were identified from each MaSS screen. Genes identified in the BH screen, in the specific example, possess the ability to functionally complement the HER2 oncogene in this inducible, in vivo cancer model (mouse). d. Identification of GP201 as a cancer gene from a Mass Screen The set of candidate genes were analyzed according to several criteria, including tumor recurrence, transcript abundance in the target tumors, and biological significance.
  • the MaSS screen identified candidate cancer genes that would functionally complement a given oncogene in its absence, leading to the successful formation of a tumor.
  • the oncogene is HER2.
  • One set of expected candidate cancer genes might be genes that are in the same pathway as HER2, or co-regulated by HER2.
  • Transcript profiling of BH cells in the presence of doxycycline (HER2 on) compared to BH cells in the absence of doxycycline (HER2 off) defined a set of genes whose mRNA expression patterns clustered with those of HER2.
  • GP201 i.e.
  • This example describes the protocols for expressing the candidate gene identified above in human cancer cells.
  • Primer pairs for each human gene were designed as described for the mouse gene. Expression of each candidate gene was assessed in a panel of 31 human cancer cell lines and 47 human primary tumors by using real-time reverse transcription PCR. The forward and reverse primers were
  • TM master mix (ABI) was mixed with the MultiScribe reverse transcriptase (ABI) and RNase inhibitor (ABI). Forward and reverse primers were added at ratios previously optimized for each gene using control human reference RNA (Stratagene). 50 ng of RNA template was used per reaction, and the reactions were performed in a total volume of 20 ⁇ l. Real-time quantification was performed using the ABI 7900HT and SDS2.0 software. RNA loading was normalized for ⁇ - actin and 18S rRNA. RNA quantity was determined relative to human universal reference RNA (Stratagene) to permit run-to-run comparisons.
  • RNA interference RNA interference
  • a pool of double-stranded siRNA oligonucleotides was purchased from a
  • the sense sequence of four independent siRNAs that inhibit expression of GP201 are shown below: 5'-GCGAGAAGAUCCUAAAUGA-3'(SEQIDNO:3); 5'-GCAAGUGGGUUGACUACUC-3' (SEQIDNO:4); 5'-GCACAUCCGUUGGCCAUCA-3' (SEQIDNO: 5);and 5'-GACCUCAAGUUGGGAAAUU-3' (SEQIDNO:6).
  • melanoma and SKOV-3 ovarian carcinoma was measured by apoptosis assay and compared to the effect of transfecting a negative control siRNA that targets firefly luciferase and a positive control siRNA that targets PLKl (GenBank NM_005030).
  • Twenty four hours after transfection with siRNA cells were plated in quadruplicate in 96-well plates at appropriate densities. Forty-eight hours after plating of cells (72 hours post-transfection) cells were assayed for apoptosis using an ELISA assay to detect free nucleosomes resulting from DNA cleavage, a result of cell apoptosis.
  • the ELISA assay was performed with the Cell Death Detection ELISA PlusTM kit (Roche; Catalog # 1920685) according to vendor's recommendations. The data are summarized in Table 2.
  • Human cancer cell lines expressing high levels of the candidate, or cell lines established from the inducible mouse cancer model described above or cells derived from MaSS screen tumors are transfected with a vector encoding a short hairpin RNA homologous to the candidate cancer-related gene. Expression of the RNA is placed under the control of an inducible U 6 promoter. Stable cell lines are established. 5 X 10 5 cells are injected subcutaneously into the flanks of 6- week- old female inbred SCID mice. Tumor formation is observed visually. For cell lines derived from the inducible mouse model, tumor formation is induced by doxycycline. Expression of the RNAi is induced once tumors were visually identified. In the case of MaSS screen-derived tumor cells, the mice are not fed with doxycycline. Tumor regression is followed using calipers to measure the shrinking tumor diameter.
  • Example 6 Tumor Formation in SCIDs
  • Tumor cells derived from the tumor suppressor null (INK4/arf -/-) doxycycline-inducible oncogene mouse model are infected with retrovirus encoding the candidate gene under the control of an IPTG-inducible promoter. Stable cell lines are established. Approximately 10 6 cells are injected subcutaneously into the flank of 6 week old female inbred SCID mice. Mice are fed with doxycycline for 7-12 days. 24 hours prior to doxycycline withdrawal, mice are fed IPTG. IPTG feeding is maintained after withdrawal of doxycycline and tumor regression is monitored using calipers.
  • casein is a substrate for PLK3 (Ouyang et al., 1999, Oncogene, 18:6029-6036).
  • PLK3 a coupled enzyme assay system that allows for a convenient and rapid continuous assay of GP201 (PLK3).
  • the PLK3 reaction which uses casein as a substrate, is coupled to a pyruvate kinase/lactate dehydrogenase coupled assay system, as shown in the following reaction scheme.
  • PLK3 lactate
  • the PLK3 reaction is monitored indirectly by observing the decrease in NADH by either absorption or fluorescence spectroscopy.
  • Casein, ATP, phosphoenol- pyruvate (PEP), NADH, PK, and LDH are combined in a single reaction mixture.
  • the reaction is started by addition of PLK3.
  • This coupled assay system can be used to screen for inhibitors for PLK3.
  • Specificity of PLK3 inhibitory compounds can be determined by examining the ability of these compounds to inhibit related kinases.
  • specificity for PLK3 in cell-based assays can be determined by identifying those compounds that induce apoptosis or inhibit growth in soft agar in the same cell lines that are similarly affected by genetic inhibition of PLK3 by siRNA.
  • This example describes the protocols used to demonstrate the ability of PLK3 (GP201) cDNA to complement a non-induced HER2 oncogene in mouse breast cells, thereby producing a tumor phenotype.
  • the vector pB-PLK3 were constructed as follows. A 2.1 kb human PLK3 cDNA fragment (OriGene, Rockville, MD, cat# TCl 17577) was cloned into vector pENTRl 1 (Invitrogen; cat#l 1819-018) to generate vector pENTR- PLK3. A recombination reaction was performed between vector pENTR- PLK3 and vector pBGD-1 using the Gateway ® LR method. The resulting vector, pB- PLK3, was confirmed by restriction enzyme digestion and nucleic acid sequencing. b.
  • EcoPack2-293 and PhoenixTM were obtained from BD Biosciences Clontech (Palo Alto, CA; cat#631507) and Orbigene Inc. (San Diego, CA; cat# PVL-10014).
  • EcoPack2-293 or PhoenixTM cells were cultured in DMEM medium (containing 10% FBS, 50 U/ml penicillin, 50 mg/ml streptomycin) until 70% confluent.
  • 20 mg DNA of pB- PLK3 retroviral vector was transfected into EcoPack2-293 or PhoenixTM cells using Fugene ⁇ transfection reagent (Roche Applied Science, Indianapolis, IN; cat# 11814443001). Transfection efficiency was monitored by GFP visualization at 24 hours after transfection.
  • Retrovirus was harvested at 48 hours after transfection by filtering the medium supernatant through a 0.45 micron filter. The filtered supernatant was stored at -8O 0 C. c. Retroviral infection of tumor cells
  • Mouse breast HER2 tumor cells were cultured in RPMI 1640 medium (containing 10% FBS, 50 U/ml penicillin, 50 mg/ml streptomycin and 2 mg/ml doxycycline). At approximately 18-24 hours after plating, or when the plated cells are 70-80% confluent, the breast tumor cells were infected with thawed retroviral supernatant in the presence of polybrene (8 mg/ml). d. Generation of complemented tumor
  • infected breast tumor cells were trypsinized, rinsed and resuspended in Hans's Balanced Salt Solution.
  • Tumors complemented with pB- PLK3 retrovirus were observed after approximately 28 days in 3 out of 6 injection sites.
  • human PLK3 expression levels in complemented tumors were about 2-5 fold higher than a normal human reference.
  • the expression of retroviral constructs in tumor cells was also confirmed by GFP protein immunohistochemistry on formalin fixed tumor samples.

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Abstract

Utilisation de molécules relatives au gène GP201 (PLK3) pour le traitement du cancer et d'autres états hyperprolifératifs. Mammifères non humains présentant une modification génétique associée au gène GP201, et leur utilisation comme modèles d'expérimentation contre le cancer.
PCT/US2005/040738 2004-11-12 2005-11-12 Gp201: procedes et compositions de traitement du cancer WO2006053125A2 (fr)

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WO2007146436A3 (fr) * 2006-06-14 2008-04-17 Vertex Pharma Structure cristalline de la kinase plk3 (polo-like kinase 3) et de ses poches de liaison

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WO2004007754A2 (fr) * 2002-07-12 2004-01-22 Rigel Pharmaceuticals, Inc. Modulateurs de la proliferation cellulaire
US20040101857A1 (en) * 2002-11-23 2004-05-27 Isis Pharmaceuticals Inc. Modulation of cytokine-inducible kinase expression

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WO2004007754A2 (fr) * 2002-07-12 2004-01-22 Rigel Pharmaceuticals, Inc. Modulateurs de la proliferation cellulaire
US20040101857A1 (en) * 2002-11-23 2004-05-27 Isis Pharmaceuticals Inc. Modulation of cytokine-inducible kinase expression

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007146436A3 (fr) * 2006-06-14 2008-04-17 Vertex Pharma Structure cristalline de la kinase plk3 (polo-like kinase 3) et de ses poches de liaison
US7700340B2 (en) 2006-06-14 2010-04-20 Vertex Pharmaceuticals Incorporated Crystal structure of polo-like kinase 3 (PLK3) and binding pockets thereof

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